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?' ---------------------------------------------------------- 45 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 44952 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 44 strain 8 isolate 8 infection 8 PCR 6 study 6 result 6 patient 6 gram 6 MRSA 6 IBV 5 virus 5 method 5 dna 5 Fig 5 ESBL 5 China 4 resistance 4 Staphylococcus 4 MIC 3 objective 3 mouse 3 figure 3 PFGE 3 NCCLS 2 gene 2 effect 2 disease 2 cell 2 canine 2 bat 2 bacillus 2 animal 2 University 2 Salmonella 2 PVL 2 PEDV 2 MHV 2 LCMV 2 Institute 2 ICU 2 GRN 2 Escherichia 2 ELISA 2 Department 2 Candida 2 CFU 2 16S 1 vr-2332 1 vp7 1 tumor Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 7498 % 6063 strain 3802 infection 3356 patient 2974 mouse 2580 study 2444 virus 2376 gene 2372 result 2274 isolate 2256 method 2077 resistance 2055 cell 1453 group 1420 sequence 1408 analysis 1342 treatment 1319 disease 1303 case 1286 activity 1270 day 1267 protein 1239 sample 1087 type 1081 conclusion 1030 effect 1027 culture 984 time 963 year 931 production 920 concentration 907 rate 898 p 897 level 859 datum 824 test 824 acid 814 system 808 specie 805 control 796 hospital 763 susceptibility 758 use 745 antibiotic 738 laboratory 736 animal 722 aureus 714 genome 705 bacteria 698 enzyme Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1395 S. 1352 al 1285 . 1154 PCR 1090 et 1041 mg 798 C. 736 E. 679 MRSA 487 L 451 C 446 University 412 MIC 399 P. 398 B. 372 RNA 362 M. 358 Staphylococcus 358 A 336 M 331 S 328 L. 324 IBV 308 Fig 291 Department 282 A. 281 B 276 T 252 b 249 H. 232 ESBL 217 K. 212 USA 210 China 206 Genome 203 PFGE 195 Pseudomonas 194 II 192 RT 191 NCCLS 191 Hospital 188 IV 183 imipenem 181 Escherichia 178 ELISA 173 D 172 Salmonella 172 DNA 171 ICU 168 R. Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1662 we 1444 it 628 they 285 them 280 i 67 he 59 us 41 she 32 one 25 itself 11 themselves 6 mg 5 me 4 you 4 her 3 fusb 2 esat-6 2 ch/ 1 Þ 1 ya 1 y 1 thereof 1 talens 1 sngr 1 putk2 1 pm230 1 met198ile 1 lmb415 1 kf442963 1 kaz)objectives 1 ka.max 1 igg2c 1 igfbp2 1 hp6a 1 himself 1 h120 1 facieum 1 ermb 1 arda 1 agfa Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 34335 be 4830 have 3723 use 1722 show 1325 include 1285 isolate 1102 find 1030 determine 998 detect 937 identify 883 increase 874 compare 861 associate 838 cause 819 perform 788 do 787 base 781 obtain 753 follow 734 produce 722 test 712 occur 667 observe 662 develop 627 report 598 contain 573 study 570 suggest 552 infect 519 evaluate 504 relate 494 indicate 493 describe 492 treat 464 reveal 464 investigate 460 result 450 reduce 443 consider 437 provide 425 collect 424 carry 418 present 418 induce 417 accord 388 know 382 confirm 375 give 373 involve 372 remain Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2049 not 1782 high 1640 clinical 1622 - 1557 also 1498 other 1323 resistant 1320 different 1206 most 1152 more 1059 positive 986 only 897 respectively 879 well 851 low 796 human 783 such 777 however 751 specific 737 non 732 new 722 antibiotic 711 bacterial 702 viral 670 negative 623 first 611 significant 599 respiratory 580 common 557 as 550 important 546 genetic 542 antimicrobial 535 susceptible 527 several 504 infectious 502 molecular 486 present 479 same 460 similar 456 acute 440 many 438 large 404 further 402 severe 394 single 390 major 374 significantly 361 immune 358 very Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 275 most 182 high 129 least 104 Most 99 good 54 low 27 great 25 large 22 close 14 late 14 early 14 common 8 strong 8 -t 6 small 6 short 5 near 5 big 5 bad 3 long 2 young 2 safe 2 new 2 fast 2 broad 2 ClustalW 2 -sdrE 2 -R 1 wide 1 ureB+,cagAÀcagHÀ 1 tt 1 steep 1 simple 1 quick 1 poor 1 old 1 mPCR-1 1 hot 1 hexose 1 heavy 1 few 1 ermC 1 dxylulose 1 deadly 1 TA,10 1 Least 1 CCoV 1 /Kuj 1 -peptides Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 931 most 98 least 30 well 4 highest 1 long 1 furthest 1 -ctz Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 7 doi.org 5 www 3 www.ncbi.nlm.nih.gov 3 dx.doi.org 2 www.mbio.ncsu.edu 2 www.informatics.jax.org 2 www.frontiersin.org 2 www.eucomm.org 1 www.wcfs.nl 1 www.viprbrc.org 1 www.rzpd.de 1 www.neli.org.uk 1 www.ncbi.nlm 1 www.ncbi.nim.nih.gov 1 www.mousecanada 1 www.moseslab 1 www.mmrrc.org 1 www.megasoftware.net 1 www.knockoutmouse.org 1 www.jgi.doe.gov 1 www.ingenuity.com 1 www.generunner.com 1 www.econexus.info 1 www.ebi.ac.uk 1 www.eadgene.org 1 www.dnastar.com 1 tree.bio.ed.ac.uk 1 talk.ictvonline.org 1 sray.med.som.jhmi.edu 1 spades.bioinf 1 rrna.uia.ac.be 1 pubmlst.org 1 norcomm.phenogenomics.ca 1 neisseria.org 1 komp.org 1 jaxmice.jax.org 1 ecogenomics.github 1 dx 1 creativecommons.org 1 blast.ncbi.nlm.nih.gove 1 blast.ncbi.nlm.nih.gov Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 5 http://www 2 http://doi.org/10.1016/j.vetmic.2019.01.020 1 http://www.wcfs.nl/ 1 http://www.viprbrc.org/ 1 http://www.rzpd.de 1 http://www.neli.org.uk 1 http://www.ncbi.nlm.nih.gov/nuccore/1021673930 1 http://www.ncbi.nlm.nih.gov/gorf/Orfig.cgi 1 http://www.ncbi.nlm.nih.gov/BLAST 1 http://www.ncbi.nlm 1 http://www.ncbi.nim.nih.gov/orffinder/ 1 http://www.mousecanada 1 http://www.moseslab 1 http://www.mmrrc.org 1 http://www.megasoftware.net/ 1 http://www.mbio.ncsu.edu/bioedit.htm 1 http://www.mbio.ncsu.edu/bioEdit/bioedit 1 http://www.knockoutmouse.org 1 http://www.jgi.doe.gov/ 1 http://www.ingenuity.com 1 http://www.informatics.jax.org/mgihome 1 http://www.informatics.jax.org/ 1 http://www.generunner.com 1 http://www.frontiersin.org/articles/10.3389/fmicb.2020 1 http://www.frontiersin.org/articles/10.3389/fmicb 1 http://www.eucomm.org/docs/protocols/mouse_protocol_1_Sanger 1 http://www.eucomm.org 1 http://www.econexus.info/ 1 http://www.ebi.ac.uk/interpro/ 1 http://www.eadgene.org/ 1 http://www.dnastar.com/ 1 http://tree.bio.ed.ac.uk/software/figtree/ 1 http://talk.ictvonline.org/files/ictv 1 http://sray.med.som.jhmi.edu/SCRopftware/simplot/ 1 http://spades.bioinf 1 http://rrna.uia.ac.be/ 1 http://pubmlst.org/neisseria/ 1 http://norcomm.phenogenomics.ca/index 1 http://neisseria.org/nm/typing/ 1 http://komp.org 1 http://jaxmice.jax.org/jaxnotes/509/509j.html 1 http://ecogenomics.github 1 http://dx.doi.org/10.1016/j.virusres.2016.12.005 1 http://dx.doi.org/10.1016/j.prevetmed.2015 1 http://dx.doi.org/10.1016/j.meegid.2012 1 http://dx 1 http://doi.org/10.6084/m9 1 http://doi.org/10.1186/s13073-019-0708-9 1 http://doi.org/10.1128/ 1 http://doi.org/10.1016/j.vaccine.2020.01.001 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 3 ubakir@metu.edu.tr 2 pcalik@metu.edu.tr 2 ozdamar@eng.ankara.edu.tr 2 mnq@biocentrum.dtu.dk 2 esipov@ibch.ru 2 dpetrides@intelligen.com 2 dkilic@yildiz.edu.tr 2 calik@eng.ankara.edu.tr 2 brivas@uvigo.es 2 barslan@eng.ankara.edu.tr 2 achaudhury@umassd.edu 1 zomorodi@nrcgeb.ac.ir 1 ymkoo@inha.ac.kr 1 wonhur@kangwon.ac.kr 1 willem.devos@wur.nl 1 ut@biocentrum.dtu.dk 1 tvede@bmb.sdu.dk 1 tmatsui@comb.u-ryukyu.ac.jp 1 tig@biocentrum.dtu.dk 1 takasumi@suou.waseda.jp 1 svharten@gmail.com 1 spela.peternel@ki.si 1 sissel.lokra@lnb.hihm.no 1 silas.villas-boas@agresearch.co.nz 1 shindo@arif.pref.akita.jp 1 sh@fsc.chalmers.se 1 schang@tier.org.tw 1 s.buus@immi.ku.dk 1 rkj@imtech.res.in 1 riar5400@rediffmail.com 1 rbuxeda@uprm.edu 1 psk@bioneer.dk 1 psatora@ar.krakow.pl 1 popovic@tfh-berlin.de 1 piversen@ciphergen.com 1 peter.neubauer@oulu.fi 1 perera@bio.ucm.es 1 pcristea@dsp.pub.ro 1 paola.branduardi@unimib.it 1 oytun@hacettepe.edu.tr 1 och@bioneer.dk 1 nmacame@ull.es 1 nbvass@yahoo.com 1 naoya-s@comb.u-ryukyu.ac.jp 1 nadja.schultz@ciw.uni-karlsruhe.de 1 muffler@rhrk.uni-kl.de 1 mp2000@vet.auth.gr 1 mouritzen@exiqon.com 1 mohammad.soltany@gmail.com 1 mehmet@eng.ankara.edu.tr Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 29 isolates were susceptible 28 isolates were resistant 27 strains were resistant 23 strains were susceptible 18 samples were positive 14 infection is usually 14 isolates were also 13 % were resistant 12 activity was comparable 12 strains were also 11 strains did not 9 % were positive 8 isolates were sensitive 8 pcr was positive 7 mice are relatively 7 patients did not 6 activity was similar 6 groups were similar 6 infection is subclinical 6 mice are susceptible 6 mice do not 6 patients were clinically 6 samples were cultured 6 strain was resistant 6 strains do not 5 % did not 5 gene was not 5 genes were differentially 5 group was significantly 5 infection is not 5 mice are highly 5 mice are usually 5 patients were male 5 patients were not 5 strains are more 5 strains were not 5 strains were sensitive 5 strains were significantly 5 virus does not 5 virus is highly 4 % were male 4 disease are not 4 genes were not 4 infection is often 4 infections are subclinical 4 mice are more 4 mice are often 4 mice is subclinical 4 patients were randomly 4 resistance determining region Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 infection is not optimal 2 patients had no s. 2 patients showed no evidence 2 virus is not easily 1 activity is not essential 1 activity is not yet 1 cases is not widely 1 cells contained no activity 1 days did not substantially 1 disease are not partic 1 disease are not present 1 disease are not synonymous 1 disease is not well 1 gene is not transferable 1 genes are not subject 1 groups are not significantly 1 groups showed no significant 1 groups was not statistically 1 groups were not significant 1 groups were not significantly 1 infection has not yet 1 infection is not only 1 infection is not practical 1 infections are not detectable 1 infections are not uncommon 1 infections are not welcome 1 isolate was not sensitive 1 isolates were not statistical 1 method is not entirely 1 method is not useful 1 methods are not always 1 methods are not simple 1 methods were not significantly 1 mice are not more 1 mice do not easily 1 mice produces no immediate 1 mice show no clinical 1 mice showed no sign 1 mice were not effective 1 mouse has no sweat 1 patient had no bacterial 1 patient had no history 1 patients did not significantly 1 patients had no clinical 1 patients have not history 1 patients is not frequent 1 patients was not significantly 1 patients were not fundamentally 1 patients were not specifically 1 pcr was not positive A rudimentary bibliography -------------------------- id = cord-018061-jy3km0fr author = AL KASSAA, Imad title = Antiviral Probiotics: A New Concept in Medical Sciences date = 2016-12-02 keywords = LGG; gram; infection; lactobacillus; probiotic; strain summary = rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity doi = 10.1007/978-3-319-49688-7_1 id = cord-280334-7b7rvr25 author = Abrantes, Joana title = Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2 date = 2020-09-02 keywords = GI.2; GI.3; non; strain summary = doi = 10.1038/s41598-020-71303-4 id = cord-259959-qzd3hf8y author = Alhatami, Abdullah O. title = Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date = 2020-07-16 keywords = IBV; Iraq; strain summary = doi = 10.14202/vetworld.2020.1358-1362 id = cord-291930-n7wq09rq author = Arden, K.E. 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 date = 2010-01-27 keywords = HRVC; QCE; strain summary = doi = 10.1016/j.jcv.2010.01.001 id = cord-005057-deq5tv1d author = Bergström, T. title = Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system date = 1990 keywords = HSV; hsv-1; strain summary = doi = 10.1007/bf02184688 id = cord-281172-7di6eub3 author = Biswas, Kaushiki title = Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination date = 2016-07-06 keywords = Fig; NDM; strain summary = doi = 10.1016/j.clim.2016.07.004 id = cord-000820-5b29wtim author = Borriello, Giorgia title = Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date = 2012-10-25 keywords = Salmonella; Typhimurium; strain summary = RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The current study investigated the intestinal contents collected from 248 water buffalo calves affected by gastroenteritis with lethal outcome to: (i) evaluate the prevalence of Salmonella spp., and (ii) perform a polyphasic characterization of the collected isolates of S. The genetic characterization (Table 2) included five loci (avrA, ssaQ, mgtC, siiD, and sopB) located on SPI 1-5, respectively [8] , eight loci (gipA, gtgB, sopE, sodC1, gtgE, gogB, sspH1, and sspH2) of prophage origin [9] [10] [11] [12] [13] , the gene spvC, located on a virulence plasmid [12] , and nine genes (stfE, safC, csgA, ipfD, bcfC, stbD, pefA, fimA, and agfA) coding for bacterial fimbriae, involved in surface adhesion and gut colonization [5] . doi = 10.1186/1746-6148-8-201 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 keywords = Airway; FRC; Lung; TLC; asm; strain summary = doi = 10.1115/1.4042309 id = cord-323463-osf6t7cw author = Cercenado, Emilia title = Update on bacterial pathogens: virulence and resistance date = 2008-04-30 keywords = MRSA; PVL; Staphylococcus; infection; isolate; patient; strain; study summary = This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 . doi = 10.1016/s0213-005x(08)76378-x id = cord-299763-ttb7o8lv author = Choi, Jeong-Won title = Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date = 2016-06-01 keywords = MVC; canine; strain summary = Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains doi = 10.1007/s00705-016-2895-7 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 keywords = IBV; Poland; polish; strain summary = doi = 10.1016/j.meegid.2020.104177 id = cord-002561-7j43yic1 author = Donato, Celeste title = The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses date = 2017-05-10 keywords = Avastrovirus; HMO; figure; specie; strain summary = doi = 10.3390/v9050102 id = cord-012054-bpgb7tgo author = Ferreira, Maria Isabel M. title = Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1 date = 2008-03-01 keywords = Arthrobacter; IF1; degradation; strain summary = doi = 10.1007/s00253-008-1343-3 id = cord-306976-p2521bl4 author = Gao, Mengying title = Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date = 2016-08-15 keywords = China; IBV; strain summary = doi = 10.1016/j.vetmic.2016.05.018 id = cord-289623-7oc1ykds author = Gendy, Sherif 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 date = 2020-08-20 keywords = SRS-8-S-2018; Serratia; strain summary = doi = 10.3389/fmicb.2020.01923 id = cord-000347-gdra8xhj author = Gibbons, Henry S. title = Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant date = 2011-03-25 keywords = ATCC; Camp; Detrick; bacillus; figure; isolate; strain summary = doi = 10.1371/journal.pone.0017836 id = cord-010187-ymhcfyxx author = Gromeier, Matthias title = Mouse neuropathogenic poliovirus strains cause damage in the central nervous system distinct from poliomyelitis date = 2005-03-25 keywords = CNS; Fig; mouse; strain summary = doi = 10.1016/s0882-4010(05)80002-6 id = cord-355492-0zvqvumc author = Hamm, Ronda L title = Resistance to cyfluthrin and tetrachlorvinphos in the lesser mealworm, Alphitobius diaperinus, collected from the eastern United States date = 2006-06-12 keywords = strain summary = doi = 10.1002/ps.1230 id = cord-301347-22lt6h40 author = Jarvis, Matthew C. title = Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date = 2016-01-01 keywords = PEDV; RBD; strain summary = Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene doi = 10.1016/j.prevetmed.2015.10.020 id = cord-291510-jh2fdks4 author = Jiang, Yi title = Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity date = 2020-02-11 keywords = China; IBV; strain summary = doi = 10.1016/j.vaccine.2020.01.001 id = cord-022383-pz0htccp author = Kohn, Dennis F. title = Biology and Diseases of Rats date = 2013-11-17 keywords = Fig; SDAV; Sendai; animal; colony; disease; infection; lesion; rat; strain; tumor; virus summary = The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. doi = 10.1016/b978-0-12-263620-2.50010-0 id = cord-294509-txk1qic1 author = Li, Zi title = The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets date = 2016-09-15 keywords = CC14; China; PHEV; strain summary = doi = 10.7717/peerj.2443 id = cord-355119-sdg9zdc1 author = Lin, Huixing title = Epidemic strain YC2014 of porcine epidemic diarrhea virus could provide piglets against homologous challenge date = 2016-04-22 keywords = PEDV; YC2014; strain summary = doi = 10.1186/s12985-016-0529-z id = cord-279495-zxerb7de author = Liu, Xiaoli 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 date = 2012-11-21 keywords = IBV; LHLJ/07VII; strain summary = Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus doi = 10.1016/j.meegid.2012.09.016 id = cord-296611-ma32oz4o author = Ma, Tianxin title = Novel genotype of infectious bronchitis virus isolated in China date = 2019-01-29 keywords = China; I0636/16; IBV; strain summary = doi = 10.1016/j.vetmic.2019.01.020 id = cord-003908-wbawzbhz author = Matsushima, Yuki title = Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date = 2019-09-27 keywords = GII.P17-GII.17; VP1; figure; strain summary = doi = 10.3389/fmicb.2019.02189 id = cord-301301-ilsenpus author = Mihalov-Kovács, Eszter title = Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission date = 2017-03-15 keywords = ORF2; UTR; canine; strain summary = doi = 10.1016/j.virusres.2016.12.005 id = cord-004116-ckms25na author = Moser, Kara A. title = Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential date = 2020-01-08 keywords = CHMI; NF135.C10; NF166.C8; NF54; Plasmodium; additional; strain summary = doi = 10.1186/s13073-019-0708-9 id = cord-004751-4vl0cvyq author = Mostow, S. R. title = The behaviour in vitro of attenuated recombinant influenza viruses date = 1973 keywords = strain; virus summary = doi = 10.1007/bf01556156 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 keywords = Complete; Draft; Genome; Strain; isolate; sequence summary = doi = 10.4056/sigs.3416907 id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 keywords = ELISA; IFA; LCMV; LDV; MHV; MPV; PCR; TMEV; infection; mouse; strain; virus summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. doi = 10.1016/b978-0-12-382008-2.00019-2 id = cord-010641-hk90qx1k author = Rodrigues, Juliana Falcão title = Strain-specific transcriptional and posttranscriptional regulation of heat-labile toxin expression by enterotoxigenic Escherichia coli date = 2020-02-03 keywords = Escherichia; etec; strain summary = doi = 10.1007/s42770-020-00231-2 id = cord-347644-4qenzjiu author = Shorter, John R. title = A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size date = 2019-03-15 keywords = effect; litter; size; strain summary = doi = 10.1534/g3.118.200847 id = cord-269892-bmdpbkni author = Tabares, Paula title = Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges date = 2011-01-11 keywords = 16S; strain summary = Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The first group of sponges (Aplysina fistularis, Plakortis sp., Amphimedon compressa, Aiolochroia crassa, Agelas clathrodes, Agelas cerebrum, Ircinia felix, Scopalina ruetzleri, Erylus formosus, Chondrilla nucula, and Aplysina archeri) was collected by SCUBA diving at depths of 3-20 m in Bahamas in July 2008 (GPS-26°27′3.25″ N, 77°5 4′14.59″ W). In terms of actinomycete diversity, the 79 cultivated strains are represented by 20 different genera namely Microbacterium (21 isolates), Rhodococcus (10), Streptomyces (5), Mycobacterium (6), Micromonospora (5), Knoellia (4), Gordonia (4), Curtobacterium (4), Arthrobacter (4) Salinispora (3), Saccharopolyspora (2), Nocardioides (2), Citromicrobium (2), Sanguibacter (1), Lapillicoccus (1), Kocuria (1), Dietzia (1), Cellulosimicrobium (1) Cellulomonas (1), and Agrococcus (1; Supplementary Table 1) . A family of aeruginosin inhibitors is active against human serine proteases and was isolated from marine sponges and cyanobacterial waterblooms (Ersmark et al. Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes doi = 10.1007/s10126-010-9349-0 id = cord-267189-xq70rn1j author = Wang, Xinyu title = Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China date = 2016-01-15 keywords = CCoV; China; strain summary = doi = 10.1371/journal.pone.0146975 id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 keywords = BALB; C57BL/6; Control; Fig; Helicobacter; LCMV; MHV; PCR; SCID; animal; cell; complication; diagnosis; disease; dna; infection; laboratory; medicine; mouse; sign; strain; virus summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. doi = 10.1016/b978-0-12-409527-4.00003-1 id = cord-255137-utg8k7qs author = Yinda, Claude Kwe title = Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date = 2019-01-23 keywords = Cameroon; Fig; bat; cameroonian; human; strain; virus summary = doi = 10.1128/msphere.00585-18 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 keywords = RVA; bat; strain; vp7 summary = doi = 10.1038/srep34209 id = cord-255857-y9wjp0aj author = Yuan, Shishan title = Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date = 2001-11-05 keywords = PRRSV; RespPRRS; strain; vr-2332 summary = 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. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions. doi = 10.1016/s0168-1702(01)00295-7 id = cord-007890-bie1veti author = nan title = ECC-4 Abstracts date = 2002-04-16 keywords = Department; Diseases; ESBL; France; HAART; HCV; HIV; Hospital; IFN; Infectious; Institute; MIC; MRSA; Medical; Medicine; Microbiology; NCCLS; PCR; Purpose; RNA; Spain; Staphylococcus; University; gram; isolate; patient; resistance; result; strain; study summary = Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. doi = 10.1016/s0924-8579(02)00033-x id = cord-008777-i2reanan author = nan title = ECB12: 12th European Congess on Biotechnology date = 2005-07-19 keywords = Ankara; Biology; Biotechnology; Chemical; Denmark; Department; Engineering; Escherichia; Faculty; Germany; HPLC; Institute; PCR; Research; Science; Technical; Technology; Turkey; University; acid; activity; analysis; bacillus; cell; concentration; condition; culture; different; dna; effect; enzyme; expression; fermentation; gene; growth; high; increase; medium; method; process; produce; production; protein; result; strain; study; system summary = Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. doi = 10.1016/j.jbiotec.2005.06.005 id = cord-009664-kb9fnbgy author = nan title = Oral presentations date = 2014-12-24 keywords = CDI; CTX; Candida; ESBL; Europe; MRSA; PCR; PFGE; PVL; clinical; dna; gene; gram; infection; isolate; method; objective; patient; resistance; result; strain; study summary = Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. doi = 10.1111/j.1469-0691.2009.02857.x id = cord-019490-m1cuuehi author = nan title = Abstracts cont. date = 2015-12-28 keywords = AUC; CIP; ESBL; Enterobacteriaceae; GISA; GRN; MIC; MIC90; MRSA; NCCLS; PCR; PFGE; Staphylococcus; gram; infection; isolate; method; objective; patient; resistance; result; strain; study; test summary = Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. doi = 10.1111/j.1469-0691.2005.clm_1134_02.x id = cord-022501-9wnmdvg5 author = nan title = P1460 – P1884 date = 2015-12-28 keywords = 16S; CDAD; CFU; ELISA; ESBL; Enterococcus; GRN; ICU; MIC; MRSA; PCR; Staphylococcus; TGC; dna; gram; infection; isolate; method; objective; patient; resistance; result; strain; study summary = Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). doi = 10.1111/j.1470-9465.2006.12_4_1431.x id = cord-023592-w96h4rir author = nan title = Abstracts cont. date = 2015-12-28 keywords = CFU; Candida; ESBL; ICU; MIC; MRSA; NCCLS; NVP; PCR; PFGE; Salmonella; dna; gram; isolate; method; patient; result; strain summary = Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined. doi = 10.1111/j.1469-0691.2004.0902c.x