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?' ---------------------------------------------------------- 156 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 15635 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 78 table 78 Table 19 Fig 18 SARS 17 COVID-19 16 figure 14 patient 11 cell 10 RNA 9 virus 8 PCR 7 protein 6 infection 6 human 6 high 5 study 5 result 5 group 5 gene 5 dna 5 day 5 Hospital 5 HLA 4 sequence 4 respiratory 4 method 4 covid-19 4 compound 4 child 4 cause 4 University 4 Supplementary 4 RSV 4 ICU 4 HCV 4 China 3 water 3 sofa 3 mortality 3 introduction 3 health 3 expression 3 effect 3 conclusion 3 clinical 3 case 3 additional 3 TBI 3 Study 3 MERS Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 16002 % 15165 patient 9147 cell 6872 virus 6475 study 4814 group 4464 day 4420 infection 4165 protein 4157 blood 3957 result 3946 disease 3775 analysis 3774 time 3572 case 3460 gene 3362 influenza 3250 method 3247 datum 3242 treatment 3174 level 3109 table 2983 p 2850 sample 2771 effect 2732 year 2685 risk 2529 rate 2500 number 2461 donor 2345 response 2212 value 2133 activity 2072 system 2070 factor 2000 antibody 1996 model 1900 age 1871 mortality 1870 expression 1854 therapy 1833 type 1786 sequence 1775 use 1772 drug 1685 test 1684 outcome 1623 control 1622 figure 1620 child Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 3215 al 2606 Table 2543 et 2443 . 2385 ⁄ 1992 SARS 1695 ICU 1576 Fig 1326 HSCT 1297 C 1167 • 1111 mg 1059 RNA 1023 CoV-2 935 PCR 878 H1N1 873 COVID-19 870 T 787 GVHD 770 A 724 M 712 II 699 HLA 695 S 678 Study 671 RBC 661 L 599 kg 596 D 564 CI 559 Design 550 B 533 H5N1 518 Studies 516 IV 515 Background 509 University 509 Case 477 TOF 464 HCV 463 G 462 MS 458 N 438 K 438 IFN 435 Health 425 HRV 424 Hospital 423 SCT 419 China Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 7091 we 4253 it 1574 they 937 i 720 them 265 he 181 you 175 us 149 she 117 itself 109 one 67 themselves 26 him 16 me 10 yourself 10 her 5 s 4 ourselves 4 's 3 theirs 3 oneself 3 igg4 3 himself 2 t98hr 2 rrt 2 ns3/4a 2 imgovguarantee 2 iga1 2 if 1 ζ 1 ŝ 1 y 1 wfdc13 1 tnfsf13 1 thr399ile 1 thbs1 1 t202 1 srbcs 1 sglt2-inhibitors 1 ser146 1 s382 1 puc::447 1 p<1e-10 1 p450s 1 p-450 1 mrnas 1 magpixv 1 m 1 kf/ 1 its Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 79145 be 12229 have 8518 use 4056 show 3982 include 3117 base 2894 increase 2751 associate 2490 compare 2385 perform 2371 do 2333 identify 2309 follow 2183 find 2023 report 1834 receive 1732 develop 1730 reduce 1692 provide 1623 cause 1614 observe 1524 occur 1488 see 1488 require 1452 relate 1430 evaluate 1423 treat 1405 obtain 1368 suggest 1352 induce 1346 determine 1315 give 1298 consider 1244 result 1221 indicate 1198 detect 1178 test 1145 assess 1118 lead 1110 make 1101 contain 1084 present 1077 collect 1040 decrease 1035 bind 1024 improve 1015 demonstrate 1004 describe 998 involve 995 remain Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 6524 not 5584 - 5218 high 3895 also 3258 other 3215 more 2962 clinical 2848 low 2497 human 2301 viral 2286 such 2239 only 2191 well 2174 first 2171 most 2144 however 2128 different 2002 significant 1995 respiratory 1908 severe 1901 acute 1818 specific 1768 non 1651 positive 1630 respectively 1429 new 1420 early 1402 significantly 1402 further 1361 median 1330 large 1328 as 1259 anti 1174 small 1174 negative 1172 common 1146 long 1121 less 1091 available 1084 similar 1059 many 1059 immune 1058 same 1048 important 1014 then 1000 single 971 total 968 several 968 potential 959 present Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 636 most 334 least 322 good 295 high 271 Most 113 low 92 large 52 great 35 strong 34 late 33 small 29 early 28 near 26 bad 22 old 21 long 19 short 19 close 18 young 16 big 15 ⁄ 13 common 9 easy 8 safe 6 simple 6 new 5 poor 5 fast 4 sick 4 Least 4 -t 3 steep 3 few 2 ÀssRNA 2 wide 2 weak 2 tremeGENE 2 p=0.016 2 missfor 2 heavy 2 fresh 2 deep 2 cfDNA 1 À18.1 1 topmost 1 strict 1 slight 1 sharp 1 score=-4.49 1 rich Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 1535 most 303 least 58 well 4 highest 2 worst 2 lowest 2 early 1 near 1 long 1 hydroxyethyl-2,2,6,6-tetramethyl-4-hydroxy 1 hard 1 furthest 1 freshest 1 fast 1 clustalw 1 -monophosphate Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 39 doi.org 8 github.com 7 www 7 tools.iedb.org 6 www.mdpi.com 6 www.ebi.ac.uk 5 www.ncbi.nlm.nih.gov 5 www.cbs.dtu.dk 5 bit.ly 4 www.cdc.gov 4 orcid.org 3 www.who.int 3 www.tensorflow.org 3 creativecommons.org 2 www.illumina.com 2 www.gisaid.org 2 www.eurosurveillance.org 2 www.ddg-pharmfac.net 2 www.biocarta.com 2 www.cdc.gov 2 weblogo.berkeley.edu 2 sysbio.cvm.msstate.edu 2 keras.io 2 journal.frontiersin.org 2 covidsim.eu] 2 bat1k.ucd.ie 2 archive.is 2 adaa.org 1 zhanglab.ccmb.med.umich.edu 1 www.youtube.com 1 www.yomecorono.com 1 www.ukbiobank.ac.uk 1 www.systemsbiology.org.au 1 www.stratcomcoe.org 1 www.stat.gov.tw 1 www.snapgene.com 1 www.rcsb.org 1 www.r-project.org 1 www.premierbiosoft 1 www.plosone.org 1 www.paragongenomics.com 1 www.normativasanitaria.it 1 www.nimblegen.com 1 www.netflixprize.com 1 www.mqtldb.org 1 www.mgc.ac.cn 1 www.medsci.org 1 www.matrixscience.com 1 www.lrrfinder.com 1 www.jstatsoft.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 15 http://doi.org/10.1101/2020.10.11.20210781 8 http://doi.org/10.1101/2020.09.24.20201178 7 http://www 3 http://www.cbs.dtu.dk/services/ 3 http://doi.org/10.1101/2020.10.12.20211573 3 http://doi.org/10.1101/2020.05.27.20115113 3 http://doi.org/10 2 http://www.tensorflow.org/ 2 http://www.gisaid.org 2 http://www.eurosurveillance.org 2 http://www.biocarta.com 2 http://www.CDC.gov 2 http://weblogo.berkeley.edu/logo.cgi 2 http://tools.iedb.org/population/ 2 http://tools.iedb.org/mhcii/ 2 http://sysbio.cvm.msstate.edu/IPMiner 2 http://keras.io/ 2 http://journal.frontiersin.org/article/10.3389/fmicb 2 http://github.com/rnajena/bats 2 http://github.com/ 2 http://covidsim.eu] 1 http://zhanglab.ccmb.med.umich.edu/ModRefiner/ 1 http://www.youtube.com/watch?v=DVJNWefmHjE 1 http://www.yomecorono.com 1 http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf 1 http://www.who.int/csr/disease/avian_influenza/ 1 http://www.who.int 1 http://www.ukbiobank.ac.uk/scientists-3/genetic-data/ 1 http://www.tensorflow.org/datasets/catalog/mnist 1 http://www.systemsbiology.org.au/glycoviewer 1 http://www.stratcomcoe.org/news-hero 1 http://www.stat.gov.tw/ 1 http://www.snapgene.com/ 1 http://www.rcsb.org/ 1 http://www.r-project.org/ 1 http://www.premierbiosoft 1 http://www.plosone.org/ 1 http://www.paragongenomics.com/ 1 http://www.normativasanitaria.it 1 http://www.nimblegen.com/ 1 http://www.netflixprize.com/ 1 http://www.ncbi.nlm.nih.gov/genbank/sars-cov-2seqs/ 1 http://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/] 1 http://www.ncbi.nlm.nih.gov/genbank/ 1 http://www.ncbi.nlm.nih.gov/blast/ 1 http://www.ncbi.nlm.nih.gov/Structure/ 1 http://www.mqtldb.org/ 1 http://www.mgc.ac.cn/ 1 http://www.medsci.org/v17p2974s1.pdf 1 http://www.mdpi.com/2076-393X/8/3/408/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 3 mswolf@northwestern.edu 1 xavier.lories@arlenda.com 1 v.medvedev@univercells.com 1 stacy-bailey@northwestern.edu 1 socquahs@nus.edu.sg 1 sadlerd@ccf.org 1 lihl@whu.edu.cn 1 lena.schober@ipa.fraunhofer.de 1 journals.permissions@oup.com 1 heijden@proteonic.nl 1 akim@uchc.edu Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 22 patients are alive 20 data are available 20 patients did not 15 results are available 13 patients were alive 13 patients were male 11 % were female 11 % were male 11 levels were significantly 11 patient did not 11 patients were not 11 treatment related mortality 10 results are consistent 9 % were males 9 analysis is adequate 9 treatment is largely 8 group was significantly 8 patients do not 8 patients had more 8 samples were then 8 studies have also 8 treatment is surgical 7 cells were then 7 patients had at 7 patients received myeloablative 6 genes were also 6 groups were comparable 6 groups were similar 6 patient is able 6 patient was not 6 patients were eligible 6 patients were randomly 6 results were available 6 results were not 6 samples were not 6 studies did not 6 study did not 6 virus is also 6 virus was not 5 % were resistant 5 analysis were also 5 data were available 5 disease has not 5 infection is usually 5 levels do not 5 levels were lower 5 patient developed grade 5 patient does not 5 patient is not 5 patients are not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 3 disease has not yet 2 % were not worried 2 blood is not available 2 cases are not due 2 patient is no longer 2 patient was not statistically 2 patients do not often 2 patients were not subsequently 2 results were not available 2 results were not significant 1 % had no change 1 % had no clinical 1 % had no recovery 1 % had no risk 1 % had no significant 1 % has no negative 1 % having no acute 1 % is not much 1 analysis is not unique 1 analysis showed no difference 1 analysis was not able 1 blood are not interchangeable 1 blood is not always 1 case is not clear 1 cases are not different 1 cases had no risk 1 cases is not sufficiently 1 cases was not previously 1 cells are not available 1 cells have no entity 1 cells were no longer 1 cells were not statistically 1 data are not complete 1 data was not statistically 1 data was not symmetrically 1 data were not statistically 1 day were not fully 1 disease are not very 1 diseases are not usually 1 effects are not well 1 genes are not replaceable 1 genes were not present 1 group are not surprising 1 group had no difference 1 group had no information 1 group had no reason 1 group was not significant 1 group was not significantly 1 group were not significantly 1 groups is not really A rudimentary bibliography -------------------------- id = cord-279528-41atidai author = Abo-Elkhier, Mervat M. title = Measuring Similarity among Protein Sequences Using a New Descriptor date = 2019-11-22 keywords = Table; sequence summary = Each amino acid in the protein sequence is represented by a number, and a new 2D graphical representation is suggested. A new descriptor is introduced, comprising a vector composed of the mean and standard deviation of the total numbers of each protein sequence (A t , SA t ). e 2D graphical representation for human, chimpanzee, and opossum beta globin protein sequences is illustrated in e 2D graphical representation of TGEVG from class I and GD03T0013 from SARS_CoV protein sequences is illustrated in Figures 4(a) and 4(b) respectively. A new descriptor for protein sequences is suggested, which is a vector composed of the arithmetic mean A t and standard deviation SA t of the combined intensity level value A t (i) of the protein sequence. F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids doi = 10.1155/2019/2796971 id = cord-315193-z6v6s46n author = Adhikari, Nilanjan title = Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date = 2017-07-14 keywords = QSAR; SARS; compound; table summary = In the present report, quantitative structure-activity relationships (QSARs) techniques have been explored to understand the relation between the SARS-CoV 3CL pro and HRV 3C pro enzyme inhibitory activity with the physicochemical and structural properties of these inhibitors developed till now. (2008) reported some cinanserin analogs as SARS-CoV 3CL pro inhibitors (Table 11 .18), for which the QSAR model obtained was as shown by Eq. (2013b) reported a series of dipeptide-type SARS-CoV 3CL protease inhibitors (Table 11 .27) whose activity was shown to be controlled by the molar refractivity (CMR) and the polar volume (Pol Vol) of the compounds [Eq. QSAR models exhibited that the physicochemical parameters, such as dipole moment, PSA, polar volume, hydrophobicity, molar refractivity, SA, and molecular volume of the compounds play a crucial role in controlling both SARS-CoV 3CL pro and HRV 3C pro inhibitory activities. doi = 10.1016/b978-0-12-809712-0.00011-3 id = cord-338750-6jfw49y7 author = Albiol, Nil title = Autoimmune thrombotic thrombocytopenic purpura (TTP) associated with COVID-19 date = 2020-05-28 keywords = Table summary = A thoracic computerized tomography was normal, and a single nasopharyngeal swab (NPS) was reported as negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by a polymerase chain reaction (PCR)-based test. Because of the pandemic state of SARS-CoV-2 and associated symptoms [1] , the treating physicians considered the patient to have coronavirus disease 2019 (COVID-19) but with a false-negative result of the PCR NPS test. After initial clinical and laboratory work-up at our institution (Day 9 on Table 1 ), a diagnosis of autoimmune thrombotic thrombocytopenic purpura (TTP) was rapidly established, based on the presence of microangiopathic hemolytic anemia, severe thrombocytopenia, and very low activity (2%) of ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13) in combination with the presence of an ADAMTS-13 inhibitor, which is an autoantibody to ADAMTS-13 [2, 3] . doi = 10.1007/s00277-020-04097-0 id = cord-021951-xxvol17t author = Amos, Louella B. title = Cough date = 2017-05-12 keywords = RSV; cause; child; cough; diagnosis; pneumonia; table summary = doi = 10.1016/b978-0-323-39956-2.00002-9 id = cord-026009-rdhuc2n2 author = Anderson, Nancy L. title = Pet Rodents date = 2009-05-15 keywords = Key; Point; animal; base; cause; clinical; mouse; sign; table; treat summary = This chapter provides information needed to diagnose and treat the most frequently encountered problems of mice, rats, gerbils, hamsters, guinea pigs, and chinchillas. • Diagnosis is based on clinical signs, history, visualization of parasite, skin scrape, and cellophane tape test. • Clinical signs in adults are caused by secondary bacterial infections and are similar to those in MRM. Common primary or secondary pathogens causing respiratory signs in mice are Streptococcus pneumoniae, Corynebacterium kutscheri, Pasteurella pneumontropica, Pseudomonas aeruginosa, and Klebsiella pneumoniae. • Mouse poliomyelitis/encephalomyelitis, also known as Theiler disease, causes clinical signs in 1 in 10,000 infected mice. • In contrast to mice, Sendai virus rarely causes clinical signs in rats. • Pneumonia in guinea pigs usually is caused by infection with S. • Diagnosis of scurvy is based on clinical signs, the exclusion of other causes of diarrhea, and response to vitamin C therapy (see Table 177 -10). doi = 10.1016/b0-72-160422-6/50179-0 id = cord-266036-qhlo99l7 author = Axell-House, Dierdre B. title = The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date = 2020-08-31 keywords = PCR; SARS; Table; test summary = OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. doi = 10.1016/j.jinf.2020.08.043 id = cord-280624-7v8xuicg author = Ba Abduallah, Mohamed M. title = Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure date = 2020-08-17 keywords = MERS; Table summary = title: Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure 18 Genome analysis of MERS-CoV isolates from human and dromedary camel origins revealed a close relationship between each other, suggesting the zoonotic origin of the virus. 19, 20 Studies on MERS-CoV isolates from various countries in northern and central Africa revealed that the circulating strains of the virus in dromedary camels from these countries belong to lineage-C. Compared to the phylogenetic tree of MERS-CoV whole-genome and ORF1ab sequences (Figure 2A (Table S1 ). Comparative genome sequence analysis of the MERS-CoV of both dromedary camels and human origins revealed significant evidence for potential barcoding of the African clades based on the S gene sequences. Dromedary camels and the transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) doi = 10.1002/rmv.2150 id = cord-271599-1yu1yl12 author = Bailey, Stacy Cooper title = Changes in COVID-19 Knowledge, Beliefs, Behaviors, and Preparedness Among High-Risk Adults from the Onset to the Acceleration Phase of the US Outbreak date = 2020-09-01 keywords = COVID-19; table; wave summary = KEY RESULTS: From the onset to the acceleration phase, participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and reported greater preparedness. Individuals with low health literacy remained more likely to feel unprepared for the outbreak (RR 1.80, 95% CI 1.11–2.92, p = 0.02) and to express confidence in the federal government response (RR 2.11, 95% CI 1.49–3.00, p < 0.001) CONCLUSIONS: Adults at higher risk for COVID-19 continue to lack critical knowledge about prevention. Our first longitudinal assessment of the C3 study revealed that participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and had a greater sense of preparedness from the onset to the acceleration phase of the outbreak. doi = 10.1007/s11606-020-05980-2 id = cord-257958-yehnlabq author = Barh, Debmalya title = Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date = 2020-10-10 keywords = COVID-19; CoV-2; SARS; Table; analysis summary = In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). doi = 10.1016/j.compbiomed.2020.104051 id = cord-256065-zz2907h0 author = Barral-Arca, Ruth title = A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date = 2020-03-06 keywords = RSV; Table; respiratory summary = title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation. doi = 10.3390/ijms21051831 id = cord-281464-15ld7knm author = Belova, Natalya V. title = Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects date = 2020-05-17 keywords = GED; Table; oxide summary = The molecular structure of 4-nitropyridine N-oxide, 4-NO(2)-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM). The geometrical parameters of the calculated equilibrium structure derived with different theory methods are given in Table 2 together with the experimental results.Vibrational amplitudes and corrections, Δr=r h1 −r a , were derived from theoretical force fields (B3LYP/aug-cc-pVTZ) by Sipachev''s method (approximation with taking into account the nonlinear kinematic effects at the level of the first order perturbation theory for the transformation of Cartesian coordinates into internal coordinates), using the program SHRINK [36] [37] [38] . doi = 10.1016/j.molstruc.2020.128476 id = cord-004096-obrq7q57 author = Benghanem, Sarah title = Brainstem dysfunction in critically ill patients date = 2020-01-06 keywords = ICU; brainstem; dysfunction; patient; table summary = OCR: oculocephalic reflex BRASS is a clinical score that has been developed for scoring brainstem dysfunction in deeply sedated, non-brain-injured, mechanically ventilated, critically ill patients and ranges from 0 to 7 The BRASS has prognostic value, as 28-day mortality proportionally increases with the BRASS score applicable to ICU patients. The "brainstem dysfunction" hypothesis originates from our study on usefulness of neurological examination in non-brain-injured critically ill patients who required deep sedation. In deeply sedated non-brain-injured critically ill patients, the cessation of brainstem responses follows two distinct patterns. Middle latency BAEP responses and SSEP latencies were increased in 24% and 45% of deeply sedated non-brain-injured critically ill patients, respectively [34] , indicating an impairment of the brainstem conduction. Brainstem dysfunction can present with central sensory and motor deficits, cranial nerve palsies and abnormal brainstem reflexes, disorders of consciousness, respiratory failure, and dysautonomia. doi = 10.1186/s13054-019-2718-9 id = cord-319460-n4ezxnjc author = Bertasio, Cristina title = Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date = 2016-12-15 keywords = PCR; PEDV; Table summary = During summer 2014, animals on two farms displaying mild clinical signs were detected as positive for PEDV by PCR (Boniotti et al., 2016) , and at the beginning of 2015 a new severe epidemic wave occurred (Efsa Ahaw Panel, 2014) . We conducted a longitudinal study by sampling the feces and blood of piglet groups from each farm at fixed intervals during a 2-5 months period, and then we determined PEDV shedding and the antibody presence. The highest fecal PEDV RNA shedding titer was observed in 3-6 day-old piglets with mean values (among shedding animals) of 5.9, 5.6, 5.6, and 6.2 log 10 copies/mL on F1, F2, F3, and F4, respectively ( Figure 1B; Supplementary Table 3 ). Determining the viral loads and shedding rates of PEDV in real field situations during outbreaks is important in evaluating the virulence of a strain and in predicting the susceptibility of infected animals, at different ages and in the various farm units, within a herd. doi = 10.3389/fmicb.2016.02009 id = cord-009969-ln91qfg4 author = Bertolesi, Gabriel E. title = Plasticity for colour adaptation in vertebrates explained by the evolution of the genes pomc, pmch and pmchl date = 2019-03-10 keywords = MCH; MCHL; MSH; Table; background; figure; group summary = doi = 10.1111/pcmr.12776 id = cord-028751-71bf4w44 author = Betten, Anton title = Classifying Simplicial Dissections of Convex Polyhedra with Symmetry date = 2020-06-06 keywords = Table summary = A convex polyhedron is the convex hull of a finite set of points in [Formula: see text] A triangulation of a convex polyhedron is a decomposition into a finite number of 3-simplices such that any two intersect in a common face or are disjoint. We present an algorithm to classify the simplicial dissections of a regular polyhedron under the symmetry group of the prolyhedron. The classification algorithm utilizes the concept of a partially ordered set under a group action, using the theory developed by Plesken [9] as a framework. The number of equivalence classes of simplicial dissections of the cube under its automorphism group of order 48 is exactly 10. By using Nauty to solve the isomorphism problem for the associated graphs, the combinatorial objects at hand are classified as well. The poset of orbits for the action of the group of the cube on the partial dissections is shown in Fig. 3 . doi = 10.1007/978-3-030-52200-1_14 id = cord-306189-ugxou9z1 author = Bherwani, Hemant title = Valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under COVID-19 lockdown date = 2020-06-10 keywords = Table; Wuhan summary = The air quality during the lockdown period for majorly polluted cities (i.e., Delhi, Wuhan, Paris, and London) is of high significance in determining the baseline pollution level and attributable health risk, to evaluate the potential fluctuation in monetary damages. An unprecedented attempt has been made to quantify the economic benefit due to reduction in an excess number of health risk subject to mortality/morbidity attributable to lower air pollutant (PM 2.5 , PM 10 , NO 2 , and SO 2 ) concentration in Wuhan, Paris, London, and Delhi. Ambient air quality for Delhi, London, Paris, and Wuhan cities for the lockdown month with the number of days for the years 2019 and 2020 as shown in Table 1 is considered for calculating the health damage cost due to air pollutants. doi = 10.1007/s11869-020-00845-3 id = cord-257969-2tax8ajw author = Bhopal, Raj S. title = COVID-19 zugzwang: potential public health moves towards population (herd) immunity date = 2020-07-15 keywords = COVID-19; Lancet; population; table summary = Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. People in these groups could minimise their risk of exposure to COVID-19, await effective vaccination and benefit indirectly as population immunity through natural infection increases (Column 2, table 1). The pandemic needs to be prevented from returning year-on-year, potentially more severely, especially in young people and children, and mandating repeated lockdowns.(3) We urgently need to consider all reasonable public health actions and plans (table 1) . doi = 10.1016/j.puhip.2020.100031 id = cord-304869-l6a68tqn author = Bielińska-Wąż, Dorota title = Graphical and numerical representations of DNA sequences: statistical aspects of similarity date = 2011-08-28 keywords = Fig; Table; dna; sequence summary = As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. How to restrict the graphs representing the sequences to two-dimensional plots and how to avoid degeneracies has been the subject of numerous studies which resulted in many graphical representations (see subsequent chapters). It is shown in the last chapter of this work that by using the four-component spectral representation one can recognize the difference in one base between a pair of sequences so it can be used for single nucleotide polymorfism (SNP) analyses which is subject of many investigation, as for example, in a recent work by Bhasi et al. doi = 10.1007/s10910-011-9890-8 id = cord-339039-6gyo9rya author = Bonvehí, Pablo E. title = Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date = 2018-04-30 keywords = RSV; infection; respiratory; table summary = The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . doi = 10.1007/s40506-018-0163-y id = cord-001567-3bw7jbzq author = Borlak, Jürgen title = Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events date = 2015-02-25 keywords = EGF; EGFR; HCC; additional; expression; figure; liver; protein; table; tumour summary = doi = 10.1186/s12864-015-1312-z id = cord-033453-557obi3r author = Bretscher, Lorenzo title = COVID-19 and the Cross-Section of Equity Returns: Impact and Transmission date = 2020-09-24 keywords = Table; covid-19; day; firm; return summary = Using the first reported case of COVID-19 in a given U.S. county as the event day, we find that firms headquartered in an affected county experience, on average, a 27-bps lower return in the 10-day post-event window. The regression results show that the average daily return of a labor-intensive firm residing in a high intensity county is 1% lower in the 10-day post-event window. To this end, we use analysts'' forecast data from the I/B/E/S database and document that the first reported coronavirus case results in downward revision of earnings estimates of firms located in the same county. Second, and related, a unique advantage of our natural experiment is that it allows us to examine the relative strength of various channels (specifically, the labor supply channel, the uncertainty channel, the government policy channel, and the cash flow news channel) through which the COVID-19 shock affects firm valuations. doi = 10.1093/rapstu/raaa017 id = cord-329999-flzqm3wh author = Buchanan, Tom title = Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date = 2020-10-07 keywords = Facebook; Study; Table; Twitter; share summary = Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Descriptive statistics for participant characteristics (personality, conservatism, new media literacy and age) and their reactions to the stimuli (likelihood of sharing, belief the stories were likely to be true, and rating of likelihood that they had seen them before) are summarised in Table 2 . This evaluated the extent to which digital media literacy (NMLS), authority of the message source, consensus, belief in veracity of the messages, consistency with participant beliefs (operationalised as the total SECS conservatism scale score), age and personality (Extraversion, Conscientiousness, Agreeableness, Openness to Experience and Neuroticism), predicted self-rated likelihood of sharing the posts. doi = 10.1371/journal.pone.0239666 id = cord-015684-q10sx1dm author = Cacabelos, Ramón title = Pharmacogenomic Biomarkers in Neuropsychiatry: The Path to Personalized Medicine in Mental Disorders date = 2009 keywords = APOE; APOE-4/4; Alzheimer; CNS; CYP2D6; disorder; drug; gene; table summary = With the advent of recent knowledge on the human genome 69,70 and the identifi cation and characterization of many genes associated with CNS disorders, 8, 19 as well as novel data regarding CYP family genes and other genes whose enzymatic products are responsible for drug metabolism in the liver (e.g., NATs, ABCBs/ MDRs, TPMT), it has been convincingly postulated that the incorporation of pharmacogenetic and pharmacogenomic procedures ( Fig. 40 .6) in drug development might bring about substantial benefi ts in terms of therapeutics optimization in CNS disorders and in many other complex disorders, assuming that genetic factors are determinant for both neuronal dysregulation (and/or neuronal death) 8,16-22 and drug metabolism. The natural course of technical events to achieve effi cient goals in pharmacogenetics and pharmacogenomics include the following steps: (a) genetic testing of mutant genes and/or polymorphic variants of risk; (b) genomic screening, and understanding of transcriptomic, proteomic, and metabolomic networks; (c) functional genomics studies and genotype-phenotype correlation analysis; and (d) pharmacogenetics and pharmacogenomics developments, addressing drug safety and effi cacy, respectively. doi = 10.1007/978-90-481-2298-1_1 id = cord-002139-zlqh436d author = Chasman, Deborah title = Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens date = 2016-07-12 keywords = Fig; LASSO; MERLIN; MTG; Table; module; regulator summary = This integrated regulatory module network enabled (3) prioritization of regulators for validation of their ability to modulate viral replication, (4) an examination of network dynamics across virus treatments, and (5) a further integration with external protein-protein interactions to predict directed physical connections between the mRNA, protein-based regulators and known influenza host response genes. We used a recently developed network inference algorithm, ''Modular regulatory network learning with per gene information'' (MERLIN [22] ) that uses genome-wide mRNA levels from multiple biological samples (time points or treatments) to predict regulatory relationships between regulators (e.g. transcription factors or signaling proteins) and target genes. Based on a hypergeometric test with FDR correction (FDR<0.05), 32 out of the 41 human Calu-3 modules (40 of 56 mouse modules) exhibited enrichment in one or more of the annotation categories representing Gene Ontology processes, KEGG pathways, and influenza related gene sets identified from 10 high-throughput RNAi studies and viral-host protein-protein interaction screens (Fig 2, S1 Fig, S1 Table, S2 Table) . doi = 10.1371/journal.pcbi.1005013 id = cord-305378-jmcuq9c5 author = Chen, Hui title = Liquid–liquid phase separation by SARS-CoV-2 nucleocapsid protein and RNA date = 2020-09-08 keywords = Table summary = title: Liquid–liquid phase separation by SARS-CoV-2 nucleocapsid protein and RNA well refolded proteins were concentrated and further purified with anion exchange chromatography column and size exclusion chromatography. The N protein RNA N1541 (1541 nt; Supplementary information, Table S1 ) and A85 H20 (20 nt), A20 (20 nt) and poly-U RNA oligos of different lengths (U10, U20, U40, U60; Supplementary information, Table S1) with HEX labeling were purchased from Sangon Biotech (Shanghai China). All RNA sequences were listed in Supplementary information, Table S1 . Phase separation was induced with RNA addition and then transferred in 96-well plate at room temperature for 1 h. Samples were prepared by mixing indicated concentration of protein and RNA. The particle size of N protein was detected by a DynaPro NanoStar (Wyatt Technology) which was equipped with a 660 nm laser, detector angle was fixed at 90°. doi = 10.1038/s41422-020-00408-2 id = cord-275720-kf9m4zho author = Cho, Won Kyong title = Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date = 2012-05-06 keywords = RNA; figure; gene; table summary = At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. For example, according to the qRT-PCR and microarray results, the transcript levels for three genes, including FGSG_01379, FGSG_03143, and FGSG_03911, were highly reduced at both 36 h and 120 h, whereas FGSG_03788, FGSG_00023, FGSG_07804, FGSG_07801, and FGSG_13222 were strongly induced regardless of the time point ( Figure 3A -C). graminearum harboring FgV1-DK21 in detail, samples were harvested at two different time points, thus providing lists of differentially expressed genes early and late in the host containing FgV1-DK21 as compared to an uninfected strain. doi = 10.1186/1471-2164-13-173 id = cord-322756-ouvn71r9 author = Chow, Michael Y.T. title = Inhaled RNA Therapy: From Promise to Reality date = 2020-09-04 keywords = RNA; delivery; lung; pulmonary; table summary = Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. Interestingly, it has been known for over a decade that naked RNA, including both siRNA and mRNA, can be transfected in the lung following pulmonary delivery, as shown in many in vivo studies [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] . Both studies demonstrated a gene-silencing effect of the powder formulations in lung tissues following intratracheal administration in mouse models of lung cancer, taking these delivery systems one step closer to clinical application. To take advantage of this phenomenon, pulmonary surfactant and surfactant protein B-coated dextran-based nanoparticles were developed for siRNA delivery, with successful gene-silencing effects observed in healthy mice and in a model of acute lung injury (ALI), respectively, following pulmonary administration [29, 69] (Table 1) . doi = 10.1016/j.tips.2020.08.002 id = cord-255140-3dwqqgv1 author = Christian, Michael D. title = Biowarfare and Bioterrorism date = 2013-07-04 keywords = agent; anthrax; bioterrorism; case; clinical; table; toxin summary = doi = 10.1016/j.ccc.2013.03.015 id = cord-016308-qzkcwrit author = Cochran, Christina L. title = Neonatal Emergencies date = 2015-11-06 keywords = newborn; patient; present; table summary = • Initial signs of respiratory distress include tachypnoea and increased work of breathing (Table 11 .1 ) • As distress progresses, newborns are at risk of developing respiratory failure and apnoea. • RDS presents in the fi rst days of life (Table 11 .2 ) • Bronchiolitis is a clinical diagnosis based on physical exam and history [ 3 ] . • Consider hypoglycaemia, metabolic dysfunction, hyperbilirubinemia, congenital heart conditions, and neurologic dysfunction when assessing a patient with the above features. • Most cases of hyperbilirubinemia are physiologic, or secondary to normal delayed conjugation and excretion of bilirubin in the newborn, though pathologic aetiologies must be considered. • Management of Hirschsprung''s Disease is reviewed in Table 11 .11 • In the case of toxic megacolon, provide resuscitation as clinically indicated and IV antibiotics • Consider thyroid studies in patients with clinical signs or maternal history of antithyroid antibodies. doi = 10.1007/978-81-322-2713-7_11 id = cord-264976-6n9cdex6 author = Corse, Tanner title = Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date = 2020-10-18 keywords = SARS; covid-19; table summary = The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. doi = 10.7150/ijms.50537 id = cord-295689-me50th40 author = Cox, E. title = Effect of antisecretory drugs on experimentally induced weanling diarrhoea in piglets date = 1989 keywords = TGE; etec; table summary = Significant differences from the values prior to infection (day 3) are indicated by *(p