Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 140 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 10042 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 43 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 140 antibody 29 cell 20 SARS 17 virus 12 patient 10 protein 9 human 9 dna 9 Fig 9 ELISA 9 COVID-19 8 PCR 8 HIV 7 study 6 phage 6 infection 6 figure 5 vaccine 5 display 5 RNA 5 HLA 5 HIV-1 5 HCV 4 test 4 response 4 platelet 4 monoclonal 4 immune 4 donor 4 blood 4 anti 4 animal 4 TRALI 4 NAT 4 HBV 4 CoV-2 3 treatment 3 system 3 result 3 peptide 3 method 3 library 3 immunoglobulin 3 group 3 disease 3 car 3 Transfusion 3 SLE 3 RHD 3 RBD Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 15907 antibody 8197 cell 6626 blood 5663 % 5225 virus 5142 patient 3631 protein 3555 infection 3308 antigen 3302 study 2857 donor 2729 disease 2625 transfusion 2610 response 2591 result 2274 vaccine 2254 method 2067 system 1922 sample 1866 serum 1837 group 1743 mouse 1720 test 1697 platelet 1684 day 1684 case 1667 assay 1663 treatment 1637 use 1634 therapy 1605 level 1567 time 1498 plasma 1493 effect 1338 type 1336 activity 1330 detection 1292 b 1290 receptor 1274 epitope 1271 control 1250 analysis 1229 phage 1207 animal 1205 year 1196 number 1152 gene 1142 development 1120 factor 1115 reaction Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2694 al 2252 et 1992 . 1568 SARS 956 IgG 762 Fc 745 HIV-1 684 sera 673 ELISA 668 C 666 IgA 659 CoV-2 651 HCV 647 T 627 PCR 591 HIV 577 IgM 569 B 553 RBC 534 mAbs 495 - 487 A 479 RNA 474 S 469 Fig 413 HBV 399 CoV 366 Blood 363 HLA 358 • 349 D 343 M 321 COVID-19 302 E. 300 mg 289 Hb 288 SLE 282 anti 280 DNA 278 IVIG 276 Fab 274 Table 270 Antibody 261 II 260 Transfusion 237 RHD 232 MAbs 231 scFv 230 Anti 222 Rh Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2951 it 2198 we 1134 they 527 them 407 i 143 he 113 us 105 one 93 she 63 itself 54 you 40 themselves 12 me 10 himself 8 him 7 ourselves 7 m19fc 7 igg1 6 trim21 6 p210bcr 6 igg4 4 mg 3 mine 3 her 2 s 2 imagej 2 iga1 2 em 1 yourself 1 y453f 1 tnfsf13 1 tgn1412 1 spvb 1 samples:"you 1 s_tmhmm 1 phosphonylmethoxy)propyl]cytosine 1 particle‖ 1 oneself 1 mrnas 1 itims 1 interleukin-15 1 ilc1s 1 gviiip 1 epcam 1 ecovs 1 dmabs 1 cr4098 1 cord-004247-lagv3tp7 1 cord-002846-la9svzml 1 3times Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 47042 be 8320 have 5271 use 2478 show 1967 bind 1843 neutralize 1581 base 1511 include 1392 do 1365 increase 1279 detect 1226 develop 1201 find 1124 provide 1114 follow 1083 perform 1074 associate 1072 produce 1063 induce 1040 identify 1025 test 1004 compare 955 reduce 938 contain 923 require 899 report 853 demonstrate 845 mediate 843 give 841 obtain 828 determine 814 infect 800 make 792 suggest 784 occur 765 target 764 result 719 observe 710 cause 707 express 695 treat 664 lead 662 evaluate 656 describe 653 indicate 636 generate 634 improve 613 select 612 relate 601 derive Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 5315 - 3761 not 3251 anti 3091 human 2878 high 2487 also 2483 specific 2338 immune 2005 other 1950 clinical 1915 more 1844 viral 1801 positive 1753 such 1713 monoclonal 1687 only 1600 well 1573 different 1356 low 1348 however 1310 most 1221 first 1204 single 1095 as 1013 new 1012 negative 983 therapeutic 935 non 864 several 811 significant 789 many 786 important 783 red 753 severe 752 recombinant 748 further 736 infectious 712 large 710 early 705 bacterial 702 same 689 effective 674 thus 674 respiratory 636 whole 617 acute 615 available 605 small 599 possible 580 major Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 408 most 190 least 150 Most 146 good 132 high 51 low 34 large 33 great 17 strong 16 safe 15 early 14 close 14 bad 12 small 12 big 10 simple 10 common 8 young 8 late 6 fast 5 old 5 near 4 easy 4 clear 3 wide 3 postsurgery 3 E(13.4 3 226/303 3 -H 3 -E 3 -Diagast 2 new 2 broad 2 B27 2 -displayed 1 αGal 1 ~3 1 weak 1 thin 1 tDC 1 short 1 ripe 1 rich 1 rare 1 randomfor 1 nAbs 1 long 1 fit 1 fair 1 deadly Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 902 most 136 least 46 well 3 fast 2 ckv061 1 youngest 1 worst 1 smallest 1 highest 1 hard 1 greatest 1 furthest 1 farthest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 9 doi.org 3 www.nrlqa.net 3 www.ncbi.nlm.nih.gov 3 www.mederrors.com. 3 www.hsph.harvard.edu 2 www.who.int 2 www 2 orcid.org 2 github.com 2 clinicaltrials.gov 1 zdock.bu.edu 1 www.synabs.be 1 www.retroscreen 1 www.imgt.org 1 www.hku.hk 1 www.fbi.gov 1 www.ebi.ac.uk 1 www.dhs 1 www.chinarareblood.cn)was 1 www.chictr.org 1 www.ch.embnet.org 1 www.cdc.gov 1 www.cbs.dtu.dk 1 www.bioinf.org.uk 1 www.aarda.org 1 vaccineschedule.ecdc.europa.eu 1 users.math.msu.edu 1 rbm.who.int 1 opig.stats.ox.ac.uk 1 ncov.schanglab.org.cn 1 mendel 1 map.ox.ac.uk 1 iuis.org 1 gbcloning.upv.es 1 eu.idtdna.com 1 esid.org 1 creativecommons.org 1 creat 1 covid19.who.int 1 covid-19tracker.milkeninstitute.org 1 bioinformatics 1 base.thep.lu.se Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://www.nrlqa.net 3 http://www.mederrors.com. 3 http://www.hsph.harvard.edu/cearegistry 3 http://doi.org/10.1101/2020.06.21.20132944 2 http://www 1 http://zdock.bu.edu 1 http://www.who.int/topics/vaccines/en/ 1 http://www.who.int/emergencies/diseases/novel-coronavirus-2019/ 1 http://www.synabs.be/2019/ 1 http://www.retroscreen 1 http://www.ncbi.nlm.nih.gov/pubmed 1 http://www.ncbi.nlm.nih.gov/genbank/ 1 http://www.ncbi.nlm.nih.gov/BLAST 1 http://www.imgt.org/mAb-DB/query.action 1 http://www.hku.hk/ctc/sars 1 http://www.fbi.gov 1 http://www.ebi.ac.uk/ipd/imgt/hla/ 1 http://www.dhs 1 http://www.chinarareblood.cn)was 1 http://www.chictr.org/en/ 1 http://www.ch.embnet.org/software/TMPRED_ 1 http://www.cdc.gov 1 http://www.cbs.dtu.dk/services/ 1 http://www.bioinf.org.uk/abysis 1 http://www.aarda.org/diseaselist/ 1 http://vaccineschedule.ecdc.europa.eu/Scheduler/ByDisease? 1 http://users.math.msu.edu/users/weig/SARS-CoV-2 1 http://rbm.who.int 1 http://orcid.org/0000-0002-4823-3829 1 http://orcid.org/0000-0001-5829-648X 1 http://opig.stats.ox.ac.uk/resources 1 http://ncov.schanglab.org.cn 1 http://mendel 1 http://map.ox.ac.uk 1 http://iuis.org/ 1 http://github.com/sophiamersmann/molecular-counting 1 http://github.com/eliberis/parapred 1 http://gbcloning.upv.es 1 http://eu.idtdna.com/CodonOpt 1 http://esid.org 1 http://doi.org/10.1371/journal.ppat.1007836.g004 1 http://doi.org/10.1038/s41598-020-63553-z.Correspondence 1 http://doi.org/10.1038/s41598-020-63553-z 1 http://doi.org/10.1016/j.intimp.2020.106639 1 http://doi.org/10.1016/j.bbrc.2018.01.141 1 http://doi.org/10 1 http://creativecommons.org/licenses/by/4.0/ 1 http://creat 1 http://covid19.who.int/ 1 http://covid-19tracker.milkeninstitute.org/#vaccines Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 zhang@bio.uminho.pt 1 yangyuan@tmu.edu.tw 1 soumya.palliyil@abdn.ac.uk Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 13 cells did not 12 antibody was not 12 patients were positive 11 antibodies were also 10 antibodies are not 10 antibodies are present 9 % tested patients 9 antibodies did not 9 antibodies were able 9 antibodies were not 9 antibody test results 9 cells do not 9 platelets were not 8 % were positive 8 antibody binding site 8 results do not 8 samples were then 7 antibodies do not 7 antibody does not 7 cases were positive 7 cells are also 7 results were not 7 test is not 7 virus neutralizing antibodies 6 % had low 6 % were passive 6 % were regular 6 antibodies are anti 6 antibody binding sites 6 antibody was detectable 6 cells were also 6 cells were then 6 days is not 6 donors is essential 6 donors was not 6 infection does not 6 patients are not 6 patients are often 6 patients were negative 6 patients were randomly 6 results were very 6 studies comparing different 6 studies comparing ffp 6 studies have also 6 tests using nacl 6 transfusions were ineffective 5 antibodies are also 5 antibodies are capable 5 antibodies are currently 5 antibodies are unable Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 5 test is not available 4 patients is not clear 3 antibodies are not clinically 3 antibodies had no apparent 3 antibodies had no effect 3 antibodies were not anymore 3 blood was not less 3 cell was not present 3 cells are not available 3 cells do not consistently 3 donors had no major 3 donors have no intention 3 groups did not significantly 3 groups has not statistical 3 methods are not sufficiently 3 patient had no history 3 patient had no transfusion 3 patient was not essentially 3 platelets were not available 3 results show no evidence 3 results showed no discrepancies 3 transfusion are not well 3 transfusions are not consistent 2 % had no confidence 2 antibodies are not present 2 cells has not only 2 patients are not possible 1 % showed no antibody 1 antibodies are no longer 1 antibodies are not effective 1 antibodies are not strictly 1 antibodies are not systemically 1 antibodies do not directly 1 antibodies do not necessarily 1 antibodies have not yet 1 antibodies is not sufficient 1 antibodies provides no information 1 antibodies were not constantly 1 antibodies were not highly 1 antibody are no longer 1 antibody does not precisely 1 antibody does not subsequently 1 antibody had no detectable 1 antibody had no effect 1 antibody had no reactivity 1 antibody had no such 1 antibody is not always 1 antibody was no greater 1 antibody was no longer 1 antibody was no more A rudimentary bibliography -------------------------- id = cord-030999-27wennun author = Altmann, Daniel M title = Adaptive immunity to SARS-CoV-2 date = 2020-07-09 keywords = SARS; antibody; response summary = The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. Since many key questions about durability of the antibody response and about correlates of protection have been hard to address in this short timeframe, there has been value in recourse to the coronavirus immunology literature, especially in relation to SARS and MERS [16] [17] [18] [19] . Experience to date with SARS-CoV-2 suggests that this may not prove to be an infection that throws up insurmountable confounders to vaccine design-approaches that can safely and durably elicit neutralizing antibody look likely to work. Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals doi = 10.1093/oxfimm/iqaa003 id = cord-321369-xzu2faol author = Andreano, Emanuele title = Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date = 2020-10-07 keywords = Fig; SARS; antibody summary = By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. As for the authentic virus neutralization assay, supernatants containing naturally produced IgG or IgA were tested for their ability to protect the layer of Vero E6 cells from the cytopathic effect triggered by SARS-CoV-2 infection (Fig. S2) . This work describes a systematic screening of memory B cells from convalescent people to identify extremely potent human monoclonal antibodies against the spike protein of the SARS-CoV-2 virus, to be used for prevention and therapy of Covid-19. doi = 10.1101/2020.10.07.328302 id = cord-001060-9g8rwsm1 author = Arruebo, Manuel title = Assessment of the Evolution of Cancer Treatment Therapies date = 2011-08-12 keywords = antibody; cancer; cell; gene; nanoparticle; target; therapy; tumor summary = These therapies can be used in isolation or in combination with other cancer treatments, thereby taking advantage of their ability to target tumors (actively or passively), to respond to physical or chemical stimulation (internal or external) and to deliver therapeutic genes to the cell nuclei. Compared to conventional therapies, nanoparticles show six clear advantages in cancer treatment and/or diagnosis: (1) they can be synthesized in specific sizes and with surface characteristics to penetrate tumors by taking advantage of the enhanced permeation and retention effect (EPR) (a mechanism known as passive targeting); (2) they can be engineered to target tumor cells by surface functionalization with biomolecules that attach to tumor-specific cell markers (a mechanism known as active targeting); (3) they can be engineered to penetrate cells and physiological barriers (e.g., blood-brain barrier, blood-retinal barrier); (4) they can increase the plasma half-life of carried chemotherapeutic drugs, which are usually highly hydrophobic; (5) they can protect a therapeutic payload from biological degradation; and (6) they can be synthesized as multifunctional platforms for combined imaging and therapeutic applications (theragnostic nanoparticles). doi = 10.3390/cancers3033279 id = cord-023053-j061ywrl author = BARLOUGH, J. E. title = Cats, coronaviruses and coronavirus antibody tests date = 2008-04-10 keywords = FIPV; Weiss; antibody summary = In domestic and exotic cats, FIPV is the aetiologic agent of a lethal disease-feline infectious peritonitis (FIP)-characterized by fibrinous serositis, vasculitis, and formation of disseminated pyogranulomas (Wolfe & Griesemer. Laboratory test procedures for detection of coronavirus antibody in feline sera include biological assays such as virus neutralization (VN); non-biological, immunochemical techniques such as indirect immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA), and kinetics-based ELISA (KELA); and other methods such as agar gel immunodiffusion and passive haemagglutination , though the availability of such tests varies worldwide. The serodiagnostic potential of these assays (i.e., their ability to identify cats with active FIP and/or potential virus carriers/excretors) is thus limited not only by the widespread distribution of serum coronavirus antibody in the feline population, but also by the possibility that non-FIPV coronaviruses may be responsible for some of the seroconversions that they detect. doi = 10.1111/j.1748-5827.1985.tb02210.x id = cord-305893-2vcy0f6i author = Bagheri, Vahid title = Neutralizing human recombinant antibodies against herpes simplex virus type 1 glycoproteins B from a phage-displayed scFv antibody library date = 2017-01-15 keywords = antibody; hsv-1 summary = title: Neutralizing human recombinant antibodies against herpes simplex virus type 1 glycoproteins B from a phage-displayed scFv antibody library Our present study focused on the selection of neutralizing single-chain Fv (scFv) antibodies of a phage-displayed nonimmune human scFv antibody library against gB of HSV-1. described a neutralizing scFv-phage antibody against glycoprotein D of HSV-1 with neutralizing effect of 76%, which was capable of neutralizing HSV-1 and inhibiting virus entry to host cell [21] . Here, we selected two neutralizing anti-gB scFv antibodies to inhibit cytopathic effects in Vero cells infected with HSV-1. Neutralizing human single-chain antibodies against herpes simplex virus type 1 glycoprotein D from a phage display library Directed selection of recombinant human monoclonal antibodies to herpes simplex virus glycoproteins from phage display libraries doi = 10.1016/j.lfs.2016.11.018 id = cord-016960-xhzvp35g author = Berencsi, György title = Fetal and Neonatal Illnesses Caused or Influenced by Maternal Transplacental IgG and/or Therapeutic Antibodies Applied During Pregnancy date = 2012-03-08 keywords = CTLA-4; Nieri; SLE; TNF; antibody; cell; disease; neonatal; patient; pregnancy; treatment summary = The importance of maternal anti-idiotypic antibodies are believed to prime the fetal immune system with epitopes of etiologic agents infected the mother during her whole life before pregnancy and delivery. Neonatal lupus is a model of passively acquired autoimmunity in which a mother-, who may have systemic lupus erythematosus (SLE) or Sj€ ogren''s syndrome (SS) or may be entirely asymptomatic-synthesizes antibodies to SSA/Ro and/or SSB/ La ribonucleoproteins that enter the fetal circulation via trophoblast FcRn receptors and presumably cause tissue injury (Lee 1990 ) as mentioned above. Teplizumab (CD3-specific, hOKT3g1-Ala-Ala), a humanized Fc mutated anti-CD3 monoclonal antibody induced tolerance, on the progression of type 1 diabetes in patients with recent-onset disease even 2 years after the first diagnosis (Herold et al. Clinical and immune responses in resected colon cancer patients treated with anti-idiotype monoclonal antibody vaccine that mimics the carcinoembryonic antigen Clinical use of anti-CD25 antibody daclizumab to enhance immune responses to tumor antigen vaccination by targeting regulatory T cells doi = 10.1007/978-94-007-4216-1_9 id = cord-277076-yvsyo4l9 author = Berger, A. title = SARS date = 2019-09-12 keywords = CoV; SARS; antibody; human summary = Measures including source isolation of patientswho only became infectious after onset of clinical symptomsstrict infection control in health care facilities, timely identification and quarantining of exposed contacts, and perhaps also measures to increase social distance, such as travel warnings and screening of travelers, had led to this remarkable and remarkably rapid success. A further, small SARS outbreak occurred again in Guangdong in late 2003/early 2004; molecular analysis of virus isolates from human cases and animals sampled at the same place and time confirmed that this was zoonotically acquired from Paguma larvata. The laboratory diagnosis of SARS remains a challenge; in fact, despite the rapid identification of SARS-CoV as the etiological agent, testing contributed little to the successful control of the 2003 outbreak. A negative antibody test result later than 21 days after the onset of illness is likely to indicate that no infection with SARS-CoV has taken place. doi = 10.1016/b978-0-444-63951-6.00624-0 id = cord-354325-r73datur author = Berger, Mitchell title = Therapeutic Applications of Monoclonal Antibodies date = 2002-07-31 keywords = CMV; MAbs; antibody; antigen; cell; human; monoclonal; mouse summary = Attempts to use mouse myeloma cells to create hybrids and derive human MAbs led to the loss of human chromosomes and the inability to make human Igs. 13 Unfortunately, in vitro immunization is limited by its inability to produce a secondary response and by the absence of the affinity maturation process that occurs in vivo. In these transgenic mouse models, human antibodies with high affinity to an immunized antigen are naturally selected by the murine immune system via an affinity maturation process, and thereby show increased diversity of the MAbs. Transgenic mice may be a suitable alternative to chimeric or humanized antibody production or the use of phage display systems to create less immunogenic or novel antibodies. [43] [44] [45] Humanizing Monoclonal Antibodies Rodent MAbs with excellent affinities and specificities have been generated using conventional hybridoma technology, but their use in clinical medicine is limited due to the immune responses they elicit in humans. doi = 10.1097/00000441-200207000-00004 id = cord-296576-d23b9fjl author = Bernard, Serge title = Lactogenic Immunity to Transmissible Gastroenteritis (TGE) of swine induced by the attenuated nouzilly strain of TGE virus: Passive protection of piglets and detection of serum and milk antibody classes by ELISA date = 1990-01-31 keywords = TGE; antibody summary = title: Lactogenic Immunity to Transmissible Gastroenteritis (TGE) of swine induced by the attenuated nouzilly strain of TGE virus: Passive protection of piglets and detection of serum and milk antibody classes by ELISA After natural infection or experimental oral infection of pregnant sows with a virulent strain of TGE virus, lactogenic immunity is highly protective for piglets, and neutralizing antibodies in milk are mainly associated with the IgA fraction (Bohl, 1981) . TABLE 3 Relationship between passive protection rate and titre of specific anti-TGE antibody classes ( IgG, IgA, IgM) in serum and milk, on the day and 10 days after challenge The most interesting result of the preliminary report about the immune response of sows vaccinated with N strain of TGE (Shira''i et al., 1988) was the absence of correlation between the passive protection rate of the litter and the neutralizing antibody titre in serum or milk of sows on the day of challenge. doi = 10.1016/0165-2427(90)90076-5 id = cord-324316-ulb8d5fe author = Bramstedt, Katrina A. title = Antibodies as Currency: COVID-19’s Golden Passport date = 2020-08-25 keywords = COVID-19; antibody summary = Due to COVID-19, the fragile economy, travel restrictions, and generalized anxieties, the concept of antibodies as a "declaration of immunity" or "passport" is sweeping the world. Numerous scientific and ethical issues confound the concept of an antibody passport; nonetheless, antibodies can be seen as a potential currency to allow movement of people and resuscitation of global economics. In this way, antibodies for SARS-CoV-2 (severe acute respiratory syndrome coronavirus type 2-the COVID-19 coronavirus) are potentially the new golden passport, but the concept is a moving target with clinical unknowns, as well as legal and ethical complexity (Phelan 2020; Persad and Emanuel 2020) . With the COVID-19 pandemic causing a fragile worldwide economy and millions of people unemployed (Congressional Research Service 2020), there is a risk of antibody certificates being viewed as the "golden passport" to return to work and travel. Show me your passport: Ethical concerns about Covid-19 antibody testing as key to reopening public life doi = 10.1007/s11673-020-09996-5 id = cord-336280-tsx409e3 author = Byrne, Barry title = Antibody-Based Sensors: Principles, Problems and Potential for Detection of Pathogens and Associated Toxins date = 2009-06-05 keywords = CFU; O157; Salmonella; antibody; assay; detection summary = Particular emphasis is placed on the detection of foodborne bacterial pathogens, such as Escherichia coli and Listeria monocytogenes, and additional examples relating to the monitoring of fungal pathogens, viruses, mycotoxins, marine toxins and parasites are also provided. It describes the development of electrochemical, potentiometric, piezoelectric and optical platforms for the monitoring of foodborne bacterial pathogens by incorporating monoclonal, polyclonal or recombinant antibodies in a variety of different assay formats. Polyclonal antibodies (pAb) are typically raised in rabbits, goats or sheep [29] , and their popularity is illustrated by the fact that they are frequently selected in immunosensor-based assays for pathogen detection. Hence, the selection of a highly-specific epitope on the pathogen is a key consideration, since many bacterial strains share homologues of surface-presented proteins which can lead to the detection of multiple cell-types by a single antibody. Muhammad-Tahir and Alocilja [74] developed a conductimetric biosensor incorporating a polyclonal antibody-based sandwich assay format in which the detection antibody was labelled with polyaniline. doi = 10.3390/s90604407 id = cord-282817-vtzpf2wr author = Byrne, Hannah title = A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications date = 2013-10-02 keywords = CD3; SARS; antibody; bispecific; cell; figure summary = Despite significant positive clinical results, especially in the case of hematological malignancies, adverse clinical outcomes and animal studies have highlighted underlying limitations of mAbs. Accordingly, many strategies have been developed in order to improve the specificity and control the functions of antibodies. The BiTE format potentially overcomes several limiting factors relating to the biological activity of tumor-directed bsAbs. BiTEs combine the minimal binding domains (Fv fragments) of two different mAbs fused together by a short flexible linker that allows free rotation of the two arms, and thus facilitates optimal antibody:antigen interaction [28] . bsAbs are attractive in such assays because they simplify the detection steps and are currently used for the development of simple, rapid, and highly sensitive immunoassays for the detection of bacterial and viral infectious diseases and in cancer diagnostics. CD40-targeted adenoviral gene transfer to dendritic cells through the use of a novel bispecific single-chain Fv antibody enhances cytotoxic T cell activation doi = 10.1016/j.tibtech.2013.08.007 id = cord-010570-ytv7dwr0 author = Casadevall, Arturo title = Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date = 1995-07-17 keywords = antibody; human; infection; serum; therapy; treatment summary = In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. We briefly review the use of antibody-based therapy in the early 20th century and make the case for reintroducing passive antibody administration for the treatment ofinfectious diseases. Given the diminishing efficacy of existing antimicrobials because of widespread resistance and the difficulties of treating infections in immunosuppressed individuals, the reintroduction of antibody-based therapies is an option that should be given serious consideration. Thus, antibody therapy is still widely used in medicine, but its role in the treatment of infections is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. In the past, serum therapy was effective against various pathogens despite the fact that immune sera contained only small amounts of specific antibody. Antibody-based therapies have traditionally been most effective in infections where viral and toxin neutralization modifies the course of the disease. doi = 10.1093/clinids/21.1.150 id = cord-335311-l73hsik0 author = Chan, Conrad E. Z. title = The role of phage display in therapeutic antibody discovery date = 2014-08-18 keywords = antibody; display; human; library; phage summary = The defining attribute of all phage display libraries is the physical linking of antibody phenotype (specificity and affinity) with genotype (sequence) via the phage particle-this allows for in vitro selection on immobilized antigen or whole cells (Fig. 2) . In particular, a phage library constructed with the heavy chain CDR3 enriched for basic residues to improve binding to negatively charged carbohydrates produced anti-carbohydrate antibodies that had relatively high affinity (K D ≈ 50 nM) and excellent specificity (40) . Phage display is also likely to remain useful for discovery of antibodies against non-protein targets, evolution of dual-binding antibodies and for affinity maturation, due to the limitations of the natural immune system. Comparison of the efficiency of antibody selection from semi-synthetic scFv and non-immune Fab phage display libraries against protein targets for rapid development of diagnostic immunoassays The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies doi = 10.1093/intimm/dxu082 id = cord-329857-pcsuu597 author = Chan, Kuan Rong title = Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date = 2015-11-02 keywords = ADCC; antibody; virus summary = The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. doi = 10.1586/14787210.2015.1079127 id = cord-133453-23rfdkuw author = Chen, Jiahui title = Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies date = 2020-10-13 keywords = ACE2; BFE; RBD; SARS; antibody summary = By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. The vaccination mechanism is to stimulate the primary immune response of the human body, which will activate T cells and B cells to generate the antibodies and long-lived memory cells that prevent infectious diseases, which is one of the most effective and economical means for combating with COVID-19 at this stage. Notably, understanding how mutations have changed the SARS-CoV-2 structure, function, infectivity, activity, and virulence is of great importance for coming up with life-saving strategies in virus control, containment, prevention, and medication, especially in the antibodies and vaccines development. Next, we study the BFE changes ∆∆G induced by 39 mutations on the SARS-CoV-2 S protein RBD for the antibody Fab 2-4 (PDB: 6XEY) in Figure 6 . doi = nan id = cord-255683-2eq24jth author = Chen, Weizao title = Cross-Reactive Human IgM-Derived Monoclonal Antibodies that Bind to HIV-1 Envelope Glycoproteins date = 2010-02-04 keywords = Envs; HIV-1; antibody; figure summary = Ig Ms (IgMs) are on average significantly less divergent from germline antibodies and are relevant for the development of vaccine immunogens but are underexplored compared to IgGs. Here we describe the identification and characterization of several human IgM-derived mAbs against HIV-1 which were selected from a large phage-displayed naive human antibody library constructed from blood, lymph nodes and spleens of 59 healthy donors. To find whether the activity of the antibodies is related to antibody size and how the viral infection could be affected by cross-linking of HIV-1 Envs, we generated a single-chain Fv fragment (scFv) (scFv m19) of m19 and a human IgG1 Fc-fusion protein (m19Fc) of scFv m19; m19 was selected for further characterization because its light chain was relatively less divergent from the germline ( Figure 1b) and was the only one which did not contain any somatic mutations in the CDR3 of the light chain. doi = 10.3390/v2020547 id = cord-275946-ofd2ipvs author = Cheng, Matthew P. title = Serodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review date = 2020-06-04 keywords = COVID-19; CoV-2; SARS; antibody summary = Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation. Appropriately designed seroepidemiologic studies will play an essential part in the public health response to the COVID-19 pandemic by characterizing transmission dynamics, refining disease burden estimates, and providing insight into the kinetics of humoral immunity to SARS-CoV-2. Serologic surveillance studies can also assess the accumulation of persons with antibody responses over time to estimate incidence of SARS-CoV-2 infection (57, 58) and can track age-and jurisdiction-specific disease susceptibility and identify at-risk populations (59) . doi = 10.7326/m20-2854 id = cord-260340-dujd28gg author = Chenoweth, Alicia M title = Harnessing the immune system via FcγR function in immune therapy: a pathway to next‐gen mAbs date = 2020-04-12 keywords = FccR; MOA; antibody; cell summary = This is most evident for antibodies targeting cancer cells inducing antibody‐dependent killing or phagocytosis but is also true to some degree for the mAbs that neutralize or remove small macromolecules such as cytokines or other Igs. The use of mAb therapeutics has also revealed a "scaffolding" role for FcγR which, in different contexts, may either underpin the therapeutic mAb action such as immune agonism or trigger catastrophic adverse effects. Most therapeutic mAbs are IgG in origin and the heavy-chain subclass determines many of their biological properties including their long plasma half-life 3 ; complement activation, which is important in the action of some cytotoxic mAbs [4] [5] [6] and importantly engagement by their fragment crystallizable (Fc) region with specific cell surface receptors, called FccR, the subject of this review. Therapy with an IgG1 anti-cancer cell mAb may then be compromised by the inhibitory action of FccRIIb upon the ITAM signaling of the activating FccR as both types of receptor would be coengaged on such an effector cell by the mAb bound to the target cell. doi = 10.1111/imcb.12326 id = cord-005409-8mbqkzpu author = Cichon, G title = Complement activation by recombinant adenoviruses date = 2002-01-24 keywords = activation; antibody; complement summary = We have determined the level of C3a (the most reactive complement component) generated in isolated citrate plasma of healthy individuals after challenge with recombinant and wild-type adenoviruses in amounts corresponding to virus blood levels to be expected in patients during adenoviral gene therapy. It has been known for a long time that adenoviruses are able to induce an antibody-dependent activation of the complement system in human plasma, but the level of activation which is reached during clinical adenoviral gene therapy (especially in intravascular infusions) might have been underestimated in the past. We will show that challenge of isolated human plasma with serotype 5 adenoviruses in amounts corresponding to blood levels reached in the above-mentioned trial, generates a level of complement activation, which holds the potency to induce serious inflammatory reactions. 13 Systemic activation of the complement system, as known from patients suffering from sepsis, severe burns or injuries, could induce autodestructive inflammatory reactions, such as adult respiratory distress syndrome (ARDS) or multiple organ failure (MOF). doi = 10.1038/sj.gt.3301611 id = cord-340305-jtvn9tlm author = Cimolai, Nevio title = A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19 date = 2020-09-19 keywords = COVID-19; CoV-2; SARS; antibody summary = At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Others have found strong correlations between neutralizing antibodies and EIA-detected antibodies to various SARS-CoV-2 antigens [41, 42] .Some have found diversity in immune responses contingent on the nature of presenting disease [38, 43] . With the availability of viral antigen, most scientists in the know-how would be able to fashion a test for antibody determination in short order and most would likely choose an enzyme immunoassay (EIA) (or nearly equivalent non-enzymebased assay) for its potential of automation and widespread use. Sensitive and specific detection of low-level antibody responses in mild Middle East Respiratory Syndrome coronavirus infections A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients doi = 10.1007/s42399-020-00533-4 id = cord-285760-y37ji92k author = Connell, Anna R. title = Mumps Outbreaks in Vaccinated Populations—Is It Time to Re-assess the Clinical Efficacy of Vaccines? date = 2020-09-18 keywords = Immunization; MMR; antibody; mumps; outbreak; vaccination; vaccine summary = Although a rise in IgG titer may also not occur in vaccinated individuals (87, 137) , numerous studies have documented a rapid, variable increase in mumps-specific IgG levels, with neutralization antibody concentrations present up to 10 months post-infection (130, 138, 139) . Potential waning immunity has been documented in the current mumps outbreaks seen in Europe and the USA, mostly affecting young adults within highly vaccinated populations attending tertiary education who have received two doses of the MMR vaccine in early childhood (40, 110, 126, 144, 145, (175) (176) (177) (178) (179) (180) (181) . Although MuV can be clinically asymptomatic in about 15-30% of those who become infected, the vaccine against mumps confers protection in a dose response manner; unvaccinated individuals saw an attack rate of Based on the reduction seen upon the introduction of a mumps vaccine, it has been proposed that MMR vaccination also prevents the transmission of the virus. doi = 10.3389/fimmu.2020.02089 id = cord-261274-y74smbtd author = Crouch, C. F title = Lactogenic immunity following vaccination of cattle with bovine coronavirus date = 2000-09-15 keywords = antibody summary = Abstract In order to investigate the ability of an oil adjuvanted vaccine containing bovine coronavirus antigen to enhance lactogenic immunity in the calf, pregnant cows and heifers were vaccinated and specific virus neutralising antibody levels determined in serum, colostrum and milk. Pre-existing antibody titres (as a result of natural infection) in the serum of these animals were found to be significantly increased as a result of a single shot vaccination carried out between 2 and 12 weeks before calving. This hypothesis was supported by the observations on the magnitude of the antibody titres found in the colostrum and milk of cows vaccinated at dierent times pre-calving with a vaccine containing 150 antigen units of BCoV. This report indicates that a single dose of coronavirus vaccine administered to the pregnant heifer 2 to 12 weeks before calving is capable of signi®cantly increasing the titre and duration of speci®c antibody present in colostrum and milk. doi = 10.1016/s0264-410x(00)00177-8 id = cord-290783-ipoelk4h author = Crouch, C. F. title = Vaccination against enteric rota and coronaviruses in cattle and pigs: Enhancement of lactogenic immunity date = 1985-09-30 keywords = antibody; calf; infection; rotavirus summary = This article examines methods currently used to enhance the titre and duration of specific antibody in the mammary secretions of cows and pigs with particular reference to rotavirus and coronavirus infections. The situation in neonatal piglets is less clear, rotavirus infections are apparently common 6.t4-tt, w.hilst transmissible gastroenteritis virus (TGEV), the prototype enteric coronavirus in swine, is an example of a seasonal cold-weather disease, probably related to both the thermal sensitivity of the virus ~ and the effect of cold-stress on converting subclinical to clinical infections ~8. It is apparent that the enhancement of lactogenic immunity through the vaccination of the dam provides a suitable mechanism by which neonatal pigs and calves can be protected against rotavirus and coronavirus infections. Passive immunity in calf rotavirus infections: Maternal vaccination increases and prolongs immunoglobulin G 1 antibody secretion in milk Antibody responses in serum, colostrum and milk of swine after infection or vaccination with transmissible gastroenteritis virus doi = 10.1016/s0264-410x(85)90056-8 id = cord-004167-r2s0gks8 author = Cutts, Julia C. title = Pregnancy-specific malarial immunity and risk of malaria in pregnancy and adverse birth outcomes: a systematic review date = 2020-01-16 keywords = Plasmodium; VAR2CSA; antibody; study summary = Antibody responses to pregnancy-specific pRBC and VAR2CSA antigens, measured at delivery, were associated with placental malaria (9 studies) and may therefore represent markers of infection, rather than correlates of protection. To summarize, evidence from studies included in narrative terms suggests that whilst high avidity Abs and anti-adhesion Abs measured at delivery may be associated with protection from placental infection [65] and reduced placental parasitaemia [38] , respectively, total IgG responses to VAR2CSA antigens and pregnancy-specific pRBC are positively associated with the presence of placental malaria [34, 39, 64, [68] [69] [70] [71] [72] 76] . Overall, the majority of estimates included in this review, and studies included in narrative terms, indicate that when measured at delivery, antibody responses to pregnancy-specific pRBC and VAR2CSA antigens are associated with the presence of placental infection and may therefore represent markers of infection, rather than correlates of protection. doi = 10.1186/s12916-019-1467-6 id = cord-022439-8wy7rpqv author = DENMAN, A.M. title = Viral Etiology of Polymyositis/Dermatomyositis date = 2013-11-17 keywords = antibody; cell; viral; virus summary = doi = 10.1016/b978-0-409-95191-2.50010-0 id = cord-103255-4k13re9y author = Daniell, Henry title = Medical molecular farming: production of antibodies, biopharmaceuticals and edible vaccines in plants date = 2001-05-01 keywords = antibody; plant; protein; transgenic summary = The production of recombinant proteins in plants has many potential advantages for generating biopharmaceuticals relevant to clinical medicine. In the decade since the expression and assembly of immunoglobulin (Ig) heavy and light chains into functional antibodies was first shown in transgenic tobacco, plants have proven to be versatile production systems for many forms of antibodies. Other advantages of tobacco include its relative ease of genetic manipulation, production of large numbers of seeds (up to a million per plant) and an impending need to explore alternate uses for this hazardous crop. However, the most attractive species for expressing subunit vaccine components should have high levels of soluble protein that is stable during storage; seed crops such as cereals are particularly suitable. Induction of a protective antibody response to foot and mouth disease in mice following oral or parenteral immunization with alfalfa transgenic plants expressing the viral structural protein VP1 doi = 10.1016/s1360-1385(01)01922-7 id = cord-339879-92esdjy9 author = Delhalle, Sylvie title = Phages and HIV-1: From Display to Interplay date = 2012-04-13 keywords = CCR5; CD4; Fab; HIV-1; antibody; display; epitope; peptide; phage; rpl summary = The BNtAb IgG1 b12 was the first neutralizing MAb selected from a phage-displayed Fab (antibody fragment composed of one constant and one variable domain of the heavy (CH1 and VH) and the light (CL and VL) chains linked together) library derived from an HIV-1-infected donor (See section 3.1.1.1.1.) [41] . At the end of the second round, selected phages displaying longer inserts of 40 to 50 AA corresponding to the N-and C-terminal regions of Gag were identified, revealing the presence of two distinct antigenic regions in Gag. This study demonstrated that gene-fragment phage display could be used to identify epitopes targeted by polyclonal Abs. Although they occur at a very low frequency in humans, antibodies targeting host proteins involved in HIV-1 infection have been reported in immunized animals. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries doi = 10.3390/ijms13044727 id = cord-275402-z92b18mb author = Diamant, Eran title = Monoclonal Antibody Combinations that Present Synergistic Neutralizing Activity: A Platform for Next-Generation Anti-Toxin Drugs date = 2015-05-29 keywords = MAbs; antibody; combination; neutralization; toxin summary = doi = 10.3390/toxins7061854 id = cord-331786-wgt7kg6f author = Diego-Martin, Borja title = Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date = 2020-10-13 keywords = Fig; RBD; SARS; antibody summary = For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. doi = 10.1101/2020.10.13.331306 id = cord-017070-05vlz5dn author = Dimitrov, Dimiter S. title = Human Monoclonal Antibodies Against HIV and Emerging Viruses date = 2008 keywords = HIV; SARS; antibody; virus summary = These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1007/978-1-59745-569-5_34 id = cord-297684-9q3oopaz author = Dobaño, Carlota title = Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date = 2020-06-12 keywords = ELISA; SARS; antibody; figure summary = doi = 10.1101/2020.06.11.147363 id = cord-018404-jdu4h00e author = DuBourdieu, Dan title = Colostrum Antibodies, Egg Antibodies and Monoclonal Antibodies Providing Passive Immunity for Animals date = 2019-03-11 keywords = animal; antibody; calf; colostrum; passive summary = doi = 10.1007/978-3-030-04624-8_18 id = cord-023731-jqgervt7 author = FENNER, FRANK title = Laboratory Diagnosis of Viral Diseases date = 2014-06-27 keywords = animal; antibody; diagnosis; viral; virus summary = Having allocated it to a particular family (e.g., Adenoviridae), one can then go on to determine the species or serotype (e.g., canine Immunodiffusion Antibody neutralizes infectivity of virion; inhibits cytopathology, reduces plaques, or protects animals Antibody inhibits viral hemagglutination Antigen-antibody complex binds complement, which is thereafter unavailable for the lysis of hemolysissensitized sheep red blood cells Antibody-aggregated virions are visible by electron microscopy Antibody labeled with fluorochrome binds to intracellular antigen; fluoresces by UV microscopy Peroxidase-labeled antibody binds to intracellular antigen; colored precipitate forms on adding substrate Enzyme-labeled antibody (or antigen) binds to antigen (or antibody); substrate changes color Radiolabeled antibody (or antigen) binds to antigen (or antibody), e.g., attached to solid phase Antibodies and soluble antigens produce visible lines of precipitate in a gel adenovirus 1) by more discriminating serological procedures. doi = 10.1016/b978-0-12-253055-5.50017-7 id = cord-257465-9yrf7ofy author = Finlay, William J. J. title = Phage Display: A Powerful Technology for the Generation of High-Specificity Affinity Reagents from Alternative Immune Sources date = 2016-05-23 keywords = antibody; phage; protein summary = These libraries are analogous to the naïve antibody repertoire in an animal, and selecting from them can result in the identifi cation of antibody fragments that exhibit high specifi city and occasionally high affi nity for the target protein. This process utilizes phage display for selection from germline targeting combinatorial libraries which results in the identifi cation of CDR residues amenable to human germ-lining without compromising on specifi city and affi nity. Nevertheless, phage display can be a relatively simple technology to use and when employed to harness natural repertoires of antibodies from immunized animals, it can offer a rapid path to highly specifi c, high-affi nity antibodies against problematic antigens . The immunized chickens appear to react to the proteins fully independently, as the phage display libraries generate individual scFv antibody clones that are fully specifi c by western blot and ELISA , showing no reactivity to their co-immunogens [ 37 , 59 ] . doi = 10.1007/978-1-4939-6412-3_6 id = cord-305039-grsv06j7 author = Flego, Michela title = Clinical development of monoclonal antibody-based drugs in HIV and HCV diseases date = 2013-01-04 keywords = HCV; HIV; HIV-1; PD-1; antibody; cell summary = As for HIV, mAbs directed against spike viral proteins, as well as against host receptors, may act at an early stage of infection by preventing the binding of the virus on the cell surface. In some chronic viral infections, virus-specific immune cells may persist in a ''non-functional'' state, because of an imbalance of immunoregulatory signals involving multiple inhibitory and activating receptors, triggered by soluble factors and/or cell surface ligands. Therapeutic approaches using specific mAbs to block host immunosuppressive molecules (antagonism) or to trigger activating receptors (agonism) may be a valid strategy to restore immune cell function and treat various chronic viral infections. In a proof-of-concept passive immunization trial with humans, it has been demonstrated that a cocktail of the three broadly neutralizing mAbs -2G12, 4E10 and 2F5was able to delay viral rebound in patients whose infections were fully suppressed by antiretroviral treatment before administration of the antibodies [76] . doi = 10.1186/1741-7015-11-4 id = cord-282081-qaagup4d author = Flicker, Sabine title = Nanobodies—Useful Tools for Allergy Treatment? date = 2020-09-30 keywords = AIT; allergen; antibody; nanobodie; specific summary = Their superior properties such as chemical stability, high affinity to a broad spectrum of epitopes, low immunogenicity, ease of their generation, selection and production proved nanobodies also to be remarkable to investigate their efficacy for passive treatment of type I allergy, an exaggerated immune reaction to foreign antigens with increasing global prevalence. Similar to the evaluation of conventional antibodies with the focus to identify effective protective monoclones, generated nanobodies have to be assessed first for their allergen specificity, epitope recognition, cross-reactivity to homologous allergens present in related species, for their affinity to their corresponding allergens and most importantly for their ability to inhibit patients''IgE binding to these allergens (Figures 2A-C) . doi = 10.3389/fimmu.2020.576255 id = cord-330218-l5q3n3ri author = Foss, Stian title = TRIM21: a cytosolic Fc receptor with broad antibody isotype specificity date = 2015-10-26 keywords = ADIN; PRYSPRY; antibody; trim21 summary = Neutralization of viruses by antibodies is predicted to depend on high-affinity binding to specific epitopes of surface-exposed viral proteins that are required for binding to target cell receptors (4) . These effector functions are induced upon binding of antibody-virus immune complexes to classical Fc c receptors (FccRs) expressed on the surface of hematopoietic cells such as natural killer (NK) cells, macrophages, and dendritic cells, which results in clearance and induction of T-cell responses (8) . Low antibody-virus stoichiometry may also result in inefficient FccR-mediated effector functions by immune cells as efficient phagocytosis requires the formation of immune complexes and cross-binding to cell-surface FccRs. In addition, as TRIM21 also engages IgM and IgA, it is likely to contribute to early protection, and at the gate of entry of most viral pathogens, the mucosal barrier. doi = 10.1111/imr.12363 id = cord-015742-nt44jcjm author = Garwes, D.J. title = Antigenicity of structural components from porcine transmissible gastroenteritis virus date = 2002-11-13 keywords = TGEV; antibody summary = Incubation of 3H-uridine TGEV with sera from sows inoculated with viral antigen resulted in the formation of immune complexes that were retained by membrane filters (Fig. 2) . Sera from sows inoculated with whole virus, SP antigen or SVP antigen preparations produced virus complexes that were retained most efficient Samples of 3H-uridine labelled TGEV containing 4000 ct/min were incubated for 2 h at 37°C in dilutions of test sera followed by incubation with rabbit anti-porcine IgG serum. Analysis of the immunoglobulin classes responsible for neutralising activity after inoculation of sows by the intramammary route showed that IgG was the predominant antibody species in both serum and colostrum, consistent with previous findings with inactivated TGEV Lucas et al., 1974) but differing from the stimulation of IgA to ferritin reported by Bourne et al. 9, which received SP antigen, produced neutralising antibody of the IgA class in the colostrum and was the only animal capable of protecting her piglets against challenge with live virus. doi = 10.1016/0378-1135(79)90034-8 id = cord-341305-zf97tcwe author = Ge, Shikun title = Canine Parvovirus is diagnosed and neutralized by chicken IgY-scFv generated against the virus capsid protein date = 2020-09-03 keywords = CPV; antibody; figure; vp2 summary = The CPV-VLP and CPV-VP2 protein showed similar reaction values to the purified scFv in the ELISA test, and the results of ELISA analysis using IgY-scFv toward CPV clinical samples were consistent with commercial immunochromatographic assay (ICA) and PCR detection, the scFv did not show cross reactivity with canine distemper virus (CDV) and canine coronavirus (CCV). This study revealed the feasibility of a novel functional antibody fragment development strategy by generating diversified avian IgY-scFv libraries towards the pathogenic target of interest for both detection and therapeutic purposes in veterinary medicine. Functional antibody fragments (i.e.: scFv, Fab) generated by phage-display technology have been not yet routinely evaluated and applied in the veterinary medicine despite it has been well confirmed that such engineered antibodies offer a series of advantages over polyclonal and full-length monoclonal antibodies. doi = 10.1186/s13567-020-00832-7 id = cord-342242-cynpob7b author = Godakova, Svetlana A. title = Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice date = 2019-08-07 keywords = BoNT; USA; antibody; vhh summary = Based on the analysis of B11-Fc and G3-Fc clones'' circulation time in the serum (presence of antibodies 14 days after injection), we decided to conduct an experiment on the survival of these mice, which previously received a single injection of the VHHs with the Fc fragment, with a repeated administration of only the lethal toxin dose 14 days after the original administration. Overall, we obtained numerous clones after two rounds of biopanning; we selected 15 clones for initial analysis based on their CDR3s, chose two clones (B11 and G3) with the best pre-mixed results in phage form in vivo, produced them in protein form, and modified their structure and characteristics by dimerization via a (Gly4Ser) 3 linker and fusion to a human IgG Fc fragment to enhance their protective activity. doi = 10.3390/toxins11080464 id = cord-015683-a9a82of4 author = Gupta, Varsha title = Molecular Diagnostics date = 2016-10-23 keywords = ELISA; PCR; antibody; dna summary = Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Binding of another antigen-specifi c antibody linked with enzyme results in color formation upon addition of the substrate 9.2 Diagnosis of Bacterial, Viral, and Parasitic Diseases peptide may react in some assays but not in others as some regions of a peptide may be more immunogenic than others. Because of the specifi city, homogeneity, and unlimited availability of the MAbs, vast amount of work has been carried out on the production/development The immuno-diagnoses of protozoan and parasitic diseases have signifi cantly been improved by MAb technology because the tests involving MAb as diagnostic reagents overcome the limitations of polyclonal antibodies. The sensitivity and specifi city of a PCR assay is dependent on target genes, primer sequences, PCR techniques, DNA extraction procedures, and PCR product detection methods. doi = 10.1007/978-981-10-0875-7_9 id = cord-001726-d7iwkatn author = Henry, Kevin A. title = Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date = 2015-08-04 keywords = M13; antibody; display; filamentous; peptide; phage; protein summary = Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage''s potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage''s large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. While in some cases the results of these studies have been promising, antibody epitope-based peptide vaccines are no longer an area of active research for several reasons: (i) in many cases, peptides incompletely or inadequately mimic epitopes on folded proteins (Irving et al., 2010 ; see below); (ii) antibodies against a single epitope may be of limited utility, especially for highly variable pathogens (Van Regenmortel, 2012); and (iii) for pathogens for which protective immune responses are generated efficiently during natural infection, peptide vaccines offer few advantages over recombinant subunit and live vector vaccines, which have become easier to produce over time. doi = 10.3389/fmicb.2015.00755 id = cord-327629-ep28ay11 author = Herron, J.B.T. title = Coronavirus antibody positive tests and continued use of personal protective equipment throughout the pandemic date = 2020-06-20 keywords = COVID-19; antibody summary = authors: Herron, J.B.T.; Dennis, J.; Brennan, P.A. title: Coronavirus antibody positive tests and continued use of personal protective equipment throughout the pandemic Antibody testing has rapidly been deployed but it is creating challenges for staff and patients. Mask use has come to the forefront and human factor (HF) strategies must be examined to reduce risk associated with lack of engagement from both healthcare staff and patients. Suggested plans have included developing a cohort of immune staff to care for COVID-19 patients allowing for a relaxation of overstretched personal protection equipment (PPE) resources. Masks reduce nosocomial spread and are important, particularly for healthcare staff (19) . For the antibody test, even after the exact nature of protection is determined, basic public health measures are not forgotten and that staff feel able to challenge those in more authoritative positions regarding PPE. Personal protective equipment and Covid 19-a risk to healthcare staff? doi = 10.1016/j.bjoms.2020.06.021 id = cord-345296-4z7yfj5s author = Ho, Mei-Shang title = Neutralizing Antibody Response and SARS Severity date = 2005-11-17 keywords = SARS; antibody; patient summary = Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. To adjust the time effects and other covariates of interest, the relationship between antibody titer, based on logarithmic transformation of base 2 (serum dilution) and other potential factors, i.e., age, sex, infection source, and duration of illness, was quantified by linear mixed models (18) , which took into account the correlation between repeated measurements of each study participants. In the model, patients with a more severe clinical course had earlier and higher antibody responses; we then examined the death rate of the early responders (Table 6 ). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways doi = 10.3201/eid1111.040659 id = cord-328935-mn8r972x author = Hodgins, Douglas C. title = Mucosal Veterinary Vaccines: Comparative Vaccinology date = 2015-03-13 keywords = PRRSV; Saif; TGEV; antibody; response; vaccine summary = Studies of the potential of novel adjuvants to improve vaccine efficacy against genetically unstable, immune-subverting RNA viruses, such as porcine reproductive and respiratory syndrome virus in pigs, should assist in the control of pathogens with similar characteristics in other species. However, a recent study showed that an inactivated reassortant RV strain (CDC-9 strain) formulated with aluminum phosphate and administered systemically in gnotobiotic pigs resulted in induction of serum IgG antibody titers, coinciding with partial protection against shedding and diarrhea, suggesting that adjuvant may have stimulated local specific (gut IgA antibodies) or nonspecific immune responses, which were not assessed in this study (Wang et al., 2010) . Intranasal delivery of whole cell lysate of Mycobacterium tuberculosis induces protective immune responses to a modified live porcine reproductive and respiratory syndrome virus vaccine in pigs doi = 10.1016/b978-0-12-415847-4.00068-9 id = cord-296928-wu14k7u9 author = Hofmann, Tim title = Greatest Hits—Innovative Technologies for High Throughput Identification of Bispecific Antibodies date = 2020-09-08 keywords = antibody; bispecific; cell; protein; screening summary = In this review, we provide an overview of the most relevant methodologies for bispecific screening purposes—the DuoBody concept, paired light chain single cell production approaches, Sortase A and Transglutaminase, the SpyTag/SpyCatcher system, and inteins—and elaborate on the benefits as well as drawbacks of the different technologies. In order to overcome this bottleneck, technologies such as controlled Fab-arm exchange used for DuoBodies [22] , paired light chain single cell production approaches [23] , microbial transglutaminase [24] or Sortase A [25] mediated bioconjugation, the SpyTag/SpyCatcher system [26, 27] , or split inteins [28] were adapted to enable broad bispecific antibody screening ( Figure 1 ). In order to overcome this bottleneck, technologies such as controlled Fab-arm exchange used for DuoBodies [22] , paired light chain single cell production approaches [23] , microbial transglutaminase [24] or Sortase A [25] mediated bioconjugation, the SpyTag/SpyCatcher system [26, 27] , or split inteins [28] were adapted to enable broad bispecific antibody screening ( Figure 1 ). doi = 10.3390/ijms21186551 id = cord-004247-lagv3tp7 author = Hooft van Huijsduijnen, Rob title = Reassessing therapeutic antibodies for neglected and tropical diseases date = 2020-01-30 keywords = Cryptococcus; HIV; Pneumocystis; antibody; cell; infection summary = This mAb was protective in an in vitro, antigen-dependent, cellular cytotoxicity assay with rat macrophages or eosinophils and also in vivo during the early phase of infection Second, beyond the cell-surface proteins, schistosomes also express a large number of glycans as part of their glycoprotein and glycolipid repertoire, and an antibody response against those glycans is mounted by the infected host [80] . In addition to antibodies that directly target and inhibit the fungal pathogen, mAbs can be directed to checkpoints that control the host immune response. In addition to highlighting the potential of mAbs as therapeutics, these studies have demonstrated the diversity of inhibitory actions that mAbs can perform on cryptococcal cells, which can include opsonization and increased phagocytosis, inhibition of fungal growth, capsular polysaccharide release and biofilm formation, antibody-mediated target cleavage, and augmentation of the host response [104] [105] [106] [107] . doi = 10.1371/journal.pntd.0007860 id = cord-001435-ebl8yc92 author = Hoppe, Sebastian title = Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date = 2014-10-21 keywords = A.U.; KPN_00363; PCR; antibody; protein summary = Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen. Incubation with antibodies reactive to either of those two bacterial species resulted in signal intensities in the neighbourhood of the negative control independent of sequence alterations, see Figure 11 . In contrast, the other two proteins displaying linear epitopes, KPN_00363 and KPN_00459, indicated some specificity with the antibodies tested and two linear consensus sequences could be derived, GAVVALSTTFA and GIAFGAVELFD, respectively. doi = 10.1371/journal.pone.0110703 id = cord-355610-7xy4s483 author = Hu, Dan title = A broadly neutralizing germline-like human monoclonal antibody against dengue virus envelope domain III date = 2019-06-26 keywords = DENV; DIII; Fig; antibody; m366.6 summary = Here, by using sequential antigen panning of a yeast antibody library derived from healthy donors against the DENV envelop protein domain III (DIII) combined with depletion by an entry defective DIII mutant, we identified a cross-reactive human monoclonal antibody (mAb), m366.6, which bound with high affinity to DENV DIII from all four DENV serotypes. Furthermore, as the first germline-like mAb derived from a naïve antibody library that could neutralize all four DENV serotypes, the m366.6 can be a tool for exploring mechanisms of DENV infection, and is a promising therapeutic candidate. Its fully human origin, the germline-like nature, combined with high-affinity and broad neutralizing activity toward all DENV serotypes, suggest that m366.6 is a promising candidate antiviral agent and may also provide a unique template for designing effective dengue vaccine immunogens. Two antibodies, designated as m360 and m366, bound potently to DENV DIIIs. Their scFv gene were fused with human IgG1 Fc for protein expression, and surface plasmon resonance (SPR) experiments were used to evaluate the antigens binding. doi = 10.1371/journal.ppat.1007836 id = cord-032598-i0jm3p1s author = Hu, Jing title = Direct imaging of antigen–antibody binding by atomic force microscopy date = 2020-09-24 keywords = Fig; IgE; antibody summary = In this study, the morphology of biotinylated antibody-specific Immunoglobulin E (IgE) immune complexes has been successfully imaged by atomic force microscopy (AFM) in the tapping-mode. The AFM images indicated that the individual immune complex was composed of an IgE and a biotinylated antibody. To the best of our knowledge, the biotinylated antibody-specific IgE immune complexes imaged by AFM have never been reported. Meanwhile, Fig. 6d , h and l would represent the biotinylated antibody-specific IgE immune complex adsorbed on the mica surface by the IgE fragment and the two Fab fragments of biotinylated antibody. In this paper, the morphology and length of IgE, biotinylated antibodies and biotinylated antibody-specific IgE immune complexes were analyzed by AFM, respectively. The results of AFM imaging demonstrated that the immune complexes exhibited various morphologies, and we were able to identify the IgE and biotinylated antibody based on the protein morphology in most cases. doi = 10.1007/s13204-020-01558-w id = cord-009581-bvihkf1r author = Hurd, Eric R. title = Virus antibody levels in systemic lupus erythematosus date = 2005-11-22 keywords = SLE; antibody summary = Antibody titers to a group of viral antigens have been determined in sera from patients with systemic lupus erythematosus (SLE), control groups with inflammatory diseases and normals. In a preliminary study in this laboratory (23) of viral antibody titers in patients with lupus nephritis and matched normal controls, complement fixing antibody titers were significantly elevated to a number of myxoviruses, coronavirus OC 43 and herpes simplex virus. In the present study, an attempt has been made to compare viral antibody titers in SLE with those of control groups with inflammatory diseases as well as normal individuals. However, it is possible that the tubular structures are evidence of chronic infection in S L E with a passenger virus of a type which might act as an adjuvant for the overall elevation in viral antibody titer observed. doi = 10.1002/art.1780150308 id = cord-300701-vkzya7uq author = Ijaz, M. K. title = Effect of different routes of immunization with bovine rotavirus on lactogenic antibody response in mice date = 1987-12-31 keywords = BRV; ELISA; antibody summary = Summary The effect of different routes of immunization with either live or killed bovine rotavirus (BRV) on the production of lactogenic antibody response in mice was evaluated. Taking this into consideration, we have utilized the murine model to study the influence of different routes of immunization with either live or killed BRV on the rate of decline of antibody titers and different subtypes in the lacteal secretions of the da-m following parturition up to eleven days. Titers of anti-rotavirus antibodies in lacteal secretions, as determined by ELISA, also revealed a similar pattern as seen in the groups immunized with killed BRV. Although administration of live or killed BRV at mucosal sites (intestine and mammary regions) not only induced a significant elevation of IgA, IgM and IgG antibodies in lacteal secretions there was also a marked increase in serum anti-rotavirus antibodies as determined by ELISA. doi = 10.1016/s0166-3542(87)80006-2 id = cord-254821-px4fe7mn author = Infantino, Maria title = Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date = 2020-05-10 keywords = SARS; antibody summary = Sixty‐one COVID‐19 patients and 64 patients from a control group were tested by iFlash1800 CLIA analyzer for anti‐SARS CoV‐2 antibodies IgM and IgG. The more relaxed rules of the FDA''s "Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency" issued on 16 March 2020, 9 has allowed the market easier access to these tests as well as easier and faster diagnostics, but the lack of control in the production process is also dangerous making these tests potentially less reliable. 11 The aim of the this study was to assess the diagnostic performance of a novel fully automated CLIA for the quantitative detection of anti-SARS-CoV-2 IgM and IgG antibodies. 16 As with most existing studies on the diagnostic performance of the SARS-CoV-2 antibodies, our preliminary data showed that most COVID-19 patients have both IgM and IgG, and only few of them have isolated IgG or IgM antibodies. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Assessment of immune response to SARS-CoV-2 with fully-automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays doi = 10.1002/jmv.25932 id = cord-335121-ro3x3qa3 author = Ingram, George A. title = A comparative assessment of four serological methods used in the detection and measurement of anti-parasite antibodies in the serum of the amphibian, bufo viridis date = 1988-04-30 keywords = ELISA; PBS; antibody summary = Abstract Antibodies against Crithidia fasciculata choanomastigotes were detected in green toad (Bufo viridis) sera by direct agglutination, indirect haemagglutination (IHA), complement-fixation test (CFT) and enzyme-linked immunosorbent assay (ELISA), Correlation coefficients (r) were calculated for comparisons between each of the techniques and regression formulae derived in order to convert antibody levels as determined by one immunological method to that of another. In this paper we present the results of acomparative assessment of four serological tests (direct agglutination, indirect haemagglutination, complement-fixation test and ELISA) used to detect and to determine the levels of antibodies in the sera of green toads (B. fasciculata and the number of control and immune sera containing detectable antibodies were the lowest for DA and CFT, intermediate for IHA and highest for the ELISA method (Table 1) . Nevertheless the method of antigen preparation ma> not be a salient criterion for antibody estimation in immune sera because correlation values of over 89% (f''< 0.001) were found when IHA titres were compared to those of ELISA. doi = 10.1016/0020-7519(88)90147-6 id = cord-338517-1mxcssjj author = Ishay, Yuval title = Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date = 2020-08-26 keywords = COVID-19; RBD; SARS; antibody; patient summary = The phage display method, allowing rapid and wide display of proteins directly correlated to their associated genes, can detect NAbs against SARS-CoV from both naïve and immune antibody libraries, capable of blocking the binding of S1 domain, thereby showing virus neutralization and prophylaxis capability either in vitro or in the animal models (31, 33, 36) . Another method, possibly allowing the production and utilization of existing NAbs, may include the use of Epstein-Barr virus (EBV) transformation of human B cells to improve the isolation of NAbs from the memory B cells harvested from the SARS-CoV infected patients (11) . Experimental and clinical data on the use of convalescent plasma products and humanized monoclonal antibodies for H5N1 influenza infection have also shown positive outcomes, and this treatment was proposed as a mean for overcoming anti-viral drug resistance (62, 79, 80) . In a study involving 20 patients with severe pandemic influenza A (H1N1) 2009 virus infection, administration of convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality (81) . doi = 10.1002/hep4.1600 id = cord-255936-hfa9w2dg author = Jin, Junyeong title = The level of decoy epitope in PCV2 vaccine affects the neutralizing activity of sera in the immunized animals date = 2018-02-12 keywords = PCV2; antibody summary = In this study, we tested this hypothesis by generating an antibody specific to the decoy epitope on the capsid protein of porcine circovirus type 2 (PCV2). To monitor the reactivity of sera to the CP 169e180 epitope, enzyme immunoassays, using BSA-conjugated CP 169e180 peptides and HRPconjugated anti-guinea pig IgG antibodies (Bethyl Laboratories), were performed as described previously. In a competition enzyme immunoassay employing a microtiter plate coated with BSA-conjugated CP 169e180 peptide and HRP-conjugated anti-porcine IgG antibody, the recombinant anti-CP 169e180 antibody almost completely inhibited the binding of naturally occurring anti-CP 169e180 antibody to the peptide in a PCV2-infected pig''s sera (Fig. 2) . In an enzyme immunoassay employing a microtiter plate coated with BSA-conjugated CP 169e180 peptide, sera from animals immunized with vaccine A had a significantly higher antibody titer than vaccine B-vaccinated animals (p < 0.01) (Fig. 3D) . doi = 10.1016/j.bbrc.2018.01.141 id = cord-267736-rya9w6sh author = Kang, Xiaoping title = Development of an ELISA-array for simultaneous detection of five encephalitis viruses date = 2012-02-27 keywords = ELISA; PBS; antibody summary = The ELISA-array assay is based on a "sandwich" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that this method combined the advantage of ELISA and protein array (multiplex and ease of use) and has potential for the identification of clinical encephalitis virus. When spotting, different spotting buffers and concentrations of capture monoclonal antibodies were evaluated to optimize the ELISA-array assay. To verify the results tested by ELISA-array, RNA extracted from chicken eggs was applied to a real time-RT-PCR assay using primers and probes targeting TBEV. In this study, we developed a multiplex ELISA-based method in a double-antibody sandwich format for the simultaneous detection of five encephalitis-associated viral pathogens. doi = 10.1186/1743-422x-9-56 id = cord-018840-ts2g1ux7 author = Katragkou, Aspasia title = Role of Immunoglobulin Therapy to Prevent and Treat Infections date = 2018-06-19 keywords = IVIG; antibody; immunoglobulin; patient; sepsis summary = While the main clinical applications of immunoglobulin therapy concern their use as replacement for patients with primary immunodeficiencies, or as treatment for autoimmune and inflammatory disorders, their role in infectious disease is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. The first clinical trial, which evaluated the effect of IgMA-enriched immunoglobulin preparation (7.8 g IgM, 7.8 g IgA, and 49.4 g IgG), which have shown to contain superior antibody content against bacterial lipopolysaccharides, in an appreciable number of neutropenic patients with hematologic malignancies and sepsis or septic shock, showed that immunoglobulins had no beneficial effects [51] . A controlled trial of long-term administration of intravenous immunoglobulin to prevent late infection and chronic graft-vs.-host disease after marrow transplantation: clinical outcome and effect on subsequent immune recovery doi = 10.1007/978-3-319-77674-3_17 id = cord-309067-aemjbkfj author = Kennedy, Melissa title = Methodology in diagnostic virology date = 2005-03-01 keywords = Fig; antibody; assay; virus summary = doi = 10.1016/j.cvex.2004.09.009 id = cord-326673-p8qbxi57 author = Kitching, R. P. title = The interference by maternally-derived antibody with active immunization of farm animals against foot-and-mouth disease date = 1995-12-31 keywords = FMD; MDA; antibody; vaccination summary = This maternally-derived antibody (MDA) provides immediate protection against infection with FMD virus, but also interferes with the development of active immunity following vaccination. However, this maternally derived antibody (MDA) is equally effective in preventing the response to active vaccination in the young animal as it is in providing protection against disease. In the case of FMD vaccination in pigs, Francis and Black (1986) concluded that the complete immunological unresponsiveness seen in the first 2 weeks of life was due to immaturity of the immune system and antigen blockade by high titre MDA, and as this titre declined an active suppression of T and/or B cells occurred to variable degrees. Francis and Black (1984) found no evidence in the pig that vaccination in the presence of MDA depressed the specific antibody to FMD virus. The effect of maternally derived antibodies on the response of calves to vaccination against foot-and-mouth disease doi = 10.1016/s0007-1935(95)80127-8 id = cord-009446-8keu2uay author = Kreer, Christoph title = Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies date = 2020-01-01 keywords = HIV-1; antibody; cell summary = Focusing on the development of highly potent broadly neutralizing antibodies against HIV-1, we discuss how a detailed knowledge of the human B cell repertoire may support the development of novel vaccination strategies. Indeed, the generation of optimized bait proteins [30] or native-like envelope trimers [45] were critical steps to improve the isolation of potent HIV-1 broadly neutralizing antibodies (bNAbs) by antigen-specific sorting strategies [31, [46] [47] [48] . Only a small fraction of HIV-1-infected individuals develop highly potent bNAbs and detailed analyses of B cell receptors and antibodies at a single cell level have been limited to a few dozen subjects. Thus, a detailed understanding of the naïve B cell receptor repertoire and the constantly adapting antibody response in the context of HIV-1 infection can be highly informative for vaccine design. doi = 10.3390/vaccines8010013 id = cord-317501-yblzopc3 author = Kuhn, Philipp title = Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date = 2016-06-21 keywords = Fab; antibody; display; human; library; phage; single; virus summary = Panning against peptides, recombinant viral proteins, or complete virus particles has led to the identification of antibodies directed against human pathogenic viruses such as Sin nombre virus [100] , Dengue virus [101, 102] , Influenza virus [103, 104] , VEEV [105] , Norovirus [106] , SARS coronavirus [107] , or Hepatitis C [108] from naïve antibody gene libraries. A naïve human Fab-phage library was screened for NS5-specific antibody fragments using various NS5 variants from Dengue Virus serotypes 1-4 as antigens for panning and characterization [128] . [180] reported the isolation of a human monoclonal antibody against the Block 2 region of Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) by phage display from a malaria patient derived scFv library. In this context, the antibody phage display offers a powerful tool for antibody selection and allows the isolation of neutralizing antibodies against complete active toxins or special domains by using different human naïve antibody libraries with high diversity [185] [186] [187] . Single chain variable fragment antibodies against Shiga toxins isolated from a human antibody phage display library doi = 10.1002/prca.201600002 id = cord-328753-qwdxgk4z author = Lafaye, Pierre title = Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date = 2018-09-25 keywords = antibody; domain; single; vhh; virus summary = The antigen-binding region of such homodimeric heavy-chain only antibodies consists of one single domain, called VHH. VHHs provide many advantages over conventional full-sized antibodies and currently used antibody-based fragments (Fab, scFv), including high specificity, stability and solubility, and small size, allowing them to recognize unusual antigenic sites and deeply penetrate tissues. The active antigen-binding fragment of heavy chain antibodies can be cloned and expressed in the form of VHH, which consists of only one domain (Fig. 1) . Gene therapy with an adenoviral vector expressing a bispecific VHH, consisting of two linked VHHs targeting different PA-neutralizing epitopes, was tested in mice, and found to protect them from anthrax toxin challenge and anthrax spore infection [55] . [92] have been found in the sera of infected camels, whereas antibodies against rabies virus, vesicular stomatitis virus, and FMD virus have been detected in llamas [93] and could lead to the possible isolation of specific broadly neutralizing VHHs. Many neutralizing VHHs that bind to different sites on the same target, including hidden antigenic sites, can be isolated from immunized or infected camelids. doi = 10.1016/j.cimid.2018.09.009 id = cord-354790-xx6imhzb author = Lambour, Jennifer title = Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play date = 2016-08-17 keywords = HIV; antibody; response summary = 31 In addition to controlling the viral propagation by these mechanisms, the opsonization of viral particles and/or infected cells by therapeutic antiviral mAbs of the IgG type leads to the formation of immune complexes (ICs) recognizable by the FcγRs expressed on antigen-presenting cells (APCs) such as DCs. This can potentially affect the endogenous antiviral adaptive immune response of passive immunotherapy-treated individuals. Moreover, as the in vivo activity of anti-HIV-1 bNAbs, including viral load control, was recently shown to crucially depend on Fc effector functions, 53,54 an important issue is identifying that Fc-FcγRs interactions are involved in the induction of vaccinelike effects by antiviral mAbs. To understand the mechanisms underlying the enhancement of antiviral responses by ICs, several in vitro studies have addressed whether antibody-mediated viral uptake by DCs could lead to stronger activation of these cells and the development of stronger virus-specific CD4 + and CD8 + T-cell responses in an Fc-dependent manner. doi = 10.1038/emi.2016.97 id = cord-354700-bdpp3qmf author = Lanzavecchia, Antonio title = Dissecting human antibody responses: useful, basic and surprising findings date = 2018-01-23 keywords = antibody; cell summary = I will discuss how a target‐agnostic approach based on high‐throughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host–pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. I will discuss how a target-agnostic approach based on highthroughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host-pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. doi = 10.15252/emmm.201808879 id = cord-022310-yc6xtw0s author = Lappin, Michael R. title = Microbiology and Infectious Disease date = 2011-12-15 keywords = Artifacts; Bartonella; ELISA; IFA; Interpretation; PCR; antibody summary = 47 Because of these findings, it is currently recommended to combine serologic test results with those of blood culture or PCR assay results when evaluating clinically ill cats for bartonellosis. Because serologic test results do not accurately correlate with presence of bacteremia and individual culture or PCR assay results can be falsely negative, there is no indication for testing healthy cats for Bartonella spp. T. gondii-specific IgM is detectable in serum by ELISA in approximately 80% of subclinically ill cats 2 to 4 weeks after experimental induction of toxoplasmosis; these titers generally are negative less than 16 weeks after infection. The author, however, has demonstrated IgG antibody titers greater than 1 : 16,384 in subclinically ill cats 5 years after experimental induction In chronic disease or asymptomatic carriers, demonstration of organisms is unreliable, and a tentative diagnosis is based on clinical signs and a positive titer. gondii-specific antibodies can also be detected in the serum, CSF, and aqueous humor of healthy, infected animals, one cannot assay results in clinically ill dogs, E. doi = 10.1016/b978-1-4377-0657-4.00015-6 id = cord-279105-e2zjxjox author = Lee, Cheryl Yi-Pin title = Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control date = 2020-04-24 keywords = CoV-2; SARS; antibody summary = With the limitations of qRT-PCR, immunoassays may offer another FIGURE 2 | Schematic illustration on the window period of detection for either viral RNA or antibodies in SARS-CoV-2-infected individuals. However, interestingly, one study demonstrated that longitudinal profiling of both antibodies in a population of 63 COVID-19 patients showed no specific chronological order in terms of IgM and IgG seroconversion (10) , which was also observed in patients infected with SARS-CoV and another human coronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV) (22, 23) . These findings on SARS-CoV-2-specific antibodies seroconversion against the S viral protein suggest the importance to test for both IgM and IgG antibodies to confirm a positive infection. With the availability of immunoassays utilizing various coronavirus structural proteins, the use of more than one different antigen-based serological approach may be essential to establish a true positive SARS-CoV-2 infection. doi = 10.3389/fimmu.2020.00879 id = cord-267744-asjvf123 author = Lee, Yu-Ching title = Chicken single-chain variable fragments against the SARS-CoV spike protein date = 2007-07-23 keywords = SARS; antibody summary = Following the immunization of chickens with these recombinant spike proteins, two single-chain variable fragment (scFv) antibody libraries were established with short or long linkers to contain 5 × 10(7) and 9 × 10(6) transformants, respectively. In a comparison of nucleotide sequences with the chicken germline gene, we found that all clones varied in the complementarity-determining regions, that two scFv antibodies reacted significantly with SARS-CoV-infected Vero cells, and that those two specific scFv antibodies recognized the same region of the spike protein spanning amino acid residues 750–1000. The current study aimed to show that monoclonal IgY scFv antibodies which bind specifically to the S protein and SARS-CoV-infected Vero cells can be isolated from chickens immunized with Escherichia coli-derived S proteins. Cellular lysates containing single-chain variable fragment (scFv) antibodies from various Ssc (A) and Lsc (B) library clones were examined for their binding to SARS-CoV-infected cell lysates using a commercially available kit. doi = 10.1016/j.jviromet.2007.06.010 id = cord-298910-2601n7a9 author = Leu, Sy-Jye title = Generation and characterization of anti-α-enolase single-chain antibodies in chicken date = 2010-10-15 keywords = Fig; antibody; scfv summary = The expressed heavy and light chain variable genes (VH and VL) were isolated from spleen B cells and amplified to construct phage antibody libraries containing scFv molecules. After four rounds of panning selection, the scFv antibodies of randomly chosen clones were expressed and their binding specificity to α-enolase protein was verified using competitive ELISA, flow cytometry and immunofluorescence staining. Accordingly, in the present study, we generated and characterized the anti-␣-enolase polyclonal IgY antibodies in chicken and monoclonal scFv antibodies by a phage display system using ELISA, Western blotting, flow cytometry and immunofluorescence staining. EnL2 and EnL5 scFv antibodies purified as a single band on SDS-PAGE (data not shown) were able to detect ␣-enolase protein in PE089 cells, and the binding signal is comparable to that of commercially available rabbit polyclonal antibodies specific for ␣-enolase as demonstrated in Fig. 7 . doi = 10.1016/j.vetimm.2010.06.001 id = cord-312787-j7ye7ed5 author = Loemba, H. D. title = Kinetics of humoral immune response to the major structural proteins of the porcine reproductive and respiratory syndrome virus date = 1996 keywords = IIF; PRRSV; antibody summary = coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. Summary. coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. The porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped RNA virus which has been found to be responsible for reproductive failure in sows of any parities (late-term abortions, increased numbers of stillborn, mummified and weakborn pigs) and respiratory problems affecting pigs of all ages [8, 20] . doi = 10.1007/bf01718333 id = cord-103077-sh4w2mye author = Lu, Shuai title = Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction date = 2020-10-16 keywords = AUC; antibody; residue summary = In this article, we propose a method to identify which amino acid residues of an antibody directly interact with its associated antigen based on the features from sequence and structure. Our algorithm uses convolution neural networks (CNNs) linked with graph convolution networks (GCNs) to make use of information from both sequential and spatial neighbors to understand more about the local environment of the target amino acid residue. According to the type of selecting neighbors of target residue for representing and predicting, the machine learning-based methods can be divided into two categories, leveraging sequential neighbors or spatial neighbors. And the stateof-art method [19] represented an antibody as a graph where each amino acid residue was a node and K nearest spatial neighbors were used in the convolution operator. In this work, we utilize the sequential and spatial neighbors of the target antibody residue by using Convolutional Neural Networks (CNNs) linked with Graph Neural Networks (GCNs) for paratope prediction. doi = 10.1101/2020.10.15.339168 id = cord-335316-x2t5h5gu author = Madariaga, M. L. L. title = Clinical predictors of donor antibody titer and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial date = 2020-06-23 keywords = COVID-19; antibody; plasma; rbd summary = This was a prospective open label clinical study to assess the feasibility, safety and immunological impact of delivering anti-SARS-CoV-2 convalescent plasma to hospitalized patients aged 18 years or older with severe or life-threatening COVID-19 disease within 21 days from the onset of their illness. Univariate regression analysis for antibody titer (anti-RBD and anti-spike) was conducted against age, sex, body mass index (BMI), previous pregnancy, previous blood donation, blood type, symptoms (fever, cough, sore throat, dyspnea, abdominal pain, aguesia, anosmia, fatigue, myalgia, headache), co-morbidities (respiratory, cardiovascular, renal, diabetes, autoimmune disease, cancer, liver disease), smoking history, travel in the past 3 months to the United States, Asia or Europe, symptom duration, interval from symptoms resolution to plasma donation, and hospitalization. To determine predictors of anti-RBD and anti-spike antibody titer, we performed best subset multivariable analysis including age, sex, blood type, history of previous blood donation, fever, cough, fatigue, myalgia, symptom duration, hospitalization and travel in the United States within the past 3 months. doi = 10.1101/2020.06.21.20132944 id = cord-339520-odly2fwg author = Madic, J. title = Isotype-specific antibody responses to bovine herpesvirus 1 in sera and mucosal secretions of calves after experimental reinfection and after reactivation date = 1995-07-31 keywords = PRD; antibody summary = Abstract Isotype-specific antibody responses to bovine herpesvirus 1 (BHV1) were measured in sera, nasal, ocular and genital secretions of calves that were reinfected with BHV1 and 6 weeks later treated with corticosteroids to reactivate putative latent virus. The control calves, which were infected for the first time, developed an IgM antibody response in serum, nasal and ocular secretions that was first detected on PRD 8 and lasted until PRD 27. Calves in which no virus excretion after reinfection and/or corticosteroid treatment was detected yet developed an antibody response against BHVl, mainly of the IgA isotype. However, it may be the serum IgA response seems to be a much more sensitive indicator for reinfection with or reactivation of BHVl than detection of nasal and ocular virus shedding. After corticosteroid treatment, virus-positive nasal secretions were detected in 20 of 26 reinfected calves, and a significant increase in serum IgGl and IgG2 antibody titre in 17 and 12 calves, respectively. doi = 10.1016/0165-2427(94)05379-7 id = cord-268417-6eyetb5i author = Mandel, Benjamin title = Neutralization of Animal Viruses date = 1978-12-31 keywords = Fab; Mandel; Yoshino; antibody; complement; neutralization; study; virus summary = Somewhat earlier, Morgan (1945''1 had reported that discrepancies in the quantitative aspects of the neutralization of WEE virus by immune rabbit sera were related to the use of fresh or heated serum, and that the addition of complement to the latter tended to eliminate the discrepancies. Further studies (Radwan et al., 1973) showed that the addition of complement to virus complexed with dependent antibody eventually resulted in lysis of the viral membrane. It was also shown (Yoshino and Taniguchi, 1966 ) that antibodies induced in guinea pigs by immunization, and in humans following herpes infection, were initially dependent and later independent of complement for neutralizing activity. A relevant observation has been made in several studies; neutralization of infectious virus-antibody complexes by antiglobulin also shows a single-hit mechanism, and at a rate that exceeds the rate of the homotypic reaction. doi = 10.1016/s0065-3527(08)60101-3 id = cord-302974-t1t89p8y author = Mathur, Gagan title = Antibody Testing For Covid-19: Can It Be Used As A Screening Tool In Areas With Low Prevalence? date = 2020-05-15 keywords = antibody summary = Soon after detection of spread of SARS-CoV-2 in the United States (US), focus was on developing molecular nucleic acid detection tests (real-time reverse transcriptase polymerase chain reaction [RT-PCR]) for early diagnosis of infection in symptomatic patients, patients with known exposure, and patients who are at risk. The Trump administration and the media have been promoting antibody tests as a screening tool to allow individuals with positive results to get back to work and open our economy. The assumption is that the individuals with positive antibody tests have recovered from COVID-19 (symptomatic or asymptomatic) infection and have developed immunity to the virus. As of April 30, 2020, 10 antibody tests have been approved by the US Food and Drug Administration (FDA) under emergency use authorizations. Prematurely promoting antibody tests as a screening tool all over the US will give individuals, who test positive and are not actually immune to COVID-19, a false sense of protection. doi = 10.1093/ajcp/aqaa082 id = cord-005913-1vo1o6w8 author = Matis, Louis A. title = Complement-specific antibodies: Designing novel anti-inflammatories date = 1995 keywords = antibody summary = The complement system is composed of more than 20 serum proteins that interact in a precise series of enzymatic cleavage and membrane binding events leading to the generation of products with immunoprotective, immunoregulatory, and proinflammatory properties 12 • Complement can be activated through either of two distinct enzymatic cascades, referred to as the classical and alternative pathways (Fig. 1) . Using a monoclonal antibody specific for mouse CS, we have shown that systemic anti-CS monoclonal antibody administration efficiently inhibited complement in vivo (inhibiting serum haemolytic activity for as long as six to seven days after a single intravenous injection), and that treatment with anti-CS monoclonal antibody was therapeutically effective in two distinct models of immune complex nephritis and autoimmune disease (Y. In addition, humanized recombinant anti-CS monoclonal antibody and scFv that retain the binding affinity and complement inhibitory activity of their murine counterparts have been produced by CDR grafting (M. doi = 10.1038/nm0895-839 id = cord-010578-uib9h1lb author = Mawle, Alison C. title = Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study date = 1995-12-17 keywords = CFS; ELISA; antibody summary = We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We conducted serological tests for a large number of infectious agents as part of a case-control study assessing risk factors for CFS. Antibodies against human T-lymphotrophic virus types I and II were detected with an ELISA, and confirmatory testing was performed by western blotting [5] . All other agents tested were detected in ;;:::25% of CFS cases, and antibody levels were compared between cases and controls. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illness: elevated anti-early antigen antibodies doi = 10.1093/clinids/21.6.1386 id = cord-327287-e5k2gcse author = May, Jori E. title = The challenges of diagnosing heparin‐induced thrombocytopenia in patients with COVID‐19 date = 2020-08-02 keywords = antibody summary = key: cord-327287-e5k2gcse authors: May, Jori E.; Siniard, Rance C.; Marques, Marisa title: The challenges of diagnosing heparin‐induced thrombocytopenia in patients with COVID‐19 cord_uid: e5k2gcse To the Editor, Riker EIAs are sensitive, but not specific, for HIT diagnosis because they detect all anti-platelet factor 4 (PF4)/heparin antibodies, including those that are nonpathogenic. 3 In contrast, functional assays (including SRA) identify only antibodies with the pathogenic ability to activate platelets and therefore have increased specificity. 3 Given that severe COVID-19 is a hyperinflammatory state, it is plausible that the increased immunoreactivity also increases production of anti-PF4/heparin antibodies; however, they may not result in clinical HIT but may instead increase potential for false-positive EIAs. Herein, we report our experience with hospitalized patients with The authors have no conflicts of interest to disclose. Heparin-induced thrombocytopenia with thrombosis in COVID-19 adult respiratory distress syndrome COVID-19 and its implications for thrombosis and anticoagulation Testing for heparin-induced thrombocytopenia antibodies doi = 10.1002/rth2.12416 id = cord-350029-1y5ex4d5 author = McDade, Thomas W. title = Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date = 2020-08-09 keywords = COVID-19; SARS; antibody summary = Serological testing is a complementary approach that detects the presence of antibodies against SARS-CoV-2 in blood samples from exposed individuals (World Health Organization, 2020). If sufficient time has passed since the initial infection, the presence of IgM antibodies against SARS-CoV-2 antigens can be used to confirm a clinical case of COVID-19. In developing a low-cost ELISA for SARS-CoV-2 antibodies, our hope is that others can draw on the longstanding tradition of methodological innovation in human biology to promote community-based research on COVID-19. Human biologists are also well-positioned to consider a life course perspective on variation in outcomes in response to SARS-CoV-2 infection. Human biologists are uniquely positioned to make important contributions to our understanding of COVID-19, and methods that facilitate research in community-based settings globally will be central to that effort. Enzyme immunoassay for SARS-CoV-2 antibodies in dried blood spot samples: A minimally-invasive approach to facilitate community-and population-based screening doi = 10.1002/ajhb.23483 id = cord-102908-sr7j8z9c author = Mersmann, Sophia F. title = Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date = 2020-07-24 keywords = antibody; figure; particle; virus summary = We used differential binary labelling and statistical modelling to extract estimates of stoichiometry, our strategy is outlined in Figure 1 ; note that this approach can be generalised to apply to many other multi-component systems (i.e. how many protein x are found in assembly y?). As described above, our experimental design utilizes antibody labelled with spectrally distinct dyes allowing binary scoring of individual virus particles as positive if they interact with at least one Ab B molecule ( Figure 1 ). We have demonstrated quantitative analysis of 9C12 interaction with individual Adv particles ( Figure 3) ; we have confirmed that differential labelling of antibody does not bias binding ( Figure 4A & B) ; and that we could detect single molecules of 9C12 Biotin allowing discrimination of positive and negative AdV-9C12 complexes ( Figure 4C & D). However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. doi = 10.1101/2020.07.23.217745 id = cord-254531-pv55re2x author = Mestecky, Jiri title = Specific antibody activity, glycan heterogeneity and polyreactivity contribute to the protective activity of S-IgA at mucosal surfaces date = 2009-06-04 keywords = IgA; antibody; mucosal summary = In addition to mechanical barriers and a variety of innate defense factors, mucosal immunoglobulins (Igs) provide protection by two complementary mechanisms: specific antibody activity and innate, Ig glycan-mediated binding, both of which serve to contain the mucosal microbiota in its physiological niche. Bacteria Table 1 Examples of glycans as adhesion sites and receptors for selected bacteria and viruses that colonize, or infect, mucosal surfaces (adapted from [1, 26, 29, [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] 132] endogenous to the intestinal tract, oral cavity, and probably also the respiratory and genital tracts, are coated in vivo with S-IgA [9, 13, 17, [31] [32] [33] [34] [35] [36] [37] [38] [39] that limits their epithelial adherence and penetration, thereby confining them to the mucosal surfaces. Parallel structural and functional exploration of the principles of adaptive (specific antibody) and innate (glycan) S-IgA-mediated immunity is likely to generate novel approaches to the design of broadly protective compounds that work by selectively interfering with the adherence and penetration of pathogens, or that contain the commensal microbiota residing at mucosal surfaces. doi = 10.1016/j.imlet.2009.03.013 id = cord-102704-wfuzk2dp author = Meza, Diana K. title = Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date = 2020-04-30 keywords = Rabies; antibody; test; virus summary = Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 doi = 10.1101/2020.04.24.060095 id = cord-313312-h607itv2 author = Mok, Darren Z. L. title = The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date = 2020-05-08 keywords = LAV; antibody; existing; virus summary = Pre-existing antibodies, derived from either from maternal–fetal transmission, or by previous infection or vaccination, have been demonstrated to interfere with vaccine immunogenicity of measles, adenovirus, and influenza LAVs. Immune interference of LAVs can be caused by the formation of virus–antibody complexes that neutralize virus infection in antigen-presenting cells, or by the cross-linking of the B-cell receptor with the inhibitory receptor, FcγRIIB. The clinical trial finding that subjects with a limited range of cross-reactive antibodies from a prior Japanese Encephalitis vaccine were able to enhance yellow fever vaccination, by prolonging vaccine viremia duration that leads to higher antibody titers, thus hints at the possibility that whether pre-existing antibodies inhibit or augment flavivirus infection will depend on both antibody titers and the type/specificity of antibodies produced [85] . By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. doi = 10.3390/v12050520 id = cord-269023-g21a9ik2 author = Mukherjee, Siddhartha title = Before Virus, After Virus: A Reckoning date = 2020-10-15 keywords = antibody; cell; immune summary = doi = 10.1016/j.cell.2020.09.042 id = cord-277894-0qw0t78s author = NAYLOR, MJ title = Canine coronavirus in Australian dogs date = 2008-03-10 keywords = Australia; CCV; antibody summary = Objective To estimate the frequency of serum antibodies (IgG and IgM) to canine coronavirus (CCV) in the Australian dog population and evaluate the role of CCV as a causative agent of gastroenteritis. Of those dogs that were presented with clinical signs of gastroenteritis such as diarrhoea and vomiting(n = 29), 85% were positive in the IgM ELISA and 85.7% in the IgG ELISA for antibodies to CCV. In this study we determine the prevalence of serum IgG and IgM antibodies to CCV from a larger number of dogs sampled from throughout Australia. 7, 8 In the open population of 1107 dogs tested we found 15.8% positive for anti-CCV IgG antibody, which reflects past exposure and infection with CCV whereas the electron microscopic studies detected only those dogs currently infected and shedding virus in their faeces. doi = 10.1111/j.1751-0813.2001.tb10718.x id = cord-278281-bdoavpsb author = NEMOTO, Manabu title = Antibody response to equine coronavirus in horses inoculated with a bovine coronavirus vaccine date = 2017-10-06 keywords = antibody summary = Virus neutralization tests showed that antibody titers against ECoV increased in all six horses tested at 14 days post inoculation, although the antibody titers were lower against ECoV than against BCoV. The virus-neutralizing antibody titers of horses inoculated with 1 or 2 ml of the BCoV vaccine are shown in Table 1 . In horses inoculated with 1 ml of vaccine, the geometric mean antibody titers against BCoV at 0, 7, 14, 28, 42 and 56 dpi were 4, 5, 32, 102, 645 and 323, respectively, and the geometric mean antibody titers against ECoV were 4, 6, 20, 25, 40 and 51 (Table 1) . Nevertheless, the antibody titers of all vaccinated horses in the present study were no more than 128, and we therefore consider that the BCoV vaccine will have limited efficacy against ECoV infection in horses. doi = 10.1292/jvms.17-0414 id = cord-319884-d8n0aokl author = Natesan, Mohan title = Protein Microarrays and Biomarkers of Infectious Disease date = 2010-12-16 keywords = USA; antibody; dna; microarray; protein summary = Fluorescencebased detection of protein interactions is similar to gene array methods, and data analysis often employs approaches previously developed for genome and transcription studies. A standard assay for measuring antibody interactions with proteins of the vaccinia proteome microarray was first developed with a pool of therapeutic human sera collected from vaccinia-immune individuals (VIg) and this data was compared to results obtained from individuals vaccinated against smallpox using Dryvax. Results from this study suggested that antibodies from vaccination recognized a small number of proteins shared with pathogenic viral strains, while recovery from infection also involved humoral immunity to antigens uniquely recognized within the monkeypox virus proteome (unpublished data). For example, a protein array produced from the outer membrane proteins of Pseudomonas aeruginosa was constructed [38] to study the immune response in patients, and several antibody-binding antigens were identified by this group as potential diagnostic markers. doi = 10.3390/ijms11125165 id = cord-048239-oluq7v0h author = Oliphant, Theodore title = Development of a humanized monoclonal antibody with therapeutic potential against West Nile virus date = 2005-04-24 keywords = DIII; E16; Fig; WNV; antibody summary = Using random mutagenesis and yeast surface display, we defined individual contact residues of 14 newly generated monoclonal antibodies against domain III of the WNV E protein. Development of a humanized monoclonal antibody with therapeutic potential against West Nile virus E protein by nickel-affinity chromatography (data not shown). 24 ), yet was virus specific, as it neither recognized nor neutralized other flaviviruses including distantly related dengue and yellow fever viruses (data not shown) and closely related Japanese and St. Louis encephalitis viruses (Supplementary Table 2 Figure 1 Mapping of monoclonal antibodies to DIII with yeast. None of the mutations identified by loss-of-binding sorts for E2 or E22 had any effect on two other non-neutralizing monoclonal Individual WNV-specific monoclonal antibodies (25 µg/ml) were mixed with yeast that displayed wild-type or mutant DIII on their surface. To determine whether human antibodies specific for WNV recognize the neutralizing epitope on DIII during infection, plasma was obtained from WNV-positive individuals. doi = 10.1038/nm1240 id = cord-302382-eifh95zm author = Owji, Hajar title = Immunotherapeutic approaches to curtail COVID-19 date = 2020-08-21 keywords = ACE2; COVID-19; CoV-2; SARS; antibody; cell; immune; patient summary = doi = 10.1016/j.intimp.2020.106924 id = cord-018811-zhwr3h07 author = Oxford, John title = Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date = 2010-06-18 keywords = H1N1; H3N2; antibody; influenza; vaccine; virus summary = doi = 10.1007/978-3-0346-0279-2_6 id = cord-295033-5fd9bu60 author = Parma, Y.R. title = Antibodies anti-Shiga toxin 2 B subunit from chicken egg yolk: Isolation, purification and neutralization efficacy date = 2011-09-15 keywords = Escherichia; PBS; Shiga; Stx2; antibody summary = The data suggest that immunization of hens with Stx2B could be a strategy to obtain at low cost a relatively high concentration of anti-Stx2 egg yolk IgY, able to neutralize Stx2 lethal activity. The data suggest that immunization of hens with Stx2B could be a strategy to obtain at low cost a relatively high concentration of anti-Stx2 egg yolk IgY, able to neutralize Stx2 lethal activity. Specific anti-Stx2B polyclonal antibodies obtained from chicken egg yolk and rabbit sera recognized not only the denatured and native form of B subunit, used for immunization but the antibodies were also able to recognize the denatured and native wild type Stx2 holotoxin in western blot (Fig. 3) , indirect ELISA (Fig. 4) and sandwich ELISA (Fig. 5) . In the present report, specific egg yolk IgY antibodies with binding and neutralizing capabilities against the wild type Stx2 toxin were obtained after immunization of laying hens. doi = 10.1016/j.toxicon.2011.07.009 id = cord-337464-otwps68u author = Parray, Hilal Ahmed title = Hybridoma technology a versatile method for isolation of monoclonal antibodies, its applicability across species, limitations, advancement and future perspectives date = 2020-05-27 keywords = antibody; cell; human; hybridoma; mouse; technology; therapeutic summary = Even with the recent development of high throughput mAb generation technologies, hybridoma is the most favoured method due to its indigenous nature to preserve natural cognate antibody pairing information and preserves innate functions of immune cells. This review also summarizes the challenges and recent progress associated with hybridoma development, and how it has been overcome in these years to provide new insights for the isolation of mAbs. Antibodies are the glycoproteins produced by the B-cells also known as immunoglobulins, which are present in higher eukaryotes. The mice hybridoma technology is a multi-step process that takes advantage of a host animal''s natural ability to produce highly specific, high-affinity and fully functional mAbs. It involves the development and optimization of specific immunogenic antigen (Ag). doi = 10.1016/j.intimp.2020.106639 id = cord-010680-lc1onm53 author = Patel, Ami title = In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies date = 2020-03-10 keywords = AAV; RNA; antibody; delivery; dna; expression; study summary = Some of these hurdles may be overcome through transient in vivo gene delivery platforms, such as non-viral synthetic plasmid DNA and messenger RNA vectors that are engineered to encode optimized mAb genes. In this review, we focus on nucleic acid delivery of antibody employing synthetic plasmid DNA vector platforms, and RNA delivery, these being important approaches that are advancing simple, rapid, in vivo expression and having an impact in animal models of infectious diseases and cancer, among others. The original studies surrounding in vivo antibody gene delivery focused primarily on gene delivery using recombinant viral vectors such as AAV and adenovirus (Ad), which were advanced clinically, building on work in the traditional gene therapy-based field. Additional studies to help evaluate fully human pDNA-mAbs in mouse models would be highly informative for both non-viral and viral delivery and provide an important path forward for preclinical evaluation of in vivo-delivered antibodies [109] . doi = 10.1007/s40259-020-00412-3 id = cord-291626-lxa8pvt3 author = Pelfrene, E. title = Monoclonal antibodies as anti-infective products: a promising future? date = 2019-01-31 keywords = FDA; antibody; mAbs; monoclonal summary = Additionally, the FDA recently licensed ibalizumab as a rescue therapy in heavily treatmentexperienced adults with multidrug-resistant HIV-1 infection and also previously approved raxibacumab (in 2012) and obiltoxaximab (in 2016), both intended for treatment of inhalational anthrax (in combination with appropriate antibacterial medicines) and for prophylaxis when alternative therapies are not available or are not appropriate [5e7] . François et al., ''Safety and tolerability of a single administration of AR-301, a human monoclonal antibody, in patients with severe pneumonia caused by Staphylococcus aureus: first in man trial,'' abstract 1992, paper presented at European Congress of Clinical Microbiology and Infectious Diseases 2017) [34, 38] . Compassionate use Benefits seriously ill patients who cannot be treated satisfactorily or cannot enrol in ongoing clinical trials Pertains to unauthorized medicinal products for chronically, seriously debilitating or life-threatening diseases, with no satisfactory treatment authorized in EU; targeted at a group of patients rather than individual; or undergoing centralized MAA or clinical trials EMA, European Medicines Agency; FDA, US Food and Drug Administration; HTA, health technology assessment bodies; MAA, marketing authorization application; SA, scientific advice. doi = 10.1016/j.cmi.2018.04.024 id = cord-281760-34wuttqw author = Pereira, E.P.V. title = Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review date = 2019-05-22 keywords = ELISA; antibody; egg; igy; specific; yolk summary = Considering the fast development of IgY technology, this work aims to review its applications in human and animal health, in addition to increasing the potential use of these antibodies among researchers and consequently promoting the reduced use of non-invasive procedures on animals. extracted IgY from hens immunized with the recombinant protein FanC, from enterotoxigenic Escherichia coli (ETEC) and these antibodies bound specifically to FanC in ELISA, Western blot and Dot-blotting [59] , demanding, thus, more investigations to evaluate its viability as a potential immunotherapeutic compound. Anti-DENV2 IgY produced in goose was able to neutralize the virus in vitro and in vivo without binding to Fcγ receptors on myeloid cells and generating ADE (antibody dependent enhancement) in mice [57] . Hen egg yolk antibodies (IgY), production and use for passive immunization against bacterial enteric infections in chicken: a review Preventive effect of anti-VacA egg yolk immunoglobulin (IgY) on Helicobacter pylori-infected mice doi = 10.1016/j.intimp.2019.05.015 id = cord-302312-1pm17l5d author = Quinteros, Daniela A. title = Therapeutic use of monoclonal antibodies: general aspects and challenges for drug delivery date = 2017-03-31 keywords = Mabs; antibody; cell; drug; nanoparticle; target summary = In therapy, the development of targeted drug delivery represents, together with tissue repair, the main applications of antibody-conjugated nanoparticles. In addition to their own properties as pathogens or toxin neutralizers, as well as in the recruitment of immune elements (complement, improving phagocytosis, cytotoxicity antibody dependent by natural killer cells, etc.), they could carry several elements (toxins, drugs, fluorochroms, or even nanoparticles, etc.) and be used in several diagnostic procedures, or even in therapy to destroy a specific target. To treat HER2 positive breast cancer, anti-HER2 humanized Mabs are commonly used, although advances can be made in targeted cellular localization via conjugation strategy through a nano-particulate system focusing on surface modified ligand/receptor-mediated nano-therapy to target the tumor cell at the molecular level. Bio-conjugation strategies of therapeutic agents loaded nanoparticles with Mabs have exhibited a targeted drug delivery approach both in vitro and in vivo. doi = 10.1016/b978-0-323-46143-6.00025-7 id = cord-010991-fp8hljbq author = Rather, Shabeer Ahmad title = Antibodies generated against dextransucrase exhibit potential anticariostatic properties in Streptococcus mutans date = 2020-01-03 keywords = antibody; dextransucrase; mutan summary = For vaccine development, attention was paid on the purified antigens involved in the pathogenesis of dental caries for the development of potentially safer vaccines, which may reduce the viability of bacteria in the saliva, impairing the surface adhesion and inhibiting the metabolically active enzymes involved in caries formation (Chen and Wang 2010) . mutans have shown encouraging results related to dental caries protection, but were limited by the cross-reactive epitopes against human heart and skeleton muscle tissues as detected by indirect immunofluorescence and crossed immunoelectrophoresis (Kt et al. In the present study, we have tried to evaluate the effect of anti-dextransucrase antibodies on caries formation by using purified dextransucrase as the antigen from S. Protein samples of the liver, heart, spleen, kidney of mice, rat and liver, kidney of rabbit were analysed by western blot analysis to evaluate the cross reactivity of purified antibody with mammalian tissues Fig. 5a . doi = 10.1007/s00253-019-10327-x id = cord-021402-wq770ik9 author = Relford, Roberta L. title = New Diagnostic Tools for Infectious Disease date = 2009-05-15 keywords = PCR; antibody; organism summary = The most common laboratory methodologies used to identify an infectious agent include visualization of the organism via cytology/biopsy, isolation of the agent in microbiological culture, immunodiagnostics/serology, and nucleic acid technology. Fluorescent antibody and immunoblot assays are performed in commercial laboratories, whereas numerous patient-side rapid ELISA and latex agglutination kits are available for antigen detection. Until the introduction of nucleic acid amplification by the PCR, detection of an organism''s DNA or RNA often was impossible because of the small amount of antigen present in a sample. In the ELISA and IFA antibody assays, a specific antigen from the infectious agent in question is fixed to a solid surface (microtiter plate or glass slide, respectively) and the patient''s serum is added. The SVN assay evaluates the ability of antibodies in a patient''s serum to prevent the infection of culture cells or embryonated eggs with a known specific virus. doi = 10.1016/b0-72-160423-4/50009-3 id = cord-267601-3ahmyicn author = Renegar, Kathryn B. title = Passive Immunization: Systemic and Mucosal date = 2007-05-09 keywords = IgA; antibody summary = Both rats and mice can actively transport IgG from the gut into the serum for approximately 2 weeks (see Combined Prenatal and Postnatal Transfer earlier in this chapter); thus, observed protection could be due either to antibody in the milk bathing the mucosal surfaces or to maternal antibody being transported into the serum and secretions of the offspring. Only a limited number of studies on the transport of antibodies into respiratory secretions have been reported, but the results have shown that selective transport of passively administered serum IgA into the respiratory tract is possible in sheep and mice. (1994) determined that passively administered monoclonal pIgA isotype-switch variants, generated from IgG hybridomas producing antibodies specific for bacterial respiratory tract pathogens, were selectively transported relative to IgG into both the upper and lower respiratory tract secretions of mice. To determine whether intravenously administered pIgA antiinfluenza monoclonal antibody could mediate protection against local influenza virus challenge, passively immunized mice were challenged intranasally while awake with influenza virus. doi = 10.1016/b978-012491543-5/50050-4 id = cord-103432-cdmoazrl author = Richardson, Eve title = A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-Pertussis toxoid antibodies date = 2020-06-02 keywords = antibody; cdrh3; clonotype summary = To test the ability of paratyping and clonotyping to group antibodies that target the same epitope we performed a test in a single-cell (paired VH/VL) data set of 1290 antibodies isolated from genetically engineered mice that have a full set of human immunoglobulin variable region genes [31] immunised with Pertussis toxoid (PTx). Each of the PTx-binders is referred to as a "probe" antibody; sequences that are within the same paratype or clonotype as the probe are predicted to bind PTx. The precision and recall of the two methods (calculated over the aggregate of predictions) for repertoire mining are comparable ( Figure 2 , Table 1 ). In a test system of transgenic mice immunised with Pertussis toxoid (PTx), we show for the first time that prediction and comparison of paratopes can be used to group antigen-specific antibodies in both an enriched, single-cell data set and non-enriched bulk heavy chain repertoires. doi = 10.1101/2020.06.02.121129 id = cord-321901-zpi7uis1 author = Roberts, Anjeanette title = Animal models and antibody assays for evaluating candidate SARS vaccines: Summary of a technical meeting 25–26 August 2005, London, UK date = 2006-11-30 keywords = CoV; SARS; animal; antibody; vaccine summary = Scientists at the WHO Technical Meeting on Animal Models and Antibody Assays for Evaluating Candidate SARS Vaccines held on 25-26 August 2005 in South Mimms, UK, discussed many aspects of research pertaining to the use of animal models in vaccine development including available animal models, suitability of the various models, correlates of protection, critical components of potential vaccines, and the potential for disease enhancement in vaccinated animals following exposure to SARS-CoV. It may actually be worthwhile to enhance the virulence of a SARS-CoV isolate by serial passages in an animal model to produce a challenge virus stock for vaccine studies that would elicit more reproducible disease in the animals. Although none of the studies to date have shown enhanced respiratory disease following SARS-CoV challenge in previously immunized animals, further studies in this area are warranted in view of some of the available in vitro data. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice doi = 10.1016/j.vaccine.2006.07.009 id = cord-304214-66nxk4e8 author = Sanders, John W. title = Vectored immunoprophylaxis: an emerging adjunct to traditional vaccination date = 2017-02-10 keywords = HIV; antibody; vector summary = Rather than passively transfering pre-formed antibodies, VIP is a process in which genes encoding previously characterized neutralizing antibodies are vectored into non-hematopoietic cells which then secrete the monoclonal antibodes encoded by those genes [1] (See Fig. 1 .) This vectored delivery and production of specified antibodies allows for protection without generating a standard immune response and results in endogenous antibody production that has the potential to be sustained [9] . Saunders, et al., used an rAAV serotype 8 vector to produce a full length IgG of a simianized form of the broadly neutralizing antibody VRC07 in macaques which was protective against simian-human immunodeficiency virus (SHIV) infection 5.5 weeks after treatment [24] . Using HIV-1-infected humanized mice, Horwitz, et al., demonstrated that following initial treatment with anti-retroviral therapy (ART), a single injection of adeno-associated virus directing expression of broadly neutralizing antibody 10-1074, produced durable viremic control after the ART was stopped [26] . doi = 10.1186/s40794-017-0046-0 id = cord-319746-6bccxgbd author = Saxena, Latika title = Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date = 2015-12-31 keywords = antibody; cell; virus summary = title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. doi = 10.1016/j.provac.2015.05.009 id = cord-003435-ke0az7nf author = Schlake, Thomas title = mRNA as novel technology for passive immunotherapy date = 2018-10-17 keywords = RNA; TCR; antibody; car; cell; expression; mrna; protein summary = Recombinant technologies further expanded the available therapies based on mAbs. In vitro antibody selection technologies like phage or ribosome display were developed to enable the generation of highly specific human mAbs out of libraries that may even be naïve for the specific antigens [31] [32] [33] [34] [35] [36] 1 Schematic illustration comparing active immunization and passive antibody immunotherapies. While T cell engineering for adoptive transfer inevitably requires the use of nucleic acids encoding a target-specific receptor, antibody immunotherapy can deploy recombinant proteins. However, the effects of mRNA modifications on translation, immunostimulation and resulting protein expression appear to be variable, for instance dependent on the type of target cells. In comparison to a single transfer of cells with retroviral CAR expression, an mRNA-encoded receptor required three consecutive lymphocyte infusions to obtain a comparable antitumor effect [262] . doi = 10.1007/s00018-018-2935-4 id = cord-005827-wjkbrfkn author = Schmidt, Rüdiger title = Antiphospholipidantikörpersyndrom date = 1999 keywords = Patienten; antibody; antiphospholipid; der; syndrome summary = Other clinical manifestations associated with APA include migraine, chorea, hemolytic anemia, heart valve disease, Budd-Chiari syndrome, perpetual pancreatitic episodes, intestinal infarctions, malignant hypertension, livedo reticularis, pre-eclampsia, fetal growth retardation or catastrophic antiphospholipid syndrome. 1Kfidiger Schmidt I , Ernst-Heinrich Scheuermann ~ , Achim Viertel 1, Helmut Geiger 1 , lnge Scharrer 2 Budd-Chiari-Syndrom, rezidivierende Pankreaufiden, intestinale Apoplexie, maligne Hypertonie;Livedo reticularis, Pr~ieklampsie, fetate WachstumsverzSgenmgen oder das sogenannte,,katastrophale Antiphospholipidantik6rpersy ndrom,_ Ira Gegensatzzum ,prim~en Antiphospholipidantik6rpersyndrom''" rinden sich Lupusantikoagulanziea und An¡250 beim ,,se-kund~iren Antiphospholipidantik/Srpersyndrom" im t(ahmen ron Autoimmun-erkrankutlget1, von.Neoplasfen und Infektionen oder sind mit dem Gebrauch bestimmter Medikamente assoziiert. Other clinical manifestations associated with APA include migraine, ch0rea, hemolytic anemia, heart Valve disease, Budd-Chiari syndrome, perpemal pancreatitic episodes, intestinal infarcfions, malignant hypertension, livedo reticularis, pre-eclampsia, fetal growth retardation or catastrophic anfiphos[10] ; dieses zeigt zudem eine fa-mili~ire H~iufung [48] sowie eine Assoziation mit HLA DR.7, DR4, DQw7 und DR.w53 [75] . el al Antiphospholipid antibodies and the anti-phospholipid syndrome in systemic lupus erythematosus doi = 10.1007/bf03044707 id = cord-311811-nrodyagi author = Schutzer, Steven E. title = The use of host factors in microbial forensics date = 2019-12-06 keywords = ELISA; antibody; response summary = doi = 10.1016/b978-0-12-815379-6.00014-3 id = cord-001074-qevosik3 author = Selvarajah, Suganya title = A Neutralizing Monoclonal Antibody Targeting the Acid-Sensitive Region in Chikungunya Virus E2 Protects from Disease date = 2013-09-12 keywords = CHIKV; antibody summary = C9 was determined to be a potent virus neutralizing antibody and a biosensor antibody binding study demonstrated it recognized residues on intact CHIKV VLPs. Shotgun mutagenesis alanine scanning of 98 percent of the residues in the E1 and E2 glycoproteins of CHIKV envelope showed that the epitope bound by C9 included amino-acid 162 in the acid-sensitive region (ASR) of the CHIKV E2 glycoprotein. The neutralizing epitope bound by C9 mapped to the acid-sensitive region (ASR) that is critical for the rearrangement of CHIKV E2 during fusion and viral entry into host cells. Therefore, C9 is a potent neutralizing antibody that can therapeutically protect wild-type neonate mice from a lethal dose of virus at 8 and 18 hours post CHIKV inoculation. This study describes the isolation and characterization of two human monoclonal antibodies, C9 and E8, from CHIKV infected and recovered individuals. doi = 10.1371/journal.pntd.0002423 id = cord-010248-ln800g5z author = Sissons, J.G. Patrick title = Antibody-Mediated Destruction of Virus-Infected Cells date = 2008-02-29 keywords = ADCC; Oldstone; PBL; antibody; cell; virus summary = When lz5I-1abeled IgG antibody was bound to the surface of measles virus-infected cells at the start of the culture period, under the conditions described above for antigenic modulation, about 40% of the radioactivity was still cell associated at 12 hours and nearly all was protein bound Perrin and Oldstone, 1977) . Lysis by human serum of cells infected with HSV types 1 and 2, influenza A, parainfluenza 1, 2, 3, and 4, mumps, and measles viruses was dependent on the presence in serum of IgG antibody specific for the relevant virus and of complement (reviewed by Oldstone and Lampert, 1979) . The use of this system, composed of 11 highly purified complement proteins, provided conclusive evidence that the known proteins of the alternative and membrane attack pathways with IgG antibody are sufficient for lysis of the measles virus-infected cell, without other serum factors. It is apparent that considerably more surface-bound IgG is required to induce complement-dependent lysis of virus-infected cells than is required for antigenic modulation or antibody-dependent cell-mediated cytotoxicity. doi = 10.1016/s0065-2776(08)60045-0 id = cord-021770-zn7na974 author = Slifka, Mark K. title = Passive Immunization date = 2017-07-17 keywords = antibody; human; infection; monoclonal; passive; serum; treatment; virus summary = [26] [27] [28] [29] Recent studies verify these earlier results, demonstrating a 90% to 91% vaccine efficacy against whooping cough among infants younger than 2 months of nonlymphoid tissues and to penetrate mucosal sites of infection is likely to explain why it is often considered the best immunoglobulin isotype for routine passive immunization and has shown clinical benefit ranging from reduced clinical symptoms to nearly complete protection from lethal infection in a number of infectious disease models (Table 8 .3). 118 With the recent development of polyclonal and monoclonal antibodies that show protective efficacy against tularemia in animal models, [119] [120] [121] it may be possible to incorporate both passive immunotherapy and antibiotic treatment into clinical practice not only for tularemia, but for other bacterial diseases, especially in cases in which antibiotic resistance is becoming more widespread. doi = 10.1016/b978-0-323-35761-6.00008-0 id = cord-274557-2071770h author = Späth, Peter J. title = On the Dark Side of Therapies with Immunoglobulin Concentrates: The Adverse Events date = 2015-02-05 keywords = IVIG; anti; antibody; high; immunoglobulin; intravenous; patient summary = i.e., cold-ethanol or ion-exchange chromatography, contaminants, route of application, i.e., intra muscular (IMIG), intravenous (IVIG), or subcutaneous (SCIG), the rate of increase of the exogenous IgG in the circulation of the recipient over time and, last but not least an eventually existing risk factor from patients'' side ( Figure 1 ) as well as incorrect handling of the concentrate are factors having a role in inducing non-infectious AEs related to administration of IgG concentrates ( Table 1) . The complement-mediated AEs were considered to be caused by aggregates in the product ("spontaneous complement activation" or anti-complementary activity or ACA) or by in vivo formation of immune complexes (ICs, patient''s condition related; e.g., subclinical infections or the unnoticed presence of anti-IgA antibodies) and therefore only IgG concentrates with low or absent ACA is accepted by authorities for human use. doi = 10.3389/fimmu.2015.00011 id = cord-349669-o3eelqcw author = Stadlbauer, Daniel title = Anti‐SARS‐CoV‐2 Spike Antibodies are Stable in Convalescent Plasma when Stored at 4° Celsius for at Least 6 Weeks date = 2020-08-14 keywords = antibody summary = Convalescent plasma (CP) has presented another option, with its use and safety supported by numerous case series and retrospective studies [2] [3] [4] . Studies demonstrating antibody stability under refrigerated conditions have largely focused on peripheral blood samples stored for several days 7, 8 . Here, we demonstrate the long-term stability of anti-SARS-CoV-2 spike antibodies in donor CP samples collected at a local blood donor center for transfusion. After thawing of fifteen CP units, segments were sampled and anti-spike antibody titers were determined via enzyme-linked immunosorbent assays (ELISAs) 9 . While our study does not address the neutralization capacity of these antibodies, previous studies demonstrate significant correlation between spike antibody titers and neutralization capacity of plasma and serum samples 9 . Treatment of COVID-19 Patients with Convalescent Plasma Early safety indicators of COVID-19 convalescent plasma in 5,000 patients Convalescent plasma treatment of severe COVID-19: A matched control study Long-term stability of trastuzumab in plasma and whole blood samples stored under different conditions doi = 10.1111/trf.16047 id = cord-283826-lgyc3sro author = Stiehm, E. Richard title = Therapeutic Use of Immunoglobulins date = 2010-11-05 keywords = CMV; IGIV; IVIG; antibody; immunoglobulin; infection; patient summary = medical science and thereby placed in the hands of the physician a victorious weapon against illness and death.'' '' Since then antibodies in multiple forms (animal and human serums, immune globulins and monoclonal antibodies) have been developed, primarily for prevention of infectious diseases, and less commonly for their treatment. Thus regular use of IVIG in antibody-deficient patients in doses of 400 to 600 mg/kg every 3 to 4 weeks or an equivalent amount given subcutaneously decreases the frequency and severity of otitis and other respiratory tract infections [27, 28] . High-dose IVIG (sufficient to increase the serum IgG levels to 1000 mg/mL) has been used successfully in immunodeficient patients with enteroviral encephalomyelitis [80] [81] [82] [83] . Because IgG represents the major defense of humoral immunity against infection, these patients also require immunoglobulin replacement therapy. Individualizing the dose of intravenous immune serum globulin for therapy of patients with primary humoral immunodeficiency doi = 10.1016/j.yapd.2010.08.005 id = cord-352172-g0jiaenw author = Stoevesandt, Oda title = Protein microarrays: high-throughput tools for proteomics date = 2014-01-09 keywords = antibody; array; dna; microarray; protein summary = While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. Protein microarray technology has rapidly developed into one of the most active areas in biotechnology today, and is being increasingly applied for the high-throughput discovery of molecular interactions, profiling of protein expression and monitoring of protein modifications. While genome sequencing and annotations provide comprehensive information on protein-encoding genes, and DNA arrays analyze gene expression at the mRNA level, these technologies need to be complemented by functional proteomic studies in order to better understand protein activities, expression levels and interactions at the system level. A reverse-phase micro array approach has been successfully applied to discover distinct pathway-activation differences among breast cancer cell lines, demonstrating the use of array-based ana lysis for multiple pharmacodynamic biomarkers responding to targeted kinase inhibitors [108] . doi = 10.1586/epr.09.2 id = cord-002846-la9svzml author = Strohl, William R. title = Current progress in innovative engineered antibodies date = 2017-08-18 keywords = Strohl; Table; antibody; car; cell summary = The second most targeted protein is CD3E, found in 32 clinical stage or approved molecules, of which 26 are T cell-redirecting bispecific antibody candidates (Table 6) . For example, 10 of them bind two soluble antigens such as IL13 and IL4 (e.g., SAR156597; NCT02345070), nine bind two receptors on the , IgG-scFv fusion, Mabtyrin (IgG with non-antibody binding scaffold "centyrin" fused to C-terminal end of heavy chains); (C) IgGs to which additional antigen combining sites have been added within the structure (e.g., two-in-one antibodies, MAT "Modular Antibody Technology" platform from F-Star); (D) Engineered antibody fragments linked by short peptide linkers which can be made into bivalent, trivalent, or tetravalent formats addressing two to three targets (e.g., bispecific T-cell engager (BiTE), Nanobody platform, dual-affinity re-targeting (DART) antibodies, "tandem antibody" structures (TandAbs)); (E) Chemically coupled IgGs. Brennan et al., 1985; Garrido et al., 1990 Innovative antibodies Mack et al., 1995; Schlereth et al., 2005; Baeuerle et al., 2008 TandAb Antibody fragmentWilliam R. doi = 10.1007/s13238-017-0457-8 id = cord-295099-ghc85pf5 author = Sun, Zehua title = Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date = 2018-01-02 keywords = HIV-1; antibody; cell summary = doi = 10.1016/j.virusres.2017.10.011 id = cord-292874-6zjqflhz author = SØRENSEN, MORTEN DRÆBY title = Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date = 2006-05-10 keywords = SARS; antibody summary = abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV. In February 2003, the new and previously unknown deadly coronavirus causing severe acute respiratory syndrome (SARS-CoV) was brought to the attention of the World Health Organization (WHO) by Dr. Carlo Urbani and his colleagues. Creation of immune phage-display libraries for immunized donors has shown a particular efficiency in selecting neutralizing antibodies (NABs) against different viruses, for example, rabies, 39 varicella-zoster, 40 hepatitis A 41 and E, 42 measles, 43 and respiratory syncytial virus. doi = 10.1196/annals.1354.072 id = cord-256652-ent4vu3z author = Tan, Joshua title = A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein date = 2018-03-19 keywords = Fig; NANP; Plasmodium; Supplementary; VH3; antibody summary = investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. These findings, combined with data from peptide array experiments ( Supplementary Fig. 7) , identify the N-terminal junction binding site of the most potent neutralizing antibodies as including the first unit of the NANP repeat region and flanking non-repeat sequences, providing a molecular basis for the dual specificity of these antibodies. doi = 10.1038/nm.4513 id = cord-002710-e8im13go author = Taschuk, Ryan title = Induction of PrP(Sc)-specific systemic and mucosal immune responses in white-tailed deer with an oral vaccine for chronic wasting disease date = 2017-10-02 keywords = CWD; antibody summary = title: Induction of PrP(Sc)-specific systemic and mucosal immune responses in white-tailed deer with an oral vaccine for chronic wasting disease Oral immunization of white-tailed deer with hAd5:tgG-RL induced PrP(Sc)-specific systemic and mucosal antibody responses with an encouraging safety profile in terms of no adverse health effects nor prolonged vector shedding. To assess the immunogenicity of hAd5:tgG-RL white-tail deer (n D 5/group) were orally immunized and epitope-specific antibody titers in serum and feces were quantified with a peptide ELISA. These results confirm that oral delivery of a recombinant viral vector, expressing an appropriate DSE and carrier molecule, is capable of inducing both systemic and mucosal antibody responses in white-tailed deer. To determine if the antibodies induced by oral immunization retained the same PrP Sc specificity as previously characterized for the parenteral vaccine, serum from hAd5:tgG-RL vaccinated animals was assayed for PrP C reactivity by ELISA, using recombinant cervid PrP 90-231 for antibody capture. doi = 10.1080/19336896.2017.1367083 id = cord-009690-kbwz7xop author = Toubanaki, Dimitra K. title = Development of a Nanoparticle-based Lateral Flow Strip Biosensor for Visual Detection of Whole Nervous Necrosis Virus Particles date = 2020-04-16 keywords = Fig; LFB; antibody; nodavirus summary = title: Development of a Nanoparticle-based Lateral Flow Strip Biosensor for Visual Detection of Whole Nervous Necrosis Virus Particles The principle of viral particles detection based on lateral flow biosensor with functionalized nanoparticles is presented in Fig. 1 . Nodavirus intact particles (virions), obtained either from SSN-1 cell culture supernatants or homogenized tissue samples, are directly applied on the LFB. The sample contains the nodavirus particles (virions) and is applied on the conjugation pad next to functionalized gold nanoparticles (Au) with polyclonal anti-nodavirus antibody. Application of that conjugate on the LFB resulted in a strong signal in the control zone, confirming the successful conjugation of anti-nodavirus antibody to Au nanoparticles (Fig. 2e) . To enable on site analysis of nodavirus, we developed and optimized a paper LFB based on gold nanoparticles for easy, specific and sensitive visual detection of nodavirus viral particles (virions) in biological samples. doi = 10.1038/s41598-020-63553-z id = cord-307320-fxs31d66 author = Ubah, Obinna title = Monoclonal Antibodies and Antibody Like Fragments Derived from Immunised Phage Display Libraries date = 2018-03-17 keywords = antibody; display; human; library; monoclonal; phage summary = However, by combining the power of immunisation with phage display, several high affinity monoclonal antibodies against "difficult" antigenic targets have been isolated from relative small antibody libraries and where traditional approaches have failed [33, 98] . The above study demonstrates the power of animal immunisation and phage display based selection strategies to isolate high affinity monoclonal antibodies towards non-antigenic targets which inherently lack properties like aromaticity and charge. Spleen samples from mice immunised with gamma inactivated Brucella melitensis strain 16 M bacteria was used to construct a phage display library and isolate monoclonal antibody fragments that specifically recognise Brucella species. Similarly high affinity neutralising antibody fragments against the protective antigen (PA) of anthrax toxin was isolated from a Macaca immunised phage display library. Lymphocytes from the bone marrow cells of two chimpanzees immunised with anthrax toxin PA, LF and Edema factor (EF) were used to construct scFv phage display libraries and neutralising antibodies were isolated against PA and LF proteins. doi = 10.1007/978-3-319-72077-7_6 id = cord-283641-2u16otbf author = Vainionpää, R. title = Diagnostic Techniques: Serological and Molecular Approaches date = 2015-03-06 keywords = PCR; antibody; virus summary = For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient''s specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. doi = 10.1016/b978-0-12-801238-3.02558-7 id = cord-344445-slv7r9u7 author = Vakharia, Kunal title = The right to know: ethical implications of antibody testing for healthcare workers and overlooked societal implications date = 2020-06-03 keywords = COVID-19; antibody summary = The discussion that has continued since the initial severe acute respiratory syndrome virus and avian influenza epidemics has focused on the potential for immunity among the general population and the moral obligation to treat that is often faced by healthcare professionals and institutions. With the growing literature and data suggesting the possibility of mutations, unequal impacts on different people and the potential repercussions of the spike protein for those with IgG immunity already, can society in good faith adopt a moral prerogative to put antibody-positive people in the front line? Healthcare workers form a group of individuals who recognise the potential of COVID-19, the impact it has had, and are still willing to go to work and continue to face the challenge. With limited knowledge about the significance of COVID-19 antibody testing at this time, it is hard to use this to stratify work in a healthcare setting or to use it for any purpose beyond epidemiological studies on the spread of the disease. doi = 10.1136/medethics-2020-106467 id = cord-274756-nnm1n09a author = Varadé, Jezabel title = Human immunology and immunotherapy: main achievements and challenges date = 2020-09-02 keywords = CD4; antibody; car; cell; disease; human; immune; tumor; vaccine summary = The development of different types of immunotherapies, including vaccines (prophylactic and therapeutic), and the use of pathogens, monoclonal antibodies, recombinant proteins, cytokines, and cellular immunotherapies, are changing the way in which we approach many diseases, especially cancer. In addition to those showing the essential role of LTi cells in the formation of secondary lymphoid organs during embryogenesis and the postnatal development of intestinal lymphoid clusters, recent studies also provide evidence that subsets of ILCs express multiple factors that modulate the adaptive immune response in health and disease 27, 28 . Autoimmunity: In the case of therapeutic vaccines for autoimmune diseases, such as multiple sclerosis, diabetes, Myasthenia gravis or Guillain Barré syndrome, the intention is to induce tolerance to self-antigens through the activation of regulatory cells (Tregs and Bregs) and tolerogenic dendritic cells, thus avoiding the immune response to self-components 211 . doi = 10.1038/s41423-020-00530-6 id = cord-016966-b23o5roz author = Verhoef, Jan title = Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites date = 2005 keywords = antibody; cell; immune; infection summary = Effective treatment, however, was not possible at that time; prevention and spread of infectious diseases depended solely on proper hygienic means.At the beginning of the 20th century, passive and active vaccination procedures were developed against a number of these pathogenic micro-organisms in order to prevent the diseases in question (rabies, diphtheria, tetanus, etc.) and due to the discovery of antimicrobial chemicals (Ehrlich) and antibiotics (Fleming), the threat of infectious diseases seemed to be minimized. CYTOKINES, such as IL-2 (INTERLEUKIN-2), GM-CSF (granulocyte-macrophage colony-stimulating factor), and TNF-α (TUMOR NECROSIS FACTOR α), stimulate non-specifically the proliferation, maturation, and Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Jan Verhoef and Harm Snippe A7 function of the cells involved in defence (see Chapter A.4). doi = 10.1007/3-7643-7408-x_7 id = cord-048360-n9sih438 author = Villard, Viviane title = Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date = 2007-07-25 keywords = antibody; figure; peptide; protein; table summary = To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates. doi = 10.1371/journal.pone.0000645 id = cord-354137-6oe8nj1j author = Wang, Hua title = Aspects of recent development of immunosensors date = 2008-05-20 keywords = antibody; antigen; base; detection; immobilization; immunosensor; surface summary = Development of microfluidic immunosensor systems for proteomics and drug discovery have also been reported in recent years where the microfluidic system integrates multiple processes in a single device to improve analytical performance by reducing the reagent consumption and the analysis time, and increasing reliability and sensitivity through automation. A capacitive immunoassay based on antibody-embedded ultra-thin alumina sol-gel fi lms (∼20 to 40 nm) was reported and used for direct determination of antigens with a detection limit as low as ϳ1 ng mL Ϫ1 [92] . reported a successful integration of the lateral fl ow immunoassay format and impedance detection for prostate-specifi c antigen of tumor marker, where the electrochemical transducer was coated with a pH-sensitive polymer layer [93] . Based on the modifi cation of mixed SAMs on gold electrodes for covalently binding antigens, another piezoelectric immunosensor has been recently developed to detect antisperm antibody [153] . doi = 10.1016/b978-012373738-0.50011-8 id = cord-002153-e0zhq18g author = Yang, Danlin title = Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses date = 2016-07-29 keywords = BAFF; IL-13; SPR; antibody summary = Our workflow consists of the following two steps: 1) the use of surface plasmon resonance to quantify antigen-specific antibodies and evaluate their apparent binding affinities, and 2) the recovery of serum IgGs using an automated small scale purification system, followed by the determination of their epitope diversity using hydrogen deuterium exchange coupled with mass spectrometry. To increase the efficiency of our therapeutic antibody generation process to achieve long term success, we developed alternative methods for assessing the quality of polyclonal antibodies in immune sera, surface plasmon resonance (SPR) 2 and hydrogen deuterium exchange (HDX) coupled with mass spectrometry. In this report, we describe the following: the method development and establishment of the detection limits of our techniques, a proof-of-concept study using sera from IL-13 immunized mice, the creation of a workflow named Quality of Antibody Response (QAR), and finally the implementation of this workflow for a therapeutic anti-B-cell activating factor (BAFF) antibody generation campaign to guide the selection of optimal animal donors for hybridoma generation. doi = 10.1074/jbc.m116.736660 id = cord-316287-4i1grvlr author = Yim, Sung Sun title = Rapid Isolation of Antibody from a Synthetic Human Antibody Library by Repeated Fluorescence-Activated Cell Sorting (FACS) date = 2014-10-10 keywords = FACS; antibody; cell summary = During the cultivation for regeneration of sorted cells, differential growth rates among various clones (particularly non-specific clones) due to unregulated protein expression and differing cell viability can decrease the library screening efficiency, resulting in more rounds of sorting (longer duration) to isolate the potential antibody candidate [12] . The whole FACS screening rounds of the synthetic human antibody library against each viral antigen could be done in one day, and these results show that repeated FACS screening without regeneration of the sorted cells can be a rapid and efficient method to isolate potential antibody candidates in case of urgent requirements. For the FACS screening of a human synthetic antibody (scFv) library, three fluorescent antigen probes were chemically synthesized: (i) FITC-CRDNWHGSNRPW as an N1 epitope of H1N1 influenza virus [13] ; (ii) FITC-NSTTFHQALLDPRVRGLYF-PAGG as a PreS2 epitope of HBV [14] ; and (iii) FITC-PVTNVRGDLQVLAQK as a VP1 epitope of FMDV [15] . doi = 10.1371/journal.pone.0108225 id = cord-330324-4hqhty5o author = Yu, Meng title = Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date = 2008-02-29 keywords = SARS; antibody; western summary = title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. In this study we identified and characterized the major immunodominant domains of the SARS-CoV N and S proteins recognized by different animal species, and then developed competition ELISAs based on these findings. The specificity of the antibody was further confirmed using Western blot against viral antigen (data not shown) and IFAT using SARS-CoV infected Vero cells. One of the main aims of this study was to assess the feasibility of developing a competition ELISA for detection of SARS-CoV antibodies from different animal species. Inhibition of binding of mono-specific chicken antibodies to SARS-CoV by sera from different species. doi = 10.1016/j.jim.2007.11.009 id = cord-031060-0o9agjiq author = Yuan, Tom Z title = Rapid exploration of the epitope coverage produced by an Ebola survivor to guide the discovery of therapeutic antibody cocktails date = 2020-08-01 keywords = Ebola; antibody summary = Incorporating epitope binning on hundreds of antibodies during early stage antibody characterization ensures access to a library''s full epitope coverage, aids in the identification of high quality reagents within the library that recapitulate this diversity for use in other studies, and ultimately enables the rational development of therapeutic cocktails that take advantage of multiple mechanisms of action such as cooperative synergistic effects to enhance neutralization function and minimize the risk of mutagenic escape. Despite ligand attrition and the stringent requirement for premixed antibodies to achieve antigen saturation, which reduced our heat map to 52 analytes x 233 ligands, we were able in this non-optimized ''first pass'' binning to assign 234 antibodies to one of seven epitope communities without the use of benchmark antibodies (Supplemental Table S1 ). doi = 10.1093/abt/tbaa016 id = cord-001566-kkaxha7d author = Zhang, Mao-Yu title = Development of Monoclonal Antibodies in China: Overview and Prospects date = 2015-02-25 keywords = China; antibody; mAbs summary = This paper aims to provide a comprehensive review of mAbs development in China through systematic analysis of drug registry, patent applications, clinical trials, academic publication, and ongoing R&D projects. Over the past three decades, monoclonal antibodies (mAbs) have achieved a dramatic development from scientific tools to powerful human therapeutic agents [1] (see Figure 1 ). Development of this class of therapeutic agents started as early as 1980s but achieved no clinical or commercial success until 2002 when adalimumab became the first human mAb approved by the US Food and Drug Administration (FDA) [14] . R&D of mAbs in China began in the 1980s [16] and the first mAb therapeutic agent (Murine Monoclonal Antibody against Human CD3 Antigen of T Lymphocyte for Injection) was introduced in 1999 [17] . This paper aims to provide a comprehensive review of mAb development in China through systematic analysis of product registry, patent application, clinical trials, academic publication, and ongoing R&D projects. doi = 10.1155/2015/168935 id = cord-267015-mprsdi2e author = Zhu, Zhongyu title = Exceptionally Potent Cross-Reactive Neutralization of Nipah and Hendra Viruses by a Human Monoclonal Antibody date = 2008-03-15 keywords = antibody; hev summary = One of these antibodies, m102, which exhibited the highest level of cross-reactive neutralization of both NiV and HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavy-chain variable domain and panning against sG(HeV). We have previously identified neutralizing human monoclonal antibodies against Nipah virus (NiV) and Hendra virus (HeV) by panning a large nonimmune antibody library against a soluble form of the HeV attachment-envelope glycoprotein G (sG HeV ). One of these antibodies, m102, which exhibited the highest level of cross-reactive neutralization of both NiV and HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavychain variable domain and panning against sG HeV . To demonstrate that m102.4 measured in plasma was biologically active, serum collected on days 1, 4, and 8 was evaluated using virus neutralization assays, as described above (data not shown). Receptor binding, fusion inhibition, and induction of cross-reactive neutralizing antibodies by a soluble G glycoprotein of Hendra virus doi = 10.1086/528801 id = cord-009571-mygj2nd4 author = nan title = Proceedings of the 42nd annual meeting of the american rheumatism association a section of the arthritis foundation june 1 & 2, 1978 new york city abstracts of papers presented date = 2005-11-23 keywords = HLA; SLE; antibody; cell; disease; dna; normal; nzb; patient; study summary = Levels of Ty cells as well as total T lymphocytes were measured in 19 patients with systemic lupus erythematosus (SLE), 11 with active and 8 with inactive disease, and in 47 normal subjects. The diagnosis of GC arthritis were studied for the presence of GC antigen (AG) and anti-in all seven patients was made by typical clinical presentation, body (AB) in serum and synovial fluid by counter-positive local culture for Ngonorrhoeae (NG) , and response to treatment. A retrospective study was instituted on 10 patients in the UCLA lupus nephritis clinic in an attempt to determine the ability of three serologic indicators-specifically immune complexes (IC), anti-DNA antibodies (DNA-ab), and C3-to predict the activity of SLE renal disease as indicated by changes in 24 hour proteinuria, serum creatinine, and creatinine clearance. doi = 10.1002/art.1780210508 id = cord-010088-s9tfvtao author = nan title = Oral Abstracts date = 2013-11-01 keywords = HBV; HCV; HLA; HNA; HPA; ISBT; Japan; NAT; PRT; TRALI; antibody; blood; cell; donor; patient; platelet; transfusion summary = These include ''incorrect blood component transfused'' events, where the blood component was intended for another recipient (frequently due to errors in patient identification at the time of collection of the pre-transfusion sample, or at the time of bedside administration), or did not meet the patient''s special needs (such as a patient with a red cell antibody who did not receive the required antigen-negative unit). Methods: Eligibility criteria for inclusion in the study included the following: transfusion of Rh D positive platelets, no anti D detectable before transfusion, no previous exposure to Rh D positive blood components, and results of follow-up testing of anti-D in patients serum available. In addition, the allelic frequency of Hpdel was calculated to be 0.015 by a genetic study of a limited number of the Japanese individuals, suggesting that Hp deficiency might distribute among the Japanese population as a phenotype of serum Hp. Aims: In this report, we present the results obtained from a hemovigilance survey carried out between 1998 and 2012, in which Hp deficiency was identified among Japanese patients who had experienced nonhemolytic TRs (NHTRs), and those obtained from a screening of Hp-deficient Japanese healthy blood donors. doi = 10.1111/vox.12100_1 id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00652.x id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00654.x id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00651.x id = cord-104226-bb4lyvhy author = nan title = Monoclonal antiprothrombinase (3D4.3) prevents mortality from murine hepatitis virus (MHV-3) infection date = 1992-09-01 keywords = MHV-3; PCA; animal; antibody summary = The induction of monocyte/macrophage procoagulant activity (PCA) has been implicated in the pathogenesis of murine hepatitis virus strain 3 (MHV-3) infection and disease. The results reported here demonstrate that a neutralizing antibody to PCA protects animals from fulminant hepatitis and death associated with MHV-3 infection, and supports the notion that PCA is a potent inflammatory mediator that plays a pivotal role in the pathogenesis of liver injury resulting from MHV-3 infection. In contrast, mice infected with MHV-3 but treated with antibody to PCA showed a marked reduction in liver disease in all groups (25, 50 , and 100/.r ( were a few small loci of inflammatory cells with no necrosis (Fig. 2 D) . No fibrin was seen in the livers of infected mice treated with 100/~g of mAb. Treatment with anti-PCA alone resulted in no detectable histological evidence of liver disease in nonirLf~ed animals. doi = nan id = cord-327883-s9nbr5y8 author = nan title = Section Virology date = 1990-03-31 keywords = EBV; HCMV; HSV; antibody; cell; dna; protein; virus summary = By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC). doi = 10.1016/s0934-8840(11)80039-3