# bib

id: cord-004751-4vl0cvyq
author: Mostow, S. R.
title: The behaviour in vitro of attenuated recombinant influenza viruses
date: 1973
extension: .txt
mime: text/plain
words: 2250
sentence: 95
flesch: 54
cache: cache/cord-004751-4vl0cvyq.txt
txt: txt/cord-004751-4vl0cvyq.txt
summary:
  Attenuated influenza viruses have been produced recently by genetic recombination of avirulent laboratory-adapted strains and virulent parents (BEARE and HALL, 1971; McCAHo~ and SCHILD, 1972) . It has been shown that influenza viruses which have squired ts markers as a result of recombination with mutagen-treated strains are attenuated for man (C~ANOCK, personal communication) .


id: cord-355492-0zvqvumc
author: Hamm, Ronda L
date: 2006-06-12
extension: .txt
mime: text/plain
words: 2423
sentence: 97
flesch: 48
cache: cache/cord-355492-0zvqvumc.txt
txt: txt/cord-355492-0zvqvumc.txt
title:
  Resistance to cyfluthrin and tetrachlorvinphos in the lesser mealworm, Alphitobius diaperinus, collected from the eastern United States

summary:
  10, 11 The 1996 cost of lesser mealworm control in Georgia alone was over $1 000 000, with estimated damage costs of $8 476 000. Alphitobius diaperinus is likely affected by insecticides used for housefly (and possibly ectoparasite) control in poultry facilities, as well as insecticides used specifically for lesser mealworm control.


id: cord-259959-qzd3hf8y
author: Alhatami, Abdullah O.
date: 2020-07-16
extension: .txt
mime: text/plain
words: 2365
sentence: 99
flesch: 42
cache: cache/cord-259959-qzd3hf8y.txt
txt: txt/cord-259959-qzd3hf8y.txt
title:
  Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq

summary:
  IBV vaccine strains can perform recombination with field strains, reversing virulence [16] . Therefore, sequencing the S1 gene of IBV strains detected in the field is critical for control programs and epidemiological purposes.


id: cord-355119-sdg9zdc1
author: Lin, Huixing
date: 2016-04-22
extension: .txt
mime: text/plain
words: 3062
sentence: 120
flesch: 50
cache: cache/cord-355119-sdg9zdc1.txt
txt: txt/cord-355119-sdg9zdc1.txt
title:
  Epidemic strain YC2014 of porcine epidemic diarrhea virus could provide piglets against homologous challenge

summary:
  Submit your next manuscript to BioMed Central and we will help you at every step: Pathogenesis of porcine epidemic diarrhea virus isolate (US/Iowa/18984/2013) in 3-week-old weaned pigs Epidemic of diarrhoea caused by porcine epidemic diarrhoea virus in Italy New variants of porcine epidemic diarrhea virus, China Molecular characterization and phylogenetic analysis of new variants of the porcine epidemic diarrhea virus in Gansu Complete genome sequence of a Chinese virulent porcine epidemic diarrhea virus strain Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States Complete Genome Sequence of Porcine Epidemic Diarrhea Virus Strain USA/Colorado/2013 from the United States Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus The GPRLQPY motif located at the carboxyterminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus Identification of two novel B cell epitopes on porcine epidemic diarrhea virus spike protein Oral efficacy of Vero cell attenuated porcine epidemic diarrhea virus DR13 strain Propagation of the virus of porcine epidemic diarrhea in cell culture Detection and genetic diversity of porcine group A rotaviruses in historic (2004) and recent (2011 and 2012) Approximately 80 to 100% of PEDV-infected piglets die within 24 h of being infected with virulent PEDV strains, resulting in tremendous economic losses to the swine industry


id: cord-267189-xq70rn1j
author: Wang, Xinyu
date: 2016-01-15
extension: .txt
mime: text/plain
words: 3049
sentence: 112
flesch: 48
cache: cache/cord-267189-xq70rn1j.txt
txt: txt/cord-267189-xq70rn1j.txt
title:
  Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China

summary:
  For the phylogenetic analysis, partial sequences of the M and S genes of CCoV strains, including CCoV-I, CCoV-IIa, and CCoV-IIb strains, were retrieved from GenBank. Nucleotide sequences of the partial S gene of CCoV strains identified in our study were shown in Supporting Information (S2 Fig).


id: cord-005057-deq5tv1d
author: Bergström, T.
date: 1990
extension: .txt
mime: text/plain
words: 3492
sentence: 117
flesch: 40
cache: cache/cord-005057-deq5tv1d.txt
txt: txt/cord-005057-deq5tv1d.txt
title:
  Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system

summary:
  HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only. HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only.


id: cord-291930-n7wq09rq
author: Arden, K.E.
date: 2010-01-27
extension: .txt
mime: text/plain
words: 3297
sentence: 108
flesch: 38
cache: cache/cord-291930-n7wq09rq.txt
txt: txt/cord-291930-n7wq09rq.txt
title:
  Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003

summary:
  Disappointingly, the possibility that discrete HRV strains exist as distinct viral entities is not accounted for in asymptomatic control populations because strain identification is not routinely conducted. Many HRV strains have distinct genetic, antigenic, immunogenic and epidemiologic profiles which are similar in nature to those of other respiratory virus species including human respiratory syncytial virus (HRSV).


id: cord-294509-txk1qic1
author: Li, Zi
date: 2016-09-15
extension: .txt
mime: text/plain
words: 4052
sentence: 154
flesch: 48
cache: cache/cord-294509-txk1qic1.txt
txt: txt/cord-294509-txk1qic1.txt
title:
  The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets

summary:
  Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development. In China, PHEV infection first occurred in Beijing in 1985, and the outbreaks caused enormous economic losses for the pig industry (Chen et al., 2012; Dong et al., 2014; Gao et al., 2011) .


id: cord-014461-2ubh9u8r
author: Nelson, Oranmiyan W.
title: Genome sequences published outside of Standards in Genomic Sciences, July - October 2012
date: 2012-10-10
extension: .txt
mime: text/plain
words: 4132
sentence: 196
flesch: 32
cache: cache/cord-014461-2ubh9u8r.txt
txt: txt/cord-014461-2ubh9u8r.txt
summary:
  carotovorum Bacteriophage PP1 Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L Genome sequence of the phage clP1, which infects the beer spoilage bacterium Pediococcus damnosus Complete Genome Sequence of Pseudomonas aeruginosa Siphophage MP1412 Complete Genome Sequences of Two Pseudomonas aeruginosa Temperate Phages, MP29 and MP42, Which Lack the Phage-Host CRISPR Interaction Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1 Complete Genome Sequence of Pseudomonas aeruginosa Siphophage MP1412 Complete Genome Sequence of Staphylococcus aureus Bacteriophage GH15 Complete Genome Sequence of Vibrio vulnificus Bacteriophage SSP002 Whole genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species Complete Genome Sequence of an Avian Leukosis Virus Isolate Associated with Hemangioma and Myeloid Leukosis in Egg-Type and Meat-Type Chickens Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus in Southern China Complete Genome Sequence of an H5N2 Avian Influenza Virus Isolated from a Parrot in Southern China Complete Genome Sequence of an Avian-Like H4N8 Swine Influenza Virus Discovered in Southern China Complete Genome Sequence of a Novel Avian Paramyxovirus Complete Genome Sequence of Avian Tembusu-Related Virus Strain WR Isolated from White Kaiya Ducks in Fujian Complete Genome Sequence of Bluetongue Virus Serotype 9: Implications for Serotyping Complete Genome Sequence of Bluetongue Virus Serotype 16 of Goat Origin from India Genome Sequence of a Bombyx mori Nucleopolyhedrovirus Strain with Cubic Occlusion Bodies Complete Genome Sequence of a Bovine Viral Diarrhea Virus 2 from Commercial Fetal Bovine Serum Complete Genome Sequences of Two Novel European Clade Bovine Foamy Viruses from Germany and Poland Complete Genome Sequences of Novel Canine Noroviruses in Hong Kong Complete Genome Sequence Analysis of a Recent Chicken Anemia Virus Isolate and Comparison with a Chicken Anemia Virus Isolate from Human Fecal Samples in China Complete Genome Sequence of a Chikungunya Virus Isolated in Guangdong Complete Genome Sequences of Two Chinese Virulent Avian Coronavirus Infectious Bronchitis Virus Variants Complete Genome Sequence of a Recombinant Coxsackievirus B4 from a Patient with a Fatal Case of Hand, Foot, and Mouth Disease in Guangxi Complete Genome Sequence of a Novel Human Enterovirus C (HEV-C117) Identified in a Child with Community-Acquired Pneumonia Complete Genome Sequence of the Genotype 4 Hepatitis E Virus Strain Prevalent in Swine in Jiangsu Province, China, Reveals a Close Relationship with That from the Human Population in This Area Complete Genome Sequence of an H10N8 Avian Influenza Virus Isolated from a Live Bird Market in Southern China Complete Genome Sequence of a Novel H9N2 Subtype Influenza Virus FJG9 Strain in China Reveals a Natural Reassortant Event Characterization and Complete Genome Sequence of Human Coronavirus NL63 Isolated in China Whole genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species Complete Genome Sequence of Ikoma Lyssavirus Analysis of the complete genome sequence of two Korean sacbrood viruses in the Honey bee, Apis mellifera The complete mitochondrial genome sequence of the western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) contains triplicate putative control regions Genome Sequence of Methylobacterium sp. Complete Genome Sequence of a Street Rabies Virus from Mexico Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4 Jenny)


id: cord-255857-y9wjp0aj
author: Yuan, Shishan
date: 2001-11-05
extension: .txt
mime: text/plain
words: 4291
sentence: 151
flesch: 45
cache: cache/cord-255857-y9wjp0aj.txt
txt: txt/cord-255857-y9wjp0aj.txt
title:
  Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains”

summary:
  key: cord-255857-y9wjp0aj authors: Yuan, Shishan; Mickelson, Daniel; Murtaugh, Michael P.; Faaberg, Kay S. title: Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date: 2001-11-05 journal: Virus Res DOI: 10.1016/s0168-1702(01)00295-7 sha: doc_id: 255857 cord_uid: y9wjp0aj Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. Initially, several standard 5%-RACE was performed on passage 2 from the original VR-2332 field isolate brain homogenate, passage 31 of strain VR-2332 and passage 4 of RespPRRS vaccine strain (Frohman, 1994) .


id: cord-000820-5b29wtim
author: Borriello, Giorgia
date: 2012-10-25
extension: .txt
mime: text/plain
words: 4322
sentence: 181
flesch: 41
cache: cache/cord-000820-5b29wtim.txt
txt: txt/cord-000820-5b29wtim.txt
title:
  Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis

summary:
  FAO Regional Office for Europe Inter-Regional Cooperative Research Network on Buffalo Veterinary microbiology and Microbial disease Infectious diseases Pathophysiology of diarrhea in calves Pathogenesis of bacterial infections in animals Studies on enteritis in buffalo calves Scientific Opinion on monitoring and assessment of the public health risk of Salmonella Typhimurium-like strains Virulotyping and antimicrobial resistance typing of Salmonella enterica serovars relevant to human health in Europe Characterization of Salmonella enterica serovar Typhimurium strains of veterinary origin by molecular typing methods Variability in occurrence of multiple prophage genes in Salmonella Typhimurium strains isolated in Slovack Republic Transposition of the heat-stable toxin astA gene into a Gifsy-2-related prophage of Salmonella enterica serovar abortusovis Rapid identification of Salmonella serovars in feces by specific detection of virulence genes, invA and spvC, by an enrichment broth culture-multiplex PCR combination assay Human Salmonella clinical isolates distinct from those of animal origin Salmonella Muenster infection in a dairy herd Outbreak of Salmonella Give in the province of Quebec Frequency and polymorphism of sopE in isolates of Salmonella enterica belonging to the ten most prevalent serotypes in England and Wales Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain Elucidation of antimicrobial susceptibility profiles and genotyping of Salmonella enterica isolates from clinical cases of salmonellosis in New Mexico in DNA-based diagnostic tests for Salmonella species targeting agfA, the structural gene for thin, aggregative fimbriae Characterization of Salmonella isolates from captive lizards Annex D Detection of Salmonella spp. S. Typhimurium and monophasic S. Typhimurium strains were further characterized by the molecular detection of 24 genes coding for virulence factors.


id: cord-288451-npefpo3t
author: Yinda, Claude Kwe
title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis
date: 2016-09-26
extension: .txt
mime: text/plain
words: 4459
sentence: 164
flesch: 47
cache: cache/cord-288451-npefpo3t.txt
txt: txt/cord-288451-npefpo3t.txt
summary:
  Therefore, zoonotic events of bat RVA strains could easily be missed with the current screening primers depending on the primer combinations, PCR conditions and/or circulating zoonotic strains. Even though there exists a considerable genetic divergence between bat RVA and human RVA, suggestions have been made about potential interspecies transmission of Chinese and Kenyan bat RVA strains.


id: cord-306976-p2521bl4
author: Gao, Mengying
date: 2016-08-15
extension: .txt
mime: text/plain
words: 5125
sentence: 165
flesch: 48
cache: cache/cord-306976-p2521bl4.txt
txt: txt/cord-306976-p2521bl4.txt
title:
  Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China

summary:
  Experimental infection of IS/885/00-like infectious bronchitis virus in specific pathogen free and commercial broiler chicks Comparison of the pathogenicity of QX-like, M41 and 793/B infectious bronchitis strains from different pathological conditions Effects of infectious bronchitis on egg production Effects of infectious bronchitis in baby chicks Infectious bronchitis Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China Pathogenicity of four serotypes of avian infectious bronchitis virus for the oviduct of young chickens of varying ages Egg quality and production following infectious bronchitis virus exposure at one day old Induction of cystic oviducts and protection against early challenge with infectious bronchitis virus serotype D388 (genotype QX) by maternally derived antibodies and by early vaccination Infection of day old chicks with infectious bronchitis (IB) virus and subsequent anatomical abnormalities A comparative study of pigeons and chickens experimentally infected with PPMV-1 to determine antigenic relationships between PPMV-1 and NDV strains A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China Fine level epitope mapping and conservation analysis of two novel linear B-cell epitopes of the avian infectious bronchitis coronavirus nucleocapsid protein Identification of previously unknown antigenic epitopes on the S and N proteins of avian infectious bronchitis virus Persistence of virus in the tissues and development of the oviduct in the fowl following infection at day old with infectious bronchitis virus Altered pathogenicity, immunogenicity, tissue tropism and 3 0 -7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos Evaluation of the protection conferred by commercial vaccines and attenuated heterologous isolates in China against the ck/CH/LDL/97I strain of infectious bronchitis coronavirus Characterization of a recombinant coronavirus infectious bronchitis virus with distinct S1 subunits of spike and nucleocapsid genes and a 3 0 untranslated region Identification of a novel nephropathogenic infectious bronchitis virus in Israel A simple method of estimating fifty percent endpoints MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan Emergence of novel nephropathogenic infectious bronchitis viruses currently circulating in Chinese chicken flocks Serotype shift of a 793/B genotype infectious bronchitis coronavirus by natural recombination key: cord-306976-p2521bl4 authors: Gao, Mengying; Wang, Qiuling; Zhao, Wenjun; Chen, Yuqiu; Zhang, Tingting; Han, Zongxi; Xu, Qianqian; Kong, Xiangang; Liu, Shengwang title: Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date: 2016-08-15 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2016.05.018 sha: doc_id: 306976 cord_uid: p2521bl4 Since 2009, strains of the naturally recombinant TW I genotype of infectious bronchitis virus (IBV) have caused considerable damage to the Chinese poultry industry.


id: cord-010187-ymhcfyxx
author: Gromeier, Matthias
date: 2005-03-25
extension: .txt
mime: text/plain
words: 5150
sentence: 221
flesch: 37
cache: cache/cord-010187-ymhcfyxx.txt
txt: txt/cord-010187-ymhcfyxx.txt
title:
  Mouse neuropathogenic poliovirus strains cause damage in the central nervous system distinct from poliomyelitis

summary:
  Mouse neurovirulent strains of poliovirus type 2 differed from mouse neurovirulent poliovirus type 1 derivatives in their ability to induce CNS lesions. The outcome of infection of mice with mouse-adapted poliovirus strains has been described previously mainly in terms of paralysis and death, and it was generally assumed that these strains produce the same disease syndromes in normal mice and in mice transgenic for the human poliovirus receptor (hPVR-tg mice).


id: cord-012054-bpgb7tgo
author: Ferreira, Maria Isabel M.
title: Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1
date: 2008-03-01
extension: .txt
mime: text/plain
words: 5273
sentence: 204
flesch: 45
cache: cache/cord-012054-bpgb7tgo.txt
txt: txt/cord-012054-bpgb7tgo.txt
summary:
  Enzyme activitiesTo test inducibility of enzymes involved in 4-FP degradation, cells of Arthrobacter sp. strain IF1 were grown on glucose or 4-FP, washed, and tested for oxygen consumption in the presence of different substrates. When the supernatant of IF1 cells growing on 4 mM 4-FP were subjected to HPLC analysis, four peaks were detected (Table 1) .


id: cord-279495-zxerb7de
author: Liu, Xiaoli
date: 2012-11-21
extension: .txt
mime: text/plain
words: 5252
sentence: 152
flesch: 42
cache: cache/cord-279495-zxerb7de.txt
txt: txt/cord-279495-zxerb7de.txt
title:
  Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome

summary:
  A filterable virus, distinct from that of laryngotracheitis, the cause of a respiratory disease of chicks Development and use of the H strain of avian infectious bronchitis virus from the Netherlands as a vaccine: a review An efficient ribosomal frame-shifting signal in the polymeraseencoding region of the coronavirus IBV Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism Commentary: a nomenclature for avian coronavirus isolates and the question of species status Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Coronaviruses in poultry and other birds Coronavirus avian infectious bronchitis virus Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes Infectious bronchitis Variations in the spike protein of the 793/B type of infectious bronchitis virus in the field and during alternate passage in chickens and embryonated eggs A cis-acting function for the coronavirus leader in defective interfering RNA replication Virus Taxonomy, Classification and Nomenclature of Viruses, Ninth Report of the International Committee on Taxonomy of Viruses, International Union of Microbiological Societies, Virology Division Molecular epidemiology and evolution of avian infectious bronchitis virus in Spain over a fourteen-year period The early history of infectious bronchitis Evidence for variable rates of recombination in the MHV genome Map locations of mouse hepatitis virus temperature sensitive mutants: confirmation of variable rates of recombination A hypervariable region within the 3 0 cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus The present of viral subpopulations in an infectious bronchitis virus vaccine with differing pathogenicity -a preliminary study Recombinational histories of avian infectious bronchitis virus and turkey coronavirus Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase A novel variant of infectious bronchitis virus resulting from recombination among three different strains The neutralizing characteristics of strains of infectious bronchitis virus as measured by the constant virus variable serum methods in chicken tracheal cultures Experimental evidence of recombination in coronavirus infectious bronchitis virus Molecular analysis of infectious bronchitis viruses isolated in Slovenia between 1990 and 2005: a retrospective study Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Origin and evolution of Georgia 98 (GA98), a new serotype of avian infectious bronchitis virus The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments Molecular characterization and pathogenicity of infectious bronchitis coronaviruses: complicated evolution and epidemiology in China caused by cocirculation of multiple types of infectious bronchitis coronaviruses Genetic diversity of avian infectious bronchitis coronavirus in recent years in China High-frequency RNA recombination of murine coronaviruses The molecular biology of coronaviruses Isolation and characterization of a novel antigenic subtype of infectious bronchitis virus serotype DE072 Stem-loop III in the 5 0 untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Stem-loop IV in the 5 0 untranslated region is a cisacting element in bovine coronavirus defective interfering RNA replication Molecular characterization of avian infectious bronchitis virus strains from outbreaks in Argentina Infectious bronchitis virus in Jordanian chickens: seroprevalence and detection An apparently new respiratory disease of chicks Evolutionary implications of avian infectious bronchitis virus (AIBV) analysis Unique and conserved features of genome and proteonome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and pathogenicity and evaluation of protection induced by Mass serotype H120 vaccine against strains of the LX4-type (QX) Differential stepwise evolution of SARS coronavirus functional proteins in different host species Evidence of natural recombination within the S1 gene of infectious bronchitis virus Evolutionary aspects of recombination in RNA viruses Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups Virus-encoded proteinases and proteolytic processing in the Nidovirales The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond Genetic interactions between an essential 3 0 cis-acting RNA pseudoknot, replicase gene products, and the extreme 3 0 end of the mouse coronavirus genome Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.meegid.2012. The etiology of IB, which was first demonstrated by Beach and Schalm (1936) , is infectious bronchitis virus (IBV).


id: cord-010641-hk90qx1k
author: Rodrigues, Juliana Falcão
date: 2020-02-03
extension: .txt
mime: text/plain
words: 5524
sentence: 213
flesch: 43
cache: cache/cord-010641-hk90qx1k.txt
txt: txt/cord-010641-hk90qx1k.txt
title:
  Strain-specific transcriptional and posttranscriptional regulation of heat-labile toxin expression by enterotoxigenic Escherichia coli

summary:
  Considering that the level of LT production and secretion may contribute to the severity of diarrhea, further studies focused on the diversity of LT expression, and the virulence of the strain shall contribute to the design of more rational preventive and therapeutic approaches to control diarrhea associated with ETEC infection. For RNA isolation, ETEC strains were grown in CA-YE medium to an OD 600 nm of 5.0.


id: cord-281172-7di6eub3
author: Biswas, Kaushiki
date: 2016-07-06
extension: .txt
mime: text/plain
words: 6088
sentence: 230
flesch: 39
cache: cache/cord-281172-7di6eub3.txt
txt: txt/cord-281172-7di6eub3.txt
title:
  Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination

summary:
  cDNA was synthesized using the Ovation Pico WTA system V2 (Nugen Technologies), fragmented, and labeled with biotin followed by hybridization with Affymetrix gene chip mouse gene 1.0 ST array that contains 750,000 unique 25mer oligonucleotide features for 28,000 gene level probe sets. A. Venn diagram depicts number of genes whose expression changed by at least 1.5 fold during DM strain infection (left circle) compared to mock infected controls, during NDM infection (right circle) compared to mock infected controls, and during DM strain infection compared to NDM infection (bottom circle).


id: cord-296611-ma32oz4o
author: Ma, Tianxin
title: Novel genotype of infectious bronchitis virus isolated in China
date: 2019-01-29
extension: .txt
mime: text/plain
words: 5923
sentence: 194
flesch: 42
cache: cache/cord-296611-ma32oz4o.txt
txt: txt/cord-296611-ma32oz4o.txt
summary:
  Phylogenetic and evolutionary relationships among torovirus field variants: evidence for multiple intertypic recombination events S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification Relationship between serotypes and genotypes based on the hypervariable region of the S1 gene of infectious bronchitis virus Emergence of novel nephropathogenic infectious bronchitis viruses currently circulating in Chinese chicken flocks Genetic diversity of avian infectious bronchitis virus in China in recent years Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens Sequencing and serologic identification of S1 genes of infectious bronchitis viruses isolated during 2012-2013 in Guangxi Province, China The authors declare that they have no competing interests. Infection with strain LGX/111119 resulted in significantly higher production of infectious viruses in trachea, lung, kidney, proventriculus, and cecal tonsil tissues than those of corresponding tissues of chickens infected with strain I0636/16 (Fig. 4B) .


id: cord-269892-bmdpbkni
author: Tabares, Paula
title: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges
date: 2011-01-11
extension: .txt
mime: text/plain
words: 5415
sentence: 198
flesch: 38
cache: cache/cord-269892-bmdpbkni.txt
txt: txt/cord-269892-bmdpbkni.txt
summary:
  The genus-level affiliation of the isolates was validated using the Ribosomal Database Project Classifier (Wang et al. 2007 ). Several recent publications have shown that Streptomyces, Micromonospora, and Rhodococcus are among the dominant genera commonly isolated from marine sponges (Abdelmohsen et al. 2010; Schneemann et al. 2010; Sun et al. 2010; ).


id: cord-003908-wbawzbhz
author: Matsushima, Yuki
date: 2019-09-27
extension: .txt
mime: text/plain
words: 6029
sentence: 208
flesch: 46
cache: cache/cord-003908-wbawzbhz.txt
txt: txt/cord-003908-wbawzbhz.txt
title:
  Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017

summary:
  Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. Phylogenetic distances between GII.17 strains were calculated by Patristic software (Fourment and Gibbs, 2006) .


id: cord-271897-9oqzsd70
author: Domanska-Blicharz, Katarzyna
title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017
date: 2020-01-07
extension: .txt
mime: text/plain
words: 6560
sentence: 215
flesch: 46
cache: cache/cord-271897-9oqzsd70.txt
txt: txt/cord-271897-9oqzsd70.txt
summary:
  The recombination analysis showed that Polish strains are a mosaic of different parental viruses most likely resulting from recombination events involving different IBV lineages, most frequently GI-13 and GI-19. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths.


id: cord-002561-7j43yic1
author: Donato, Celeste
title: The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses
date: 2017-05-10
extension: .txt
mime: text/plain
words: 7438
sentence: 287
flesch: 32
cache: cache/cord-002561-7j43yic1.txt
txt: txt/cord-002561-7j43yic1.txt
summary:
  Astrovirus strains identified from fecal samples of multiple non-human primate species from wild, captive, and peri-urban environments in Bangladesh and Cambodia reveal multiple interspecies transmission events, with viruses closely related to the VA/HMO lineage of human viruses, and non-human mammalian and avian astroviruses (Figure 1a,b) In addition to interspecies transmission which generates significant diversity in astrovirus species, both intra-species and inter-species recombination can rapidly generate novel, divergent viruses.


id: cord-291510-jh2fdks4
author: Jiang, Yi
date: 2020-02-11
extension: .txt
mime: text/plain
words: 8033
sentence: 304
flesch: 46
cache: cache/cord-291510-jh2fdks4.txt
txt: txt/cord-291510-jh2fdks4.txt
title:
  Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity

summary:
  Sheng Zhou: Conceptualization, Validation, Resources, Writing -original draft The long view: 40 years of infectious bronchitis research Coronaviruses in poultry and other birds Review of infectious bronchitis virus around the world Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism Coronavirus avian infectious bronchitis virus Infectious bronchitis virus variants: molecular analysis and pathogenicity investigation Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Progress and challenges toward the development of vaccines against avian infectious bronchitis A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China Genetic diversity of avian infectious bronchitis coronavirus in recent years in China Analysis of S1 gene of avian infectious bronchitis virus isolated in southern China during Genetic analysis revealed LX4 genotype strains of avian infectious bronchitis virus became predominant in recent years in Sichuan area Current status of veterinary vaccines Protection of laying hens against infectious bronchitis with inactivated emulsion vaccines Avian infectious bronchitis: the protection afforded by an inactivated virus vaccine IgM responses in chicken serum to live and inactivated infectious bronchitis virus vaccines Molecular characterization and pathogenicity of infectious bronchitis coronaviruses: complicated evolution and epidemiology in china caused by cocirculation of multiple types of infectious bronchitis coronaviruses Molecular characterization of an infectious bronchitis virus strain isolated from northern China in 2012 Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine Attenuation, safety, and efficacy of a QX-like infectious bronchitis virus serotype vaccine Preparation and protective efficacy of a chicken embryo kidney cell-attenuation GI-19/QX-like avian infectious bronchitis virus vaccine Rapid development and evaluation of a live-attenuated QX-like infectious bronchitis virus vaccine Efficacy and safety of an attenuated live QX-like infectious bronchitis virus strain as a vaccine for chickens Safety and efficacy of an infectious bronchitis virus used for chicken embryo vaccination Embryo vaccination of chickens with infectious bronchitis virus: histologic and ultrastructural lesion response and immunologic response to vaccination Attenuated vaccines can recombine to form virulent field viruses Recombinant infectious bronchitis viruses expressing chimeric spike glycoproteins induce partial protective immunity against homologous challenge despite limited replication in vivo Recombinant live attenuated avian coronavirus vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious bronchitis in chickens Recombinant infectious bronchitis viruses expressing heterologous S1 subunits: potential for a new generation of vaccines that replicate in Vero cells Reverse genetics system for the avian coronavirus infectious bronchitis virus Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120 Infectious bronchitis virus as a vector for the expression of heterologous genes The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Construction of an infectious fulllength cDNA clone of infectious bronchitis virus H120 vaccine strain Expression of green fluorescent protein using an infectious cDNA clone of infectious bronchitis virus The causative agent of IB is infectious bronchitis virus (IBV), a non-segmented, positive-sense, single-stranded RNA virus, which belongs to the genus Gammacoronavirus, family Coronaviridae, in the order Nidovirales


id: cord-299763-ttb7o8lv
author: Choi, Jeong-Won
date: 2016-06-01
extension: .txt
mime: text/plain
words: 2621
sentence: 92
flesch: 41
cache: cache/cord-299763-ttb7o8lv.txt
txt: txt/cord-299763-ttb7o8lv.txt
title:
  Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog

summary:
  Although liver degeneration in canines has also been described at post-mortem examination of a pup infected with MVC [6] , and a novel bocavirus (KC580640) that was highly divergent from known MVC strains has been isolated from canine liver [11] , hepatitis with evidence of intranuclear inclusion bodies that correspond to MVC infection has not yet been reported. ORF1 of the 15D009 strain encodes a 776-aa non-structural (NS) protein, which is 2-60 aa longer than the NS protein of other MVC strains.


id: cord-301347-22lt6h40
author: Jarvis, Matthew C.
date: 2016-01-01
extension: .txt
mime: text/plain
words: 4265
sentence: 149
flesch: 43
cache: cache/cord-301347-22lt6h40.txt
txt: txt/cord-301347-22lt6h40.txt
title:
  Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

summary:
  The major clade of US PEDV strains was supported by high posterior probability (100%) and appears to have diverged further into two highly supported sublineages (99% and 100% posterior probability). The estimated tMRCA of the minor clade of US PEDV strains is July 2009-2011, and the estimated tMRCA of the major clade of US PEDV strains is September 2010-August 2012.


id: cord-000347-gdra8xhj
author: Gibbons, Henry S.
date: 2011-03-25
extension: .txt
mime: text/plain
words: 9621
sentence: 379
flesch: 38
cache: cache/cord-000347-gdra8xhj.txt
txt: txt/cord-000347-gdra8xhj.txt
title:
  Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant

summary:
  Phase-contrast microscopy of BG strains after two days of growth on SBA. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the “military” isolates.


id: cord-289623-7oc1ykds
author: Gendy, Sherif
date: 2020-08-20
extension: .txt
mime: text/plain
words: 9880
sentence: 293
flesch: 27
cache: cache/cord-289623-7oc1ykds.txt
txt: txt/cord-289623-7oc1ykds.txt
title:
  Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018

summary:
  Despite the fact that many of these SRS native soil bacteria are bioremediative being armed with an arsenal of metal resistance genes (MRGs), but they can also pose public health risks by virtue of their acquired antibiotic resistance(s), via the activity of antibiotic resistant genes (ARGs), thus strongly negating their beneficial properties. To validate the phenomic response indicating carriage of broad antibiotic resistance in SRS-8-S-2018, a comprehensive survey of antibiotic resistance genes (ARGs) was performed employing PATRIC, CARD, and RAST pipelines.


id: cord-301301-ilsenpus
author: Mihalov-Kovács, Eszter
date: 2017-03-15
extension: .txt
mime: text/plain
words: 4874
sentence: 187
flesch: 47
cache: cache/cord-301301-ilsenpus.txt
txt: txt/cord-301301-ilsenpus.txt
title:
  Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission

summary:
  Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics Nineteen New Species in the Genus Mamastrovirus in the Astroviridae Family Complete genome sequence of canine astrovirus with molecular and epidemiological characterisation of UK strains Novel astroviruses in insectivorous bats Astrovirus infections in humans and animals-molecular biology, genetic diversity, and interspecies transmissions Viral genome sequencing by random priming methods Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea Human stool contains a previously unrecognized diversity of novel astroviruses Complete sequence of a duck astrovirus associated with fatal hepatitis in ducklings Prevalence and risk factors of astrovirus infection in puppies from French breeding kennels Avian Nephritis Virus (ANV) as a new member of the family Astroviridae and construction of infectious ANV cDNA Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server Viruses and virus-like particles in the faeces of dogs with and without diarrhoea Astroviruses in dogs Detection and characterization of canine astroviruses Enteric disease in dogs naturally infected by a novel canine astrovirus Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system Astroviruses Characterization of human astrovirus cell entry Enteric viral infections of sheltered dogs in Hungary Candidate new rotavirus species in sheltered dogs Molecular characterisation of the 3'-end of the astrovirus genome Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus) Astrovirus Research. Essential Ideas, Everyday Impacts, Future Directions Detection and characterization of avastrovirus associated with diarrhea isolated from minks in China Detection of canine astrovirus in dogs with diarrhea in Japan MEGA6: molecular evolutionary genetics analysis version 6.0 Genetic characterization of a new astrovirus detected in dogs suffering from diarrhoea Electron microscopic demonstration of viruses in feces of dogs with diarrhea Astrovirus infection in children Astrovirus-like, coronavirus-like, and parvovirus-like particles detected in the diarrheal stools of beagle pups Isolation and characterization of canine astrovirus in China


id: cord-255137-utg8k7qs
author: Yinda, Claude Kwe
date: 2019-01-23
extension: .txt
mime: text/plain
words: 9795
sentence: 378
flesch: 40
cache: cache/cord-255137-utg8k7qs.txt
txt: txt/cord-255137-utg8k7qs.txt
title:
  Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses

summary:
  VIRSorter_NODE_210_length_3873_cov_4_79189-cat_1 VIRSorter_NODE_388_length_2881_cov_7_17939-cat_1 VIRSorter_NODE_5_length_42493_cov_21_423-circular-cat_1 VIRSorter_NODE_8_length_45832_cov_51_2672-cat_1 VIRSorter_NODE_4_length_43684_cov_82_015-circular-cat_2 VIRSorter_NODE_15_length_28369_cov_37_8786-cat_2 VIRSorter_NODE_16_length_34096_cov_10_5837-cat_1 VIRSorter_NODE_7_length_23030_cov_44_5743-cat_2 VIRSorter_NODE_4_length_46080_cov_143_372-circular-cat_1 VIRSorter_NODE_154_length_5846_cov_32_8156-cat_2 VIRSorter_NODE_2_length_40986_cov_83_5436-cat_2 VIRSorter_NODE_14_length_28627_cov_424_601-cat_2 VIRSorter_NODE_130_length_7398_cov_6_88034-cat_2 VIRSorter_NODE_911_length_1516_cov_2_82279-cat_2 VIRSorter_NODE_60_length_9439_cov_32_4934-cat_1 VIRSorter_NODE_98_length_5449_cov_11_7885-cat_1 VIRSorter_NODE_193_length_2388_cov_2_87797-cat_2 VIRSorter_NODE_25_length_14198_cov_12_3353-cat_2 VIRSorter_NODE_83_length_6779_cov_23_1462-cat_1 VIRSorter_NODE_37_length_8496_cov_10_6883-cat_1 VIRSorter_NODE_97_length_6417_cov_22_439-cat_2 VIRSorter_NODE_20_length_3093_cov_15_1522-cat_1 VIRSorter_NODE_794_length_2121_cov_3_72505-cat_2 VIRSorter_NODE_510_length_2453_cov_9_21212-cat_2 VIRSorter_NODE_11_length_24212_cov_31_2924-cat_1 VIRSorter_NODE_16_length_17400_cov_20_1101-cat_2 VIRSorter_NODE_1_length_45933_cov_26_6238-cat_1 VIRSorter_NODE_4_length_46625_cov_133_007-circular-cat_1 VIRSorter_NODE_52_length_9386_cov_11_0833-cat_2 VIRSorter_NODE_229_length_1757_cov_2_47857-cat_2 VIRSorter_NODE_11_length_20025_cov_19_5373-cat_1 VIRSorter_NODE_22_length_11775_cov_21_2965-cat_1 VIRSorter_NODE_107_length_7429_cov_59_5487-cat_2 VIRSorter_NODE_5_length_61314_cov_65_5801-cat_2 VIRSorter_NODE_8_length_28098_cov_49_3527-cat_2 VIRSorter_NODE_59_length_6288_cov_49_065-cat_1 VIRSorter_NODE_6_length_39977_cov_34_3534-cat_2 VIRSorter_NODE_145_length_6050_cov_14_9503-cat_2 VIRSorter_NODE_3_length_55511_cov_174_071-cat_2 VIRSorter_NODE_512_length_1992_cov_5_2329-cat_1 VIRSorter_NODE_43_length_9047_cov_24_7407-cat_1 VIRSorter_NODE_7_length_27940_cov_25_4928-cat_2 VIRSorter_NODE_30_length_20704_cov_18_18-cat_2 VIRSorter_NODE_284_length_3092_cov_4_56783-cat_2 VIRSorter_NODE_21_length_10227_cov_70_6216_ID_1234280-cat_1 VIRSorter_NODE_244_length_3185_cov_5_53925-cat_1 VIRSorter_NODE_9_length_14015_cov_52_0782-cat_2 VIRSorter_NODE_483_length_3784_cov_3_74777-cat_2 VIRSorter_NODE_163_length_1997_cov_6_07969-cat_1 VIRSorter_NODE_73_length_9441_cov_6_50694-cat_1 VIRSorter_NODE_391_length_2005_cov_13_5311-cat_2 VIRSorter_NODE_48_length_4545_cov_11_4716-cat_2 VIRSorter_NODE_274_length_2499_cov_6_84104-cat_1 VIRSorter_NODE_5_length_45101_cov_33_3939-cat_2 VIRSorter_NODE_84_length_5772_cov_5_66831-cat_1 VIRSorter_NODE_228_length_3330_cov_15_3372-cat_1 VIRSorter_NODE_38_length_6638_cov_33_8407-cat_2 VIRSorter_NODE_110_length_3327_cov_40_0329_ID_1235347-cat_2 VIRSorter_NODE_292_length_3977_cov_5_20205-cat_2 VIRSorter_NODE_73_length_4137_cov_29_2744-cat_2 VIRSorter_NODE_109_length_3682_cov_5_79945-cat_2 VIRSorter_NODE_2060_length_1098_cov_2_56024-cat_2 VIRSorter_NODE_186_length_5287_cov_24_3374-cat_2 VIRSorter_NODE_128_length_4404_cov_8_8202-cat_2 VIRSorter_NODE_8_length_40727_cov_52_8639-circular-cat_1 VIRSorter_NODE_241_length_2048_cov_3_82192-cat_2 VIRSorter_NODE_566_length_1570_cov_4_87877-cat_1 VIRSorter_NODE_236_length_2071_cov_8_333-cat_2 VIRSorter_NODE_21_length_8643_cov_7_23897-cat_1 Halocynthia~phage~JM-2012 Bacillus~phage~NotTheCreek Bacillus~phage~Belinda Listeria~phage~LP-083-2 VIRSorter_NODE_12_length_23882_cov_20_202-cat_2 Bacillus~phage~W.Ph. Enterococcus~phage~EFLK1 VIRSorter_NODE_421_length_3484_cov_2_88788-cat_2 VIRSorter_NODE_51_length_6073_cov_24_308-cat_2 VIRSorter_NODE_126_length_4338_cov_7_34968-cat_2 VIRSorter_NODE_743_length_2937_cov_5_76678-cat_2 VIRSorter_NODE_572_length_1258_cov_4_2989-cat_2 VIRSorter_NODE_511_length_1714_cov_9_19609-cat_2 VIRSorter_NODE_105_length_2295_cov_5_80162_ID_209_GC022959_GC022959-cat_2 VIRSorter_NODE_351_length_1653_cov_3_89784-cat_2 VIRSorter_NODE_62_length_4317_cov_5_92123_GC022960_GC022960-cat_2 VIRSorter_NODE_70_length_5230_cov_7_68756-cat_1 VIRSorter_NODE_59_length_5445_cov_7_07004-cat_2 VIRSorter_NODE_151_length_2931_cov_21_0263-cat_2 VIRSorter_NODE_87_length_2972_cov_3_15406-cat_2 VIRSorter_NODE_52_length_12117_cov_12_12-cat_2 VIRSorter_NODE_11_length_18974_cov_17_7842-cat_2 VIRSorter_NODE_2774_length_1414_cov_2_55497-cat_2 VIRSorter_NODE_250_length_2007_cov_4_84663-cat_2 VIRSorter_NODE_92_length_4947_cov_8_09199-cat_2 VIRSorter_NODE_1203_length_1540_cov_6_38619-cat_2 VIRSorter_NODE_46_length_7537_cov_11_1706-cat_2 VIRSorter_NODE_2982_length_1113_cov_2_02703-cat_2 VIRSorter_NODE_150_length_2967_cov_3_60415-cat_2 VIRSorter_NODE_856_length_1683_cov_5_93275-cat_2 VIRSorter_NODE_297_length_2600_cov_4_91082-cat_2 VIRSorter_NODE_891_length_1502_cov_2_53754-cat_2 VIRSorter_NODE_234_length_5884_cov_5_88807-cat_2 VIRSorter_NODE_142_length_4144_cov_6_25424-cat_2 VIRSorter_NODE_1046_length_1299_cov_4_62684-cat_2 VIRSorter_NODE_150_length_4016_cov_26_916-cat_1 VIRSorter_NODE_29_length_15514_cov_39_9365-cat_2 VIRSorter_NODE_315_length_2377_cov_6_79043-cat_2 VIRSorter_NODE_53_length_6164_cov_14_1464-cat_2 VIRSorter_NODE_324_length_2523_cov_8_04415-cat_2 VIRSorter_NODE_234_length_3252_cov_10_1729-cat_2 VIRSorter_NODE_14_length_18167_cov_39_9557-cat_2 VIRSorter_NODE_240_length_2054_cov_3_92817-cat_2 VIRSorter_NODE_846_length_2391_cov_4_03933-cat_2 VIRSorter_NODE_476_length_1954_cov_5_94406_GC021836_GC021836-cat_2 VIRSorter_NODE_74_length_3590_cov_49_2966-cat_2 VIRSorter_NODE_568_length_1984_cov_4_76403-cat_2 VIRSorter_NODE_13_length_17922_cov_52_6305-cat_1 VIRSorter_NODE_433_length_2253_cov_3_42233-cat_2 VIRSorter_NODE_335_length_2021_cov_4_10391_GC021842_GC021842-cat_2 VIRSorter_NODE_138_length_3112_cov_4_00791-cat_2 VIRSorter_NODE_1458_length_1041_cov_2_11722_GC021830_GC021830-cat_2 VIRSorter_NODE_42_length_4096_cov_4_64369-cat_1 VIRSorter_NODE_76_length_2941_cov_3_10859_ID_151_GC022959_GC022959-cat_2 VIRSorter_NODE_590_length_1526_cov_7_29262_GC021830_GC021830-cat_2 VIRSorter_NODE_271_length_4659_cov_16_1942-cat_2 VIRSorter_NODE_54_length_4664_cov_9_37127-cat_2 VIRSorter_NODE_407_length_2846_cov_138_023_GC021836_GC021836-cat_1 VIRSorter_NODE_1721_length_1996_cov_5_9359-cat_2 VIRSorter_NODE_428_length_2323_cov_3_73776-cat_2 VIRSorter_NODE_356_length_2384_cov_8_9935-cat_2 VIRSorter_NODE_332_length_2175_cov_10_2507-cat_2 VIRSorter_NODE_1147_length_1321_cov_3_40756-cat_1 VIRSorter_NODE_100_length_4424_cov_7_35335-cat_2 VIRSorter_NODE_1703_length_1463_cov_2_22872-cat_2 VIRSorter_NODE_366_length_3576_cov_8_32009_GC021836_GC021836-cat_2 VIRSorter_NODE_725_length_1855_cov_10_6147-cat_2 VIRSorter_NODE_1238_length_1327_cov_2_0664-cat_2 VIRSorter_NODE_672_length_1295_cov_4_3514-cat_2 VIRSorter_NODE_79_length_6354_cov_62_2409-cat_2 VIRSorter_NODE_78_length_6260_cov_45_9512-cat_2


id: cord-004116-ckms25na
author: Moser, Kara A.
date: 2020-01-08
extension: .txt
mime: text/plain
words: 10816
sentence: 371
flesch: 39
cache: cache/cord-004116-ckms25na.txt
txt: txt/cord-004116-ckms25na.txt
title:
  Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

summary:
  Here, reference assemblies for NF54, 7G8, NF166.C8, and NF135.C10 (hereafter referred to as PfSPZ strains) were generated using approaches to take advantage of the resolution power of long-read sequencing data and the low error rate of short-read sequencing platforms. NF135.C10 had the highest number of unique SNPs genome-wide (SNPs not shared with other PfSPZ strains), with 5% more unique SNPs than NF166.C8 and 33% more than 7G8 (Additional file 2: Figure S6) .


id: cord-280334-7b7rvr25
author: Abrantes, Joana
date: 2020-09-02
extension: .txt
mime: text/plain
words: 4627
sentence: 163
flesch: 42
cache: cache/cord-280334-7b7rvr25.txt
txt: txt/cord-280334-7b7rvr25.txt
title:
  Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2

summary:
  Rabbit haemorrhagic disease virus 2 (GI.2) is replacing endemic strains of RHDV in the Australian landscape within 18 months of its arrival Epidemiology of RHDV2 (Lagovirus europaeus/GI.2) in free-living wild European rabbits in Portugal Full genomic analysis of new variant Rabbit Hemorrhagic Disease Virus revealed multiple recombination events Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains A strain-specific multiplex RT-PCR for Australian rabbit haemorrhagic disease viruses uncovers a new recombinant virus variant in rabbits and hares Recombination in rabbit haemorrhagic disease virus: possible impact on evolution and epidemiology Emergence of pathogenicity in lagoviruses: evolution from pre-existing nonpathogenic strains or through a species jump Bat caliciviruses and human noroviruses are antigenically similar and have overlapping histo-blood group antigen binding profiles First complete genome sequence of a European non-pathogenic rabbit calicivirus (lagovirus GI.3) Detection of positive selection in the major capsid protein VP60 of the rabbit haemorrhagic disease virus (RHDV) RDP4: detection and analysis of recombination patterns in virus genomes Benign rabbit caliciviruses exhibit similar evolutionary dynamics to their virulent relatives Immunogenicity in rabbits of virus-like particles from a contemporary rabbit haemorrhagic disease virus type 2 (GI2/RHDV2/b) isolated in the Netherlands Full genome sequences are key to disclose RHDV2 emergence in the Macaronesian islands Norovirus recombination in ORF1/ORF2 overlap Recombination of Feline calicivirus within an endemically infected cat colony Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles Caliciviruses: Molecular and Cellular Virology Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus Ancient recombination events and the origins of hepatitis E virus RNA recombination in vivo in the absence of viral replication Norovirus recombinants: recurrent in the field, recalcitrant in the lab-a scoping review of recombination and recombinant types of noroviruses Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates The performance of the date-randomization test in phylogenetic analyses of time-structured virus data Rabbit haemorrhagic disease virus 2-like variant in Great Britain Characterization of old RHDV strains by complete genome sequencing identifies a novel genetic group Recombination patterns in aphthoviruses mirror those found in other picornaviruses Recombination in circulating human enterovirus B: independent evolution of structural and non-structural genome regions Pressure for pattern-specific intertypic recombination between sabin polioviruses: evolutionary implications The complete nucleotide sequence of rabbit haemorrhagic disease virus (Czech strain V351): use of the polymerase chain reaction to detect replication in Australian vertebrates and analysis of viral population sequence variation Response of the North Island brown kiwi, Apteryx australis mantelli and the lesser short-tailed bat, Mystacina tuberculata to a measured dose of rabbit haemorrhagic disease virus Antibody response to rabbit viral hemorrhagic disease virus in red foxes (Vulpes vulpes) consuming livers of infected rabbits (Oryctolagus cuniculus) Detection of rabbit haemorrhagic disease virus (RHDV) in nonspecific vertebrate hosts sympatric to the European wild rabbit (Oryctolagus cuniculus) Beneficial coinfection can promote within-host viral diversity. Thus, according to RDP all these sequences (GI.2 strains from the early outbreaks and GI.2 non-recombinant strains) are GI.3/GI.2 recombinants.


id: cord-347644-4qenzjiu
author: Shorter, John R.
date: 2019-03-15
extension: .txt
mime: text/plain
words: 6977
sentence: 222
flesch: 38
cache: cache/cord-347644-4qenzjiu.txt
txt: txt/cord-347644-4qenzjiu.txt
title:
  A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size

summary:
  Litter size is moderately heritable, and maternal effects account for the majority of explained variation To estimate founder strain effects on litter size, we used a Bayesian regression model that decomposes the phenotypic variation in the diallel into genetic and parent-of-origin contributions (Lenarcic et al. 2012 ). Under the general effects, we see significant positive additive effects on average litter size from B6, NOD, and NZO and significant negative additive effects on litter size from CAST, PWK, and WSB strain dosages.


id: cord-018061-jy3km0fr
author: AL KASSAA, Imad
title: Antiviral Probiotics: A New Concept in Medical Sciences
date: 2016-12-02
extension: .txt
mime: text/plain
words: 13244
sentence: 553
flesch: 36
cache: cache/cord-018061-jy3km0fr.txt
txt: txt/cord-018061-jy3km0fr.txt
summary:
  Otherwise, orally administered probiotics can change the composition of the gut microbiota by increasing the number of probiotic cells and decreasing commensal and Gram-negative bacteria . The meaning of direct mechanism is when the EnVs interact directly with probiotic cells and/or their metabolic compounds.


id: cord-009764-m9flptcv
author: Bossé, Ynuk
title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity
date: 2019-01-18
extension: .txt
mime: text/plain
words: 15772
sentence: 743
flesch: 52
cache: cache/cord-009764-m9flptcv.txt
txt: txt/cord-009764-m9flptcv.txt
summary:
  They are also unable to distinguish between radial versus longitudinal airway strain. Since ASM is embedded within the airway wall in an orientation that is nearly orthogonal to the long axis of the airways [97, 98] , an increase in airway caliber necessarily implies that ASM is transiently elongated.


id: cord-323463-osf6t7cw
author: Cercenado, Emilia
title: Update on bacterial pathogens: virulence and resistance
date: 2008-04-30
extension: .txt
mime: text/plain
words: 15034
sentence: 589
flesch: 38
cache: cache/cord-323463-osf6t7cw.txt
txt: txt/cord-323463-osf6t7cw.txt
summary:
  CA-MRSA infections refer to MRSA infections in patients lacking established MRSA risk factors and without a previous history of MRSA infection or colonization: they do not have a medical history in the past year of hospitalization, healthcare-related admission (to a nursing home, skilled nursing facility or hospice), dialysis, surgery, or implantation of a permanent indwelling catheter or other medical devices 8, 14 . However, there is now an increasing number of reports of MRSA infections in the community that have not escaped from the hospitals, and no longer can MRSA be considered as an exclusively nosocomial pathogen.


id: cord-022383-pz0htccp
author: Kohn, Dennis F.
title: Biology and Diseases of Rats
date: 2013-11-17
extension: .txt
mime: text/plain
words: 20192
sentence: 1081
flesch: 48
cache: cache/cord-022383-pz0htccp.txt
txt: txt/cord-022383-pz0htccp.txt
summary:
  It must, there- fore, be assumed that seropositive rats are persistently infected and can serve as a source of infection to other rats. Attempts to induce the disease in other rats with this agent have yielded inconsistent results (Fox et al, 1977) .


id: cord-353190-7qcoxl81
author: Nicklas, Werner
title: Viral Infections of Laboratory Mice
date: 2012-05-17
extension: .txt
mime: text/plain
words: 27792
sentence: 1326
flesch: 37
cache: cache/cord-353190-7qcoxl81.txt
txt: txt/cord-353190-7qcoxl81.txt
summary:
  The term murine hepatitis virus (MHV; commonly referred to as 'mouse hepatitis virus') A model for the study of viral infection, pathogenesis, and clearance Histopathological characterization of the naturally occurring hepatotropic virus infections of nude mice Detection methods for the identification of rodent viral and mycoplasmal infections Reverse transcriptionpolymerase chain reaction detection and nucleic acid sequence confirmation of reovirus infection in laboratory mice with discordant serologic indirect immunofluorescence assay and enzyme-linked immunosorbent assay results Diagnosis of murine infections in relation to test methods employed Reovirus 3 not detected by reverse transcriptase-mediated polymerase chain reaction analysis of preserved tissue from infants with cholestatic liver disease Detection of reovirus type 3 by use of fluorogenic nuclease reverse transcriptase polymerase chain reaction Detection of reovirus by reverse transcription-polymerase chain reaction using primers corresponding to conserved regions of the viral L1 genome segment Isolation of a non-pathogenic tumour-destroying virus from mouse ascites An oncolytic virus recovered from Swiss mice during passage of an ascites tumour Mouse hepatitis virus Enterotropic mouse hepatitis virus Effects of air temperature and relative humidity on coronavirus survival on surfaces Asymptomatic infection of mouse hepatitis virus in the rat Effects of experimental infection of the deer mouse (Peromyscus maniculatus) with mouse hepatitis virus Isolation of a latent murine hepatitis virus from cultured mouse liver cells Induction of lytic plaques by murine leukemia virus in murine sarcoma virus-transformed nonproducer mouse cells persistently infected with mouse hepatitis virus MHV-S Mouse hepatitis virus biology and epizootiology The cellular and molecular pathogenesis of coronaviruses Enterotropic coronavirus (mouse hepatitis virus) in mice: influence of host age and strain on infection and disease Response of genetically susceptible and resistant mice to intranasal inoculation with mouse hepatitis virus JHM Duration of mouse hepatitis virus infection: studies in immunocompetent and chemically immunosuppressed mice Effective clearance of mouse hepatitis virus from the central nervous system requires both CD4þ and CD8þ T cells Role of CD4þ and CD8þ T cells in mouse hepatitis virus infection in mice Antibody prevents virus reactivation within the central nervous system Mouse hepatitis virus Enterotropic mouse hepatitis virus infection in nude mice Persistent transmission of mouse hepatitis virus by transgenic mice Duration of challenge immunity to coronavirus JHM in mice Virus strain specificity of challenge immunity to coronavirus Duration and strain-specificity of immunity to enterotropic mouse hepatitis virus Passively acquired challenge immunity to enterotropic coronavirus in mice Epizootic coronaviral typhlocolitis in suckling mice Isolation of mouse hepatitis virus from infant mice with fatal diarrhea Thymus involution induced by mouse hepatitis virus A59 in BALB/c mice Adverse effects of mouse hepatitis virus on ascites myeloma passage in the BALB/eJ mouse Murine hepatitis virus strain 1 produces a clinically relevant model of severe acute respiratory syndrome in A/J mice Tolllike receptor 4 deficiency increases disease and mortality after mouse hepatitis virus type 1 infection of susceptible C3H mice Granulomatous peritonitis and pleuritis in interferon-gamma gene knockout mice naturally infected with mouse hepatitis virus Pathogenesis of enterotropic mouse hepatitis virus in immunocompetent and immunodeficient mice Vertical transmission of mouse hepatitis virus infection in mice Tissue distribution and duration of mouse hepatitis virus in naturally infected immunocompetent ICR (CD-1) and immunodeficient athymic nudenu mouse strains used for ovarian transplantation and in vitro fertilization Rederivation of inbred strains of mice by means of embryo transfer Risk assessment of mouse hepatitis virus infection via in vitro fertilization and embryo transfer by the use of zona-intact and laser-microdissected oocytes Mouse hepatitis virus immunofluorescence in formalin-or Bouin's-fixed tissues using trypsin digestion Comparison of isolation in cell culture with conventional and modified mouse antibody production tests for detection of murine viruses Monoclonal antibody solution hybridization assay for detection of mouse hepatitis virus infection Detection of rodent coronaviruses in tissues and cell cultures by using polymerase chain reaction Sequence analysis and molecular detection of mouse hepatitis virus using the polymerase chain reaction Detection of mouse hepatitis virus by the polymerase chain reaction and its application to the rapid diagnosis of infection Detection of rodent coronaviruses by use of fluorogenic reverse transcriptase-polymerase chain reaction analysis An immunofluorescence test for detection of serum antibody to rodent coronaviruses Simultaneous detection of antibodies to mouse hepatitis virus recombinant structural proteins by a microsphere-based multiplex fluorescence immunoassay Differences in antibody production against mouse hepatitis virus (MHV) among mouse strains Maternally-derived passive immunity to enterotropic mouse hepatitis virus Mouse hepatitis virus: molecular biology and implications for pathogenesis Maintenance of pluripotency in mouse embryonic stem cells persistently infected with murine coronavirus Replication of murine coronaviruses in mouse embryonic stem cell lines.


id: cord-009664-kb9fnbgy
title: Oral presentations
date: 2014-12-24
extension: .txt
mime: text/plain
words: 71226
sentence: 3280
flesch: 44
cache: cache/cord-009664-kb9fnbgy.txt
txt: txt/cord-009664-kb9fnbgy.txt
summary:
  Resistance to penicillin, clindamycin and tetracycline fluctuated over time at~75%, 4−8% and 2−10% respectively. The median expected power was 10.0% (IQR, 7.2−13.6%) for a risk ratio for mortality of 0.85 between the compared groups; 14.7% (IQR, 10.6−21.8%) for a risk ratio of 0.80; and 7.9% (IQR, 6.3−10.2%) for a reduction in mortality from 30% to 25%.


id: cord-267671-ys43n672
author: Whary, Mark T.
title: Biology and Diseases of Mice
date: 2015-07-10
extension: .txt
mime: text/plain
words: 63704
sentence: 3050
flesch: 37
cache: cache/cord-267671-ys43n672.txt
txt: txt/cord-267671-ys43n672.txt
summary:
  If an endogenous retrovirus is still infectious to other mouse cell targets, it is termed ecotropic, whereas if it is no longer infectious for mouse cells, but can infect cells of other species, it is termed xenotropic. Recombinant viruses have recently been discovered that can infect mouse cells and heterologous cells and are associated with spontaneous leukemia development in high leukemia strains such as AKR mice.


id: cord-023592-w96h4rir
title: Abstracts cont.
date: 2015-12-28
extension: .txt
mime: text/plain
words: 67976
sentence: 3236
flesch: 48
cache: cache/cord-023592-w96h4rir.txt
txt: txt/cord-023592-w96h4rir.txt
summary:
  The maximum amino acid identities of genes among different non-antibiotic-producing bacterial isolates were close to 100% for most genes, but those between antibiotic-producing and human or animal bacteria ranged from <28 to <77%. Results: Seven or eight participants provided qualifying results in the two separate QC studies, and the calculated (proposed) ranges were (range; % results in range): E. faecalis ATCC 29212 (2-8 mg/ L; 95.6), S. aureus ATCC 29213 (0.5-2 mg/L; 99.4), S. pneumoniae ATCC 49619 (0.25-1 mg/L; 97.5 and 30-37 mm; 97.6), H. influenzae ATCC 49247 (1-4 mg/L; 97.5 and 24-32 mm; 99.8), and S. aureus ATCC 25923


id: cord-007890-bie1veti
title: ECC-4 Abstracts
date: 2002-04-16
extension: .txt
mime: text/plain
words: 86133
sentence: 4193
flesch: 45
cache: cache/cord-007890-bie1veti.txt
txt: txt/cord-007890-bie1veti.txt
summary:
  On the whole, E. coli showed an elevated sensitivity rate ( !/90% of tested strains) to nitrofurantoin, gentamicin, amikacin, and 2nd-and 3rd-generation cephalosporins, while only amoxicillin and piperacillin had a mean resistance rate !/30 % for M41L, D67N, K103N, M184V, L210W, T215YF, and for L10I, M36I, L63P, A71VT, L90M for P Inhibitors (PI).


id: cord-019490-m1cuuehi
title: Abstracts cont.
date: 2015-12-28
extension: .txt
mime: text/plain
words: 93719
sentence: 4340
flesch: 45
cache: cache/cord-019490-m1cuuehi.txt
txt: txt/cord-019490-m1cuuehi.txt
summary:
  Mean age (78 vs 77), Charlson score (2.5 vs. 2.6), neoplasm (22% vs. 21%), HIV (0.7% vs. 0.8%), chronic liver disease (9% vs.7%), diabetes mellitus ( 19% vs.22%), ICU admission (4% vs. 4%), monotherapy (63% vs. 66%), and aetiology (S. pneumoniae 34% vs. 36%; L. pneumophila 3% vs.2%; others 8% vs.11%; unknown 54% vs.51%) were similar. The same was found for mecillinam, i.e. no correlation for AUC/MIC vs. CFÚ s in urine or organs, while Time > MIC % significantly (P < 0.05) correlated with CFÚ s in urine (R 2 = 0.48), and kidney tissue (R 2 = 0.82), respectively.


id: cord-022501-9wnmdvg5
title: P1460 – P1884
date: 2015-12-28
extension: .txt
mime: text/plain
words: 128422
sentence: 6046
flesch: 46
cache: cache/cord-022501-9wnmdvg5.txt
txt: txt/cord-022501-9wnmdvg5.txt
summary:
  In the first half-year of 2005 family doctors most often prescribed penicyllins -(44.8%), makrolids -(27.1%), cephalosporins -(12.5%), tetracyclins -(9.4%) and lincozamidsbased (3.1%) treatments Specialist doctors, on the other hand, prescribed penicllins (41.7%), makrolids (17.9%), cephalosporins (17.7%), tetracyclins (12.1%), lincozamids (5.2%) and chinolons (3%). State-wide antibiotic consumption in the AC setting during the same time was 12 DID (~85% of total consumption).


id: cord-008777-i2reanan
title: ECB12: 12th European Congess on Biotechnology
date: 2005-07-19
extension: .txt
mime: text/plain
words: 151661
sentence: 6588
flesch: 40
cache: cache/cord-008777-i2reanan.txt
txt: txt/cord-008777-i2reanan.txt
summary:
  During the process development for protein production, short time to market and the demand for cheap processes dominate today's process development. Interdependence of the impact of methanol and oxygen supply on protein production with recombinant Pichia pastoris N.K. Khatri, F. Hoffmann Martin-Luther-University Halle-Wittenberg, Institute for Biotechnology, Halle D-06120, Germany.


# ent

id: cord-255137-utg8k7qs
sid: 247
eid: 27
type: PERSON
entity:
  ~rap44 virsorter_node_185_length_4953_cov_6_15402-cat_1 virsorter_node_1708_length_1576_cov_4_20547-cat_2


