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?' ---------------------------------------------------------- 55 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 18405 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 53 type 13 cell 8 IFN 6 patient 6 diabetes 5 study 5 figure 5 disease 5 SARS 4 infection 4 dna 4 PCR 4 COVID-19 3 virus 3 result 3 pulmonary 3 lung 3 lesion 3 increase 3 gene 3 University 3 T2DM 3 HIV 3 HCV 3 Fig 2 tissue 2 sample 2 receptor 2 level 2 human 2 expression 2 drug 2 conclusion 2 cause 2 Type 2 Pasteurella 2 Hospital 2 HLA 1 turbulence 1 tumor 1 tularensis 1 tularaemia 1 treatment 1 transfusion 1 test 1 term 1 table 1 syndrome 1 sting 1 stain Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 5293 cell 4722 % 4427 type 4229 patient 2477 blood 2316 study 2035 infection 1795 disease 1651 result 1511 protein 1473 virus 1227 gene 1222 method 1192 lung 1187 case 1186 sample 1177 drug 1147 transfusion 1143 level 1109 treatment 1080 response 1077 donor 1073 time 1064 group 1029 day 988 analysis 962 antibody 941 receptor 939 expression 935 system 935 number 904 year 877 effect 870 unit 858 datum 843 factor 836 platelet 832 diabetes 820 conclusion 793 finding 778 tissue 766 mouse 748 product 747 hospital 722 risk 687 role 684 medication 679 use 679 change 678 rate Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1397 IFN 924 al 747 et 727 . 580 RBC 565 Study 526 Design 492 Background 489 Case 484 Studies 460 SARS 419 C 395 T 383 Fig 376 I 339 II 317 RNA 294 A 267 B 264 Blood 259 PCR 253 University 238 CoV-2 217 HIV 212 HCV 205 - 197 HLA 196 S 193 D 193 COVID-19 191 Hospital 184 ABO 179 M 177 FCoV 175 E. 170 Type 170 T2DM 169 mg 168 RHD 167 Health 166 PLT 165 K 151 CoV 144 Rh 143 TRAIL 141 L 132 RT 129 Listeria 129 Disease 128 NPY Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2161 we 1506 it 1262 i 594 they 256 them 118 he 86 us 47 she 40 itself 37 one 22 you 21 themselves 7 him 5 ifnar1 4 me 4 isgf3 3 s 3 pdcs 3 ourselves 3 his 3 himself 3 her 2 igg4 2 ifnyr-/-mice 1 λr1 1 y401 1 w@ 1 theremaindwareeitherent~~ympas 1 srbcs 1 q656 1 p62 1 oneself 1 mine 1 mg 1 magpixv 1 irf8 1 iosns 1 immunosuppression 1 ilc1s 1 iiandciniii.usinganiemps/2 1 hpv120 1 em 1 easel 1 ca 1 c.1136c 1 a4bll Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 29073 be 4767 have 2670 use 1529 include 1416 show 1051 increase 1048 see 978 identify 948 find 907 induce 903 associate 875 cause 787 perform 783 do 751 follow 725 compare 709 base 702 report 607 reduce 607 contain 600 occur 571 suggest 563 provide 560 relate 553 lead 553 determine 544 require 519 involve 510 test 507 observe 504 express 503 develop 491 indicate 489 result 465 evaluate 460 detect 458 know 455 receive 452 treat 451 signal 430 demonstrate 429 describe 421 reveal 411 collect 411 bind 410 give 406 decrease 382 produce 374 make 364 activate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2273 not 2130 - 1679 also 1492 high 1377 other 1156 clinical 1039 more 956 most 907 such 905 viral 884 human 798 only 787 positive 781 pulmonary 767 low 750 however 734 specific 731 well 730 different 690 anti 646 non 586 immune 572 first 565 acute 559 large 555 respiratory 539 severe 534 chronic 520 negative 520 common 520 as 502 significant 496 new 459 possible 446 present 432 many 427 bacterial 426 further 423 important 420 abstract 415 inflammatory 405 several 399 similar 394 patient 392 small 385 significantly 385 potential 381 red 378 early 377 main Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 262 most 122 least 102 high 79 Most 73 good 35 low 30 great 26 large 12 late 8 old 7 early 6 strong 6 small 6 near 3 young 3 simple 3 fast 3 common 3 close 3 bad 2 short 2 new 2 fresh 2 easy 1 weak 1 tight 1 strict 1 steep 1 slow 1 sharp 1 safe 1 rich 1 postt 1 poor 1 pSARS 1 narrow 1 mild 1 mean:-42 1 long 1 heavy 1 estandsmall 1 ear{i 1 dense 1 deadly 1 cord-254404-lrsqrc2u 1 case(centra1andperipheralparliansaf 1 bottommost 1 START2014 1 S1P 1 Least Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 694 most 143 least 22 well 1 highest 1 freshest 1 cuituredonboneslicesbothin Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 33 doi.org 5 bit.ly 4 orcid.org 3 www.who.int 3 www.ncbi.nlm.nih.gov 3 github.com 2 zeus2.itb.cnr.it 2 www.bioinformatics.babraham.ac.uk 2 dx.doi.org 1 zenodo.org 1 www.worldometers.info 1 www.who-umc 1 www.thegpm.org 1 www.r-project.org 1 www.mdpi.com 1 www.isbtweb.org 1 www.gutenberg.org 1 www.gisaid.org 1 www.genomique.eu 1 www.fruitfly.org 1 www.fda.gov 1 www.ensembl.org 1 www.cbs.dtu.dk 1 www.astrazeneca.com 1 www 1 web.expasy.org 1 trna.bioinf.uni-leipzig 1 swissmodel.expasy.org 1 scope.aertslab.org 1 pfam 1 nmdc.cn 1 nls-mapper.iab.keio.ac.jp 1 gitlab.com 1 clinicalcodes.rss.mhs.man.ac.uk 1 blast.ncbi.nlm 1 bit Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 18 http://doi.org/10.1101/2020.08.10.20172189 10 http://doi.org/10.1101/2020.10.25.20200675 3 http://doi.org/10.1101/2020 2 http://zeus2.itb.cnr.it/~webgene/ 2 http://github.com/pasquelab/scPancreasAtlas 1 http://zenodo.org/record/3837351 1 http://www.worldometers.info/coronavirus/ 1 http://www.who.int/medicines/access/controlled-substances/ 1 http://www.who.int/health-topics/coronavirus#tab= 1 http://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ 1 http://www.who-umc 1 http://www.thegpm.org/cRAP/index.html 1 http://www.r-project.org 1 http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi 1 http://www.ncbi.nlm.nih.gov/genbank 1 http://www.ncbi.nlm.nih.gov/Traces/sra/ 1 http://www.mdpi.com/1999-4915/11/8/743/ 1 http://www.isbtweb.org/working-parties/red-cell-immunogenetics-and-bloodgroup-terminology/ 1 http://www.gutenberg.org/ebooks/1342 1 http://www.gisaid.org/ 1 http://www.genomique.eu/cellbrowser/HCA/ 1 http://www.fruitfly.org/ 1 http://www.fda.gov/safety/ 1 http://www.ensembl.org/index.html 1 http://www.cbs.dtu.dk/services/ 1 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 1 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 1 http://www.astrazeneca.com/ 1 http://www 1 http://web.expasy.org/translate/ 1 http://trna.bioinf.uni-leipzig 1 http://swissmodel.expasy.org/ 1 http://scope.aertslab.org/#/PancreasAtlas/*/welcome 1 http://pfam 1 http://orcid.org/0000-0003-3104-8800 1 http://orcid.org/0000-0003-0831-199X 1 http://orcid.org/0000-0002-8958-7404 1 http://orcid.org/0000-0002-0995-5714 1 http://nmdc.cn/#/nCoV 1 http://nls-mapper.iab.keio.ac.jp/ 1 http://gitlab.com/compstorylab/allotaxonometer 1 http://github.com/NicolasLagaillardie/mpst 1 http://dx.doi.org/10.1016 1 http://dx.doi.org/10 1 http://doi.org/10.1093/nsr/nwaa036 1 http://doi.org/10.1007/s40200-020-00656-4 1 http://clinicalcodes.rss.mhs.man.ac.uk 1 http://blast.ncbi.nlm 1 http://bit.ly/2q51heq 1 http://bit.ly/2pDplF8 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 vincent.pasque@kuleuven.be 1 ronald.kostoff@pubpolicy.gatech.edu 1 peter.dodds@uvm.edu Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 16 drug related problems 6 patient did not 5 % were male 5 cells are also 5 patients are more 5 samples were also 5 samples were then 4 % were female 4 * see also 4 cells is not 4 infection is usually 4 patients had at 4 patients were not 4 results are consistent 4 studies are available 4 type is more 3 % had severe 3 % were men 3 % were women 3 cells did not 3 donors were igm 3 drug related problem 3 gene is not 3 genes are also 3 genes including ace2 3 infection is not 3 infections are more 3 lungs are notably 3 lungs is not 3 patient does not 3 patient had symptoms 3 patient was not 3 patient was successfully 3 patients are not 3 patients did not 3 patients do not 3 patients had more 3 patients using manually 3 patients were eligible 3 receptors are orthologs 3 results did not 3 results were not 3 samples did not 3 samples were not 3 studies are necessary 3 studies are not 3 study provides new 3 time was similar 3 transfusion related acute 3 transfusions were not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 donors were not able 2 patients were not subsequently 2 response has not only 2 studies are not available 2 transfusion had no effect 1 % had no change 1 % had no clinical 1 % had no indication 1 antibodies are not detectable 1 antibodies had no effect 1 antibodies were not routinely 1 antibody is not demonstrable 1 blood is not always 1 blood is not available 1 cases is not yet 1 cases was not previously 1 cells are not available 1 cells are not only 1 cells is not as 1 cells is not clear 1 cells is not possible 1 disease are no longer 1 donor had no identifiable 1 donor has not yet 1 donor reported no clinical 1 donor were not significant 1 donors reported no significant 1 drug is not available 1 drugs having no justification 1 drugs is not negligible 1 gene is not essential 1 gene is not lethal 1 groups was not statistically 1 groups were not significantly 1 infection are not identical 1 infection are not well 1 infection is not always 1 infection was not clearly 1 infections did not significantly 1 infections is not fully 1 infections is not well 1 lungs are not fully 1 lungs is not well 1 methods are not available 1 patient had no change 1 patient had no other 1 patient was not recently 1 patient was not statistically 1 patients are not subsequently 1 patients had no chronic A rudimentary bibliography -------------------------- id = cord-347207-1u4i6qmc author = Almomani, Huda Y. title = Randomised controlled trial of pharmacist-led patient counselling in controlling hypoglycaemic attacks in older adults with type 2 diabetes mellitus (rose-adam): A study protocol date = 2020-07-29 keywords = diabetes; intervention; study; type summary = title: Randomised controlled trial of pharmacist-led patient counselling in controlling hypoglycaemic attacks in older adults with type 2 diabetes mellitus (rose-adam): A study protocol Several studies have established the important positive role of educational interventions on achieving glycaemic control and other clinical outcomes, however, there is still a lack in studies that evaluate the impact of such type of interventions on hypoglycaemia risk in elderly patients with type 2 diabetes. The purpose of this research is to evaluate the effectiveness of pharmacist-led patient counselling on reducing hypoglycaemic attacks in older adults with type 2 diabetes mellitus. Participants who are elderly (age ≥ 65 years), diagnosed with type 2 diabetes mellitus, and taking insulin, sulfonylurea, or any three anti-diabetic medications will be randomly assigned to intervention (SUGAR Handshake) and control (usual care) groups. doi = 10.1016/j.sapharm.2020.07.012 id = cord-315094-pzixgqcy author = Benetka, Viviane title = Prevalence of feline coronavirus types I and II in cats with histopathologically verified feline infectious peritonitis date = 2004-03-26 keywords = FIP; PCR; type summary = doi = 10.1016/j.vetmic.2003.07.010 id = cord-260793-bb4h255w author = Brann, David H. title = Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date = 2020-05-18 keywords = ACE2; SARS; TMPRSS2; cell; figure; gene; olfactory; type summary = It has recently been demonstrated through single cell RNA sequencing analysis (referred to herein as scSeq) that cells from the human upper airway -including nasal RE goblet, basal and ciliated cells -express high levels of ACE2 and TMPRSS2, suggesting that these RE cell types may serve as a viral reservoir during CoV-2 infection (33) . The presence of Ace2 and Tmprss2 transcripts in mouse WOM and their (near total) absence in purified OSNs suggest that the molecular components that enable CoV-2 entry into cells are expressed in non-neuronal cell types in the mouse nasal epithelium. An independent mouse scSeq data set (obtained using the 10x Chromium platform, see Methods) revealed that olfactory sensory neurons did not express Ace2 (2 of 28769 mature OSNs were positive for Ace2), while expression was observed in a fraction of Bowman''s gland cells and HBCs ( Figure S4 , see methods). doi = 10.1101/2020.03.25.009084 id = cord-343982-ymaql0hx author = Carr, M. J. title = Impact of COVID-19 on the diagnoses, HbA1c monitoring and mortality in people with type 2 diabetes: a UK-wide cohort study involving 13 million people in primary care date = 2020-10-27 keywords = COVID-19; type summary = ; https://doi.org/10.1101/2020.10.25.20200675 doi: medRxiv preprint Supplementary figure 2: Comparison of monthly HbA1c testing rates in people with type 2 diabetes in primary care by age, gender, deprivation level and by region before and after the first COVID-19 peak in England (CPRD Aurum) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint ; https://doi.org/10.1101/2020.10.25.20200675 doi: medRxiv preprint Supplementary figure 6: Comparison of observed and expected monthly incidence rates for type 2 diabetes in primary care, HbA1c monitoring and new prescriptions for metformin and insulin before and after the first COVID-19 peak in Northern Ireland, Scotland and Wales (CPRD GOLD) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint doi = 10.1101/2020.10.25.20200675 id = cord-001124-qcjbtflt author = Carrero, Javier Antonio title = Confounding roles for type I interferons during bacterial and viral pathogenesis date = 2013-10-24 keywords = IFN; IFNAR; type summary = Although type I interferons (IFN-I) were initially defined as potent antiviral agents, they can also cause decreased host resistance to some bacterial and viral infections. In contrast, there is a negative effect of IFN-I on host resistance during chronic infection with lymphocytic choriomeningitis virus (LCMV) and acute infections with intracellular bacteria. Following Listeria infection, IFN-I promote the cell death of macrophages and lymphocytes, which leads to innate immune suppression. Because of the extent of the IFN-I literature, this review will mostly limit itself to experiments that have examined viral and bacterial pathogenesis in IFNAR -/mice with a particular emphasis on work that has examined lethality and pathogen burden. In the case of influenza and potentially other respiratory viruses, the type III interferon system (which comprises IFN-λ subtypes and signals using IL-10R2-IFNLR1) plays a dominant role in restricting acute epithelial cell infection, thereby limiting the requirement of IFN-I signaling (10, 11) . Production of type I IFN sensitizes macrophages to cell death induced by Listeria monocytogenes doi = 10.1093/intimm/dxt050 id = cord-293819-tbdsr5iw author = Carvalho, C.L. title = Tularaemia: A challenging zoonosis date = 2014-01-13 keywords = Dermacentor; Francisella; disease; tularaemia; tularensis; type summary = doi = 10.1016/j.cimid.2014.01.002 id = cord-028840-7n77vko9 author = Chardonnet, Kostia title = Toward a Curry-Howard Equivalence for Linear, Reversible Computation: Work-in-Progress date = 2020-06-17 keywords = type summary = In this paper, we present a linear and reversible language with inductive and coinductive types, together with a Curry-Howard correspondence with the logic [Image: see text] : linear logic extended with least and greatest fixed points allowing inductive and coinductive statements. The constructors inj l and inj r represent the choice between either the left or right-hand side of a type of the form A ⊕ B; the constructor , builds pairs of elements (with the corresponding type constructor ⊗); fold and pack respectively represent inductive and coinductive structure for the types μX.A and νX.A. A value can serve both as a result and as a pattern in the clause of an iso. We presented a higher-order, linear, reversible language with inductive and coinductive types together with an interpretation of programs into derivations in the logic . doi = 10.1007/978-3-030-52482-1_8 id = cord-336201-fl606l3b author = Daryabor, Gholamreza title = The Effects of Type 2 Diabetes Mellitus on Organ Metabolism and the Immune System date = 2020-07-22 keywords = ROS; T2DM; cell; diabetes; diabetic; increase; level; patient; type summary = Obesity-related immune cell infiltration, inflammation, and increased oxidative stress promote metabolic impairments in the insulin-sensitive tissues and finally, insulin resistance, organ failure, and premature aging occur. T2DM, the most common form of diabetes (∼90%), is characterized by a systemic inflammatory disease accompanied by insulin resistance (IR) or decreased metabolic response to insulin in several tissues, including the adipose tissue, liver, and skeletal muscle, as well as by reduced insulin synthesis by pancreatic beta cells (4, 5) . During the progression of diabetes, hyperglycemia promotes mitochondrial dysfunction and induces the formation of reactive oxygen species (ROS) that cause oxidative stress in several tissues such as blood vessels and pancreatic beta cells (7) (8) (9) . In addition, the attachment of AGEs to their receptors [e.g., CD36, galectin-3, scavenger receptors types I (SR-A1), and II (SR-A2)] on the surfaces of immune cells in the circulation and tissues activates the expression of pro-inflammatory cytokines and increases free radical generation (18) . doi = 10.3389/fimmu.2020.01582 id = cord-284514-b7no0yrv author = Davies, Robert L title = Diversity of avian Pasteurella multocida strains based on capsular PCR typing and variation of the OmpA and OmpH outer membrane proteins date = 2003-02-02 keywords = OMP; Pasteurella; type summary = title: Diversity of avian Pasteurella multocida strains based on capsular PCR typing and variation of the OmpA and OmpH outer membrane proteins One hundred avian Pasteurella multocida isolates recovered from cases of fowl cholera and related infections in England and Wales over a 13-year period were characterised by capsular PCR typing and analysis of outer membrane protein (OMP) profiles. Nineteen distinct OMP profiles (OMP-types) were identified based mainly on molecular mass heterogeneity of the heat-modifiable (OmpA) and porin (OmpH) proteins. Strains of capsular types B, D and F, as well as the untypable isolates, were associated exclusively with specific OMP-types and represent distinct and widely disseminated clonal groups. The molecular mass of OmpA (A) varied from 36.9 to 37.9 kDa and that of OmpH (H) varied from 33.1 to 38.3 kDa. The distribution of OMP-types among the avian isolates is shown in Table 1 . doi = 10.1016/s0378-1135(02)00300-0 id = cord-321878-bnjupaik author = Deliwala, Smit S. title = A 29-Year-Old Male with a Fatal Case of COVID-19 Acute Respiratory Distress Syndrome (CARDS) and Ventilator-Induced Lung Injury (VILI) date = 2020-07-23 keywords = ARDS; COVID-19; Type summary = title: A 29-Year-Old Male with a Fatal Case of COVID-19 Acute Respiratory Distress Syndrome (CARDS) and Ventilator-Induced Lung Injury (VILI) Patient: Male, 29-year-old Final Diagnosis: Acute respiratory distress syndrome (ARDS) • COVID-19 •multi organ failure/septic shock • pneumothorax Symptoms: Cough • dyspnea • fatigue • myalgia Medication:— Clinical Procedure: Mechanical ventilation • thoracentesis Specialty: Critical Care Medicine OBJECTIVE: Unknown ethiology BACKGROUND: COVID-19 patients that develop acute respiratory distress syndrome (ARDS) "CARDS" behave differently compared to patients with classic forms of ARDS. In previous cases of SARS patients, pneumothorax was noted at 14-37 days after the initial diagnosis [16] , suggesting that a sustained period of lung inflammation serves as a pre-requisite, a similar time course as our patient Recently a scoring system was proposed to predict the risk of developing critical illness in COVID-19, allowing early interventions and resource allocation to mitigate the high disease burden [17] . doi = 10.12659/ajcr.926136 id = cord-309795-2kozsv4z author = Dewidar, Bedair title = Metabolic liver disease in diabetes – from mechanisms to clinical trials date = 2020-06-20 keywords = Disease; NAFLD; NASH; T2DM; diabetes; liver; type summary = NAFLD, which affects about 25% of the population [3] , comprises a broad range of abnormalities ranging from simple fatty liver (steatosis) to non-alcoholic steatohepatitis (NASH), characterized by inflammation, necrosis, and hepatocellular ballooning, and progression to liver fibrosis, cirrhosis, and hepatocellular carcinoma (HCC) [2] . In general, both hyperglycemia and toxic lipids such as ceramides, DAG, FFA, and cholesterol can induce deleterious effects on liver cells (glucolipotoxicity), which might initiate NAFLD progression from simple steatosis to NASH and fibrosis via various mechanisms, including cell death, oxidative stress, endoplasmic reticulum (ER) stress and mitochondrial disorders [46] . BL, baseline; CCR2/5, C-C chemokine receptors type 2 and type 5; FXR, farnesoid X receptor; HbA 1c , glycated haemoglobin; LXR, Liver X receptor; MPC, mitochondrial pyruvate carrier; NA, data not available; NAFLD, non-alcoholic fatty liver disease; NFS, NAFLD fibrosis score; PPAR, peroxisome proliferator-activated receptor; NASH, non-alcoholic steatohepatitis; SCD, stearoyl-CoA desaturase; SGLT, sodium-glucose cotransporter; THR, thyroid hormone receptor; T2DM, type 2 diabetes. Potential Nexus of Non-alcoholic Fatty Liver Disease and Type 2 Diabetes Mellitus: Insulin Resistance Between Hepatic and Peripheral Tissues doi = 10.1016/j.metabol.2020.154299 id = cord-240471-rz0pj5a3 author = Dodds, P. S. title = Probability-turbulence divergence: A tunable allotaxonometric instrument for comparing heavy-tailed categorical distributions date = 2020-08-30 keywords = divergence; probability; turbulence; type summary = In Sec. IV, we show that probability-turbulence divergence is either a generalization of or may be connected to a number of other kinds of divergences and similarities (e.g., the Sørensen-Dice coefficient), and then discuss limited functional similarities with the Rényi entropy and diversity indices [20] [21] [22] [23] [24] . The dominant contributions to probability-turbulence divergence in the α → ∞ limit therefore come from the most common types in each systems, providing they are not equally abundant. For a primary, familiar example to help us explain our probability-turbulence divergence allotaxonographs, we compare the normalized usage frequency distributions of 2-gram usage between the first and second halves of Pride and Prejudice [29] . 5. Allotaxonograph using probability-turbulence divergence to compare normalized 2-gram usage ranks on two days of English-language Twitter, 2020/03/12 and 2020/05/30. Allotaxonograph using probability-turbulence divergence to compare 3-gram usage ranks on two days of English-language Twitter, 2020/03/12 and 2020/05/30. doi = nan id = cord-018595-x3tleomb author = Dodiuk-Gad, Roni P. title = Adverse Medication Reactions date = 2017-04-25 keywords = HLA; Johnson; SJS; Stevens; cutaneous; dress; drug; patient; reaction; skin; type summary = 2. Delayed-type drug hypersensitivity: Delayed-type drug hypersensitivity reactions usually take several days to weeks following drug exposure, with variable clinical presentations that may include Maculopapular Eruption (MPE), Fixed Drug Eruption (FDE), Acute Generalized Exanthematous Pustulosis (AGEP), Stevens-Johnson Syndrome (SJS), Toxic Epidermal Necrolysis (TEN) and Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS). Examples of strong associations of HLA alleles with specific drug-induced hypersensitivity reactions include abacavir, nevirapine, carbamazepine, and allopurinol (Table 25. [61] , who reported the weak associations of HLA-A29, B12, and MPE maculopapular drug eruption, DRESS drug reaction with eosinophilia and systemic symptoms, SJS/TEN Stevens-Johnson syndrome/toxic epidermal necrolysis DR7 in sulfonamide-related TEN, and HLA-A2, B12 in oxicam-related TEN in Europeans [61] . Drug specific cytotoxic T-cells in the skin lesions of a patient with toxic epidermal necrolysis doi = 10.1007/978-3-319-29785-9_25 id = cord-001273-plz1ja2e author = Dussurget, Olivier title = The bacterial pathogen Listeria monocytogenes and the interferon family: type I, type II and type III interferons date = 2014-04-28 keywords = IFN; III; Listeria; type summary = doi = 10.3389/fcimb.2014.00050 id = cord-332186-3jy9zoz2 author = Edens, FW title = Atypical Escherichia coli strains and their association with poult enteritis and mortality syndrome date = 1997-07-01 keywords = PEMS; coli; type summary = doi = 10.1093/ps/76.7.952 id = cord-335382-fk4um9nw author = Farver, Carol F. title = Molecular Basis of Pulmonary Disease date = 2012-08-10 keywords = EGFR; LAM; Molecular; Pathology; cause; cell; disease; figure; gene; lung; patient; pulmonary; tumor; type summary = When lung cancer is suspected, evaluation of the patient includes a thorough clinical, radiologic, and laboratory assessment, with collection of tissue or cytology samples to establish a pathologic diagnosis of malignancy and to classify the tumor type. Development of lung cancer occurs with multiple, complex, stepwise genetic and epigenetic changes involving allelic losses, chromosomal instability and imbalance, mutations in tumor suppressor genes (TSGs) and dominant oncogenes, epigenetic gene silencing through promoter hypermethylation, and aberrant expression of genes participating in control of cell proliferation and apoptosis [7] . In recent years, atypical adenomatous hyperplasia (AAH) has been recognized as a precursor lesion for peripheral pulmonary ACs. This lesion is defined as "a localized proliferation of mild to moderately atypical cells lining involved alveoli and, sometimes, respiratory bronchioles, resulting in focal lesions in peripheral Part IV Molecular Pathology of Human Disease alveolated lung, usually less than 5 mm in diameter and generally in the absence of underlying interstitial inflammation and fibrosis" (Figure 18 .8) [36] . doi = 10.1016/b978-0-12-374419-7.00018-4 id = cord-266488-wc6k06sm author = Feng, Mingqian title = Construction and next-generation sequencing analysis of a large phage-displayed V(NAR) single-domain antibody library from six naïve nurse sharks date = 2018-11-07 keywords = CDR3; NAR; type summary = title: Construction and next-generation sequencing analysis of a large phage-displayed V(NAR) single-domain antibody library from six naïve nurse sharks METHODS: Here, we developed a library construction method based on polymerase chain reaction (PCR)-Extension Assembly and Self-Ligation (named "EASeL") to construct a large V(NAR) antibody library with a size of 1.2 × 10(10) from six naïve adult nurse sharks (Ginglymostoma cirratum). To validate the use of the shark V(NAR) library for antibody discovery, we isolated a panel of V(NAR) phage binders to cancer therapy-related antigens, including glypican-3, human epidermal growth factor receptor 2 (HER2), and programmed cell death-1 (PD1). The isolated shark single-domain antibodies including Type I and Type II V(NAR)s were produced in Escherichia coli and validated for their antigen binding. In this study, we developed a PCR-Extension Assembly and Self-Ligation-based method (named EASeL) to make a large phage-displayed V NAR single-domain library from six nurse sharks. doi = 10.1093/abt/tby011 id = cord-025995-nxeg03xj author = Gerba, Charles P. title = Pathogen Removal from Wastewater during Groundwater Recharge date = 2013-11-17 keywords = Survival; Wastewater; Water; sewage; soil; type; virus summary = doi = 10.1016/b978-0-250-40549-7.50015-1 id = cord-343409-oao75pzy author = Hayward, Joshua A title = Identification of diverse full-length endogenous betaretroviruses in megabats and microbats date = 2013-03-27 keywords = Env; Lys; ORF; PBS; Rev; type summary = doi = 10.1186/1742-4690-10-35 id = cord-010657-5qtsj8xv author = Heckman, Carol A. title = Pathogenesis of Lesions Induced in Rat Lung by Chronic Tobacco Smoke Inhalation date = 1982-07-01 keywords = lesion; type summary = In serially killed animals, four types of lesions were found: 1) perivascular or peribronchiolar accumulation of lymphoreticular cells, 2) fibrotic and cellular enlargement of peribronchiolar septa, 3) type II cell hyperplasia with septal fibrosis, and 4) air-space enlargement (emphysema). The type II hyperplastic and peribronchiolar alveolar lesions involved larger portions of the parenchyma in fibrotic changes but differed in structure, location, and frequency. In studies by Roe''s group (1, 2) , the major lesions induced in the rat lung by lifetime exposure were columnar, cuboidal, and squamous metaplasias of the alveolar epithelium. (3) on rats exposed to tobacco smoke for 6 weeks showed characteristic lesions at the level of the respiratory bronchiole, including peribronchiolar and perivascular infiltration by lymphocytes, focal pneumonitis, and alveolar cuboidal or columnar metaplasia. The present studies have shown that the most common type of focal lesions to develop in the lungs of tobacco smoke-exposed animals consisted of accumulated lymphocytes and macrophages in the vascular adventitia. doi = 10.1093/jnci/69.1.117 id = cord-292908-rbn3foj3 author = Hohdatsu, T. title = Antigenic analysis of feline coronaviruses with monoclonal antibodies (MAbs): Preparation of MAbs which discriminate between FIPV strain 79-1146 and FECV strain 79-1683 date = 1991-06-30 keywords = FIPV; Type summary = title: Antigenic analysis of feline coronaviruses with monoclonal antibodies (MAbs): Preparation of MAbs which discriminate between FIPV strain 79-1146 and FECV strain 79-1683 Abstract We prepared 31 monoclonal antibodies (MAbs) against either FIPV strain 79-1146 or FECV strain 79-1683, and tested them for reactivity with various coronaviruses by indirect flourescent antibody assay (IFA). Sixteen MAbs which reacted with all of the 11 strains of feline coronaviruses, also reacted with canine coronavirus (CCV) and transmissible gastroenteritis virus (TGEV). For serological diagnosis of feline infectious peritonitis virus (FIPV) infection, detection of antibody by indirect fluorescent antibody assay (IFA) is popular (Pedersen, 1976b; Horzinek and Osterhaus, 1979; Scott, 1979) . They divided FIPV into Types I and II according to the presence or absence of the induction of FIP, ability of the viruses to proliferate in cell cultures, and the antigenic relationship with porcine and canine coronaviruses. doi = 10.1016/0378-1135(91)90096-x id = cord-355239-fc52dn3v author = Kato, Kentaro title = The Role of Carbohydrates in Infection Strategies of Enteric Pathogens date = 2014-11-15 keywords = Salmonella; cell; host; type summary = doi = 10.2149/tmh.2014-25 id = cord-257641-wmbgpnr9 author = Katsarou, Maria title = Acute Retrograde Type A Intramural Hematoma during SARS-CoV-2 time date = 2020-10-15 keywords = type summary = title: Acute Retrograde Type A Intramural Hematoma during SARS-CoV-2 time Retrograde type A IMH (retro-TAIMH) origins in the descending aorta and 4 extend into the arch or ascending aorta. Follow-up CTA was performed at 24 hours 13 (B) and 7 days (C) showing progressive to complete thrombosis of the entry tear, with reduction 14 in aortic diameter which is the most important predictor of IMH regression and positive 15 outcome. CoV-2 pandemic peak in Lombardy and the patient was found to be positive to the virus five 17 days after symptom onset, with progressive dyspnea and worsening findings on chest X rays (D). 4 Medical treatment appears to be appropriate in asymptomatic patients, in those 1 with non-complicated retro-TAIMH and in patients with high open surgical / TEVAR risks. The differences and similarities between intramural hematoma of the descending 6 aorta and acute type B dissection Management of retrograde type A IMH with acute arch tear/type B dissection doi = 10.1016/j.jvs.2020.09.019 id = cord-334588-2vy4xkz6 author = Klaumann, Francini title = Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry date = 2018-12-12 keywords = China; PCV-3; circovirus; porcine; type summary = (21) also performed a brief retrospective study through qPCR on serum samples from animals clinically affected by PDNS-like lesions (but negative for PCV-2 by IHC) and pigs with porcine respiratory diseases. Based on these two initial works, the name PCV-3 was proposed as the third species of circoviruses affecting pigs, since pairwise analysis demonstrated significant divergence with the existing PCVs. The novel sequences showed <70% of identity in the predicted whole genome and capsid protein amino acid (aa) sequence compared to the other members of the Circovirus genus (22) . Cloned genomic DNA of type 2 porcine circovirus is infectious when injected directly into the liver and lymph nodes of pigs: characterization of clinical disease, virus distribution, and pathologic lesions Genetic characterization of Type 2 Porcine Circovirus (PCV-2) from pigs with postweaning multisystemic wasting syndrome in different geographic regions of north America and development of a differential PCR-restriction fragment length polymorphism assay doi = 10.3389/fvets.2018.00315 id = cord-311332-n8tvglif author = Kostoff, Ronald N. title = Literature-related discovery: Potential treatments and preventatives for SARS() date = 2011-04-20 keywords = LRD; SARS; discovery; potential; type summary = doi = 10.1016/j.techfore.2011.03.022 id = cord-026548-z2ifu1d6 author = Lagaillardie, Nicolas title = Implementing Multiparty Session Types in Rust date = 2020-05-13 keywords = Rust; type summary = Multiparty Session Types (MPST) is a typing discipline for distributed protocols, which ensures communication safety and deadlock-freedom for more than two participants. In addition, since we generate the local types from a readable global specification, errors caused by an affine (and not linear) usage of channels, a well-known limitation of the previous libraries [8, 9] , are easily avoided. Our framework guarantees that processes implemented using mpst-rust primitives with Scribble-generated types are free from deadlocks, reception errors, and protocol deviations. (line 12), which is applied to a multiparty channel s of a sum type between ChoiceA::Video and ChoiceA::End. The behaviour of each branch in the protocol is implemented as an anonymous function. The types of the multiparty channel, as well as the generic types in the declaration of the mpst-rust communication functions, enable compile-time detection of protocol violations, such as swapping line 3 and line 4, using another communication primitive or using the wrong payload type. The Rust library in [8] implements binary session types, following [4] . doi = 10.1007/978-3-030-50029-0_8 id = cord-314328-gft6phd6 author = Lawrence, C. title = Increased paediatric presentations of severe diabetic ketoacidosis in an Australian tertiary centre during the COVID‐19 pandemic date = 2020-10-23 keywords = DKA; type summary = AIMS: To determine if the frequency of severe diabetic ketoacidosis at presentation of new‐onset type 1 diabetes to an Australian tertiary centre increased during the initial period of restrictions resulting from the COVID‐19 pandemic (March to May 2020). We report one Australian centre''s experience of presentations of newly diagnosed type 1 diabetes in a paediatric cohort during the COVID-19 pandemic restrictions (March to May inclusive) compared to pre-pandemic presentations in the March to May periods of the years 2015 to 2019. • We report a significant increase in the frequency of severe diabetic ketoacidosis at presentation of new-onset type 1 diabetes during the COVID-19 pandemic at our tertiary centre. This study reports a significant increase in the frequency of children and adolescents presenting with severe DKA at onset of type 1 diabetes during the COVID-19 pandemic. The increase in presentations of children and adolescents with severe DKA at diagnosis of type 1 diabetes during the COVID-19 pandemic is a major concern. doi = 10.1111/dme.14417 id = cord-329398-8o39bwv7 author = Li, Kunwei title = CT image visual quantitative evaluation and clinical classification of coronavirus disease (COVID-19) date = 2020-03-25 keywords = TSS; type summary = doi = 10.1007/s00330-020-06817-6 id = cord-332133-6hdk8801 author = Li, Mao-Zhong title = A Pneumonia Case Associated with Type 2 Polio Vaccine Strains date = 2017-01-05 keywords = OPV; type summary = title: A Pneumonia Case Associated with Type 2 Polio Vaccine Strains [1, 2] Other than VAPP cases and VDPVs, Type 2 polio vaccine strains can also cause a variety of illnesses. [3] To the best of our knowledge, no cases of pneumonia resulting from Type 2 polio vaccine strains have been reported. However, here we report an infant case associated with the Type 2 polio vaccine strain. A 3-month-old male infant with no underlying diseases was admitted to Beijing Haidian Hospital on July 31, 2015, where he was diagnosed with lobular pneumonia exactly 26 days after he had received his second dose of trivalent OPV (tOPV). However, this report provides an initial case of pneumonia, the outcomes associated with Type 2 polio vaccine strains, and the implications for the safety of attenuated OPV in the absence of wild virus diseases. doi = 10.4103/0366-6999.196575 id = cord-262545-bs8p50ig author = Luk, Andrea O. Y. title = Secular trends in incidence of type 1 and type 2 diabetes in Hong Kong: A retrospective cohort study date = 2020-02-20 keywords = Hong; Kong; type summary = From the 2012-2014 National Health Insurance Service database containing 706 physician-reported cases of type 1 diabetes in children aged <15 years in South Korea, Kim and colleagues reported an incidence of 3.2 per 100,000 person-years, which was 2.3-fold higher compared with the rate recorded in the earlier period of 1995-2000 [13] . Based on retrospective retrieval of 255 paediatric cases of newly diagnosed diabetes between 1984 and 1996, Huen and colleagues recorded an incidence of 1.4 per 100,000 person-years for type 1 diabetes in children aged <15 years in Hong Kong, which was considerably lower than our updated estimates of 5.3-6.4 per 100,000 person-years in a comparable age group [14] . In the present study, 60% of incident cases of diabetes in people aged <20 years were type 2 diabetes. In this report on the secular trend of the incidence of diabetes in Hong Kong, we revealed that the incidence of type 1 diabetes increased in people aged <20 years and was stable in other age groups. doi = 10.1371/journal.pmed.1003052 id = cord-026005-f2khcjdy author = López, Alfonso title = Respiratory System, Mediastinum, and Pleurae date = 2017-02-17 keywords = Fig; Mannheimia; Mycobacterium; Mycoplasma; Pasteurella; alveolar; cause; cell; disease; horse; infection; lesion; lung; nasal; pneumonia; pulmonary; respiratory; type summary = Microscopic examination of properly collected, stored, and processed samples may reveal many erythrocytes and siderophages in pulmonary hemorrhage or left-sided heart failure; inclusion bodies or syncytial cells in viral pneumonias; increased number of leukocytes in pulmonary inflammation; abundant mucus in asthma or equine recurrent airway obstruction (RAO); the presence of pulmonary pathogens, such as parasites, fungi, and bacteria; or tumor cells in cases of pulmonary neoplasia. The portal of entry for the respiratory form is typically aerogenous, and the disease is generally transient; thus the primary viral-induced lesions in the nasal mucosa and lungs are rarely seen at necropsy unless complicated by secondary bacterial rhinitis, pharyngitis, or bronchopneumonia. Laryngeal edema occurs in pigs with edema disease; in horses with purpura hemorrhagica; in cattle with acute interstitial pneumonia; in cats with systemic anaphylaxis; and in all species as a result of trauma, improper endotracheal tubing, inhalation of irritant gases (e.g., smoke), local inflammation, and animal species is classified as fibrinous, catarrhal, purulent, or granulomatous (Figs. doi = 10.1016/b978-0-323-35775-3.00009-6 id = cord-030631-cc79j9j4 author = Marcus, Benjamin A. title = Typ-1-Diabetes: Früherkennung und Ansätze zur Prävention: Update 2020 date = 2020-08-19 keywords = Typ-1-Diabetes; diabetes; die; type summary = Autoantikörpern markiert das Frühstadium des Typ-1-Diabetes Der Nachweis von 2 oder mehr dieser Autoantikörper beim asymptomatischen Kind ohne gestörten Glukosestoffwechsel ist inzwischen als eines der Frühstadien des Typ-1-Diabetes (Stadium 1) anerkannt. Um zu prüfen, ob Teplizumab die klinische Manifestation verhindern kann, wurden in einer TrialNet-Studie Angehörige von Personen mit Typ-1-Diabetes behandelt, die selbst bereits ein Frühstadium mit multiplen Inselautoantikörpern und eine Dysglykämie oder gestörte Glukosetoleranz (Stadium 2) entwickelt hatten. Somit konnte erstmals die Manifestation der Erkrankung wirksam hinausgezögert werden, was einen Durchbruch für die präventive Therapie des Typ-1-Diabetes darstellt. Bei 19 (43%) der 44 mit Teplizumab behandelten Teilnehmenden und 23 (72 %) von 32 in der Plazebogruppe wurde ein klinischer Typ-1-Diabetes diagnostiziert. Für eine individualisierte Sekundärprävention interessant wird die Tatsache, dass anhand von Biomarkern -HLA-Merkmalen (HLA: humanes Leukozytenantigen) und dem Fehlen von ZnT8A -abgeschätzt werden kann, bei welchen Patienten ein Ansprechen auf die Anti-CD3-Behandlung bessere Erfolgschancen hat [28] . doi = 10.1007/s11428-020-00668-x id = cord-353867-617f90wq author = Ory, Marcia G. title = Implementing a Diabetes Education Program to Reduce Health Disparities in South Texas: Application of the RE-AIM Framework for Planning and Evaluation date = 2020-08-30 keywords = Diabetes; South; Texas; type summary = This community-based initiative reached a large and diverse population, and statistically significant reductions in A1c levels (p < 0.01) were observed among participants with Type 2 diabetes at 3 months. The U.S.-Mexico border is impacted by extremely high disparities in income, education, and healthcare access, and these social determinants of health make this region among the nation''s Figure 1 illustrated the 27 counties formally included in the Healthy South Texas initiative [30] , and the counties in which the Diabetes Education Program was offered were marked with a red dot. Among participants with pre-diabetes or Type 1 diabetes, no statistically significant differences were observed based on baseline A1c level attending a follow-up session at any given time point (Table 2 ). From private and public sources, over USD 15,000,000 was identified in direct support and in-kind dollars for the Healthy South Texas initiative (including delivery of the Diabetes Education Program, as well as other disease prevention and health promotion activities) by governmental and nongovernmental entities. doi = 10.3390/ijerph17176312 id = cord-344093-3bniy5b5 author = Peteranderl, Christin title = The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date = 2017-03-22 keywords = IAV; IFN; TRAIL; cell; infection; type; virus summary = A prominent regulator of disease outcome, especially in-but not limited to-respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. (73) Cell death induction, e.g., Bcl-2-associated X protein, caspase-8, Fas-associated protein with death domain, Fas ligand, and TNF-related apoptosis-inducing ligand (TRAIL) dsRNA, polyI:C (4, 110) IAV (4, 5, 10, 115) Sendai virus (110) TRAIL Virus control by apoptosis induction in infected cells IAV (6, 170, 171) Tissue injury by apoptosis of both infected and non-infected alveolar epithelial cells, lung macrophages IAV (5, 7, 10) RSV (137) Necrosis of fibroblasts, dendritic cells, and epithelial cells IAV (146, 147, 168) Increased cellular infiltration CoV (175) Decreased expression of Na,K-ATPase, impaired epithelial fluid reabsorption IAV (11) iNTRODUCTiON In 1957, Isaacs and Lindenmann (1) first recognized the potential of a soluble and probably cell-derived factor to combat influenza virus infection and named this factor interferon [(IFN) from latin interferre, to interfere]. doi = 10.3389/fimmu.2017.00313 id = cord-031922-3pfxrhbc author = Petrie, John R title = SGLT2 inhibitors and renal complications in type 1 diabetes date = 2020-09-15 keywords = SGLT2; type summary = In this issue of The Lancet Diabetes & Endocrinology, Per-Henrik Groop and colleagues 4 report the effect of the SGLT2 inhibitor dapagliflozin on albuminuria in adults with type 1 diabetes in a post-hoc subgroup analysis of the DEPICT-1 and DEPICT-2 phase 3 trials. The UK National Institute for Healthcare Excellence (NICE) subsequently recommended both drugs (dapagliflozin in August, 2019, and sotagliflozin in February, 2020) to be cost-effective for use within the UK National Health Service for individuals who additionally had a relatively high insulin requirement (≥0·5 units/kg per day) and had completed an evidence-based qualityassured structured education programme. Effect of dapagliflozin as an adjunct to insulin over 52 weeks in individuals with type 1 diabetes: post-hoc renal analysis of the DEPICT randomised controlled trials doi = 10.1016/s2213-8587(20)30311-9 id = cord-299756-m0va36er author = Raaben, Matthijs title = Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo date = 2009-08-03 keywords = IFN; MHV; type summary = As the BALB/c and the IFNAR-/129SvEv mice demonstrated very similar viral loads in their brains, we also compared their gene expression profiles upon infection with MHV in order to identify type I IFN-dependent transcriptional responses. CONCLUSION: Transcriptional profiling of mice infected with MHV demonstrated the induction of a robust IFN response, which correlated with the viral load. Furthermore, gene expression profiling of 129SvEv mice lacking the type I IFN receptor, which are not able to control the MHV infection [11] , allowed us to identify type I IFN-independent transcriptional responses. To study the role of type I IFN-independent and -dependent gene expression in the control of MHV infection in vivo in more detail, we next made use of the IFNAR-/-mice [30] . Transcriptional profiling of mice infected with MHV demonstrated the induction of a robust IFN response, which correlated with the viral load. doi = 10.1186/1471-2164-10-350 id = cord-008700-knbf8m4x author = Rodrigues, Merlyn R. title = Methods for Rapid Detection of Human Ocular Viral Infections date = 2013-10-30 keywords = Fig; type; virus summary = Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections. Lens aspirate from a 2-year-old patient with clinical ocular rubella was examined by immunofluorescence and negative stain electron microscopy. 10 In a recent epidemic of EKC at a Vietnamese refugee camp in Florida, adenovirus type 8 was recovered in 81% of cases cultured within two weeks of onset of infection.U Dawson et aP 2 described adenovirus-like particles in the conjunctiva of one patient and in the corneal epithelium of another by transmission electron microscopy of tissue culture preparations. In the present study, the typical virions of herpes simplex keratitis were readily identified both by immunofluorescence and by negative stain transmission electron microscopy. Herpes simplex hominis type 1 was recovered in culture and demonstrated by direct immunofluorescence and negative stain electron microscopy in three patients with herpetic dendritic keratitis. doi = 10.1016/s0161-6420(79)35507-5 id = cord-312955-gs65c3fy author = Schreiber, Gideon title = The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date = 2020-09-30 keywords = COVID-19; IFN; SARS; cell; interferon; type summary = doi = 10.3389/fimmu.2020.595739 id = cord-316943-ef3i96bo author = Sciberras, Justine title = The burden of type 2 diabetes pre-and during the COVID-19 pandemic – a review date = 2020-10-19 keywords = Health; T2DM; covid-19; diabetes; type summary = doi = 10.1007/s40200-020-00656-4 id = cord-284608-ba7wq52t author = Sias, Catia title = Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date = 2019-03-04 keywords = HIV; PCR; hpv; type summary = title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . doi = 10.1186/s12985-019-1132-x id = cord-015503-j99cgsjt author = Tang, Xiaolu title = On the origin and continuing evolution of SARS-CoV-2 date = 2020-03-03 keywords = CoV-2; SARS; type summary = Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Further, the genomic sequences of SARS-CoV-2 viruses isolated from a number of patients share sequence identity higher than 99.9%, suggesting a very recent host shift into humans [1] [2] [3] . doi = 10.1093/nsr/nwaa036 id = cord-269734-u43gt8fh author = Teijaro, J.R. title = Pleiotropic Roles of Type 1 Interferons in Antiviral Immune Responses date = 2016-09-20 keywords = IFN; ifnar1; infection; type summary = doi = 10.1016/bs.ai.2016.08.001 id = cord-265005-e6rpryrh author = Tomasello, Elena title = Harnessing Mechanistic Knowledge on Beneficial Versus Deleterious IFN-I Effects to Design Innovative Immunotherapies Targeting Cytokine Activity to Specific Cell Types date = 2014-10-30 keywords = CD4; CD8; HCV; IFN; cell; figure; infection; type summary = We will discuss the expression patterns and functions of endosomal TLRs with regards to IFN production in uninfected specialized immune cell types, pDCs and XCR1 + DCs. Plasmacytoid DCs uniquely produce very large amounts of IFNs in response to in vitro stimulation with many viruses, without being infected (46) . Under these conditions, to promote health over disease, the benefits for the host of producing high circulating levels of IFNs in order to induce widespread cell-intrinsic anti-viral defenses might prevail over the deleterious effects that this could cause on certain cell types or tissues. Subcapsular sinus macrophages rapidly become infected by viruses incoming from the lymph and produce large amounts of IFNs. This altruistic suicide prevents virus dissemination to other adjacent cell types and promotes the induction of innate and adaptive anti-viral immunity (87) . doi = 10.3389/fimmu.2014.00526 id = cord-103108-vmze2mdx author = Vanheer, Lotte title = Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas date = 2020-09-25 keywords = cell; figure; human; pancreatic; type summary = doi = 10.1101/2020.09.23.310094 id = cord-307128-wwjeu8ie author = Walz, Lucas title = Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis date = 2020-08-11 keywords = COVID-19; JAK; type summary = title: Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis Janus-kinase (JAK) inhibitors and Type I interferons have emerged as potential antiviral candidates for COVID-19 patients for their proven efficacy against diseases with excessive cytokine release and by their ability to promote viral clearance in past coronaviruses, respectively. METHODS: MEDLINE and MedRxiv were searched until July 30(th), 2020, including studies that compared treatment outcomes of humans treated with JAK-inhibitor or Type I interferon against controls. Meta-analysis of 3 sets of studies with 990, 454, and 1480 patients receiving Type I interferon therapy revealed that there were no significant associations between receiving Type I interferon therapy, compared to standard of care, and ICU admittance, requiring mechanical ventilation, or developing a severe or critical case of COVID-19, respectively (p>0.05; Figure 3B ; Figure 3C ; Figure 3D ).[28-36] The analyses included 97, 167, and 537 control patients, respectively. doi = 10.1101/2020.08.10.20172189 id = cord-259748-x7dq1sy4 author = Wan, Dongshan title = Research Advances in How the cGAS-STING Pathway Controls the Cellular Inflammatory Response date = 2020-04-28 keywords = HIV-1; IFN; IRF3; TBK1; cell; cgas; dna; sting; type summary = Double-stranded DNA (dsDNA) sensor cyclic-GMP-AMP synthase (cGAS) along with the downstream stimulator of interferon genes (STING) acting as essential immune-surveillance mediators have become hot topics of research. The intrinsic function of the cGAS-STING pathway facilitates type-I interferon (IFN) inflammatory signaling responses and other cellular processes such as autophagy, cell survival, senescence. In 2008, several research teams discovered a new protein on the endoplasmic reticulum (ER) which can be activated by immune-stimulatory DNA (ISD) and initiate type-I interferon (IFN) responses, which was named "stimulator of interferon genes" (STING, also known as MITA, ERIS) (2) (3) (4) . Mitochondrial outer membrane permeabilization (MOMP) activation, which is executed by BCL-2-associated X protein (BAX) and BCL-2 antagonist or killer (BAK), is a highly controlled conserved process in regulated cell FIGURE 3 | Interaction of the cGAS-STING pathway with other DNA-sensing pathways and its role in cell survival. Human plasmacytoid dentritic cells elicit a Type I interferon response by sensing DNA via the cGAS-STING signaling pathway doi = 10.3389/fimmu.2020.00615 id = cord-259935-xyo2pe4g author = Wang, Ching-Ying title = SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date = 2017-05-02 keywords = Fig; SARS; TGF; type summary = To examine the association of SARS-CoV PLpro-induced TGF-β1 production with the collagen up-regulation, A549 lung epithelial cells transiently transfected with pcDNA3.1 and pSARS-PLpro were analyzed the production of TGF-β1 and type I collagen using Western blot, realtime RT-PCR and Sirius red staining assays (Fig. 1) . To examine whether SMAD-dependent pathways involve in TGF-β1mediated up-regulation of Type I collagen in response SARS-CoV PLpro, subcellular localization of receptor-regulated SMAD3 and inhibitory SMAD7 in transfected cells were detected using the immunofluorescent and DAPI staining (Fig. 4) . To examine the possible pathways involved in TGF-β1-dependent up-regulation of Type I collagen by SARS-CoV PLpro, the profiles of ubiquitin-conjugated proteins in transfected cells with vector control and pSARS-PLpro were determined using immune-precipitation and nanoLC-MS/MS. Subcellular localization analysis demonstrated that SMAD3 was predominant in cytoplasmic, but not in the nucleus in transfected cells with pSARS-PLpro compared to vector control (Fig. 4) , revealing that canonical Smad-dependent signaling pathway was not involved in PLpro-induced TGF-β1-dependent upregulation of Type I collagen. doi = 10.1016/j.virusres.2017.04.008 id = cord-254404-lrsqrc2u author = Yañez-Guerra, Luis Alfonso title = Echinoderms provide missing link in the evolution of PrRP/sNPF-type neuropeptide signalling date = 2020-06-24 keywords = NPF; NPY; figure; peptide; receptor; type summary = doi = 10.7554/elife.57640 id = cord-307110-eiobmxp2 author = Zhao, Shan title = Serological Screening for Coronavirus Infections in Cats date = 2019-08-13 keywords = ELISA; PEDV; type summary = In total 137 cat serum samples and 25 FCoV type 1 or type 2-specific antisera were screened for the presence of antibodies against the S1 receptor binding subunit of the CoV spike protein, which is immunogenic and possesses low amino acid sequence identity among coronavirus species. Synthetic sequences of 12 coronavirus spike S1 subunits (HCoV-HKU1 (GB: YP_173238.1), MERS-CoV (GB:YP_009047204.1), SARS-CoV (GB: AAX16192.1), HCoV-OC43 (GB: AAR01015.1), HCoV-229E (GB: NP_073551.1), HCoV-NL63 (GB: YP_003767.1), TGEV (GB: ABG89325.1), PEDV (GB: AOG30832.1), BCoV (GB: P15777.1), PDCoV (GB: AML40825.1), FCoV type 1 (GB: FJ938060.1), FCoV type 2 (GB: AY994055.1)) and different domains of PEDV S1 subunit (S1 0 and S1 A-D , as identified and described in [40] ) were cloned into pCAGGS expression plasmids as described previously [41] . doi = 10.3390/v11080743 id = cord-292344-3bj567gr author = Zimmet, P. title = The burden of type 2 diabetes: are we doing enough? date = 2003-09-30 keywords = diabetes; prevalence; type summary = Over subsequent decades, numerous reports have highlighted the high prevalence of type 2 diabetes in a number of other populations including native Americans, Afro-Americans, and Mexican Americans in the USA [4] [5] [6] [7] , native Canadians [8] , Australian Aborigines and Torres Strait islanders [9] , and Polynesians in New Zealand [10, 11] . This explosive increase in the prevalence of type 2 diabetes, and the consequences of its complications and associated disorders, represents the greatest health care challenge facing the world today [14] . The population of this nation are Asian Indian, Creole (Black) and Chinese, and these three ethnic groups account for over 66% Increasing prevalence of type 2 diabetes by region [12] . The CODE-2 data are consistent with previous estimates of the prevalence of coronary heart disease and other complications in type 2 diabetic patients in various countries (Fig 2) . doi = 10.1016/s1262-3636(03)72783-9 id = cord-004879-pgyzluwp author = nan title = Programmed cell death date = 1994 keywords = ATP; Basel; Bern; Drosophila; Institut; Lausanne; NMDA; PCR; PKC; RNA; Switzerland; TNF; University; acid; activity; cell; dna; expression; gene; high; human; increase; level; mouse; protein; receptor; result; sequence; study; type summary = Furthermore kinetic experiments after complementation of HIV=RT p66 with KIV-RT pSl indicated that HIV-RT pSl can restore rate and extent of strand displacement activity by HIV-RT p66 compared to the HIV-RT heterodimer D66/D51, suggesting a function of the 51 kDa polypeptide, The mouse mammary tumor virus proviral DNA contains an open reading frame in the 3'' long terminal repeat which can code for a 36 kDa polypeptide with a putative transmembrane sequence and five N-linked glycosylation sites. To this end we used constructs encoding the c-fos (and c-jun) genes fused to the hormone-binding domain of the human estrogen receptor, designated c-FosER (and c-JunER), We could show that short-term activation (30 mins.) of c-FosER by estradiole (E2) led to the disruption of epithelial cell polarity within 24 hours, as characterized by the expression of apical and basolateral marker proteins. doi = 10.1007/bf02033112 id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 keywords = ABO; Anti; Background; Blood; CD36; Case; Center; DAT; DTT; Design; FDA; FFP; HBV; HCV; HIV; HLA; Hospital; IPC; MTP; Medical; Medicine; NAT; PCR; PLT; RBC; RHD; Red; Studies; Study; System; TPE; University; WBC; ZIKV; Zika; cd341; cell; conclusion; day; dna; donor; finding; method; patient; platelet; result; sample; table; test; transfusion; type summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). doi = 10.1111/trf.14286 id = cord-017248-a37t31u1 author = nan title = Alphabetic Listing of Diseases and Conditions date = 2010-05-17 keywords = Associated; Related; Synonyms; acute; aortic; artery; autopsy; blood; chapter; chronic; condition; death; disease; external; heart; lung; note; poisoning; possible; procedure; pulmonary; record; sample; study; syndrome; term; tissue; type summary = doi = 10.1007/978-1-59745-127-7_17 id = cord-326785-le2t1l8g author = nan title = Pathological Society of Great Britain and Ireland. 163rd meeting, 3–5 July 1991 date = 2005-06-15 keywords = HPV; biopsy; bone; carcinoma; case; cell; change; disease; dna; expression; increase; lesion; normal; number; patient; present; renal; section; small; specimen; stain; study; tissue; type summary = doi = 10.1002/path.1711640412 id = cord-350571-6tapkjb6 author = nan title = 45th ESCP-NSF international symposium on clinical pharmacy: clinical pharmacy tackling inequalities and access to health care. Oslo, Norway, 5–7 October 2016 date = 2017-01-10 keywords = BZD; DRP; France; HCV; HIV; Hospital; January; June; Pharmacy; University; abstract; background; clinical; conclusion; descriptive; drug; medication; medicine; objective; patient; pharmacist; prescription; research; result; study; treatment; type summary = Possible solutions might be to use shared communication tools like Internet based communication programs and to introduce the patient as a participant at the IMRs. Please specify your abstract type: Research abstract Background and objective: International good pharmacy practice guidelines describe how pharmacists should counsel the patients about their medicines, offer additional services where needed, and intervene at drug related problems. Please specify your abstract type: Descriptive abstract (for projects) Background and objective: In order to improve the medication reconciliation and to implement training programs for the medical team in an associated to general hospital nursing (ASNH) home we measured the discrepancies between pharmacy registered treatments (PRT) and medical prescriptions (MP), and we analysed potentially inappropriate prescriptions according to ''''American Geriatrics Society 2015 Beers Criteria'''' and ''''STOPP-START 2014 criteria. doi = 10.1007/s11096-016-0404-4