Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 41 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 6084 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 9 figure 6 virus 6 PRRSV 5 RNA 4 cell 4 IFN 3 PEDV 2 vaccine 2 protein 2 porcine 2 pig 2 group 2 gene 2 disease 2 clostridium 2 cat 2 PCR 2 Newcastle 2 IAV 2 APMV-1 1 vp7 1 vp2 1 vac 1 toxin 1 tomatidine 1 target 1 sample 1 respiratory 1 population 1 oral 1 ns1 1 maintenance 1 intracellularis 1 infection 1 hpi 1 host 1 he52.7 1 exhibition 1 enteroid 1 dpi 1 deg 1 defective 1 cryptosporidium 1 com 1 calf 1 bridge 1 bovine 1 antibody 1 alpha 1 WSN Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 2330 cell 2240 virus 1256 infection 896 pig 833 group 824 protein 793 % 762 response 746 study 737 vaccine 606 disease 581 antibody 571 strain 542 figure 511 gene 508 host 485 influenza 484 sample 419 cat 419 analysis 404 level 403 animal 395 chicken 391 p 376 expression 376 control 345 result 336 day 335 c 334 tissue 321 type 315 ° 310 antigen 307 calf 303 time 294 pathogen 286 serum 283 lung 276 datum 273 dpi 270 difference 260 replication 257 role 247 mouse 247 blood 242 swine 240 production 238 activity 235 number 232 challenge Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 416 PEDV 384 PRRSV 372 RNA 309 IFN 284 PCR 221 USA 192 BNP 186 C. 171 NK 165 PRV 163 PBS 157 SAV 153 NKp46 146 C 140 Figure 139 MHC 123 hpi 123 T 117 M 112 al 110 Newcastle 106 Vero 105 mAb 104 L. 103 FIP 102 China 100 HE 100 ALV 94 et 94 J 93 HPAI 91 IAV 90 II 89 Mhf 88 GFP 88 A 87 FCoV 87 ELISA 87 B. 86 D7 86 BVD 84 © 84 H9N2 80 RT 80 IPEC 79 Table 78 α 78 intracellularis 78 H5N1 77 dpv Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 498 we 325 it 214 i 189 they 45 them 23 he 10 us 8 itself 6 themselves 4 you 3 one 1 tomatidine 1 themself 1 she 1 pdcs 1 interleukin-10 1 imagej 1 il-1β 1 esat6 1 apmv-1 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 8120 be 1105 use 999 have 614 show 448 infect 400 induce 301 compare 293 observe 292 detect 285 indicate 282 perform 254 identify 248 base 239 increase 229 associate 228 include 217 describe 215 find 212 follow 210 do 210 contain 207 provide 202 determine 196 collect 181 cause 178 express 172 isolate 161 bind 154 inhibit 152 result 150 treat 143 incubate 139 vaccinate 136 suggest 135 mediate 134 report 131 produce 130 obtain 129 remain 128 involve 122 reduce 120 demonstrate 120 consider 117 inactivate 116 enhance 112 test 108 reveal 108 inoculate 105 develop 105 accord Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 727 - 648 not 568 viral 559 high 551 immune 503 porcine 477 also 425 respiratory 410 different 329 specific 329 other 279 low 270 infected 262 however 250 well 245 anti 243 significantly 243 significant 243 only 242 human 227 infectious 225 avian 220 non 208 more 200 such 199 reproductive 194 additional 192 positive 189 most 178 then 178 bovine 166 innate 163 important 163 clinical 161 first 159 further 156 respectively 154 epithelial 151 early 150 feline 145 negative 145 highly 144 as 135 intestinal 134 antiviral 131 cellular 129 similar 129 same 129 experimental 120 therefore Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 58 most 52 high 38 least 17 low 14 large 14 good 7 Most 5 near 4 close 2 strong 2 old 2 long 2 late 2 great 1 young 1 steep 1 small 1 simple 1 pGemT 1 few 1 early 1 big 1 bad 1 TAdV-3-host 1 /animal Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 131 most 24 least 6 well Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 1 www.veterinaryresearch.org 1 doi.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 1 http://www.veterinaryresearch.org/content/43/1/64 1 http://doi.org/10.1186/s1356 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 zhang@bio.uminho.pt 1 torr0033@umn.edu 1 sunjhe@sjtu.edu.cn 1 resen023@umn.edu 1 nicolas.ruggli@ivi.admin.ch 1 lixiangrui@njau.edu.cn 1 lijinxiang@caas.cn Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 17 cells were pre 10 cells were then 5 group was significantly 5 levels were significantly 4 antibodies were not 4 pigs were randomly 4 pigs were significantly 4 results were consistent 4 strain was more 3 cell binding receptors 3 cells were approximately 3 disease following homologous 3 group was sham 3 group were positive 3 group were significantly 3 infection did not 3 pigs did not 3 pigs had significantly 3 pigs were humanely 3 pigs were negative 3 response following vaccination 3 results were also 3 rna was first 3 vaccines are available 2 animals do not 2 animals infected only 2 cats were not 2 cell associated markers 2 cell binding proteins 2 cells are also 2 cells expressing scfv 2 cells was not 2 cells was significantly 2 cells were also 2 cells were co 2 cells were cultured 2 cells were further 2 cells were not 2 cells were similar 2 figures indicate significant 2 group did not 2 group had significantly 2 group was lower 2 group were also 2 group were seropositive 2 groups had significantly 2 host does not 2 infection is important 2 infection is not 2 level did not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 animals do not accurately 1 antibodies are not available 1 cats showed no differences 1 cats showed no increase 1 cats were not susceptible 1 cells showed no obvious 1 cells was not higher 1 cells were not frequently 1 disease was not evident 1 gene shows no evidence 1 group had no serum 1 group had no viral 1 group showed no histological 1 host does not always 1 infection did not significantly 1 infection is not clearly 1 infection is not sufficient 1 infection was not possible 1 infections had no effects 1 level was not significantly 1 pedv has not yet 1 pigs had no fever 1 proteins have not yet 1 prrsv has not yet 1 results were not only 1 studies are not naturally 1 studies are not well 1 vaccine is not available 1 vaccine showed no clinical 1 vaccines are not available 1 vaccines is not as 1 virus did not strongly 1 virus does not productively 1 virus had not yet 1 virus was no longer 1 viruses has not yet A rudimentary bibliography -------------------------- id = cord-310194-f5jtufja author = Benedictus, Lindert title = Bovine Neonatal Pancytopenia is a heritable trait of the dam rather than the calf and correlates with the magnitude of vaccine induced maternal alloantibodies not the MHC haplotype date = 2014-12-17 keywords = BNP; BVD; MHC; Pregsure summary = Since alloantigens (including MHC I and MHC class I associated B2M) and MHC class II are genetically determined and therefore heritable, we studied whether differences in these genes between dams and/or calves may explain why BNP only occurs in part of the calves born to PregSure© BVD vaccinated dams. We conclude that the development of BNP in calves is a heritable trait of the dam rather than the calf and that genetic differences between BNP and non-BNP dams are likely due to genes controlling the quantitative alloantibody response following vaccination. We conclude that the development of BNP in calves is a heritable trait of the dam rather than the calf and that genetic differences between BNP and non-BNP dams are likely due to genes controlling the quantitative alloantibody response following vaccination. doi = 10.1186/s13567-014-0129-0 id = cord-001714-jfawhnsq author = Caron, Alexandre title = Bridge hosts, a missing link for disease ecology in multi-host systems date = 2015-07-21 keywords = bridge; host; maintenance; population; target summary = We illustrate this framework using the example of the transmission of Avian Influenza Viruses across wild bird/poultry interfaces in Africa and discuss a range of other examples that demonstrate the usefulness of our definition for other multi-host systems. Lastly, we present an operational framework to identify potential bridge host populations, using as a case study the ecology of avian influenza viruses at the wild/domestic bird interface in Africa and also giving other multi-host systems examples. As a consequence, the information available on most wild bird species is scarce and has been obtained mostly from by-catch (i.e. captured non-targeted species) of studies investigating AIV in maintenance waterfowl, resulting in small sample sizes that are inadequate to provide epidemiological understanding of the host roles in AIV ecology in Africa [26] . The range of methods available to characterize host competence for AIV and contact patterns between maintenance, potential bridge and target host populations is drawn from the fields of epidemiology and avian ecology ( Table 2) . doi = 10.1186/s13567-015-0217-9 id = cord-266199-smlq11y9 author = Dhakal, Santosh title = Nanoparticle-based vaccine development and evaluation against viral infections in pigs date = 2019-11-06 keywords = PLGA; PRRSV; pig; porcine; vaccine; virus summary = The economic burden caused by virus infections such as Porcine Reproductive and Respiratory Syndrome Virus, Swine influenza virus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus 2, Foot and Mouth Disease Virus and many others are associated with severe morbidity, mortality, loss of production, trade restrictions and investments in control and prevention practices. Likewise, DCs targeted chitosan NPs loading plasmid DNA encoding nucleocapsid protein of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) induced better nucleocapsid protein-specific mucosal IgA antibody response compared to soluble unentrapped antigens after nasal immunization in mice [57] . In this review, only studies conducted in pigs related to the development and evaluation of NPs-based vaccine candidates by using virus-like particles (VLPs), biodegradable polymers, polysaccharides and liposomes against porcine viral infections are included (Table 3) . Chitosan-based NPs are used in pigs to deliver adjuvants such as bee venom and plasmid encoding porcine IL-2 and IL-4/IL-6 genes, which improved induction of better virus-specific immune responses of respective vaccines against PRRSV and PCV2 [103, 104] . doi = 10.1186/s13567-019-0712-5 id = cord-351881-qea4b0i5 author = Eck, Melanie title = Virus replicon particles expressing porcine reproductive and respiratory syndrome virus proteins elicit immune priming but do not confer protection from viremia in pigs date = 2016-02-19 keywords = GP3; GP5; PRRSV; VRP; VSV summary = title: Virus replicon particles expressing porcine reproductive and respiratory syndrome virus proteins elicit immune priming but do not confer protection from viremia in pigs However, none of the PRRSV antigens expressed from VRP, with the exception of the N protein, did induce any detectable antibody response in pigs before challenge infection with PRRSV. These data show that the VSV replicon vector can induce immune responses to heterologous proteins in pigs, but that the PRRSV envelope proteins expressed from VSV VRP are poorly immunogenic. Again, before challenge infection, vaccination with VRP expressing the structural proteins of PRRSV did not induce any detectable antibody response against GP5, GP4 and GP3 as measured by ELISA (not shown). Following challenge infection, GP5-specific antibody responses were detected on day 7 pi in 2 out of 4 pigs, and all pigs vaccinated with VRP expressing the PRRSV proteins seroconverted to GP5 at day 11 pi (Table 3 ). doi = 10.1186/s13567-016-0318-0 id = cord-003506-ztqjo13e author = Feng, Min title = A balanced game: chicken macrophage response to ALV-J infection date = 2019-03-06 keywords = ALV; MDM; deg; hpi summary = ALV-J infection induced strong innate immune responses in chicken MDM at 3 hpi, instead of 36 hpi, according to the analysis results of Gene Ontology and KEGG pathway. In our previous study, we found that primary chicken monocyte-derived macrophages (MDM) were susceptible to ALV-J and infection resulted in expression of immune-related genes [10] . In this study, RNA-seq analysis platform and gene overexpression verification were employed to analyze chicken MDM gene expression after ALV-J infection. According to published studies [21] [22] [23] , 94 and 23 differentially expressed interferon-stimulated genes (ISG) were identified in ALV-J-infected MDM at 3 hpi and 36 hpi, respectively (Additional file 6). Overexpression of CISH, EX-FABP and SOCS3 significantly increased the expression of ALV-J env gene at protein levels ( Figures 8A and B) and mRNA levels ( Figure 8C ) in chicken MDM cells at 3 hpi. doi = 10.1186/s13567-019-0638-y id = cord-335215-h9p4kmss author = Follet, Jérôme title = Cryptosporidium infection in a veal calf cohort in France: molecular characterization of species in a longitudinal study date = 2011-12-02 keywords = France; calf; cryptosporidium summary = These studies on dairy calves reported a within herd prevalence of Cryptosporidium without identifying species or the relation to the host''s age. parvum at the age of 5 weeks were excluded because Cryptosporidium species could not be identified in all of the following samples collected in these animals. The present study based on 18S rDNA and gp60 gene analysis is the first in France to include molecular characterization to describe the prevalence and the host age related susceptibility to different Cryptosporidium species after a follow up of the same animal. This observation shows that prevalence of Cryptosporidium infection decreases with increasing age of the cattle in France as in many other countries [17, 19, [33] [34] [35] [36] [37] [38] . parvum, a prevalent zoonotic species, in 5-week-old calves was in agreement with the report of Atwill et al., who considered that the contribution of cattle to human cryptosporidiosis is limited to calves under 2 months of age [53] . doi = 10.1186/1297-9716-42-116 id = cord-341305-zf97tcwe author = Ge, Shikun title = Canine Parvovirus is diagnosed and neutralized by chicken IgY-scFv generated against the virus capsid protein date = 2020-09-03 keywords = CPV; antibody; figure; vp2 summary = The CPV-VLP and CPV-VP2 protein showed similar reaction values to the purified scFv in the ELISA test, and the results of ELISA analysis using IgY-scFv toward CPV clinical samples were consistent with commercial immunochromatographic assay (ICA) and PCR detection, the scFv did not show cross reactivity with canine distemper virus (CDV) and canine coronavirus (CCV). This study revealed the feasibility of a novel functional antibody fragment development strategy by generating diversified avian IgY-scFv libraries towards the pathogenic target of interest for both detection and therapeutic purposes in veterinary medicine. Functional antibody fragments (i.e.: scFv, Fab) generated by phage-display technology have been not yet routinely evaluated and applied in the veterinary medicine despite it has been well confirmed that such engineered antibodies offer a series of advantages over polyclonal and full-length monoclonal antibodies. doi = 10.1186/s13567-020-00832-7 id = cord-315072-b28yikvj author = Giotis, Efstathios S. title = Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) date = 2016-08-05 keywords = Affymetrix; FDR; IFN; RNA; gene summary = title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) To generate a chicken ISG database we have compared data from three transcriptomic technology platforms: (i) the classical 3′-biased GeneChip Chicken Genome Array (32K; Affymetrix, High Wycombe, UK), (ii) the Chicken Gene 1.0 Sense Target (ST) whole transcriptome Array (Affymetrix) and (iii) Illumina (Little Chesterford, UK) RNA-seq. One of the most highly-expressed contigs was one which, when analysed by BLAST, proved to represent a homologue of STAT2, which is missing from the current ENSEMBL annotated reference chicken genome In (B) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5. Technologies identifying significant IRGs are listed as "1" RNA-seq (using Kal''s Z test); "2" Affymetrix 32K GeneChip Chicken Genome Array and "3" Chicken Gene 1.0 ST Array'' . doi = 10.1186/s13567-016-0363-8 id = cord-264888-h560slug author = Goossens, Evy title = The C-terminal domain of Clostridium perfringens alpha toxin as a vaccine candidate against bovine necrohemorrhagic enteritis date = 2016-04-27 keywords = alpha; clostridium; toxin summary = title: The C-terminal domain of Clostridium perfringens alpha toxin as a vaccine candidate against bovine necrohemorrhagic enteritis Using an intestinal loop model in calves, we investigated the protection afforded by antisera raised against native alpha toxin or its non-toxic C-terminal fragment against C. The aim of this study was to evaluate whether the nontoxic C-terminal fragment of alpha toxin could be a candidate for effective vaccination of calves against bovine necrohemorrhagic enteritis. Incubation of cell-free supernatants of the wild-type strain JIR325 (concentrated tenfold using Vivaspin, Sartorius Stedim Biotech GmbH, Göttingen, Germany) on sheep blood agar at 37 °C overnight results in an inner, complete zone of hemolysis caused by perfringolysin O and a less complete outer zone caused by alpha toxin. perfringens strain by sera from calves immunized with the native alpha toxin (rCpa) or the non-toxic C-terminal fragment of the alpha toxin (Cpa 247-370 ). perfringens in the intestinal loop model was significantly reduced only by co-administration of antisera from animals vaccinated with the native alpha toxin. doi = 10.1186/s13567-016-0336-y id = cord-343421-k1dqe4lk author = Hoelzer, Karin title = Vaccines as alternatives to antibiotics for food producing animals. Part 2: new approaches and potential solutions date = 2018-07-31 keywords = Eimeria; Salmonella; clostridium; disease; oral; vaccine summary = doi = 10.1186/s13567-018-0561-7 id = cord-332881-mkm4ygh6 author = Kirchhoff, Jana title = Three viruses of the bovine respiratory disease complex apply different strategies to initiate infection date = 2014-02-18 keywords = BHV-1-GFP; BPIV3; BRSV; GFP summary = doi = 10.1186/1297-9716-45-20 id = cord-269531-7gy4epzo author = Kumar, Pankaj title = Proteomic analysis of purified turkey adenovirus 3 virions date = 2015-07-09 keywords = TAdV-3; protein summary = To develop a better understanding of virus-host interactions, we performed a comprehensive proteomic analysis of proteinase K treated purified TAdV-3 virions isolated from spleens of infected turkeys, by utilizing one-dimensional liquid chromatography mass spectrometry. The LC-MS/MS analysis of proteinase K treated CsCl 2 density gradient purified TAdV-3 virions identified eleven virus-encoded proteins (hexon, pVI, pVII, penton base, pVIII, sialidase, IIIA, adenain, pX, IVa2 and DBP) previously reported to be in other adenoviruses (Table 3 and Figure 3A ) [16] . In addition, five host proteins namely, vitronectin, collagen alpha-3 (VI) chain, collagen alpha-2 (VI) chain, tyrosine protein phosphatase and turkey heterophil peptide 2 (THP-2) were only detected in proteinase K treated TAdV-3 virions. The proteomic analysis of proteinase K treated purified virions identified eleven cellular proteins incorporated in TAdV-3, which have been identified in other viruses (Table 4 ). In addition, proteomic analysis identified seven host proteins incorporated in TAdV-3 virions (Table 4) , which have not been identified so far in any other virus. doi = 10.1186/s13567-015-0214-z id = cord-290593-vhmi2559 author = Lannes, Nils title = Interplay of foot-and-mouth disease virus, antibodies and plasmacytoid dendritic cells: virus opsonization under non-neutralizing conditions results in enhanced interferon-alpha responses date = 2012-08-30 keywords = FMDV; IFN; PBMC summary = title: Interplay of foot-and-mouth disease virus, antibodies and plasmacytoid dendritic cells: virus opsonization under non-neutralizing conditions results in enhanced interferon-alpha responses Vaccine-induced immune protection correlates with the presence of high levels of neutralizing antibodies but also opsonising antibodies have been proposed as an important mechanism of the immune response contributing to virus clearance by macrophages and leading to the production of type-I interferon (IFN) by plasmacytoid dendritic cells (pDC). The present study demonstrates that the opsonising antibody titres mediating enhanced IFN-α responses in pDC were similar to neutralizing titres, when antigenically related viruses from the same serotype were employed. Considering the possible importance of opsonising antibodies and pDC in the protection against FMDV, the main aim of this study was to characterize the relationship between neutralizing and opsonising activities of polyclonal sera from immunized pigs. Plasmacytoid dendritic cell activation by foot-and-mouth disease virus requires immune complexes doi = 10.1186/1297-9716-43-64 id = cord-003888-lgutt1r9 author = Lauterbach, Sarah E. title = Assessing exhibition swine as potential disseminators of infectious disease through the detection of five respiratory pathogens at agricultural exhibitions date = 2019-09-18 keywords = IAV; exhibition summary = title: Assessing exhibition swine as potential disseminators of infectious disease through the detection of five respiratory pathogens at agricultural exhibitions Influenza A virus remains a top threat to animal and human health, but other pathogens may be disseminated through the exhibition swine population. Influenza A virus (IAV) has been routinely detected in swine at agricultural exhibitions, where subclinical infection is common and can make recognition difficult [3] [4] [5] [6] . Continued disease surveillance is vital to understanding the epidemiology of IAV and other pathogens infecting swine at agricultural exhibitions in order to protect animal and public health. There were 18 cases of variant influenza infections associated with the IAVs detected in this population of exhibition swine, and IAV should remain a priority for infectious disease surveillance and mitigation in exhibition swine [22] . Characterization of an influenza A virus isolated from pigs during an outbreak of respiratory disease in swine and people during a county fair in the United States doi = 10.1186/s13567-019-0684-5 id = cord-025152-3wqtu9ey author = Lee, Ji Eun title = Bacillus subtilis spores as adjuvants against avian influenza H9N2 induce antigen-specific antibody and T cell responses in White Leghorn chickens date = 2020-05-24 keywords = H9N2; figure summary = title: Bacillus subtilis spores as adjuvants against avian influenza H9N2 induce antigen-specific antibody and T cell responses in White Leghorn chickens subtilis spores, as adjuvants, enhance not only H9N2 virus-specific IgG but also CD4(+) and CD8(+) T cell responses, with an increase in pro-inflammatory cytokine production. subtilis spore adjuvant in chickens produces a significant effect on antigen-specific antibody and T cell responses against avian influenza virus. B. subtilis spores not only enhance innate immunity that protects against respiratory infections [12] [13] [14] but also induce an increase in antigen-specific antibody and T cell responses when co-administered with a soluble antigen [15] [16] [17] . subtilis spores act as adjuvants in chickens, enhancing antigen-specific immune responses when immunized with the inactivated H9N2 avian influenza virus. subtilis spores could act as potential vaccine adjuvants that synergistically provide antigen-specific immune responses against the avian influenza virus H9N2 in White Leghorn chickens. doi = 10.1186/s13567-020-00788-8 id = cord-028887-eseo7lyh author = Li, Chong title = Exploring heterologous prime-boost vaccination approaches to enhance influenza control in pigs date = 2020-07-09 keywords = AUT; IAV; LAIV; WIV; com summary = We performed a vaccination-challenge study to evaluate the protective efficacy of using multivalent inactivated vaccine and/or a live attenuated IAV vaccine (LAIV) in pigs following multiple prime-boost vaccination protocols against a simultaneous H1N1 and H3N2 IAV infection. Based on the BALF samples collected from pigs receiving WIV, the least amount of virus post-contact was detected in the heterologous treatment group AUT/ COM (Table 3) . We also tested the frequency of virus-specific IFN-γ secreting cells in PBMC samples collected at 1 week after boost vaccination from pigs in selected groups (COM/COM, AUT/AUT, LAIV/ COM and LAIV/NONE) and obtained similar results between the WIV administration groups (COM/COM and AUT/AUT). We found the heterologous prime-boost vaccination protocols may have expanded the antibody response to both H1 and H3 challenge strains as demonstrated by the higher HI titers especially in pigs from AUT/COM and LAIV/COM treatment groups. doi = 10.1186/s13567-020-00810-z id = cord-033692-txfuuu7d author = Lim, Byeonghwi title = Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection date = 2020-10-13 keywords = KEGG; PRRSV; RNA; dpi; figure; gene summary = In this study, we investigated the molecular mechanisms of PRRSV infection by integrating the differences in the expression of various genes in tissues responsible for respiration (lungs) and immunity (bronchial lymph nodes [BLNs] , and tonsils) using RNA-Seq data at serial time points. To validate the results of specific groups, GSEA based on the KEGG database were performed using log 2 -normalised TMM counts at each time point for each tissue to identify the maximum gene expression changes for each group, and the GSEA results were consistent with the KEGG enrichment analyses of DEGs. GSEA using the 3-dpi data for all tissues revealed many significant pathways related to viral infection, among which influenza A showed the highest NES ( Figure 5A ). Significant KEGG terms related to viral infections and immune signalling were identified through KEGG enrichment analyses performed for each up-and down-regulated genes (343 and 287 genes, respectively), based on the time point for each tissue with a maximum FC value in the GCN, which was constructed using serial DEGs ( Figure 4A ). doi = 10.1186/s13567-020-00850-5 id = cord-010835-nnorilo6 author = Lu, Mingmin title = Proteomic analysis revealed T cell hyporesponsiveness induced by Haemonchus contortus excretory and secretory proteins date = 2020-05-13 keywords = Haemonchus; cell; figure summary = doi = 10.1186/s13567-020-00790-0 id = cord-287153-jbuuph6w author = Lund, Morten title = Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar) date = 2016-10-21 keywords = PRV; RNA; SAV; SAV3; WPC summary = doi = 10.1186/s13567-016-0389-y id = cord-004400-li1sc47z author = Ma, Jingjiao title = Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus date = 2020-02-24 keywords = IFN; WSN; ns1; protein summary = However, the growth of the deacetylated mutant virus WSN-NS1-108R was significantly impaired compared with that of the other two viruses in MDCK and A549 cells at 36 and 48 hpi, which indicated that the acetylated K108 of NS1 is important for virus replication in vitro at the late stage of infection (Figures 2A and B) . To further explore how the K108R mutation attenuated the IFN-β antagonistic ability of the NS1 protein, we co-transfected NS1 expression plasmids, an IFN-β reporter plasmid and different type I interferon pathway components, including RIG-I CARD, TBK1, and the active form of IRF3, into 293T cells. This result indicated that the deacetylation-mimic K108R substitution retained NS1 protein in the cytoplasm of infected cells, suggesting that the acetylated K108 residue is important for the nuclear localization of the NS1 protein ( Figures 5A-C ). doi = 10.1186/s13567-020-00747-3 id = cord-308298-5ntdb8yf author = Mair, Kerstin H title = Porcine CD8α(dim/-)NKp46(high) NK cells are in a highly activated state date = 2013-03-01 keywords = CD27; CD3; IFN; cell summary = Functional analyses revealed that splenic NKp46(high) NK cells produced much higher levels of Interferon-γ and Tumor Necrosis Factor-α upon stimulation with cytokines or phorbol-12-myristate-13-acetate/Ionomycin compared to the other two subsets. Splenic NKp46 high NK cells showed a significantly reduced level of CD8α expression compared to the other splenic NK-cell subsets in all animals analysed Sequences of primers (5''-3'') for target genes as well as primer positions on (+) strand, length of specific product in base pairs (bp) and product melting temperature in°C are indicated. Splenic NKp46 high NK cells showed an overall higher expression of this receptor compared to NKp46and NKp46 + NK-cell subsets from both spleen and blood. Splenic NKp46 high NK cells showed highly elevated expression of this activating receptor compared to the other two NKp46-defined subsets in spleen as well as in blood in all animals analysed, which could be demonstrated on protein as well as on mRNA level. doi = 10.1186/1297-9716-44-13 id = cord-331001-7pyuy1os author = Miyazaki, Ayako title = Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26 date = 2011-11-09 keywords = GAR; vp7 summary = title: Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26 Although a number of G and P genotypes have been identified in porcine GARs, few attempts have been made to study the molecular epidemiology of these viruses associated with diarrhea outbreaks within a farm over an extended period of time. Based on the sequence and phylogenic analysis of GAR strains detected among the four outbreaks, at least five combinations of G and P genotypes (G/P combinations) were identified: G9P [23] at the first outbreak, G9P[13]/ [22] and G9P [23] at the second, G3P [7] at the third, and G26P [7] , G9P [23] , and G5P [13] / [22] at the fourth ( Table 2) . Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-tofinish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26 doi = 10.1186/1297-9716-42-112 id = cord-350626-ov9fy10b author = Nazki, Salik title = Evaluation of local and systemic immune responses in pigs experimentally challenged with porcine reproductive and respiratory syndrome virus date = 2020-05-13 keywords = PRRSV; cell; pig summary = doi = 10.1186/s13567-020-00789-7 id = cord-344845-52rehsd5 author = Opriessnig, Tanja title = Evaluation of the efficacy of a commercial inactivated genogroup 2b-based porcine epidemic diarrhea virus (PEDV) vaccine and experimental live genogroup 1b exposure against 2b challenge date = 2017-10-26 keywords = EXP; PEDV; vac summary = title: Evaluation of the efficacy of a commercial inactivated genogroup 2b-based porcine epidemic diarrhea virus (PEDV) vaccine and experimental live genogroup 1b exposure against 2b challenge The aim of this study was to compare the ability of G1b-based live virus exposure against use of a commercial G2b–based inactivated vaccine to protect growing pigs against G2b challenge. Under the study conditions a commercial inactivated G2b-based vaccine protected pigs against G2b challenge, as evidenced by reduction of PEDV RNA in feces for 3–4 logs during peak shedding and a shorter viral shedding duration. The oral, but not the intramuscular, experimental G1b-based live virus exposure induced a high anti-PEDV IgA response prior to challenge, which apparently did not impact PEDV shedding compared to POS-CONTROL pigs. Anti-PEDV IgA antibodies in serum samples were first detected in 8/8 EXP-ORAL-1b pigs at dpv 14 ( Figure 3 ). doi = 10.1186/s13567-017-0472-z id = cord-000172-um0ds7dh author = Paul, Mathilde title = Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model date = 2009-12-16 keywords = H5N1; HPAI; Thailand summary = In this study, we investigated which anthropogenic factors played a role in the risk of HPAI in Thailand using outbreak data from the ''''second wave'''' of the epidemic (3 July 2004 to 5 May 2005 in the country. In this study, we investigated which anthropogenic factors played a role in the risk of HPAI in Thailand using outbreak data from the ''''second wave'''' of the epidemic (3 July 2004 to 5 May 2005 in the country. The risk of HPAI varies spatially according to the anthropogenic characteristics of the different geographical areas of interest, each characterized by a variety of human activities such as poultry farming practices, trade activities and market rules, land use and agro-ecosystems, and veterinary services structure and control. This analysis shows that, when adjusted for the effects of environmental and poultry variables, several anthropogenic factors were significantly associated with an increased risk of HPAI in both chicken and duck populations. doi = 10.1051/vetres/2009076 id = cord-334968-gonx5taq author = Pignatelli, Jaime title = Lineage specific antigenic differences in porcine torovirus hemagglutinin-esterase (PToV-HE) protein date = 2013-12-23 keywords = ELISA; HE52.11; figure; he52.7 summary = In the first case, the two PToV-HE lineages were detected even within the same animal at two sequential sampling time points, indicating that both PToV strains carrying different HE proteins coexisted on the same farm infecting the same piglets, and suggesting that the immune response generated against one PToV strain did not protect the animals against the infection by the other strain. Hence, in order to examine the potential existence of antigenic differences between the two lineages of PToV-HE proteins, piglet serum samples were analyzed with an HI assay to detect the presence of specific antibodies against the receptor binding domain that prevents the RBC hemagglutination. In addition, to study the antibody response against the whole protein by a different approach, soluble c-myc tagged HE52.7 and HE52.11 proteins were generated by rVV methodology to obtain highly purified coating antigens that were used in ELISA to test the same field serum samples. doi = 10.1186/1297-9716-44-126 id = cord-319685-dw0qsl4s author = Porter, Emily title = Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date = 2014-04-25 keywords = FIP; PCR; cat; sample summary = doi = 10.1186/1297-9716-45-49 id = cord-003216-5qioku84 author = Rehman, Zaib Ur. title = Pathobiology of Avian avulavirus 1: special focus on waterfowl date = 2018-09-19 keywords = APMV-1; Newcastle; disease; virus summary = Besides the strong innate immune responses, waterfowl are generally considered long-term carrier of APMV-1 and disease outbreaks have been reported since 1997 [12] [13] [14] , and were confirmed by follow up experimental studies. Host innate immune responses of ducks infected with Newcastle disease viruses of different pathogenicities Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during Histopathological alterations in immune organs of chickens and ducks after experimental infection with virulent 9a5b newcastle disease virus Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses Phylogenetic diversity among low-virulence newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates Genomic characterizations of a Newcastle disease virus isolated from ducks in live bird markets in China doi = 10.1186/s13567-018-0587-x id = cord-295661-v3q1spmm author = Resende, Talita Pilar title = Evaluation of mouse enteroids as a model for Lawsonia intracellularis infection date = 2019-07-19 keywords = Lawsonia; USA; enteroid; intracellularis summary = doi = 10.1186/s13567-019-0672-9 id = cord-326723-jiauk4fq author = Risalde, María A title = Pathogenic mechanisms implicated in the intravascular coagulation in the lungs of BVDV-infected calves challenged with BHV-1 date = 2013-03-18 keywords = BHV-1; BVDV; bovine; figure; group summary = The aim of this study was to clarify the mechanisms responsible for vascular changes occurring in the lungs of calves infected with bovine viral diarrhea virus (BVDV) and challenged later with bovine herpesvirus type 1 (BHV-1), evaluating the role of MΦs in the development of pathological lesions in this organ. Therefore, the aim of this study was to clarify the mechanisms responsible for ultrastructural and histopathological changes occurring in the lungs of calves pre-infected with BVDV and challenged later with BHV-1, as well as to analyze the role of MΦs in the appearance of the lesions. According to this, in the course of certain acute viral infections, platelets may be activated in vivo, leading to their degranulation, Figure 6 Pro-inflammatory cytokines in the lungs of calves with and without pre-existing BVDV challenged with BHV-1.1. doi = 10.1186/1297-9716-44-20 id = cord-324950-ux7shvji author = Saade, Georges title = Coinfections and their molecular consequences in the porcine respiratory tract date = 2020-06-16 keywords = PCV2; PRRSV; cell; infection; porcine; respiratory; virus summary = In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] . doi = 10.1186/s13567-020-00807-8 id = cord-278479-vl296i1b author = Samuel, Arthur S title = Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date = 2011-02-23 keywords = APMV; APMV-1; Newcastle; virus summary = In this study, groups of hamsters were infected with a prototype strain of each APMV serotype by the intranasal route and monitored for virus replication, clinical symptoms, histopathology, and seroconversion. Our results showed that each of the APMV serotypes replicated in hamsters without causing adverse clinical signs of illness, although histopathologic evidence of disease was observed in some cases, and also induced high neutralizing antibody titers. Necropsies were performed immediately postmortem and the following tissue samples were collected for immunohistochemistry (IHC), histopathology, and virus isolation: brain, nasal turbinates, lung, spleen, kidney and small intestine. Deparaffinized sections of the virus-infected and uninfected control tissue (brain, lungs, nasal turbinates, small intestine, kidney, and spleen) were immunostained using polyclonal antisera against the N protein of the homologous APMV serotypes. In animals infected with any of the other APMV serotypes, virus-specific antigens were detected on 3 dpi in the lungs and nasal turbinates (Figure 3 ). doi = 10.1186/1297-9716-42-38 id = cord-312695-1uw8xcxw author = Sugiarto, Sarah title = Passive immunization does not provide protection against experimental infection with Mycoplasma haemofelis date = 2016-08-05 keywords = Mhf; cat; figure; group summary = In the present study we investigated whether the passive transfer of antibodies from Mhf-recovered cats to naïve recipient cats provided protection against bacteremia and clinical disease following homologous challenge with Mhf; moreover, we characterized the immune response in the recipient cats. The present study aimed to investigate whether the passive transfer of antibodies from Mhf-recovered to naïve recipient cats induced partial or complete protection against bacteremia and clinical disease following homologous challenge with Mhf. Different parameters addressing the humoral and cellular immune response were monitored in passively immunized and control cats. Our study demonstrated that the passive transfer of antibodies from Mhf-recovered to naïve SPF cats does not prevent infection, high bacterial loads and the development of clinical signs following homologous challenge with Mhf. The passively immunized and control cats showed no differences in the onset and extent of bacteremia and anemia during the course of Mhf infection. doi = 10.1186/s13567-016-0361-x id = cord-330554-xg49foch author = Tanaka, Yoshikazu title = Suppression of feline coronavirus replication in vitro by cyclosporin A date = 2012-04-30 keywords = FIPV; Japan summary = Cyclosporin A (CsA), an immunosuppressive agent that targets the nuclear factor pathway of activated T-cells (NF-AT) to bind cellular cyclophilins (CyP), dose-dependently inhibited FIPV replication in vitro. Cyclophilin B (CyPB) is another target of CsA that promotes hepatitis C virus (HCV) replication by regulating the RNA-binding ability of the HCV NS5B protein. Here, we show that CsA inhibits intracellular replication of the FIPV genome and viral protein expression in vitro independently of the NF-AT pathway. After adsorption for 1 h at 37°C, the medium containing the virus was removed, and the cells were rinsed three times with phosphate-buffered saline [PBS (−)] and incubated with or without various concentrations of CsA (Sigma-Aldrich), cyclosporin H (CsH; Cosmobio, Tokyo, Japan) and FK506 (Sigma-Aldrich) for 20 h. Quantitative RT-PCR showed that 0.63 -10 μM CsA dose-dependently suppressed FIPV RNA replication, whereas FK506 did not exert significant inhibitory effects, except at 10 μM FK506 (approximately 30 % reduction compared to 0 μM FK506, P < 0.05; Figure 3A ). doi = 10.1186/1297-9716-43-41 id = cord-354114-frdsct44 author = Vogel, Liesbeth title = Pathogenic characteristics of persistent feline enteric coronavirus infection in cats date = 2010-07-23 keywords = FECV; RNA; UCD summary = FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The cats were monitored for clinical signs, body weight, faecal virus shedding and serum antibody titres for 70 days post inoculation. In all animals, the amount of virus in the faeces subsequently increased within two days to peak levels of 10 6 -10 8 genomes/lL faeces, after which shedding remained high for an extended period until day 16 and day 23 post inoculation in FECV UCD and FECV RM infected cats, respectively. In order to determine in which part(s) of the gut virus was present during viral persistence, we screened the contents of the entire intestines of two FECV UCD infected cats. doi = 10.1051/vetres/2010043 id = cord-259296-qsaewje2 author = Wang, Pengcheng title = Tomatidine inhibits porcine epidemic diarrhea virus replication by targeting 3CL protease date = 2020-11-11 keywords = DMSO; PEDV; PRRSV; figure; tomatidine summary = We screened an FDA-approved library of 911 natural products and found that tomatidine, a steroidal alkaloid extracted from the skin and leaves of tomatoes, demonstrates significant inhibition of PEDV replication in Vero and IPEC-J2 cells in vitro. After transfer, the membrane was incubated in blocking buffer (5% non-fat milk in PBST w/v) for 2 h at room temperature, washed three times with PBST, then probed with the following antibodies: anti-PEDV N-protein ( The detection of mRNA levels of TGEV, PRRSV, and SVA was performed as described previously [13, 19, 20] . When Vero cells were treated with increasing concentrations of tomatidine, the cleaved fragments clearly decreased in a dose-dependent manner ( Figure 6B ), indicating that tomatidine inhibited the activity of PEDV 3CL protease. doi = 10.1186/s13567-020-00865-y id = cord-316908-8ti75mru author = Wei, Xiaona title = PEDV enters cells through clathrin-, caveolae-, and lipid raft-mediated endocytosis and traffics via the endo-/lysosome pathway date = 2020-02-10 keywords = IPEC; PEDV; Vero summary = doi = 10.1186/s13567-020-0739-7 id = cord-275443-9ib77yws author = Xie, Xing title = Monoclonal antibody specific to HA2 glycopeptide protects mice from H3N2 influenza virus infection date = 2015-03-19 keywords = H3N2; JS/10; figure summary = Considering that mAb D7 resulted in a significant reduction in viral titers in the lungs of mice infected with three different virus strains at 6 dpi, we chose that time point to determine the viral RNA loads in different tissues and fecal samples. To compare the above results with pathological findings in mice infected with three different virus strains, and treated with mAb D7 and irrelevant mAb IgG, we chose the heart, brain and lung from different treatment groups at 6 dpi to perform histopathological and immunohistochemical analysis. To gain a better understanding of the effect of CIV on the innate immune response and to ascertain whether passive immunization with monoclonal antibody affected the levels of cytokines, we examined the levels of IFN-γ and TNF-α in the lungs of mice in the virus-infected and mAb D7 groups. doi = 10.1186/s13567-015-0146-7 id = cord-263785-0iift8zy author = Zhang, Xiaorong title = Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date = 2020-07-31 keywords = IBV; virus summary = title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. doi = 10.1186/s13567-020-00819-4 id = cord-278635-vwdxr1bl author = Świętoń, Edyta title = Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date = 2020-08-28 keywords = PCR; RNA; defective; virus summary = In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). doi = 10.1186/s13567-020-00833-6