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. Eric Lease Morgan May 27, 2019 Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 91 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 707 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 46 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 11 virus 9 cell 6 respiratory 6 RSV 6 MERS 6 Fig 5 figure 4 patient 4 influenza 4 disease 4 RNA 4 PEDV 3 SARS 3 PCR 3 Middle 3 IFN 3 East 2 vaccine 2 study 2 pandemic 2 mortality 2 model 2 lung 2 infectious 2 individual 2 animal 2 ZIKV 2 Korea 2 IBV 2 HIV-1 2 H5N1 2 Group 2 Ebola 2 CARV 2 ARDS 1 year 1 water 1 tumor 1 treatment 1 transmission 1 tissue 1 therapy 1 test 1 surveillance 1 surface 1 strategy 1 step 1 soil 1 social 1 slice Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 3896 patient 3397 % 3200 cell 3017 virus 2353 infection 2001 study 1886 disease 1184 protein 1173 datum 1131 year 1120 model 1082 treatment 1065 influenza 1038 result 1025 case 933 time 897 analysis 881 risk 876 child 860 day 848 group 791 therapy 779 response 760 vaccine 746 method 701 level 696 control 686 age 680 blood 671 antibody 664 health 657 mouse 633 p 619 sample 617 effect 614 diagnosis 590 gene 584 system 583 activity 574 use 564 population 561 factor 558 pathogen 555 rate 544 type 537 role 532 tumor 529 culture 527 number 506 test Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1410 al 1212 . 1142 et 588 MERS 458 CoV 457 de 388 RNA 384 PCR 384 Fig 334 PEDV 325 RSV 321 la 293 VLP 284 SCD 281 United 272 States 237 SARS 232 S 225 y 225 C 224 IFN 203 T 202 el 201 East 192 Hospital 189 Middle 178 Children 174 A 173 mg 173 B 172 Health 172 Background 167 L 167 HSCT 160 Table 159 ZIKV 157 PMO 155 II 153 HIV 149 University 148 S1 143 S. 141 IBV 140 AML 138 HN 137 los 135 RT 135 MHC 133 N 127 Korea Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1704 we 1129 it 446 they 241 i 202 he 183 she 137 them 39 us 31 you 19 itself 17 themselves 17 one 14 nsp15 4 me 4 her 3 irbcs 3 him 1 y903mxcj 1 s 1 ourselves 1 mrnas 1 ly294002 1 interleukin-15 1 himself 1 hhsn272200800039c 1 gammacovs 1 e15.5 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 20214 be 3894 have 2261 use 1182 include 1120 show 888 associate 787 base 701 identify 697 increase 692 do 658 report 632 follow 624 compare 569 develop 542 receive 542 find 531 perform 522 infect 515 treat 482 require 469 provide 469 induce 445 cause 427 describe 419 determine 419 demonstrate 410 suggest 409 reduce 406 present 378 detect 375 evaluate 372 improve 354 target 338 indicate 338 consider 337 give 330 decrease 327 lead 326 remain 325 occur 325 bind 319 observe 313 make 312 result 303 assess 290 collect 283 relate 281 reveal 281 know 277 analyze Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1691 not 1445 - 1213 respiratory 1207 high 1085 viral 1082 also 994 clinical 918 other 797 human 794 low 786 more 716 well 716 such 661 however 638 infectious 610 most 587 pediatric 560 significant 559 only 546 acute 517 different 508 specific 508 severe 504 first 460 positive 454 immune 441 non 438 significantly 412 as 394 important 381 further 380 large 376 early 359 new 309 common 307 old 304 similar 301 then 301 primary 298 negative 298 antiviral 297 bacterial 296 many 292 effective 292 anti 288 highly 277 long 275 several 275 respectively 275 potential Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 149 most 100 good 92 high 76 Most 66 least 54 low 45 large 17 great 8 early 8 big 7 small 6 strong 4 simple 4 poor 4 late 4 deadly 3 young 3 short 3 long 2 safe 2 old 2 liv 2 grave 2 common 2 close 2 bad 2 -I 1 â€"there 1 wide 1 vRNA 1 southernmost 1 slow 1 slight 1 preharv 1 postharv 1 mild 1 gDNA 1 fast 1 dry 1 dense 1 costly 1 cord-300459-tu2xrt9x 1 cold 1 astrocytomas 1 W553 1 MRX-2843 1 Glu389 1 D539N Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 461 most 77 least 18 well 2 youngest 1 lowest 1 fast 1 cfdna Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 13 doi.org 6 orcid.org 5 tools.iedb.org 3 www.who.int 2 www.rcsb.org 2 www.r-project.org 2 www.ncbi.nlm.nih.gov 2 www.mdpi.com 2 www 2 keras.io 2 internettrend.co.kr 1 zikalliance.tghn.org 1 www.uniprot.org 1 www.syfpeithi.de 1 www.projecthelix.eu 1 www.isglobal.org 1 www.iedb.org 1 www.emerge.rki.eu 1 www.compare-europe.eu 1 www.allelefrequencies.net 1 primerexplorer.jp 1 omics.pnl.gov 1 ndssl.vbi.vt.edu 1 longitudeprize.org 1 is.cdc.go.kr 1 imagej.nih.gov 1 imagej.net 1 embnet.vital-it.ch 1 dx 1 dpcpsi.nih.gov 1 doi 1 datalab.naver.com 1 data.kma.go.kr 1 cvc.dfci.harvard.edu 1 creativecommons.org 1 cordis 1 blast.ncbi.nlm.nih.gov 1 biocomp.chem.uw.edu.pl 1 academic Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www.r-project.org/ 2 http://www 2 http://keras.io/ 2 http://internettrend.co.kr/trendForward.tsp 2 http://doi.org/10.1128/mBio 1 http://zikalliance.tghn.org/about/ 1 http://www.who.int/influenza/human_animal_interface/2017_10_30_tableH5N1.pdf?ua=1 1 http://www.who.int/emergencies/mers-cov/en/ 1 http://www.who.int/blueprint/priority-diseases/en/ 1 http://www.uniprot.org/ 1 http://www.syfpeithi.de/0-Home 1 http://www.rcsb.org/ 1 http://www.rcsb.org 1 http://www.projecthelix.eu/en 1 http://www.ncbi.nlm.nih.gov/igblast/ 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.mdpi.com/2409-9279/1/2/12/s1 1 http://www.mdpi.com/1660-4601/15/8/1596/s1 1 http://www.isglobal.org/en/web/guest/healthisglobal/-/custom-blog-portlet/prova/5620053/7201 1 http://www.iedb.org/ 1 http://www.emerge.rki.eu/ 1 http://www.compare-europe.eu/about 1 http://www.allelefrequencies.net/default.asp 1 http://tools.iedb.org/processing/ 1 http://tools.iedb.org/population/ 1 http://tools.iedb.org/mhcii/ 1 http://tools.iedb.org/immunogenicity/ 1 http://tools.iedb.org/ 1 http://primerexplorer.jp/e/ 1 http://orcid.org/0000-0003-2613-1669 1 http://orcid.org/0000-0002-7849-7024 1 http://orcid.org/0000-0002-5930-5461 1 http://orcid.org/0000-0002-5152-3093 1 http://orcid.org/0000-0001-9131-3341 1 http://orcid.org/0000-0001-8692-5116 1 http://omics.pnl.gov 1 http://ndssl.vbi.vt.edu/ 1 http://longitudeprize.org 1 http://is.cdc.go.kr/dstat/index.jsp 1 http://imagej.nih.gov/ij/download.html 1 http://imagej.net/Introduction 1 http://embnet.vital-it.ch/software/ClustalW.html 1 http://dx 1 http://dpcpsi.nih.gov/AMRChallenge 1 http://doi.org/10.3904/kjim.2018.031 1 http://doi.org/10.1371/journal.pone.0193131.g001 1 http://doi.org/10.1371/journal.pntd.0006674.t004 1 http://doi.org/10.1371/journal.pntd.0006674.g006 1 http://doi.org/10.1016/j.tvjl.2018.11.008 1 http://doi.org/10.1016/j.jviromet.2018.03.003 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 research@f1000.com 1 parkj@korea.ac.kr 1 jean-louis.romette@univmed.fr 1 ahnik@korea.ac.kr 1 a.karampourian@sbmu.ac.ir Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 13 cells were then 8 % were male 6 patients are alive 6 patients did not 6 results were not 5 results are consistent 5 study did not 5 virus infected cells 4 patients had severe 4 results were consistent 4 study was not 3 % had adherence 3 % had at 3 % had moderate 3 % were female 3 analysis did not 3 data were available 3 disease reporting system 3 diseases are more 3 group was comparison 3 groups were significantly 3 infection was not 3 method does not 3 patients had improvement 3 patients had stage 3 patients receiving chemotherapy 3 patients receiving prone 3 patients were female 3 patients were male 3 patients were positive 3 results were negative 3 studies have also 3 therapy was not 3 treatment did not 2 % did not 2 % had aki 2 % were non 2 % were positive 2 analysis is ongoing 2 case report forms 2 cases do not 2 cases have also 2 cases were not 2 cells did not 2 cells following viral 2 cells has not 2 cells including macrophages 2 cells is dependent 2 cells using plaque 2 cells were first Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 cells has not only 2 methods were not satisfactory 2 results were not as 2 vaccines are not widely 1 % had no training 1 . are not consistent 1 . has no apparent 1 analysis showed no statistically 1 cases are not unexpected 1 cases had no bacterial 1 cases were not only 1 cells are not susceptible 1 cells showed no change 1 cells showed no differences 1 cells was no longer 1 data are not available 1 data show no notable 1 data showed no decay 1 data showed no shifts 1 data was not significant 1 days showed no significant 1 disease is not present 1 diseases are not limited 1 group had no discernable 1 groups was not statistically 1 infection are not uncommon 1 infection are not well 1 infection had no effect 1 infection had no impact 1 infection has not yet 1 infection is not entirely 1 infection requires not only 1 level is not normally 1 level was not significantly 1 levels are not significantly 1 levels were not different 1 method is no longer 1 method provided not only 1 model is not only 1 model is not suitable 1 models are not applicable 1 patient demonstrated no evidence 1 patient had no detrimental 1 patient was no longer 1 patients are no longer 1 patients are not regularly 1 patients had no phenotypic 1 patients had no previous 1 patients had no symptoms 1 patients had no systemic Sizes of items; "Measures in words, how big is each item?" ---------------------------------------------------------- 182060 cord-009997-oecpqf1j 18361 cord-301767-1jv20em8 10663 cord-252894-c02v47jz 10321 cord-003243-u744apzw 9337 cord-333639-usgpe1cz 8937 cord-006039-vbq9izw3 8021 cord-329227-sqetz7h6 7804 cord-319729-6lzjhn8j 7423 cord-273324-xhpv783y 7005 cord-003270-vu9b5a14 6732 cord-282322-ywwqnw74 6698 cord-262205-ax3i3d7f 6557 cord-344227-rdlinzrn 6536 cord-021894-lq8yr710 6514 cord-256903-8lyw27gh 6448 cord-281403-yl7jdarm 6297 cord-330296-706hf4qw 6062 cord-023200-3caevjvh 6002 cord-314340-ltx4w9zh 5987 cord-295878-pd9elo4l 5730 cord-254747-vox5xsgd 5720 cord-017272-r5en82s1 5671 cord-017463-repm1vw9 5642 cord-307547-7n3f3wrz 5565 cord-317688-mr851682 5511 cord-292830-gcfx1095 5439 cord-003018-qrt07zmz 5241 cord-265679-7gzont7l 5232 cord-289026-v09m2fzw 5054 cord-354904-7gq2e6f0 5038 cord-003138-9r1hg7ld 4969 cord-003377-9vkhptas 4901 cord-290861-5bxvenue 4879 cord-265282-v3n9ff16 4872 cord-002889-fie121ns 4846 cord-003244-abs3tc3r 4814 cord-319871-qnijw08y 4752 cord-252600-bvh1o64r 4497 cord-002932-5e7xrd1y 4463 cord-017137-6pmts7ui 4387 cord-318181-xxc7vdnt 4357 cord-003219-iryb3v0z 4346 cord-330942-x238hq9b 4343 cord-305936-tdswzj7r 4208 cord-258052-y9pzsoqa 4150 cord-346586-fxxceffl 4144 cord-351760-698voi9y 4140 cord-018066-s0zk9l6a 4077 cord-327202-2um6jmhk 4035 cord-003171-z22ekgtv 4013 cord-322201-5laifjgz 3968 cord-296992-2vp35fwv 3921 cord-348660-qnbgywgy 3883 cord-003099-a0acr28o 3831 cord-003571-upogtny6 3809 cord-329429-ur8g68vp 3795 cord-295491-zlah6u5s 3756 cord-287853-cob7ur35 3726 cord-307543-piust0s6 3692 cord-354664-mzzvmyea 3659 cord-320107-wels9wt7 3637 cord-310240-otf9ruvj 3620 cord-252355-ol21ofj9 3528 cord-323700-5awng7h1 3386 cord-328525-80xk3gln 3195 cord-270286-76mrzaxi 3140 cord-288332-y15g1yak 3112 cord-354700-bdpp3qmf 3091 cord-339871-jso21mbx 3061 cord-003655-uo0hdrgc 2928 cord-022046-q1exf47s 2917 cord-343390-y903mxcj 2910 cord-261962-sfa9d1ux 2847 cord-280374-yj0r4rwt 2839 cord-275162-2239dk45 2555 cord-275719-ru33ubss 2487 cord-309565-8syjr6k8 2340 cord-324432-k0g3r1lw 2099 cord-328086-ji2emajn 1955 cord-006325-3no74e74 1802 cord-020750-zvwy7bgt 1464 cord-325525-d1hsguds cord-003092-3owcqt3d cord-003261-fz8ucwwm cord-006892-n2ncamqh cord-268149-narre5e7 cord-298032-3zlu8g8y cord-298805-ntpm68cg cord-300459-tu2xrt9x cord-324674-yd7idp90 cord-353553-adaow2w7 Readability of items; "How difficult is each item to read?" ----------------------------------------------------------- 63.0 cord-020750-zvwy7bgt 61.0 cord-325525-d1hsguds 60.0 cord-265282-v3n9ff16 58.0 cord-261962-sfa9d1ux 57.0 cord-252894-c02v47jz 56.0 cord-003655-uo0hdrgc 56.0 cord-289026-v09m2fzw 56.0 cord-309565-8syjr6k8 55.0 cord-329227-sqetz7h6 54.0 cord-252600-bvh1o64r 54.0 cord-307543-piust0s6 53.0 cord-022046-q1exf47s 53.0 cord-254747-vox5xsgd 53.0 cord-343390-y903mxcj 52.0 cord-003171-z22ekgtv 52.0 cord-003244-abs3tc3r 52.0 cord-265679-7gzont7l 51.0 cord-003138-9r1hg7ld 51.0 cord-290861-5bxvenue 51.0 cord-295491-zlah6u5s 50.0 cord-003270-vu9b5a14 50.0 cord-018066-s0zk9l6a 50.0 cord-288332-y15g1yak 50.0 cord-310240-otf9ruvj 50.0 cord-317688-mr851682 50.0 cord-318181-xxc7vdnt 50.0 cord-319729-6lzjhn8j 50.0 cord-329429-ur8g68vp 49.0 cord-003377-9vkhptas 49.0 cord-282322-ywwqnw74 49.0 cord-323700-5awng7h1 49.0 cord-346586-fxxceffl 49.0 cord-351760-698voi9y 48.0 cord-009997-oecpqf1j 48.0 cord-328086-ji2emajn 48.0 cord-333639-usgpe1cz 48.0 cord-339871-jso21mbx 48.0 cord-354904-7gq2e6f0 47.0 cord-002889-fie121ns 47.0 cord-258052-y9pzsoqa 46.0 cord-270286-76mrzaxi 45.0 cord-262205-ax3i3d7f 45.0 cord-292830-gcfx1095 44.0 cord-002932-5e7xrd1y 44.0 cord-003219-iryb3v0z 44.0 cord-275162-2239dk45 44.0 cord-275719-ru33ubss 44.0 cord-281403-yl7jdarm 44.0 cord-296992-2vp35fwv 44.0 cord-314340-ltx4w9zh 43.0 cord-252355-ol21ofj9 43.0 cord-330942-x238hq9b 43.0 cord-344227-rdlinzrn 43.0 cord-348660-qnbgywgy 42.0 cord-017137-6pmts7ui 42.0 cord-256903-8lyw27gh 42.0 cord-307547-7n3f3wrz 42.0 cord-322201-5laifjgz 41.0 cord-003018-qrt07zmz 41.0 cord-003571-upogtny6 41.0 cord-017272-r5en82s1 41.0 cord-023200-3caevjvh 41.0 cord-273324-xhpv783y 41.0 cord-280374-yj0r4rwt 41.0 cord-295878-pd9elo4l 41.0 cord-324432-k0g3r1lw 40.0 cord-006039-vbq9izw3 40.0 cord-017463-repm1vw9 40.0 cord-301767-1jv20em8 40.0 cord-320107-wels9wt7 40.0 cord-327202-2um6jmhk 40.0 cord-328525-80xk3gln 39.0 cord-003099-a0acr28o 39.0 cord-006325-3no74e74 39.0 cord-021894-lq8yr710 39.0 cord-305936-tdswzj7r 37.0 cord-330296-706hf4qw 36.0 cord-354700-bdpp3qmf 33.0 cord-003243-u744apzw 33.0 cord-287853-cob7ur35 32.0 cord-354664-mzzvmyea 28.0 cord-319871-qnijw08y cord-003092-3owcqt3d cord-003261-fz8ucwwm cord-006892-n2ncamqh cord-268149-narre5e7 cord-298032-3zlu8g8y cord-298805-ntpm68cg cord-300459-tu2xrt9x cord-324674-yd7idp90 cord-353553-adaow2w7 Item summaries; "In a narrative form, how can each item be abstracted?" ----------------------------------------------------------------------- cord-002889-fie121ns Human and mouse mesothelin share sequence similarity, expression patterns, and biochemical characteristics, [7] , and the homeostatic function of mesothelin in mammals is unknown: the gene can be deleted without apparent effect in mice PLOS C57Bl6 mice and thus can be grown in syngeneic mice to allow for study of an anti-tumor immune response in an immunocompetent mouse model. In order to create a putative therapeutic anti-mesothelin vaccine, we inserted the mouse mesothelin gene into the poxvirus MVA genome under a viral promoter so that mesothelin would be expressed in any cells infected with the recombinant virus. To determine whether the viruses expressing mesothelin protein were able to induce an immune response in mice, we first attempted to measure anti-mesothelin antibody in vaccinated mouse sera. In comparison, there were very few spots (1-3) in response to stimulation with Lewis Lung cells that do not express mouse mesothelin, and mice vaccinated with MVA, MVAmeso and MVAmesoA35Del viruses all had good responses to restimulation with vaccinia virus (124, 147, and 148 spots respectively). cord-002932-5e7xrd1y In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. cord-003018-qrt07zmz Using a www.oncotarget.com flow cytometer-based screening assay with Dox-treated and untreated iNTCP cells, we identified a hybridoma clone producing anti-NTCP mAb, clone 9A8 ( Figure 2B ). To test whether the 9A8 antibody can inhibit HBV infection, we pretreated iNTCP cells and primary human hepatocytes with 9A8 mAb and subsequently infected cells with wild type HBV and HBV encoding a luciferase reporter gene (HBV-NL) [21] . iNTCP cells (G) and primary human hepatocytes (H) were infected with HBV or its reporter virus (HBV-NL) respectively, in the presence of 9A8 mAb. Anti-HBs mAb (clone 33A4, which recognizes the PreS1 domain) was used as a control. In this study, we generated iNTCP cells, which have high NTCP expression and high susceptibility to HBV infection, and also developed a monoclonal antibody (mAb) that recognizes cell-surface NTCP. Although primary hepatocytes express NTCP at low levels for the uptake of bile acids, endogenous NTCP in hepatocellular carcinoma cell lines is not sufficient to achieve successful infection with HBV in vitro. cord-003092-3owcqt3d cord-003099-a0acr28o In vitro studies in which influenza-infected alveolar macrophages were subsequently stimulated with bacterial lipopolysaccharide (LPS), a bacterial compound that induces a profound innate immune response, revealed increased levels of pro-inflammatory cytokines tumor necrosis factor (TNF) α, interleukin (IL)-1β, and IL-6 [4] [5] [6] [7] [8] , indicative of a priming effect on these cells by influenza. Likewise, murine influenza infection resulted in increased levels of pro-inflammatory cytokines in both plasma and lungs, and enhanced pulmonary neutrophil influx upon pneumococcal infection 7 days later [10] . In the present study, we demonstrate that a systemic LPS challenge in the acute phase of influenza infection (4 days post-infection) results in an enhanced pulmonary, but not systemic pro-inflammatory cytokine response. Our results are in accordance with in vitro data reporting a cellular priming effect of influenza observed upon secondary stimulation with LPS [4] [5] [6] [7] [8] , as well as with other murine in vivo studies that report increased inflammation and pulmonary neutrophil influx or sequestration upon a secondary bacterial infection or LPS challenge in the acute phase of influenza infection [9, 10] . cord-003138-9r1hg7ld title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial BACKGROUND: Although the use of induced blood stage malaria infection has proven to be a valuable tool for testing the efficacy of vaccines and drugs against Plasmodium falciparum, a limiting factor has been the availability of Good Manufacturing Practice (GMP)—compliant defined P. A GAP master cell bank (MCB) was manufactured by culturing parasites in an FDA approved single use, closed system sterile plastic bioreactor. falciparum in tissue culture flasks for in vitro production of Good Manufacturing Practice (GMP) grade blood stage malaria cell banks was recently described [8] . Development of cultured Plasmodium falciparum blood-stage malaria cell banks for early phase in vivo clinical trial assessment of anti-malaria drugs and vaccines cord-003171-z22ekgtv title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment METHODS: Hemagglutinin inhibition (HAI) assays against historical human and recent avian influenza A(H2N2) viruses were performed across age groups in Rochester, New York, and Hong Kong, China. In this study, we evaluated population immunity using HAI assays against human and avian H2N2 influenza strains in different age groups in the United States and Hong Kong. The prevalence of titers ≥1:40 against the test viruses is shown for sera from Rochester and Hong Kong in persons born before the 1957 H2N2 pandemic, during the years that H2N2 circulated (1957-1968), or after 1968 is shown in Figure 1 . The comparability of data from 2 geographically separated areas of the world, Rochester and Hong Kong, argues for the representativeness and generalizability of such studies that aim to assess population immunity to viruses of pandemic concern. cord-003219-iryb3v0z title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning CONCLUSIONS: In the present study, in evaluating the effect of prone positioning in patients with influenza pneumonia-related ARDS, pneumonia severity index, renal replacement therapy and increase in dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. After multivariate Cox regression analysis, PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. The present study in influenza pneumonia-related ARDS patients receiving prone positioning also found that increased dynamic driving pressure (hazard ratio 1.372, 95% confidence interval 1.095-1.718; p = 0.006) was identified as After multivariate Cox regression analysis, it was found that PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumoniarelated ARDS receiving prone positioning. cord-003243-u744apzw METHODOLOGY AND PRINCIPAL FINDINGS: We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYMFASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYM-FASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. cord-003244-abs3tc3r In 1978, the national Expanded Program on Immunization (EPI) in China started to implement a standard schedule for the routine administration of one dose of measles-containing vaccine (MCV1) among children between 8 and 24 months of age. In the present study, we compared the age-specific R of measles infections between different age groups by using laboratory and clinically confirmed data collected from 2009 to 2016. The R values estimated for children aged 7-15 years were low across the study period in general, even though the values also increased since 2012, indicating that primary and secondary school students had a limited contribution to measles transmissions. In this study, we compared the age-specific R of measles infections between different age groups, using laboratory and clinically confirmed data from 2009 to 2016 for Guangdong Province. cord-003261-fz8ucwwm cord-003270-vu9b5a14 In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens'' analyses were carried out successively by different tools. For the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and for the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens analyses were considered. In this study, the binding ability of the first step selected peptides to human and mouse MHC molecules, was analyzed by CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock/) server. In cancer immunotherapy, the CTL-mediated responses play the central role in eradication of malignant cells, and the binding of epitopes to MHC-I molecules is an essential step for antigen presentation to CTLs. Thus, in this study, predicted epitopes were primarily selected by their MHC-I binding and processing scores. cord-003377-9vkhptas title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). The indicator for wild bird habitat used in this study was the set of "Important Bird and Biodiversity Areas" (IBAs) for "migratory and congregatory waterbirds" identified by BirdLife The live poultry trade poses different avian influenza risks in different regions of the world Table 1 . Our first specification (Model 1) included a number of factors related to disease risk but excluded both live poultry imports and biosecurity measures. cord-003571-upogtny6 In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. age patterns; history of epidemiology; influenza; mortality; pandemic; prior immunity One hundred years after the fact, the 1918 influenza pandemic remains one of the most important epidemics of the modern medical era; it was significant for its impact on both human health and the development of epidemiology and other medical sciences. cord-003655-uo0hdrgc Here, we describe a protocol for the preparation and ex vivo infection of lung slices from different mammalian host species with various respiratory paramyxoviruses expressing fluorescent reporter proteins, and suggest follow-up experiments including immunohistochemistry, flow cytometry and confocal microscopy. The combination of these viable lung slices with recombinant viruses expressing fluorescent reporter proteins [7] [8] [9] allows for accurate, sensitive and reproducible assessment of respiratory virus infection and dissemination over time. We have validated this technique by infecting lung slices of multiple host species (cotton rats, ferrets, dogs and macaques) with various paramyxoviruses expressing fluorescent reporter proteins (measles virus (MV), canine distemper virus (CDV), human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV)) [10] . Using a (blunt-end) needle or flexible catheter, the fresh lungs are inflated through the trachea (or primary bronchus, if inflation of a half lung or single lobe is desired) with low-melting point agarose mixed with culture medium. cord-006039-vbq9izw3 In this Review, we emphasize the need to focus on host interactions with Plasmodium parasites at various tissue levels and the importance of targeting local and specific organ failure and/or pathologies during, as well as long after, infection. Overall, while the process of sequestration is not completely understood, it is known to cause obstruction of blood flow in small capillaries and post-capillary venules (PCVs), endothelial cell activation and inflammation and severe pathology in many organs including lung, adipose tissue, spleen and brain 52, 53, 65, 66 (FIG. This unique brain pathology, known as cerebral malaria, involves convulsions, coma and high fever and develops with the presence of mostly ring-stage infected erythrocytes in the periphery (suggesting a sequestration of late-stage parasites in the organs) [69] [70] [71] . Malaria is a serious disease with acute life-threatening and long-term complications, all of which can be attributed to local but specific organs in which Plasmodium Figure 4 | Infected red blood cells in gut and bone marrow niches. cord-006325-3no74e74 A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France cord-006892-n2ncamqh cord-009997-oecpqf1j Completed cranial radiation and proceeded to allogeneic stem cell transplant with unrelated cord marrow donor and is disease free at approximately day +200.Case 2: 5 year-old female diagnosed with FLT3 and MLL negative AML and completed treatment per COG AAML1031 study on the low risk arm without Bortezomib. Design/Method: This study was a retrospective chart review that included patients 3 to 23 years old with sickle cell disease type SS and S 0 followed at St. Christopher''s Hospital for Children. Background: Hydroxyurea, chronic blood transfusion, and bone marrow transplantation can reduce complications, and improve survival in sickle cell disease (SCD), but are associated with a significant decisional dilemma because of the inherent risk-benefit tradeoffs, and the lack of comparative studies. Brown University -Hasbro Children''s Hospital, Providence, Rhode Island, United States Background: Despite clinical advances in the treatment of sickle cell disease (SCD) in pediatric and young adult patients, pain remains a significant source of disease-related morbidity. cord-017137-6pmts7ui When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—"microbial forensics." Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Herein the microbial forensics could be defined as "the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes" [21] . Microbial forensics has a role in such cases by applying scientific methods for the analysis of evidence from such a bioterrorism attack. The most reliable technique till date for microbial forensics is metagenomics-a culture-independent approach for identifying and enumerating microbes. cord-017272-r5en82s1 [11] pointed out that due to the accumulation of highly sophisticated spatial and spatiotemporal technology like GIS, GPS, remote sensing, and computer cartography, collectively termed as geographic information science, it becomes possible to model the disease process involving multiple spatiotemporal data obtained in different disciplines. Also, mobility has been one of a classical topic in the area of human ecology since it is associated with the question of how a population utilizes the environment spatially as well as temporally (time allocation studies). Time allocation studies observe the individuals in the targeted field and record the location and type of activity for a given period, which is useful to answer some of the basic questions in human Unlikely Large ecology or other related fields as noted above. A relatively large spatial scale study has been conducted covering approximately 80 × 200 km area in Belgium [3] , which compared regional exposure estimates for two representative air pollutants, NOx and ozone, under two alternative assumptions. cord-017463-repm1vw9 We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. cord-018066-s0zk9l6a In order to achieve this, the article analyses the case of the refugee camp in city of Harmanly, close to the Bulgarian-Turkish border, and assesses the public health risks related to this specific situation. The purpose of our article is to collect, summarize and present epidemiological data related to migrants in Bulgaria and, on the basis of this information, to analyze the potential risks to public health (including risks to migrants) and to assess the capacity of Bulgaria''s healthcare system to cope with the refugee crisis. Following the 2012-2013 crisis, in February 2015 a WHO assessment mission to Bulgaria took place to access the country''s capacity to address the public health implications of sudden large-scale influxes of migrants [27] . Public health needs of migrants, refugees and asylum seekers in Europe, 2015: infectious disease aspects cord-020750-zvwy7bgt En la intersección entre el ser humano y los microbios hay un cuadrado que representa la convergencia de los factores que conducen a la aparición de una enfermedad infecciosa. Esto todavía no es realidad, pero grupos como el Global Disease Detection Program (GDD) de los CDC y la Global Outbreak Alert and Response Network de la OMS están vigilando sin descanso la evolución de la interacción entre microbios y seres humanos en todo el planeta, creando tecnología de seguimiento y respondiendo a los informes sobre el aumento de enfermedades y otras emergencias sanitarias 14 . Las enfermedades infecciosas emergentes son una amenaza para todos y cada uno de los habitantes del planeta y todo el mundo puede desempeñar un papel, ya sea en el retraso de la transmisión o la prevención. cord-021894-lq8yr710 Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis cord-022046-q1exf47s Middle East respiratory syndrome (MERS) is an emerging infectious zoonotic disease caused by a novel coronavirus (CoV). 4 Surveillance of DCs in KSA has shown that MERS-CoV clade B has been enzootic in the camel population in Arabia Genetic deep sequencing methods (i.e., high-throughput sequencing) have been readily available to researchers since the disease was first reported. 8 Nevertheless, given the prevalence of MERS-CoV infection in the Middle East''s DC population and due to the potential for spillover to the human population in direct contact with DCs, the development of a vaccine for use in DCs may be feasible. Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Detection of the Middle East respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient cord-023200-3caevjvh The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. cord-252355-ol21ofj9 title: Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens When we infected day 6 chickens with H4N6 low pathogenic avian influenza virus (LPAIV), we observed that H4N6 LPAIV infection increased the staining intensity of KUL01+ cells in trachea, lungs and duodenum of chickens at 3 days post-infection. Then, we used clodronate liposomes intra-abdominally in 5 day-old chickens and found significant reduction of staining intensity of KUL01+ cells in trachea and duodenum but not in lungs at 4 days post-treatment. We also hypothesized that the decrease of the staining intensity of KUL01 marker + cells following intra-abdominal administration of clodronate liposomes will augment replication of low pathogenic avian influenza virus (LPAIV) in respiratory and intestinal tracts of chickens. cord-252600-bvh1o64r We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). cord-252894-c02v47jz This study predicts infectious diseases by optimizing the parameters of deep learning algorithms while considering big data including social media data. The performance of the deep neural network (DNN) and long-short term memory (LSTM) learning models were compared with the autoregressive integrated moving average (ARIMA) when predicting three infectious diseases one week into the future. Therefore, the aim of this study is to design a model that uses the infectious disease occurrence data provided by the KCDC, search query data from search engines that are specialized for South Korea, Twitter social media big data, and weather data such as temperature and humidity. Figure 1 shows the overall framework of the model used in this study including the data collection process and the comparison of models designed using the deep neural network (DNN) method, the long-short term memory (LSTM) method, the autoregressive integrated moving average (ARIMA) method, and the ordinary least squares (OLS) method. cord-254747-vox5xsgd Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. cord-256903-8lyw27gh Dendritic cells (DC) as such, and their role in immunity were first described in the 1970s and in 1995 Ralph Steinman published a series of papers describing that a cellular receptor called "DEC-205" (now CD205) was expressed on mouse DC, was involved in antigen processing (58, 59) and was detected by the monoclonal antibody NLDC-145. Studies in mice, for example, have shown the efficacy of vaccines against FMDV, however these efficacy studies have failed to be translated to the target species (cattle and pigs), presumably due to fundamental differences in the immune systems of model organisms and target species and the ability of the virus to mutate in these animals (112) . The role of bovine γδ T cells and their WC1 co-receptor in response to bacterial pathogens and promoting vaccine efficacy: a model for cattle and humans cord-258052-y9pzsoqa A key method for detecting the presence of an emerging infectious disease syndrome or a biological weapons exposure in an ED patient is to develop a general approach that seeks out key historical and physical examination clues. Any suspicion of smallpox should prompt infectious disease consultation, airborne isolation procedures, and notification of local, state, and national public health authorities. Any suspicion of a VHF should prompt immediate consultation with an infectious disease physician and state and local health authorities. 20 There are several experimental treatments and vaccines (which can be used for postexposure prophylaxis) that are available for filovirus infections and arenavirus infections that would likely be used in any domestic VHF cases caused by these groups of viruses. 22 MERS should be suspected in individuals with upper or lower respiratory infection after travel to the Middle East in the prior 2 weeks, and confirmatory molecular testing can be done in conjunction with state and local health authorities. cord-261962-sfa9d1ux In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in‐flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. • Our identification of the dominated routes, that is the close contact route (large droplet) for influenza, the fomite route for norovirus, and all 3 routes for SARS CoV, suggested the relative importance of different environment intervention for different infectious diseases in air cabins and probably also in other indoor environments. F I G U R E 1 Spatial distribution for 3 in-flight infection outbreaks, (A) norovirus, 26 (B) SARS CoV, 27 and (C) influenza A H1N1 28 of infectious pathogens from the index source passenger, which is also sometimes termed indirect contact route. cord-262205-ax3i3d7f The aim of this study is to explore stakeholders'' experiences on the health system''s preparedness and challenges, and to provide suggestions for preventing infectious diseases during the Arbaeen mass gathering. Health infrastructure defects in Iraq has three sub-themes (health abandonment in Iraq, the weaknesses in health culture and problems related to the health system); poor control of the causative factors of infectious diseases has three sub-themes (the underlying factors of the prevalence of contagious diseases, health system response to communicable diseases and ignoring the risks of the Arbaeen ceremony); the low perception of risk in pilgrims has three sub-themes (lack of awareness in pilgrims, fatalism in pilgrims and unhygienic belief in pilgrims); and the ineffectiveness of health education has two sub-themes (training shortage in the targeted group and educational content problems) that shows participant''s experiences of the health system''s challenges for coping with infectious diseases during the Arbaeen ceremony. cord-265282-v3n9ff16 For the SIQ based ordinary differential equation (ODE) model, we perform the task of parameter estimation, and apply optimal control theory to the controlled SIQ model, with the goal of minimizing the infectious compartment population and the cost of implementing the quarantine and isolation strategies. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. cord-265679-7gzont7l In this study, the antiviral activity of a cationic amphibian antimicrobial peptide Caerin1.1 against porcine epidemic diarrhea virus (PEDV) was evaluated by an in vitro system using Vero cells. Vero cells cultured in 24-well plates were washed with PBS for 3 times and inoculated respectively with single medium, or single PEDV, or PEDV pre-incubated with different concentrations of Caerin1.1. PEDV suspensions containing different concentrations of Caerin1.1 were pre-incubated for 1 h at 37 • C, and were serially diluted before they were inoculated on the 80% confluent Vero cell monolayers grown in the 96-well plates, followed by washing 3 times with PBS. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. cord-268149-narre5e7 cord-270286-76mrzaxi We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In our time series analysis study, we reported that the implementation of the bacteremia prediction rule successfully reduced the blood culture rate without any significant 30-day mortality and antibiotics regimen changes. Finally the target population only included patients with CAP and this would limit the broad application of the Table 4 Blood culture results with contamination and antibiotics regimen changes before and after implementation of bacteremia prediction model. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. cord-273324-xhpv783y For example, as POC technologies for HIV viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from HIV RDTs. Malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-Saharan Africa. Although national TB programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-POC NAT assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow RDTs) and sustainability 46 , in addition to power and per-test time. Such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective ASSURED diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. cord-275162-2239dk45 On follow-up, children with viral infection (Group I) had adverse outcome in form of greater worsening of Shwachman clinical scores, number of pulmonary exacerbations requiring antibiotic usage [4 (2.1%)] and [2.8 (1.7%)], need for intravenous antibiotics 30.4% vs. CONCLUSION: Acute viral infection in children with CF affected course of illness on follow-up, including frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12–18 months. This retrospective cohort study demonstrated that CF children who had suffered a viral respiratory infection had worse outcome in follow-up in the form of lower CF scores, higher use of intravenous antibiotics, higher rate of hospitalization and higher mortality as compared with matched controls who did not have viral respiratory infection. C O N C L U S I O N Following the viral respiratory infections in children with CF who were already nutritionally compromised, there were frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12-18 months. cord-275719-ru33ubss Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients'' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. cord-280374-yj0r4rwt title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient He subsequently developed both hepatic veno-occlusive disease and busulfan-induced lung injury. In our case other bacterial infections typically seen in an immunocompromised child are also unlikely in view of sterile cultures, complete absence of fever and normal Creactive protein (CRP).Though this clinical presentation can be caused by infection with PCJ, it is an uncommon infection. The non-infective etiologies causing respiratory symptoms in a post-transplant setting can be pulmonary GvHD, Idiopathic pneumonia syndrome (IPS), Bronchiolitis obliterans syndrome (BOS), Cryptogenic organising pneumonia (COP) and SOS. The final diagnosis is neuroblastoma stage IV, day + 68 post auto-SCT (Bu-Mel) with pneumonitis, ARDS and multi-organ failure; likely etiology being fungal pneumonia or CMV pneumonia and hepatitis secondary to ischemia with underlying SOS. Hepatic veno-occlusive disease (sinusoidal obstruction syndrome) after hematopoietic stem cell transplantation cord-281403-yl7jdarm Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Survey questions included: demographic information (e.g. title, population served, state), personal protective equipment (PPE) worn in different infectious scenarios, procedures performed in different infectious scenarios, duration of training received, biosafety level (BSL) capabilities, and jurisdictional handling of highly infectious remains. Slightly more than half of respondents (56%; 61/108) stated their office staff had received training on donning and doffing PPE in suspected or confirmed cases of highly infectious remains; nearly one-third (32%) (18/56) reported the amount of cumulative training in hours per person, on average per year, was 1 h or less while 29% (16/56) spent between 1 and 2 h of training. 3. This survey, with respondents from nearly every U.S. state, revealed current levels of Medical Examiner/ Coroner training and education to address suspected or confirmed highly infectious remains. cord-282322-ywwqnw74 Our previous study in chickens has shown that inhalation of a non-adjuvanted dry powder influenza vaccine formulation during normal breathing results in partial protection against lethal influenza challenge. Upon passive inhalation of dry influenza vaccine formulations in an optimized set-up, BLP and Advax/BLP adjuvanted formulations induced significantly higher systemic immune responses than the non-adjuvanted formulation. In a previous study, we have shown that pulmonary immunization by dispersion of a dry powder influenza vaccine directly at the syrinx of chickens (active administration) was able to completely protect these animals against lethal viral challenge [11] . For this, we initially tested whether (a) BLP or Advax could be co-formulated with influenza vaccine into dry powder formulations that are suitable for pulmonary immunization; (b) the adjuvants have the potential to boost systemic and mucosal immune responses to influenza; (c) passive administration with either non-adjuvanted or adjuvanted influenza formulations would protect chickens against a lethal HPAIV challenge. cord-287853-cob7ur35 As illustrated in the following section and in Table 1 , mass spectrometry-based techniques have been used to perform the structural characterization, glycosylation profiling and antigen quantitation during the development of the HIV, influenza, Dengue, Ebola, Meningococcal, and other vaccines. The review also highlights that mass spectrometry-based methods such as glycan analysis has been used to analyze a specific envelope glycoproteins (Env) and has broad applicability to any other glycoprotein-based vaccines. 91 To improve on the conventional approaches for absolute quantitation of GP1 in Ebola virus-like particles (eVLPs), an isotope dilution full-scan liquid chromatography-high-resolution mass spectrometry method was developed using an UltiMate 3000 HPLC and an Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations Development and application of a reversed-phase high-performance liquid chromatographic method for quantitation and characterization of a Chikungunya virus-like particle vaccine cord-288332-y15g1yak PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Nasopharyngeal aspirates from all patients were obtained within 48 hours of admission for multiplex RT-PCR assay to detect the following 15 common respiratory viruses: influenza virus A and B (IFA, IFB), respiratory syncytial virus A and B (RSV A, RSV B), parainfluenza virus 1-4 (PIV 1, PIV 2, PIV 3, PIV 4), human coronavirus 229E and OC43 (hCV-229E, hCV-OC43), human rhinovirus (hRV), human enterovirus (hEV), adenovirus (AdV), human bocavirus (hBV), and human metapneumovirus (hMPV). cord-289026-v09m2fzw Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Based on the results above, recombinant pAPN ectodomain was obtained as dimers, and PEDV S1 or S1t protein existed as monomers, which showed similar natures of mammalian APN [43] and other coronavirus S proteins [48] [49] [50] as previously reported. In the current study, three canonical assays were carried out to characterize the interaction between pAPN ectodomain and PEDV S1 or S1t protein since these functional target proteins were successfully prepared. Identification and comparison of receptor binding characteristics of the spike protein of two porcine epidemic diarrhea virus strains cord-290861-5bxvenue Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). After the most stable reference genes were identified, a selection of genes previously associated with nociception in rodent models, and of interest to the authors, were examined using qPCR in the same samples to allow us to start characterizing the neurobiological signature of pain associated with DJD in cats. After a set of stable reference genes were identified for each tissue type, 13 genes associated with pain in rodents were selected (based on current knowledge of genes involved in pain states (Foulkes and Wood, 2008) and their expression levels compared in the DRG from DJD-affected and healthy samples. cord-292830-gcfx1095 Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . cord-295491-zlah6u5s The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. The aim of this study was to test specificity and sensitivity of two commercially available reaction mixtures in a reverse transcription LAMP (RT-LAMP) to detect FCoV in body cavity effusions of cats with and without FIP, and to minimize the time from sampling to obtaining results. The FIP group (n = 34) included cats with a definitive diagnosis of FIP by one or more methods: All effusions of cats with FIP tested positive for FCoV by RT-PCR by a commercial laboratory, and in 26/34 samples putative disease-causing mutations could be detected. cord-295878-pd9elo4l Based on the location-based network, we simulate influenza transmission dynamics and evaluate the efficacy of different vaccination strategies according to the identified geo-social interaction patterns. Second, the design of control strategies based on individualbased networks (e.g., vaccinate the individual with a large number of contacts) is challenging because it is infeasible to keep track of all social contacts of infections (Cohen, Havlin, & Ben-Avraham 2003; Gómez-Gardenes, Echenique, & Moreno 2006; Holme 2004 ), but the information to estimate population flows among locations based on intra-and inter-community travelers is widely available in the existing census data and travel survey reports (Mao & Bian 2010) . Thus, location-based human interaction network models are required to easily represent explicitly spatial dynamics of the disease transmission and design control strategies to target certain critical locations first rather than prioritizing individuals. cord-296992-2vp35fwv We retrospectively investigated how to use data from the International Network for Strategic Initiatives in Global HIV Trials, a global clinical influenza research network, to make more accurate case fatality ratio (CFR) estimates early in a future pandemic, an essential part of pandemic response. Since 2009, INSIGHT has undertaken 2 cohort studies-1 outpatient (FLU002) and 1 inpatient (FLU003)-specifically to address gaps in clinical research on the emerging influenza pandemic, including factors linked to disease progression and severe outcomes [24] . To underscore the importance of having baseline data, we compared the estimated pH1N1 clinical severity to that of seasonal influenza types and subtypes and noninfluenza respiratory patients in the post-pandemic period (2012) (2013) (2014) (2015) . Our analysis combining data from inpatient and outpatient INSIGHT cohorts demonstrates how preestablished global research networks could immediately begin rigorous studies to estimate the CFR, a key parameter of clinical severity of an emerging pandemic. cord-298032-3zlu8g8y cord-298805-ntpm68cg cord-300459-tu2xrt9x cord-301767-1jv20em8 Primarily, pathogens may contaminate produce ''on-field'' via various routes including; atmospheric deposition, uptake from contaminated soils and groundwater (Harris et al., 2003; Lynch et al., 2009; Mei Soon et al., 2012) , use of raw (or poorly treated) manure and compost, exposure to contaminated water (irrigation or flooding), transfer by insects, or by fecal contamination generated by livestock or wild Table 1 The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . Epidemiological investigations of food poisoning outbreaks, experimental studies examining pathogen contamination of fruits and vegetables as well as observations of increased incidence of disease in areas practicing wastewater irrigation with little or no wastewater treatment indicate that contaminated irrigation water might indeed be a source of foodborne pathogens on fresh produce (Norman and Kabler, 1953; Hern andez et al., 1997; Steele and Odumeru, 2004) . cord-305936-tdswzj7r Despite not controlling for comorbidities, climate, and vaccination, for the >70 years, ratio of respiratory diseases excess mortality rates between AH1N1 (2009) and severe year of H3N2 (2007) shows protection in the pandemic year and great vulnerability during AH3N2 virus predominance. We analyzed particularly the most predominant variants (AH1N1 and AH3N2) on excess of mortality in the adults and elderly of different age groups in a region with marked seasonality of respiratory diseases in Brazil. Among adults (24-59 years), we observe a large excess of deaths rates during the 2009 pandemic (953 obits), which correspond to 7.1 excess deaths from all causes, and 99 excess mortality from respiratory diseases associated with viral infection in every 100,000 individuals of the age group. Although the elderly are the most vulnerable group to viral respiratory infections, we found relative small excess of deaths in years of circulating AH1N1 pre pandemic (2002 and 2008) . cord-307543-piust0s6 title: Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study OBJECTIVES: To assess the nurses'' hand hygiene (HH) knowledge, perception, attitude, and self-reported performance in smalland medium-sized hospitals after Middle East Respiratory Syndrome outbreak. The questionnaire included 4 domains: (A) HH knowledge, (B) HH perceptions, (C) HH attitudes and role models, and (D) participant demographics and hospital characteristics. The attitudes and role models domain (C) was adapted from Hand Hygiene Knowledge and Performance a previous study [8] . The regression model for performance was calculated as Y4 =18.302+0.247X41 (perceptions)+0.232X42 (attitudes)+ 0.875X42 (role model); the coefficients were statistically signifiIn terms of infection control infrastructure [16] , ICDs and ICNs were not fully allocated across the hospitals analysed in this study. Consistently with previous studies [13, 21, 22, 25] , our participants'' self-reported HH performance rate of self was positively correlated with their scores for perceptions, attitudes, and role models. cord-307547-7n3f3wrz Two structurally less complex Actinomycin D analogs containing the phenoxazone chromophores, Questiomycin A and Actinocin, appear to be competitive inhibitors of both aminopeptidases, with potencies similar to the non-competitive macrocyclic parent compound (K(i) in the micromolar range). Elimination of the cyclic peptide fragments from the structure of Actinomycin D/X 2 allowed the resulting Actinocin to penetrate much further into the active sites of the studied metallopeptidases and to act as a classical competitive ligand by interacting with the metal ions (Figures 5 and 6 ). Actinomycin D is a long-known drug that was developed as an anticancer agent years before apoptosis and other cell death mechanisms and cancer progression were elucidated. Blocking the activity of MetAP2 and APN with Actinomycin D or its analogs seems to be promising for the development of new generations of potent anticancer agents that would be implicated in different mechanisms of action and directed against multiple molecular targets. cord-309565-8syjr6k8 A long-term animal experiment involving inoculation with bovine coronavirus (BCoV) was conducted to verify its persistent infection in cattle. Until the end of the experiment (1,085, 700 and 280 days, respectively), viral RNAs were detected sporadically by RT-PCR and nested PCR from plasma, nasal discharge, and feces. Samples of nasal discharge, feces, plasma, and sera were collected daily until 10 days post inoculation (dpi), followed by weekly collection until 141 dpi and then twice-weekly collection until the end of the experiment (1,085 dpi). The virus in the digestive tract might have been quickly inactivated and excreted; therefore, viral RNAs were not detected from nasal discharge and feces at 421 dpi, 10 days after the onset. This study showed that the BCoV RNA was long-lasting, having been detected from the nasal discharge of cattle that had been maintained in an isolated room of a high-containment facility to prevent virus intrusion from outside. cord-310240-otf9ruvj METHODS: ARDS patients admitted to the intensive care unit (ICU) who were placed on ECMO and treated with (IVIG group; n = 29) or without (control group; n = 28) intravenous IgM-enriched immunoglobulins for 3 days in the initial stages of ARDS were analyzed retrospectively. CONCLUSION: We conclude that administration of IgM-enriched immunoglobulins as an additional therapy did not have a beneficial effect in patients with severe ARDS requiring ECMO support. Although this treatment was omitted in recent sepsis guidelines due to a lack of supporting evidence in high-quality trials [8] , several studies, including one meta-analysis, describe beneficial effects of immunoglobulins in acute pneumonia induced by drug-resistant bacterial infections [9] [10] [11] . Based on these data, we treated patients with ARDS requiring ECMO therapy with IgM-enriched immunoglobulins immediately after intensive care unit (ICU) admission. The purpose of this analysis was to systematically investigate the potential effect of IgM-enriched immunoglobulins on the outcomes of ARDS patients requiring ECMO therapy. cord-314340-ltx4w9zh During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). Indeed, 5 µM of AA treatment could inhibit histone H3 acetylation as demonstrated by the reduced levels of H3K9ac relative to the control, but AA increased the levels of H3K9ac in the context of virus infection in comparison to the mock treated but infected cells ( Figure 3E ,F). cord-317688-mr851682 Middle East Respiratory Syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in 2012. Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in September 2012 [1] . The first patient (index case) with MERS-CoV infection was a 68-year-old Korean man returning from the Middle East. Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea Clinical implications of 5 cases of Middle East respiratory syndrome coronavirus infection in a South Korean outbreak Renal complications and their prognosis in Korean patients with Middle East respiratory syndrome-coronavirus from the central MERS-CoV designated hospital Successful treatment of suspected organizing pneumonia in a patient with Middle East respiratory syndrome coronavirus infection: a case report cord-318181-xxc7vdnt A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient''s clinical status, ''yes/no'', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). cord-319729-6lzjhn8j title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. To assess innate immune responses in astrocytes, cells were infected with DRV or B2c at an MOI of 0.1 and the expression of several proteins involved in the MAVS signaling pathway, namely, RIG-I, p-IRF7, STAT1 and IFIT1 (ISG56), was measured by Western blot. cord-319871-qnijw08y title: Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms S. aureus expresses a wide repertoire of surface proteins that recognize cellular adhesive molecules and it is therefore able to adhere to and internalize into lung epithelial cells, which protects the bacteria from the host immune system and facilitate chronic infection [20] . A recent prospective study investigated the differences in the nasopharyngeal microbiome during acute respiratory tract infections due to human rhinovirus or RSV in 135 infants aged less than 6 months [38] . Several potential mechanisms through which rhinovirus increases susceptibility to bacterial infection have been demonstrated in vitro in epithelial cells of the upper and lower airways. aureus carriage and non-influenza respiratory virus infections, as well as deeper insights into mechanisms of interactions between these different pathogens. cord-320107-wels9wt7 Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study cord-322201-5laifjgz To explore the action of nano-silver on emerging Bacillus megaterium MTCC 7192 and re-emerging Pseudomonas aeruginosa MTCC 741 pathogenic bacteria, the study includes an analysis of the bacterial membrane damage through Scanning Electron Microscope (SEM) as well as alternation of zeta potential and intracellular leakages. The comparative antibacterial activities of nano-silver and broad spectrum antibiotics was effectively accessed against emerging pathogens Bacillus megaterium MTCC 7192 and re-emerging pathogens Pseudomonas aeruginosa MTCC 741 using agar well diffusion assay method [13] . Samples from bacterial cultures (Bacillus megaterium MTCC 7192 and Pseudomonas aeruginosa MTCC 741), mixed with 100 μg/ml of nano-silver, were collected at 3 h and pre-fixed with 2.5% glutaraldehyde for 30 min; these were then washed two times in the same buffer and post-fixed for 2 h in 1% osmium tetroxide. The inhibition zones of nano-silver obtained in this study indicated that a nano-silver has potential to control emerging and re-emerging multidrug-resistant pathogens compared to tested antibiotics. cord-323700-5awng7h1 The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients cord-324432-k0g3r1lw PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually. cord-324674-yd7idp90 cord-325525-d1hsguds À l''inverse, des pathologies, comme la maladie de Glässer, sont encore susceptibles d''engendrer d''importantes pertes économiques dans des élevages à haut niveau sanitaire. En 2018, six maladies et infections à déclaration obligatoire (encéphalite à virus Nipah, gastro-entérite transmissible, cysticercose, peste porcine classique et africaine, syndrome dysgénésique et respiratoire) ont été recensées par l''Organisation mondiale de la santé animale pour les suidés 1 . Peste porcine ✦ Causée par un virus de la famille des Flaviridae, la peste porcine classique n''est actuellement plus présente en France tant dans les cheptels porcins domestiques que sauvages. Aucun traitement spécifique n''est disponible et la vaccination préventive des cheptels porcins n''est plus autorisée dans l''Union européenne depuis 1988 suite à la mise en place d''un programme d''éradication de la maladie. Cette affection, pour laquelle il n''existe ni traitement ni vaccin, résulte d''une infection par des entérovirus de la famille des Picornaviridae. cord-327202-2um6jmhk The conundrum of dual use research of concern was crystallized by the so-called "gain-of-function" type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. The major outcome of the great GOF controversy of 2012 is that it defined and crystallized some of the issues of dual-use research in biology by providing clear examples of experiments that were of great scientific value while also raising biosecurity and biosafety concerns. Consequently, when faced with GOF papers containing information that could conceivably be used to enhance the pathogenicity or transmissibility of a virus, editors and journals have almost always opted for full publication, usually requiring more details from the authors about biosafety and biosecurity methods, and often publishing an accompanying editorial emphasizing the scientifically useful aspects of the research [for examples, see Dermody et al. cord-328086-ji2emajn BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection cord-328525-80xk3gln Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. To strengthen our existing infection control measures in hematology and oncology, we subsequently implemented a systematic influenza and RSV screening of patients lacking respiratory symptoms on a pediatric and an adult hemato-oncological ward as a prophylactic infection control measure in the following winter (2016/2017). To extend our existing standard infection control measures, we introduced a prophylactic screening program for asymptomatic patients targeting RSV and influenza on an adult and a pediatric hemato-oncological ward. cord-329227-sqetz7h6 The amounts of PEDV S proteins in the ERGIC, in other organelles, or on the cell surface are likely regulated by two nearby motifs in its cytoplasmic tail (CT): a tyrosine-based motif, Yxx⌽ (x is any residue and ⌽ is a bulky hydrophobic residue: F, M, I, L, or V), and an ER retrieval signal (ERRS), KVHVQ (10) (11) (12) (13) , as well as other viral and cellular proteins. One study demonstrated that a single amino acid substitution in this motif (KVHVQ to KVRVQ) weakens the intracellular retention function of the S proteins of the 10th passage of a murine-adapted PEDV variant, MK-P10 (18) , resulting in enhanced syncytium formation in Vero cells. In this study, we evaluated the phenotypes of transiently expressed S mutants containing mutations or deletions in these two motifs in mammalian cells and the virulence of three representative recombinant PEDVs in gnotobiotic piglets. cord-329429-ur8g68vp Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . cord-330296-706hf4qw Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. cord-330942-x238hq9b The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Recent studies however, suggest that hRV may be a clinically significant pathogen with the potential to cause serious pulmonary disease in HCT recipients (Campbell et al., 2015; Seo et al., 2015 Seo et al., , 2017 Versluys et al., 2017) with risk of progression to LRTI of 9-24% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) and hRV related mortality of 4-33% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) . In 2016 a joint working group in the UK (Dignan et al., 2016) has reviewed the available literature and made recommendations for the diagnosis and management of respiratory viral infections in patients with hematological malignancies or those undergoing hematopoietic stem cell transplantation. cord-333639-usgpe1cz title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects We focus on the choice of the macromolecular backbone as a carrier for the conjugated drug and analyze blood coagulation, binding to albumin, albumin aggregation, inhibitory activity on polymerases, and cytotoxicity for polymers differed by their anionic charge (carboxylates, phosphates and phosphonates, sulfonates). As a result, we identify polymers and macromolecular prodrugs that are devoid of blood anti-coagulation activity but are strong as inhibitors of polymerases and efficacious as delivery vehicles for ribavirinthus being attractive for the development of broad-spectrum antiviral agents. This observation echoes our recent findings on the apparent unique pairing of negative character and hydrophobicity of the polymer backbone that renders PEAA an efficacious inhibitor of e.g. hepatitis C virus intracellular replication [55] and a lead polymer with broad-spectrum antiviral activity [21] . Polyanionic macromolecular prodrugs of ribavirin: antiviral agents with a broad Spectrum of activity cord-339871-jso21mbx To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea cord-343390-y903mxcj title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador cord-344227-rdlinzrn As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. cord-346586-fxxceffl CONCLUSION: The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Following the A/H1N1/2009 influenza pandemic that was associated with a high morbidity and an increased risk of mortality among particular groups [13] , a number of countries have strengthened vigilance for the surveillance of severe diseases and deaths in order to rapidly detect new viruses and to provide information in assessing the impact on the population and having operational preparedness plans. A meta-analysis of data from Africa reported that the incidence of RSV in lower acute respiratory infections that required hospitalization ranged from 10-18 per 1000 person year for infants and 3-9 per 1000 person year for children under 5 years of age [26] . cord-348660-qnbgywgy Following optimization of the ELISA protocol, 18 test sera were obtained from broiler chickens exposed to natural wild-type IBV infection, 18 test sera from broiler chickens vaccinated with a live-attenuated commercial IBV vaccine, and sera obtained at different time-points from chicks immunized with recombinant IBV N protein (described above) were analyzed to detect IBV N-specific antibodies. To assess the reliability of the performance of our in-house indirect IBV N ELISA, a panel of sera was obtained from chickens naturally infected with local wild-type IBV strains, chickens vaccinated with live-attenuated commercial IBV vaccine, and chickens immunized with recombinant IBV N protein (expressed in a baculovirus expression system). This represents the first study in Turkey that expressed recombinant IBV N protein in baculovirus and examined its reactivity against antisera obtained from Turkish chickens for potential use as antigen Fig. 5 Detection of IBV N specific antibodies in sera obtained from naturally infected chicken (a) and vaccinated chickens (b) using an in-house IBV-N ELISA and a commercial ELISA. cord-351760-698voi9y The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. In vivo study demonstrated that prophylaxis with m336 reduced virus titers in the lung of rabbits infected with MERS-CoV [15] , and m336 also provided transgenic mice expressing human DPP4 with full prophylactic and therapeutic protection from MERS-CoV [16] . A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein Prophylaxis with a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection Passive Transfer of a Germline-like Neutralizing Human Monoclonal Antibody Protects Transgenic Mice Against Lethal Middle East Respiratory Syndrome Coronavirus Infection Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV cord-353553-adaow2w7 cord-354664-mzzvmyea While population-based studies have historically suggested improved clinical outcomes with the routine use of macrolide combination therapy in hospitalized patients with CAP, emerging evidence from recent randomized controlled trials has challenged this practice. Last updated in 2007, the joint Infectious Disease Society of America (IDSA)/American Thoracic Society (ATS) guidelines for CAP recommend empiric combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone (e.g., moxifloxacin) for adult patients hospitalized with CAP in a non-ICU setting [21] . The body of evidence used to support current IDSA/ATS guideline recommendations that advocate for combination therapy with a beta-lactam plus macrolide in the management of hospitalized adult patients with CAP originates from a series of large, retrospective cohort studies that showed improved clinical outcomes in patients treated with combination therapy. Based on the findings of these large observational studies, many clinical practice guidelines recommend combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone as first-line therapy for hospitalized adult patients with CAP. cord-354700-bdpp3qmf 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. cord-354904-7gq2e6f0 We used spherical gold nanoparticles (average diameter, 15 nm) as a platform for the antigen for swine transmissible gastroenteritis virus (TGEV). The literature data demonstrate that immunization of animals with the TGEV antigen coupled to gold nanoparticles (GNPs) not only activates antigen-presenting cells but also increases the proliferative activity of splenic lymphoid (antibody-forming) cells. Immunization with the TGEV antigen conjugated to GNPs as a carrier activates the respiratory activity of lymphoid cells and peritoneal macrophages, which is directly related to their transforming activity and to the activation of antibody generation. After the virus''s nucleic acid was inactivated with ribonuclease, the resultant antigen (a mixture of viral capsid proteins) was used for conjugation with GNPs and for subsequent animal immunization. A study of the respiratory activity of splenic lymphoid cells (Fig. 5) showed that after immunization with the conjugate, the activity increased 2.2-fold, as compared to the control, whereas after immunization with TGEV antigen alone, it did not change much.