cord-000082-jy7j8sh0	2009	
cord-001116-2yvyiiuy	2013	Since those functions are associated with the hippocampus, I analyzed the global gene expression data from post-mortem hippocampal tissue of 25 old (age ≥ 60 yrs) and 15 young (age ≤ 45 yrs) cognitively intact human subjects. Having employed three different and independent methods of statistical significance, namely, ROC curve analysis, fold change, and P-value, I was able to identify 36 genes that were the most significant in terms of differential expression. The seven genes [C4A (C4B), ADORA3, MS4A7, BCL6, CD44, C3AR1, and HLA-DRB1], which are the constituent input variables of the model (F 1 super variable), and all of which are -in terms of function -inflammation or immune system activation genes (Table 1) , were all found to be over-expressed in the old subjects compared with the young subjects (Table 1) .
cord-001186-jkg7qkj6	2014	During spring-summer 2009, several observational studies from Canada reported that prior receipt of the 2008-09 trivalent inactivated influenza vaccine (TIV) was associated with increased risk of medically-attended, laboratory-confirmed A(H1N1)pdm09 illness, with estimated risk or odds ratios of 1.4-2.5 compared to those unvaccinated [1] . Protein microarray results were consistent with ELISA but in addition showed vaccine-induced HA1 antibody to the seasonal H1 antigen, for which values were significantly higher in vaccinated animals relative to pre-immunization and compared to placebo from day 28, most pronounced from day 49 after the first TIV dose (i.e. three weeks after two-dose vaccine series completion) ( Figure 2 ). Lower neutralizing antibody to A(H1N1)pdm09 even at Ch+14 among vaccinated versus placebo ferrets, although not statistically significant, is consistent with human immunogenicity trials showing blunting of pandemic H1N1 vaccine-induced responses in association with prior seasonal vaccine receipt [53] [54] [55] [56] .
cord-001521-l36f1gp7	2011	
cord-001567-3bw7jbzq	2015	
cord-001890-kbiwze0z	2015	coli, not only does AgaR regulator that belongs to the DeoR family of transcriptional factors, act as an autoregulator, but also negatively controls the expression of two aga genes (agaZ and agaS) of GalN/ GalNAc catabolism pathway via direct binding of the specific palindromes in front of these target genes (Ray and Larson 2004) . Discovery of the genome-wide regulons encoding the GalNAc/GalN utilization pathways in Lactobacillales Arrows represent the GalNAc/ GalN catabolism-related genes, and circles denote the predicted AgaR-recognizable sites. (B) Real-time qPCR assays for effects of agaR2 on expression profile of genes of GalNAc/GalN utilization pathway in Streptococcus suis. The approach includes inference of transcriptional factor-binding sites (TFBSs), construction of nucleotide positional weight matrices (PWMs) for TFBSs motifs, and reconstruction of regulons in complete genomes on the basis of prediction of putative TFBSs in the promoter gene regions. suis 05ZYH33 (Accession no.: CP000407.1) encodes a fully functional GalNAc utilization machinery and most of the genes encoding this pathway are regulated by AgaR2 (and/or AgaR1) (Fig. 1) .
cord-001933-rnjnxymc	2016	Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus whose 190 kb genome encodes more than 60 confirmed proteins (Abd-Alla et al., 2008 , 2009b Kariithi et al., 2013a) . However, detection of hytrosavirus-like infection symptoms, i.e., the salivary gland hypertrophy syndrome (SGH) in the Narcissus bulb fly Merodon equestris (Diptera; Syrphidae; Amargier et al., 1979) and in male accessory gland filaments of the parasitic wasp Diachasmimorpha longicuadata (Hymenoptera; Braconidae; Luo and Zeng, 2010) implies that the Hytrosaviridae potentially contains other members. We hypothesized that GpSGHV infection in Glossina is under the control of host-and/or virus-encoded factors (proteins/peptides) whose interactions influence the expression or lack of overt SGH symptoms. The host (and viral) proteins identified in this study are potential targets for control of GpSGHV infections in tsetse fly mass production facilities. The clear GpSGHV-induced differential modulation of SG protein expression in Glossina raises the question of what host pathways are potentially globally regulated to facilitate successful virus infection.
cord-001974-wjf3c7a7	2016	Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. The datasets went through a sequential pipeline with modules (in order) of preprocessing, computational subtraction of host sequences, low-complexity sequence removal, sequence assembly, clustering, association to metadata features, and taxonomical annotation. Associations from the shortest mode tended to have higher dispersion in the range of ORs. Furthermore, one block of clustering results using global alignment mode, alignment length based on the shortest contig, and a minimum sequence identity of 90% (c09ˆaSyG1), had an overall high range of ORs as well as the highest minimum values. The clusters are significantly associated with lowest p-values to biological features and the species annotations are described by HMP.
cord-002139-zlqh436d	2016	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) .
cord-002846-la9svzml	2017	
cord-003318-abs9rvjk	2018	Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ).
cord-003532-lcgeingz	2019	It''s proposed to evaluate the association between myocardial injury biomarkers, high-sensitive troponin T (hs-cTnT) and N-terminal pro-brain natriuretic peptide (NT-ProBNP), with inflammatory mediators (IL-6, IL-1Β , IL-8, IL-10, IL-12 / IL-23p40, IL17A, IL-21 and TNF-α ) and biomarkers, C protein reactive (CPR) and procalcitonin (PCT), in septic patients Methods: This was a prospective cohort study performed in three intensive care units, from September 2007 to September 2010 enrolling patients with sepsis (infection associated with organ dysfunction), and septic shock (hypotension refractory by fluids infusion requiring vasopressor). Blood samples were collected up to 48h after the development of first organ dysfunction (D0) and on the 7th day after inclusion in the study (D7) Results: Ninety-five patients were enrolled, with median age 64 years (interquatile?48-78), APACHE II: median 19 (14-22), SOFA: median 8 (5-10); 24.2% were admitted in ICU with sepsis and 75.8% with septic shock.
cord-003707-fbe47bgi	2019	
cord-003899-a4w2nnos	2019	title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs We found that high dose 25-hydroxyvitamin D(3) supplementation could ease intestinal injury and inhibit intestinal immune response induced by porcine epidemic diarrhea virus (PEDV), suggesting that feeding a high dose of 25-hydroxyvitamin D(3) could be used as an approach against PEDV infection. ABSTRACT: We conducted this experiment to determine if feeding 25-hydroxyvitamin D(3) (25(OH)D(3)) to weaned pigs would alleviate porcine epidemic diarrhea virus (PEDV) infection and immune response. Porcine epidemic diarrhea virus (PEDV) infection causes severe damage to the intestinal function and barrier integrity of pigs [1] , leading to diarrhea, vomiting, dehydration, and high mortality in piglets [2] . In summary, the results of the current study indicate that dietary supplementation of 155.5 µg/kg 25(OH)D 3 alleviated the severity of diarrhea of piglets infected with PEDV by improving the intestinal structure and immune response, and maintaining regular intestinal function.
cord-004016-iaktm72a	2019	
cord-004096-obrq7q57	2020	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.
cord-005460-ezrn8cva	2017	Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] .
cord-005497-w81ysjf9	2020	The positive NC group had more plasma transfusion (p-value 0.03) and a lower median hematocrit at 24 hrs (p-value 0.013), but similar hospital length of stay (p=0.17) and mortality rate (p=0.80) Conclusions: NC at ICU admission identifies subclinical AKI in TBI patients and it maight be used to predictclinical AKI. In patients with pneumonia requiring intensive care (ICU) admission, we hypothesise that abnormal right ventricular (RV) function is associated with an increased 90-day mortality. The objective of this study was to describe the incidence of each AKI stages as defined by KDIGO definition (with evaluation of urine output, serum creatinine and initiation of renal replacement therapy (RRT)), in a mixed medical and surgical population of patients hospitalized in ICU and PCU over a 10-year period (2008-2018). This study aimed at investigating the relationship of goal-directed energy and protein adequacy on clinical outcomes which includes mortality, intensive care unit(ICU) and hospital length of stay (LOS), and length of mechanical ventilation (LOMV).
cord-006984-x1r99rlm	2015	At wk 10, relative weights of liver and gizzard of Group IF were heavier (P < 0.05) than other treatments; activities of pepsin, GP, trypsin and chymotrypsin of IF pullets were significantly greater than other treatments as was mRNA expression for pepsinogens A (25.9 vs. The first experiment was designed to determine whether the addition of a commercial IF product (Arbocel RC, JRS Co. Inc., Rosenberg, Germany) in the diets of young layer-strain pullets between the ages of 8 and 18 wk influenced supply organ growth and proteolytic enzyme activities in the proventriculus, pancreas, and small intestine. Feeding the IF diet to the older pullets (13 to 18 wk of age) for 5 wk (Group C-IF) had no significant effect (compared to controls) on activities of pepsin or the three pancreatic enzymes measured (Table 4 ).
cord-007580-qwh8ei60	2014	We had three major goals: to determine the rate of viral recovery from cases of nonepidemic acute or subacute follicular conjunc tivitis; to compare the accuracy of clinical diagnoses with that achieved by culture or serologic studies, or both; and to explore the possible role of serum antibody in the forma tion and maintenance of corneal subepithelial infiltrates. 4 VIRAL KERATOCONJUNCTIVITIS 663 antibody titers to vaccinia, herpes, coxsackievirus A-9, A-16, and A-21, and four strains of acute hemorrhagic conjunctivitis virus were similarly assayed by serum neutraliza tion tests in human diploid fibroblast tissue culture. Table 2* shows the difference between the number of positive isolates ob tained by culturing before or after the eighth * All of the data for the epidemic keratoconjunc tivitis group were published elsewhere, except for the corneal quantitative material in clinical studies.'' day of illness.
cord-009424-0jh0945y	2020	To explore a more effective way to establish a novel convert communication channel over compressed speech stream, this paper presents a steganography method based on modulation of the excitation pulse positions of the G.723.1 low-bit rate codec and G.729A speech codec as the research scenario. Experimental results show that the proposed steganography algorithm of G.723.1 speech codec with an embedding rate of 3.1% and secret information transfer rate of 166 bits/s results in \ 5.7% degradations in perceptual evaluation of speech quality (PESQ) scores, which indicates a high degree of imperceptibility. As to the proposed steganography algorithm of G.729A speech codec, our method can achieve 400 bite/s secret information communication with 3% embedding rate, while the capacity and the degradation rate of the PESQ score for the carrier speech is less than 7%, indicating that the hidden method studied has good privacy and efficacy.
cord-009969-ln91qfg4	2019	
cord-010119-t1x9gknd	2017	Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip).
cord-011172-1nhvbvy8	2020	In our current study, we conducted a cross-sectional national survey of physicians in five pediatric subspecialties (neonatology, critical care, palliative care, emergency medicine, and hematology-oncology) to: (1) characterize existing institution -sponsored wellness offerings; (2) determine utilization of available institution -sponsored wellness activities; and (3) identify interventions physicians wish were available to them. Availability of debriefs/critical incident management, Schwartz Center Rounds, pet therapy, and organized team building events were significantly different across subspecialties (Supplementary There were significant differences in utilization of almost all institution-sponsored wellness activities across pediatric subspecialties (Supplementary Table S2 ). Respondents'' free-text responses (Fig. 2) for "wish lists" for specific institutional supports to combat compassion fatigue and burnout were coded into four main categories: social/emotional support, improvements to leadership, organizational support, and modifications to the physical work environment. [4] [5] [6] [7] In this cross-sectional national survey of pediatric subspecialists, we present the first comprehensive evaluation of availability and utilization of institution-sponsored physician wellness activities.
cord-014597-66vd2mdu	2018	Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line.
cord-014900-yw088jvf	2011	title: Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis Water use efficiency and the root-to-shoot ratio increased significantly in response to water deficit, indicating a high tolerance to drought. Weak water deficit did not decrease root biomass production, but significantly increased the production of glycyrrhizic acid (by 89%) and liquiritin (by 125%) in the roots. Although the responses of the metabolites to drought have been investigated in some medicinal plants [4, 10] , no reference concerning the effect of various water deficit levels on their production by lic orice roots is available. The present study aims to determine the effect of water deficit on gas exchange, biomass and secondary metabolites production in licorice plants. At 60-70% WC, the amounts of glycyrrhizic acid and liquiritin in plant roots were the highest among the studied four levels of soil water con ditions: the gain increased by 85.0 and 119.4%, respectively (Figs.
cord-015527-ph576eji	2019	Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species.
cord-015684-q10sx1dm	2009	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.
cord-016308-qzkcwrit	2015	• 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.
cord-017184-1ewi3dka	2008	In this disease, microorganism phagocytosis by polymorphonuclear (PMN) leukocytes appears annulled, and the patient is subject to severe infections supported by capsular bacteria: the deficiency, described in association with severe and recurrent infantile infections [175, 485, 487] , depends on the lack of mannose-binding lectin (MBL) [487] , its Primary Immunodeficiencies a possible atopy dependence on IgA underproduction rather than on IgE hyperproduction ( Fig. 4.1 ): in children with levels of IgA at the minimum normal level, and followed from birth until the age of 18-23 months, a greater severity of atopic manifestations and an increased cumulative incidence of asthma, AD and otitis media with effusion (OME) were observed compared to controls.
cord-017367-15o6g57q	2008	While affected by many occupational hazards, some of which are cited in Table 3 .3, women working in the cleaning industry are also disadvantaged due to the fact that (Gavana, Tsoukana, Giannakopoulos, Smyrnakis, & Benos, 2005; Gyorkos et al., 2005; Nakazono, Nii-no, & Ishi, 1985; Skillen, Olson, & Gilbert, 2001; Valeur-Jensen et al., 1999) • Vascular problems (Kovess-Masfety, Sevilla-Dedieu, Rios-Seidel, Nerriere, & Chee, 2006) of the lower extremities due to extended standing (Sandmark, Wiktorin, Hogstedt, Klenell-Hatschek, & Vingard, 1999) in upright position • Voice disorders due to overuse of vocal chords Duff, Proctor, & Yairi, 2004; Kooijman et al., 2006; Kosztyla-Hojna, Rogowski, Ruczaj, Pepinski, & Lobaczuk-Sitnik, 2004; Roy, 1999; Sliwinska-Kowalska et al., 2006; Sulkowski & Kowalska, 2005; Thibeault, Merrill, Roy, Gray, & Smith, 2004; Williams, 2003) • Exposure to increased levels of noise (Behar et al., 2004) • Musculoskeletal problems (Fjellman-Wiklund, Brulin, & Sundelin, 2003; Sandmark, 2000; Yamamoto, Saeki, & Kurumatani, 2003) (handling and lifting small children in day care centres, physical education teachers, inadequate body posture) • Work-related stress (Fjellman-Wiklund et al., 2003; Zidkova & Martinkova, 2003) • Children''s or adolescent''s violent behavior (Lawrence & Green, 2005) 
cord-017499-51yy7y9n	2008	Thus, -selective opioids like morphine, fentanyl and sufentanil, due to the high density of binding sites, mediate their main action within the brain stem and the midbrain. This sterospecificity of opiate action supports the concept of selective receptor binding to a site, which is able to distinguish in "handedness or goodness of fit" of an opioid molecule maximal response induced by administration of the active agent. On the other hand mixed agonist/antagonists, such as pentazocine, nalorphine, levallorphan, nalbuphine and butorphanol, demonstrate characteristics, which enable them to displace a pure agonist at the receptor site (antagonistic effect), but at the same time when administered by themselves, they induce opioid related effects such as analgesia and respiratory depression (agonistic effects; Table II-7) . However, a less potent opioid like codeine or tramadol, even when given in dosages higher than their therapeutic margin, will not induce a clinically relevant respiratory depressive effect ( Figure II-34) .
cord-018884-os0faovj	2019	There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. Respiratory viral infections are typically caused by rhinovirus (RhVs), coronavirus (CoV), respiratory syncytial virus (RSV), influenza (FLU), parainfluenza (PIV), human metapneumovirus (hMPV), and adenovirus (AdV) ( Table 9 .1). Antiviral resistance is of considerable concern among immunocompromised patients infected with influenza virus, and testing should be strongly considered in SOT undergoing treatment who fails to have an appropriate clinical response within 3-5 days of initiating antiviral therapy or who has a relapsing course despite ongoing therapy. Adjunctive therapy with corticosteroids has been purposed for SOT with influenza and RSV and for lung transplant recipients with any RVs with LRTI because of the risk of both acute and chronic rejection [13] . Update in the treatment of non-influenza respiratory virus infection in solid organ transplant recipients
cord-021013-xvc791wx	2008	In animals, we can observe the analogous situation in that many insects and other invertebrates (especially those which are sessile and unprotected by armor), but also some vertebrates, store secondary metabolites for their defense which are often similar in structure to plant allelochemicals (1,4,12,16,17,28-30, [494] [495] [496] 503) . During the next three decades this concept was improved experimentally, and we can summarize the present situation as follows Although the biological function of many plant-derived secondary metabolites has not been studied experimentally, it is now generally assumed that these compounds are important for the survival and fitness of a plant and that they are not useless waste products, as was suggested earlier in the twentieth century (34, 35) . These "generalists," as we can also call this subgroup of herbivores, are usually deterred from feeding on plants which store especially noxious metabolites and select those with less active ones (such as our crop species, where man has bred away many of the secondary metabolites that were originally present; see Table XI ).
cord-021951-xxvol17t	2017	
cord-022147-istz1iql	2016	• Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers'' homes, are necessary to prevent further illness.
cord-022281-xn0cf33a	2009	In the evaluation of a patient with sore throat, the primary concern is usually accurate diagnosis and treatment of pharyngitis caused by group A streptococci, which accounts for about 15% of all episodes of pharyngitis. Within 24 hours of institution of therapy with penicillin, it is difficult to isolate group A streptococci from patients with acute streptococcal pharyngitis, and infected children can return to school. In general, patients with a negative result of the rapid test do not require treatment before culture verification unless there is a particularly high suspicion group A streptococcal infection (e.g., scarlet fever, peritonsillar abscess, or tonsillar exudates in addition to tender cervical adenopathy, palatal petechiae, fever, and recent exposure to a person with group A streptococcal pharyngitis). Therapy with an appropriate antibiotic within 9 days of onset of symptoms is highly effective in preventing rheumatic fever, but acute glomerulonephritis is not prevented by treatment of the antecedent streptococcal infection.
cord-022292-msz4au4b	2009	
cord-022380-49oti4zg	2009	Because infectious diseases may represent the most common cause of time lost from work, it is important for the clinician concerned with occupational medicine to understand the relationship of specific infections to specific work environments and practices, and to give at least as much attention to prevention as to diagnosis and treatment. Susceptible household contacts of infected adults and children pose a transmission risk in the workplace during the period of virus shedding, beginning about 10 days before the development of rash (about 1 week after exposure) until 7 days after rash appears. Varicella vaccination is also recommended for susceptible adolescents and adults who will have close contact with persons at high risk for serious complications of acquired varicella, including healthcare personnel and susceptible family contacts of immunocompromised individuals. The ACIP recommends that all healthcare personnel be immune to varicella, either from a reliable history of prior varicella infection or vaccination, to reduce the risk of infection and its complications, and to decrease the possibility of transmission of varicella zoster virus to patients (Table 22.
cord-022642-f784qdr5	2006	This first detailed report of subtidal macroalgal communities in New South Wales describes a several‐year study of the benthic communities along a transect in the upper sublittoral region of a rocky headland at Plantation Point, Jervis Bay. Eighty‐nine species of algae were recorded, five of which were previously unrecorded for New South Wales. Storms, seasonal variation and longer term changes all affected the abundance and distribution of the algal species growing along the transect and hence the floristic composition of the area. However both this (with twenty species) and the next collection in July, in which twentynine species were recorded, followed closely upon storms which denuded many rock surfaces in the transect area of their algae. The following algae were to be found at most stations throughout the transect (Table 2) : Cladophora repens, Enteromorpha intestinalis, Lobophora variegata, Sphacelaria tribuloides, Stypopodium zonale, Zonaria turneriana, Acrosorium uncinatum, Fosliella farinosa, Gelidium pusillum, Heterosiphonia australis, Laurencia brongniartii, Plocamium cartilagineum, Polysiphonia sp.
cord-024981-yfuuirnw	2020	The World Health Organization and the Pan American Health Organization define a disaster as "an event that occurs in most cases suddenly and unexpectedly, causing severe disturbances to people or objects affected by it, resulting in the loss of life and harm to the health of the population, the destruction or loss of community property, and/or severe damage to the environment. After the events of 9/11, much attention has been given to the possibility of another mass casualty act of terrorism, especially with weapons of mass destruction, that include chemical, biological, nuclear, radiological, and explosive devices (CBNRE), or other forms of violence such as active shooter incidents and mass shootings (Jacobson and Severin 2012) . Antidote therapy should be given as usual for nerve agents, including atropine, diazepam, and pralidoxime chloride (United States Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, National Library of Medicine 2019; United States Department of Health and Human Services, Chemical Hazards Emergency Medical Management (CHEMM) 2019).
cord-025300-sl9kredk	2020	Tabular data to Knowledge Graph (KG) matching is the process of assigning semantic tags from KGs (e.g., Wikidata or DBpedia) to the elements of the table. We have selected the following tasks for the semantic annotation of tabular data: (i) Column-Type Annotation (CTA), (ii) Cell-Entity Annotation (CEA), and (iii) Columns-Property Annotation (CPA). The above matching tasks are challenging for various reasons including but not limited to: (i) Lack of metadata or uninformative table and column names, a typical scenario in Web tables and real-world tabular data. The final outcome is a collection of SPARQL queries, each resulting in tabular data with (i) columns that can be annotated with the expected type (class for the case of object properties), (ii) cell values that can be annotated with instance URIs, and (iii) pairs of columns that can be annotated with a property.
cord-026009-rdhuc2n2	2009	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).
cord-026031-hnf5vayd	2009	Fresh whole blood Coagulopathy with active hemorrhage (disseminated intravascular coagulation, thrombocytopenia; massive acute hemorrhage; no stored blood available) Stored whole blood Massive acute or ongoing hemorrhage; hypovolemic shock caused by hemorrhage that is unresponsive to conventional crystalloid and colloid fluid therapy; unavailability of equipment required to prepare blood components Packed red blood cells Nonregenerative anemia, immune-mediated hemolytic anemia, correction of anemia before surgery, acute or chronic blood loss Fresh frozen plasma Factor depletion associated with active hemorrhage (congenital: von Willebrand''s factor, hemophilia A, hemophilia B; acquired: vitamin K antagonist, rodenticide intoxication, DIC); acute or chronic hypoproteinemia (burns, wound exudates, body cavity effusion; hepatic, renal, or gastrointestinal loss); colostrum replacement in neonates Frozen plasma Acute plasma or protein loss; chronic hypoproteinemia; (contains stable colostrum replacement in neonates; hemophilia B and clotting factors) selected clotting factor deficiencies Platelet-rich plasma* Thrombocytopenia with active hemorrhage (immune-mediated thrombocytopenia, DIC); platelet function abnormality (congenital: thrombasthenia in Bassett hounds; acquired: NSAIDs, other drugs) Cryoprecipitate
cord-028751-71bf4w44	2020	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 .
cord-029462-jm5qwxhz	2020	We performed an epigenome-wide association study (EWAS) to identify placental DNA methylation associated with maternal plasma concentration of POPs in early gestation (10 weeks 0 days to 13 weeks 6 days) among 260 pregnant women participating in the Eunice Kennedy Shriver National Institute of Child Health and Human Development''s (NICHD) Fetal Growth Studies-Singletons cohort (which comprised 2802 pregnant women from 12 clinic sites within the USA). In total, maternal early pregnancy plasma concentrations of POPs were significantly associated with placental DNA methylation at 214 CpG sites annotated to 205 genes (BACON-corrected false discovery rate (FDR) p values < 0.05, nominal p values ranging from 2.61 × 10 −21 to 2.11 10 −7 , Supplementary Table S3 ). The correlations between DNA methylation at the POPs-associated CpG sites and neonatal anthropometry suggest that placental epigenetic mechanisms may underlie the influence of specific maternal plasma POP concentrations on fetal growth.
cord-031330-zgzq35fe	2020	Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. Designed library was used for virtually screening against nsP3 of CHIKV, to get potential lead molecules based on minimum total binding energy, drug-likeness, and bioactivity score [27] . Further, temperature dependent molecular dynamic simulations (tdMD) and MM-GBSA of screened compound-nsp3 of CHIKV complex was performed to analyze the structural stability of the complex. In this study, best five compounds from designed library were docked with active site of nsp3 of CHIKV using Pardock to elucidate their molecular interactions as in Table 9 and Figure 3 .
cord-031416-ytbs95wi	2020	In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. Where precision medicine will allow researchers to predict more accurately which therapies will work better in which groups of people, combination therapy is a keystone of cancer therapy and potentially reduces drug resistance, while simultaneously providing therapeutic anticancer benefits, such as reducing tumor growth and metastatic potential, arresting mitotically active cells, reducing cancer stem cell populations, and inducing apoptosis. In this research, we have used our previously proposed ABSM model [28] as a cancer system, i.e., we may fit it to a given patient and use it for demonstrating our system biology-based approach for designing combination therapy in cancer precision medicine.
cord-032174-qu5mm9r1	2013	The reading value of the flowmeter 20 L/min is the indication value in the calibration condition, so the actual flow rate q 1 through the flowmeter should be According to the actual collected particle concentration 18.31 L/min after correction, the calculated indoor particle concentration is 371.4#/L, so the indoor air cleanliness level does not reach Class 7. The example of the application of Fig. 16 .10 is shown as follows: When the particle counter with small sampling volume 2.83 L/min is used to detect particles with diameter 5 μm (only for this particle size) from airflow with velocity 0.5 m/s, should any correction be made? For the common particle counters with large, medium, and small sampling flow rates at home and abroad, Reynolds numbers Re in the sampling tube are shown in Table 16 .3. So the following requirement must be satisfied: For particle counter with medium and low sampling flow rates, calculation results are shown in Table 16 .4.
cord-032491-tycd2i95	2020	Between genotype analysis (Table 4 , item e) showed a similar effect of genotype following morphine as oxycodone treatment in that, when compared with flMORs, A2aflMORs showed an enhanced response at the higher doses used, 10 (p = 0.0001) and 15 (p = 0.004) mg/kg, whereas D1flMORs showed a reduced response at 15 mg/kg (p = 0.004), but not 10 mg/kg. The flMORs showed a genotype  day interaction as both oxycodone (p = 0.002) and morphine (p = 0.02), but not saline, induced sensitization ( Fig. 3D ; Table 4 , item h). The D1flMORs showed no sensitization effect following oxycodone or morphine and this response was not different from saline ( Fig. 3E ; Table 4 , item i). Our findings show that this A2a-MOR population is an apparent subset of D2 medium spiny neurons that controls the locomotor sensitivity to oxycodone and morphine and drug-seeking behavior during extinction. Deleting MORs from ChAT neurons does not alter oxycodone-induced hyperlocomotion and sensitization but does increase the locomotor effect of cocaine and drug-seeking behaviors following opioid IVSA.
cord-033453-557obi3r	2020	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.
cord-034448-wgvvdmxe	2020	title: Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed.
cord-048360-n9sih438	2007	To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates.
cord-102319-2b404su7	2020	title: Increased brain volume from cereal, decreased brain volume from coffee -shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants Results: We investigated diet effects in the UK Biobank data and discovered anti-correlated brain-wide grey matter volume (GMV)-association patterns between coffee and cereal intake, coincidence with their anti-correlated genetic constructs. These genetic factors may further affect people''s lifestyle habits and body/blood fat levels through the mediation of cereal/coffee intake, and the brain-wide expression pattern of gene CPLX3, a dedicated marker of subplate neurons that regulate cortical development and plasticity, may underlie the shared GMV-association patterns among the coffee/cereal intake and cognitive functions. To further understand the biological insights of the shared variants of cereal intake and coffee intake, we performed linear regression analysis to examine the pairwise associations between the independent lead SNPs and other diets, lifestyle, and body/blood fat covarying age, sex, the top 40 25 genetic principal components.
cord-103733-blam1f4c	2020	title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. Conclusion Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera. SUMMARY Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes. Our metagenomic analysis yielded improved 85 outcome predictions compared to 16S rRNA sequencing, and identified bacterial genes 86 associated with remaining uninfected after exposure to V. Applied to the Midani 230 2018 cohort, this model predicted outcomes significantly better than random (shuffled labels) 231 using species, strains or pathway data, but not gene families ( Table 1 ; see Table S3 for p-232 values).
cord-131094-1zz8rd3h	2020	Despite a higher computational cost, results indicated an overall higher classification accuracy, precision, recall and F1-score brought about by either quantum AFs on five of the seven bench-mark datasets, thus demonstrating its potential to be the new benchmark or gold standard AF in CNNs and aid image classification tasks involved in critical applications, such as medical diagnoses of COVID-19 and PD. Despite a higher computational cost (four-fold with respect to the other AFs except for the CReLU''s increase being almost three-fold), the results achieved by either or both the proposed QReLU and m-ReLU AFs, assessed on classification accuracy, precision, recall and F1-score, indicate an overall higher generalisation achieved on five of the seven benchmark datasets ( Table 2 on the MNIST data, Tables 3 and 5 on PD-related spiral drawings, Tables 7 and 8 on COVID-19 lung US images).
cord-253827-5vodag6c	2020	We estimate the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. 2 Counterfactual policy simulations using our empirical estimates suggest that mandating indoor masks nationwide in early July could have reduced weekly new cases in Canada by 25 to 40% on average by mid-August relative to the actually observed numbers, which translates into 700 to 1,100 fewer cases per week. Our results on business/gathering regulations and school closure suggest that reduced restrictions and the associated increase in business or workplace activity and gatherings or school re-opening can offset, in whole or in part, the estimated effect of mask mandates on case growth, both in our sample and subsequently. CKS (2020), whose estimation strategy we follow, exploit U.S. state-level variation in the timing of mask mandates for employees in public-facing businesses, and find that these mandates are associated with 9 to 10 percentage points reduction in the weekly growth rate of cases.
cord-254193-hsu0yo5c	2020	
cord-254667-yafcy8ul	2020	METHODS: Patients were consecutively enrolled during the Italian lockdown among those waiting for bariatric surgery or attending a post-bariatric follow-up, and were asked to complete through an online platform the Depression Anxiety Stress Scales-21 and a self-assessment questionnaire of 22 items evaluating the resilience, change in eating behavior and emotional responses referring to the ongoing pandemic. Univariate and multivariate logistic regression model was performed to analyze the effect of the COVID-19 pandemic (measured through a questionnaire whose scores were used as independent variable: emotionality domain, resilience domain and eating related) on DASS derived condition of depression, anxiety and stress used as the discrete dependent variable. Regarding the increased snacking, the univariate analysis showed that the three statuses from the DASS questionnaire Table 5 DASS derived depression, anxiety and stress as markers of lifestyle and eating related behavioral characteristic during COVID-19 pandemic in the post-bariatric population Oucomes: three discrete and separately analyzed outcomes from the interview questionnaire were used as dependent variables: increased hunger; increased snacking and increased impulsivity in eating.
cord-255087-fwsicgv1	2020	To better understand how science-based university spin-offs can be endowed for success, the pre-formation stage of 30 ventures co-founded over a 40 year period by a star-scientist-entrepreneur is analysed by matching his 363 co-invented US patents granted to 1476 co-authored publications and these 30 ventures. Employing the extended case method, including the analysis of extensive archival data, iterative interviews, and this unique, longitudinal, multi-level dataset, existing dynamic capabilities theory is confronted and extended with evidence as to how a star-scientist-entrepreneur senses and shapes and seizes opportunities to endow university spin-offs pre-formation. A process model was developed, depicting the key role played by the SSE in four pre-formation entrepreneurial capabilities which endow these science-based university spin-offs for success: technology-market matching, claiming and protecting the invention, attracting and mentoring the founding team, and strategic 48 timing.
cord-255140-3dwqqgv1	2013	
cord-256065-zz2907h0	2020	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.
cord-257336-rpx71ww5	2020	Given the rapidly growing number of cases, a detailed report of clinical characteristics recognized in EVALI cases with radiological findings of lung injury will not only provide a better understanding of the natural history of the disease, but also create a strong foundation for the development of evidence-based guidelines for the diagnosis, prognosis, and treatment of this condition. Here, we present data from a series of ten cases that recognize clinical characteristics in hospitalized EVALI patients with radiological findings of lung injury. Our ten-case series data recognized that clinical characteristics in hospitalized EVALI patients with radiological findings of lung injury, may include both respiratory and gastrointestinal or constitutional symptoms and based on the current literature may be misdiagnosed. E-cigarette or vaping product-use-associated lung injury (EVALI): A case report of a pneumonia mimic with severe leukocytosis and weight loss
cord-257958-yehnlabq	2020	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).
cord-257969-2tax8ajw	2020	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) .
cord-260014-q5sug7uu	2020	We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study
cord-260728-4w23kwzu	2016	Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71).
cord-262760-mf1pn587	2020	By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ).
cord-264814-v4wnmg03	2020	Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure.
cord-264976-6n9cdex6	2020	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.
cord-266036-qhlo99l7	2020	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.
cord-266255-898h9rl1	2020	Thus, in addition to a more severe LHD at baseline, patients whose TR progress represents a subset characterized by an accelerated course of LHD, including a more rapid increase in LA size, pulmonary pressures, and higher rates of new atrial fibrillation, reduction in LVEF, worsening valvular disease, and need for pacemaker or device therapy. Increased LA LGE has been found to be associated with future diagnosis of atrial arrhythmias in patients with preexisting cardiac disease (9) but no study has investigated the prognostic value of LA LGE in a population-based cohort or by use of continuous monitoring. Positron Emission Tomography) study revealed that total sympathetic denervation size independently predicts appropriate ICD therapy for fast VA (7 ACE ¼ angiotensin converting enzyme; ARB ¼ angiotensin-II-receptor blocker; CFR ¼ coronary flow reserve; CI ¼ confidence interval; HED ¼ hydroxyephedrine; HR ¼ hazard ratio; LVEDVi ¼ leftventricular end-diastolic volume index; LVEF ¼ left-ventricular ejection fraction; MBF ¼ myocardial blood flow; NT-proBNP ¼ N-terminal prohormone of brain natriuretic peptide; NYHA ¼ New York Heart Association; RI ¼ retention index.
cord-267866-854rzbrx	2020	We used a pragmatic theoretical approach with a 35 mixed methods methodology, to categorise the results within three distinct levels 36 ( individual, school/department, and institution), supporting the design and 37 implementation of resilience-building strategies for academics and institutional leaders. We used a pragmatic theoretical approach with a 35 mixed methods methodology, to categorise the results within three distinct levels 36 ( individual, school/department, and institution), supporting the design and 37 implementation of resilience-building strategies for academics and institutional leaders. Architecture and Design (SEAD) established a resilience Steering Group (i.e., a community 122 of practice and research project) to explore how we can prepare staff and learners and 123 promote L&T continuity in the event of significant disruption. The results and discussion are presented within the four major themes identified in our data 220 analysis: our community of practice''s characterisation of resilience to disruption, followed by 221 the benefits, barriers, and incentives to building resilience.
cord-268645-5op2m7pu	2015	
cord-269711-tw5armh8	2013	Abstract The effects of a number of vaccination strategies on the spread of an SIR type disease are numerically investigated for several common network topologies including random, scale-free, small world, and meta-random networks. These strategies, namely, prioritized, random, follow links and contact tracing, are compared across networks using extensive simulations with disease parameters relevant for viruses such as pandemic influenza H1N1/09. (2006) compared the efficacy of contact tracing on random and scale-free networks and found that for transmission rates greater than a certain threshold, the final epidemic size is smaller on a scale-free network than on a corresponding random network, while they considered the effects of degree correlations in Kiss et al. We investigate numerically whether network topologies affect the effectiveness of vaccination strategies started with a delay after the disease is widespread; for example, a 40 day delay as in the second wave of the 2009 influenza pandemic in British Columbia, Canada (Office of the Provincial Health Officer, 2010).
cord-270892-ycc3csyh	2010	[79] [80] [81] [82] Taken together, the results of natural cold studies as well as of experimental infection in human volunteers clearly demonstrate that HRV are able to replicate in the upper as well as in the lower airways. Such an anti-HRV drug would have to be (i) with broad spectrum activity because of the high number of HRV serotypes, (ii) administered very early in infection to demonstrate a good antiviral effect because of the fast infection kinetics, (iii) very safe because of the broad application by millions of people, and (iv) directed against a highly conserved target with low risk of resistance development. The HRV-induced CPE, infectious virus titers, viral protein expression, and RNA synthesis can be chosen as parameters to evaluate the anti-HRV activity of compounds in cell-culture based assays. Due to the lack of a small-animal model for HRV infection until 2008, the experimental human challenge model has to be used to approve effects of potential antiviral drugs under controlled conditions in preclinical studies.
cord-270940-acwkh6ed	2005	Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans.
cord-270970-9gtnsyts	2020	
cord-271032-imc6woht	2020	Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) .
cord-271599-1yu1yl12	2020	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.
cord-273906-s7l0yxc0	2020	Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] .
cord-273992-xddikzxs	2004	The main impact of the study is that the utilization of genetically modified (GM) yeast produced by recombinant DNA technology genomic strategies could circumvent the bioprocessing problems that otherwise result from the bioprocess perturbations: this is as a result of oxidative stress caused by ROS, which is avoidable by deployment of appropriate antioxidants such as vitamins E, C and D (and antioxidant proteins and enzymes often of microbial origin via recombinant DNA technology). Catalases ( Table 3 ) in yeasts and other micro-organisms (Antioxidants such as vitamins E and C chain terminate the formation of membrane-degrading ROS) relates to more than just structural damage that is sometimes obvious and predictable: functional damage may also follow. Avoidance biostrategies against ROS and RSS in many oxidatively stressed bioprocesses that utilise yeasts (and other micro-organisms) are essential where human therapeutic proteins are expected to be produced in high yield.
cord-275258-azpg5yrh	2019	title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. We then present the first use of force-directed graphs to produce an intuitive visualization of sequence space, and select target RdRPs without solved structures for homology modelling. The solved structure has 10 other sequences in its proximity in the three-dimensional space, roughly Table 5 Homology modelling at intra-order, inter-family level.
cord-275720-kf9m4zho	2012	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.
cord-279528-41atidai	2019	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
cord-279551-py2awuav	2015	title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain.
cord-280624-7v8xuicg	2020	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)
cord-281464-15ld7knm	2020	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] .
cord-281668-960trqex	2020	These inhibitors further provided the option of varying the leaving group that targets S2� site; more hydrophobic substituents were preferred at this position as comparison of ki/Ki values of the inactivation exhibited the following trend for Aa: Gly < Ala < Val < Leu < Phe < 4-NO2-Ph. The nitrophenyl analog (Entry 7, Table 2 ) which incur both hydrophobicity and electron-withdrawing property exerted the maximum potency and selectivity for cathepsin L over other tested cysteine proteases. These inhibitors further provided the option of varying the leaving group that targets S2� site; more hydrophobic substituents were preferred at this position as comparison of ki/Ki values of the inactivation exhibited the following trend for Aa: Gly < Ala < Val < Leu < Phe < 4-NO2-Ph. The nitrophenyl analog (Entry 7, Table 2 ) which incur both hydrophobicity and electron-withdrawing property exerted the maximum potency and selectivity for cathepsin L over other tested cysteine proteases.
cord-282783-ps5jyjkl	2020	The Childhood Cancer Survivor Study showed a 10-fold higher risk of pericardial disease in all CCS versus siblings (30year cumulative incidence, 3 .0%) and a dose-response relation with chest RT (11) . The literature on ECG abnormalities in large cohorts of long-term CCS is sparse (46, 47) , Data on the use of ambulatory ECG monitoring to define the prevalence of brady-and tachyarrhythmias induced by cardiotoxic cancer treatments are needed, but must be carefully weighed against the potential patient burden and clinical significance. Interestingly, a prior study in testicular cancer survivors showed that those patients who were exposed to cisplatin-based chemotherapy nearly 3 to more than 20 years ago had a more severe reduction in FMD and higher levels of circulating endothelial cells than those not exposed (13) .
cord-287136-3cml1shh	2020	RESULTS: In the four weeks after lockdown in Germany began, we observed a massive drop of 63.8% in pediatric emergency healthcare utilization (mean daily visits 26.8 ± SEM 1.5 in 2019 vs. Severe cases of COVID-19 remained comparatively low in Germany (n = 163,175 confirmed SARS-CoV-2 infections with 6.692 fatalities as of May 4th 2020 [13] ), and the healthcare system has thus far been spared an untenable influx of critically ill patients. When we compared daily visit frequencies between 2019 and 2020, we observed a striking reduction in the number of patients presenting to the ED after March 16th 2020, the day that school closures and a nationwide lockdown began (Fig. 1a) . The proportion of daily patients with infectious diseases or signs and symptoms of infection, however, did not differ significantly between calendar weeks 12 to 15 from one year to another (Table 1 ; Fig. 2e ).
cord-287684-z3l9tsir	2020	Our aim was to inform further research and service responses by conducting, in the early stages of the COVID-19 pandemic, a survey of the perspectives and experiences of staff working in inpatient and community settings across the UK health and social care sectors.
cord-287711-gw8mgg4m	2017	Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters.
cord-288644-ywaefpe8	2020	We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir.
cord-288842-qr8bzp4r	2004	However, a 1,25-(OH)(2)D(3) suppression of several intra-/intercellular matrix modeling proteins such as sodium/potassium ATPase, claudin 3, aquaporin 8, cadherin 17, and RhoA suggests a vitamin D regulation of tight junction permeability and paracellular calcium transport. The maximum fold change of the expression level of calbindin D 9k -the vitamin D-dependent cytosolic calcium binding protein within 6 h after the treatment, was 1.6-fold at 3 h (at 1 h after injection there was 1.4-fold increase) ( Table 2 ). Our data confirm previously published data that 1,25-(OH) 2 D 3 up-regulates expression of transcellular calcium transport genes such as calbindin D 9k , plasma membrane Ca 2+ ATPase, epithelial calcium channels, TRPV5, and TRPV6 (Table 2 and Fig. 1 ) [1, 4, 7, 8, [12] [13] [14] [15] .
cord-290788-6y0vjhux	2020	The combination of sorting antigen-specific memory B cells with determining immunoglobulin (Ig) genes at the single-cell level enables the isolation of monoclonal antibodies (mAbs) in individuals. Currently, multiple strategies have been reported to generate human neutralizing mAbs against Zika infection, including sequencing antigen-specific memory B cells [8, 9] or generating Epstein-Barr virus-immortalized memory B cells from Zika patient samples [10] , and identifying functional mAbs from phage display naïve antibody libraries [11] . Here, we introduce a method to apply Zika envelope (E) glycoproteins, which play pivotal roles in virus entry and contain important neutralizing epitopes, to sort single memory B cells from a convalescent Zika patient. Fig. 4 Strategy to clone and express Zika E-specific human mAbs. The Ig genes from the sorted cells were determined and cloned into the expression vectors by a reported approach with some modifications [13, 18] .
cord-291032-l813q689	2020	These results indicate the livelihoods of urban Kenyan families were deleteriously affected by COVID-19 lockdown, with a likely rise in household air pollution from community-level increases in polluting fuel use. [8] [9] [10] To combat the adverse health, environmental and social effects of reliance on polluting fuels and associated HAP exposures, 11, 12 several African countries (e.g. Kenya, Ghana, Cameroon), have set aspirational targets for rapid market expansion of liquefied petroleum gas (LPG) for cooking. This timely pre-post study documented an extremely high proportion (88%; n=180) of households experiencing food insecurity due to income decline/cessation during the COVID-19 lockdown in a Kenyan urban informal settlement ( Table 3) . Elevated HAP exposures among the study population may offset potential health benefits from the decrease in ambient air pollution levels during COVID-19 lockdown ( Figure 3 ), 39 which were documented in studies conducted in high-income countries.
cord-292698-w7wrwj95	2020	The extended durations of these closures present unique challenges, as many families rely on the school as a source of physical activity, mental health services, psychosocial support, child care, and food security. NASN also provides, "Guidance for School Nurses to Safely Send and Receive Resources Between School and Home During COVID-19," to ensure safe transfer of both student and school property, including backpacks, student medication, school supplies, electronic devices, and ongoing food services to socially and medically disadvantaged families (NASN, 2020). On the national level, the Families First Coronavirus Response Act includes a provision that expands protection for employees that during a public health emergency are unable to work due to a need for leave to care for their child because the school or day care has been closed or the child care provider is unavailable (Moss et al., 2020) . To provide families in your community with outdoor physical activities that follow social distancing guidelines, visit the Healthy Children website in Table 1 .
cord-293857-o8rlqsq5	2015	Also, we will outline successful designs of organic carbamates, including a variety of cyclic ether-derived carbamates, as suitable amide bond surrogates leading to a wide range of novel organic carbamates as potent HIV-1 protease, βsecretase, serine protease, and cysteine protease inhibitors. 172−174 A number of FDA-approved HIV protease inhibitor drugs contain an important carbamate functionality. 179, 230 Further development of carbamate-derived novel HIV-1 protease inhibitors is shown in Figure 12 . This backbone binding strategy to combat drug resistance led to the development of a series of very potent carbamate-derived protease inhibitors. Carbamate derivative 281 (Figure 24 ), a diphenyl phosphonate ester containing a Cbz group and bearing a single amino acid side chain, showed very good inhibitory activity against human plasma kallikrein, useful for the treatment of hereditary angioedema. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation
cord-295028-vlj2ay6d	2020	title: Probability estimation model for the cancellation of container slot booking in long-haul transports of intercontinental liner shipping services To fill this research gap, this study aims to estimate the probability for the cancellation of container slot booking in the long haul transports of the intercontinental liner shipping service by considering the primary influential factors of cancellation behavior. g., booking time, booked volume), the container shipping market (e.g., shipping index, market volatility) and customer information The developed model can assist the container shipping company to improve the loading rate of the ship and to understand how the internal and external influential factors affecting the slot cancellation. The objective of this study is to develop a container booking data-driven model for estimating the probability that a slot booking is cancelled prior to the loading time in a long-haul leg of an intercontinental liner container shipping service.
cord-295689-me50th40	1989	Significant differences from the values prior to infection (day 3) are indicated by *(p<O.O5); **(p<O.Ol) and ***(pc0.001) Treatment with the low dose of chlorpromazine at 1 mg/kg/24 h was without beneficial effect on diarrhoea score, vomiting or survival (Table I) . The decrease in body temperature observed in control piglets after TGE virus and ETEC inoculation was not influenced by the calcium antagonist, whereas administration of the b-adrenergic antagonist resulted in an increase in temperature (Table II) . In the present study most dually infected piglets in the control group and also in some of the treatment groups developed hypovolaemic shock as a result of vomiting, induced by the TGE virus, and diarrhoea, probably induced by a combination of malabsorption (TGE virus) and hypersecretion (ETEC) (Cox, Charlier and Houvenaghel, 1988) . Our results suggest that, of the drugs studied, only chlorpromazine and clonidine are likely to be of value in the treatment of severe diarrhoea of mixed viral-ETEC nature in newly-weaned piglets.
cord-297742-0pfrk5uk	2020	METHODS: We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. The objectives of the Zambia-ISSS were to: (i) monitor the temporal trends of influenza virus circulation; (ii) monitor the circulating influenza virus types and subtypes annually, including pandemic strains; (iii) assess the proportion of patients meeting the ILI and SARI case definition attributable to influenza virus infection; (iv) assess risk factors for influenza-associated severe illness; (v) assess the burden of influenza-associated illness; and (vi) obtain and share clinical samples for annual selection of influenza virus strains for influenza vaccine formulation under the WHO-Global Influenza Surveillance and Response Network.
cord-301150-41lfsedz	2020	title: Assessment of Lockdown Effect in Some States and Overall India: A Predictive Mathematical Study on COVID-19 Outbreak By validating our model to the data on notified cases from five different states and overall India, we estimated several epidemiologically important parameters as well as the basic reproduction number (R(0)). Our result suggests that lockdown will be effective in those locations where a higher percentage of symptomatic infection exists in the population. Furthermore, the trend of the effective reproduction number (R(t)) during the projection period indicates if the lockdown measures are completely removed after May 17, 2020, a high spike in notified cases may be seen in those locations. • Using current estimate of the lockdown rate and different parameters of our mathe-230 matical model (see Table 1 and Therefore, lockdown will be effective in those region where higher 310 percentage of symptomatic infection is found in the population and also larger COVID-19 311 mass testing will be required to isolate the cases.
cord-302414-g5onwhg1	2020	Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches.
cord-302543-ipaoge55	2015	In this chapter we analyze the binding and dissociation kinetics (if applicable) of (1) IFN-gamma as a function of aptamer variants and inclusion of spacer in addition to spacer (Tuleuova et al., 2010) , (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to an LPSCF fiber-optic biosensor (Huang et al., 2009) , (3) cytochrome c mutant to a superoxide biosensor (Wegerich et al., 2009) , (4) CA-II to an ABS ligand on an SPR biosensor surface (Williams et al., 2009 ), (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay (Clark et al., 2010) , and (6) different concentrations of CRP in solution to a sandwich-type assay using a label-free detection method, reflectometric interference spectroscopy (Albrecht et al., 2010) .
cord-303300-89v1weno	2020	The critical procedural pillars of any behavioral study are: (1) programming an experiment in the preferred software (e.g., E-prime, PsychoPy, PsychToolbox, etc.); (2) setting-up the testing machine (e.g., lab-computer, multi-unit testing facility, etc.) and (3) recruiting participants to conduct the study. In comparison to the hegemony of Java, Python, C++ and MATLAB libraries for experimental programming of lab-based studies, Javascript (JS) is the language of choice for online experiments. In comparison to the hegemony of Java, Python, C++ and MATLAB libraries for experimental programming of lab-based studies, Javascript (JS) is the language of choice for online experiments. Generally speaking, what researchers need for online experimentation is the same as what they need for lab-based studies (Figure 1) : (1) a programmed experiment, (2) a server to host the study and (3) a recruiting platform which advertises to participants. The Timing Mega-Study: Comparing a Range of Experiment Generators, Both Lab-Based and Online
cord-304375-l5gvpat3	2012	Some of the compounds showed in vitro anti-plasmodial activity against drug-sensitive CQ(S) (3D7) and drug-resistant CQ(R) (K1) strains of Plasmodium falciparum in the nM range. In this communication, we report synthesis of a set of compounds that possess basic, hydrophobic as well as hydrogen bonding substituents, required for targeting either or both heme as well as DNA, thus providing new antimalarial agents active against chloroquine resistant strains of P. We have evaluated their anti-plasmodial activity, cytotoxicity and cytostatic activity, binding studies with DNA and heme (monomeric as well as m-oxo dimeric) using UVevisible, fluorescence spectrophotometry as well as NMR analysis. The comparison of association constants of 10r and 10c for monomeric and m-oxo heme reveals that both compounds bind strongly with m-oxo heme than monomeric heme and inhibit hemozoin formation by blocking the growing face of heme resulting in the observed anti-plasmodial activity.
cord-304869-l6a68tqn	2011	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.
cord-304909-3wmrjlhy	2016	No attempt has yet been made to collate the current knowledge of potential pathogens detected from species within the family Viverridae (Shepherd, 2008; Bongiovanni et al., 2014) despite the family''s long history of exploitation for human consumption (Abebe, 2003; Shepherd and Shepherd, 2010) , the management of threatened viverrids for conservation (Roberton et al., 2002) , the peri-urban habitation of many species within the family (King et al., 1993; Ninomiya et al., 2003; Sato et al., 2013) and their susceptibility to a number of important zoonotic pathogens including the novel coronavirus responsible for the outbreak of severe acute respiratory syndrome (SARS) (Guan et al., 2003; Tu, 2004) , rabies virus (Matsumoto et al., 2011) and highly pathogenic avian influenza H5N1 (HPAI H5N1) (Roberton et al., 2006) .
cord-305378-jmcuq9c5	2020	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°.
cord-305745-9lngdjow	2020	Chalcones isolated from Angelica keiskei were shown to inhibit both SARS-CoV proteases PLpro and 3CLpro in enzymatic, FRET-based (Table 2) and molecular docking studies (Park et al. As Table 2 demonstrates, the compounds showed generally higher inhibitory potential against SARS-CoV PLpro than when tested against the other viral proteases using fluorogenic methods, which is likely related to genomic variations in the single amino acid sequences. In particular, herbacetin, quercetin and isobavachalcone (Fig. 3) were identified as promising antiviral leads against SARS-and MERS-CoV based on their broad-spectrum activity against the viral proteases 3CL and PL of both CoVs, the number of relevant literature data, and the availability of the compounds from different plant sources. However, despite some promising inhibitory activities of flavonoids against SARS-and MERS-CoV in vitro, none of these compounds have been tested in vivo using animal and/or human cell models.
cord-305900-ht7hb2rc	2012	Therefore, we inoculated ferrets with seasonal H3N2, pandemic H1N1 (pH1N1), and highly pathogenic avian H5N1 influenza virus and performed detailed virological and pathological analyses at time points from 0.5 to 14 days post inoculation (dpi), as well as describing clinical signs and hematological parameters. To this end, we inoculated ferrets with either seasonal human H3N2, pH1N1, or HPAI H5N1 virus, and performed detailed virological and pathological analyses at time points from 0.5 to 14 dpi, as well as measuring virus excretion, clinical signs, and hematological parameters. Comparable with the pattern of antigen expression in the respiratory tissues, high virus titers were seen in the nasal concha from 0.5 to 4 dpi with a peak on 1 dpi (Figure 3) . However, in the current study, we found very little H3N2 infection (based on virus antigen expression) in any cell types of the ferret lower respiratory tract ( Figure 3 ).
cord-306189-ugxou9z1	2020	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.
cord-306535-j26eqmxt	2020	The majority of candidate genes identified in our screen that were testis-specific were already identified by the Human Protein Atlas [9] and/or our reanalysis of (See figure on previous page.) Fig. 1 Summary of the human and mouse RNA-seq samples used in the identification of novel male reproductive tract-specific drug targets. Additional file 14: Fig. S6 shows the complete list of male reproductive tract-specific human genes for which a previously generated mouse model shows male infertility phenotype, as identified in each of the respective cell and/or tissue datasets. Through the integration of hundreds of published and newly acquired human and mouse reproductive and non-reproductive tissue and cell RNA-seq datasets, we have generated a list of novel genes expressed predominantly or exclusively in the male reproductive tract that are worthy of consideration for functional validation in an animal model and potential targeting for a male contraceptive.
cord-307338-4nta9b6w	2010	Fifteen of these specimens (six swabs and nine tissues) were shown to be Avian influenza viruses, with highly pathogenic (HP) H5 and H7 isolates indicated positive for H1N1v by non-RRT PCR approaches (Table 3) , i.e. amplification of RNA extracted from the clinical specimen by conventional RT PCR using primers that had been designed specifically for the HA gene of current H1N1v isolates, available at: http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf Amplicons were electrophoresed in 2% agarose and stained with RedSafeÔ (iNtRON Biotechnology, Kyungki-Do, Korea) for visualisation, excised and purified from agarose using the QIAquick Ò Gel Extraction Kit (Qiagen, Crawley, UK). These test results with archived tissue specimens obtained from the field reinforced the observation that the ''''perfect match'''' M gene RRT PCR is the most sensitive for detecting contemporary European and UK SIVs. All 31 archived UK tissue samples from SIV-positive pigs were negative by the ''''H1-118'''' RRT PCR assay (Table 2) .
cord-307632-x9bxnrtn	2018	Five virus strains identified from Microtus clarkei, Eothenomys inez, Eothenomys melanogaster, Myodes rufocanus, and Cricetulus longicaudatus in five provinces appeared to be closely related to porcine reproductive and respiratory syndrome virus (PRRSV) with higher sequence similarity than those with other members of the family Arteriviridae (60.1-73.7% versus 25.7-54.2% aa identity for ORF1b, compared with equine arteritis virus, lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus, and wobbly possum disease virus; Additional file 1: Table S6 ). Pairwise similarity and phylogenetic analysis ( Fig. 5a and Additional file 3: Figure S6 ) revealed that 29 viruses formed diverse evolutionary clades in lineage A under the genus Betacoronavirus, with sequence identities between 88.1 and 98.9% (RdRp aa identity).
cord-313355-166b6fep	2020	To examine endpoints as a time to mortality in the statin and the non-statin group, we performed a Cox proportional hazards model adjusting for age, gender, blood pressure (SBP and DBP), preexisting comorbidities (DM, hypertension, coronary heart disease, cerebral arterial disease, and chronic kidney disease), indicators of disease severity and organ injuries (lesions in chest CT, neutrophil counts increase, procalcitonin increase, D-dimer increase, ALT increase, AST increase, creatinine increase, and SpO2), LDL-c increase, cholesterol increase, medications at admission, using invasive mechanical ventilation support, and days from symptom onset to hospitalization covariates with statin therapy as a time-varying exposure. Baseline characteristic, including age, gender, blood pressure (SBP and DBP), pre-existing comorbidities (DM, hypertension, coronary heart disease, cerebrovascular disease, and chronic kidney disease), indicators of disease severity and organ injuries (lesions in lung CT, neutrophil counts increase, procalcitonin increase, D-dimer increase, creatine increase, and SpO2), LDL-c increase, cholesterol increase, medications at admission, using invasive mechanical ventilation support, and days from symptom onset to hospitalization were adjusted in the model.
cord-314372-knhkdlq7	2008	The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus–host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs. The second set of data illustrates the overlapping at npeptide level (with n from 5 to 16 amino acids) from the 30 viral proteomes versus the 30 human sub-proteomes (Table 8, columns 7 and 8) . A similar observation holds in considering the viral peptide overlapping to the 30 human sub-proteomes at higher n-mer level (Table 8, columns 7 and 8) .
cord-314908-kp2jznwb	2020	To better predict these behaviors, we introduce the concept of job crafting self-efficacy (JCSE) and define it as an individual''s beliefs about their capability to modify the demands and resources of their job to better fit their needs. In this project we integrate Social Cognitive Theory and the Job Demands-Resources model [6, 7] to introduce the concept of job crafting self-efficacy (JCSE). Based on the assumptions of Social Cognitive Theory, we also expect that these specific beliefs predict matching job-crafting behaviors, for example, individuals who feel self-efficacious with respect to increasing challenging job demands are more likely to start new projects or learn about new developments at work and try them out.
cord-315193-z6v6s46n	2017	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.
cord-315931-kc8gnj6z	2020	During the first attempt, thirty libraries (including 4 positive and 2 negative controls) were prepared in three plexes (10 samples each, see Supplementary Table S1 ) employing NEBNext ® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) followed by capture-based workflow utilizing the Twist SARS-CoV-2 Research Panel (Twist Bioscience). Compare to NEB+TWIST the capture-based Illumina approach data showed in average a lower percentage of mapped reads (Supplementary Table S1 ), this consequence could be related to the lower specificity of Respiratory Oligo Viral Panel designed next to the SARS-CoV-2 also for other pathogens (see https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/ngsenrichment-coronavirus-app-note-1270-2020-002.pdf). Also, the viral load in a sample (corresponding to sample Ct value ≤ 23.29 or positive control value ≤ 25.84) showed to be the limiting factor in case of each workflow, samples with higher Ct value resulted in either poor genome coverage (NEB+Twist workflow and Illumina workflow) or in absence of expected library preparation product (Paragon workflow).
cord-316983-h4mtpcyc	2016	We have identified here the main venom proteins of two braconid wasps, Psyttalia lounsburyi (two strains from South Africa and Kenya) and P. To assess whether this variation between two figitid species that differ in their host range similarly exists in other parasitoid taxa, we compared here the venom composition of two braconid wasps, Psyttalia lounsburyi and P. This resulted in a total of 32 and 30 putative venom proteins for Pl and Pc respectively (Tables 1 and 2), whose relative abundance was compared using (i) the RPKM normalized number of Illumina reads from Pl and Pc venom apparatus, mapped to the assembled transcriptomes and (ii) the number of peptides matches in Mascot searches. Interestingly, most of the proteins identified in the proteomics of the reservoir (detection of the most abundant putative venom proteins only, data not shown), such as actin or paramyosin, had a predicted muscular function, as expected from microscopy observations (see above; Fig. 1 ).
cord-318339-j35w1vsw	2006	METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients.
cord-319460-n4ezxnjc	2016	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.
cord-320208-uih4jf8w	2020	In this article, we propose a CorExQ9 algorithm that integrates a Correlation Explanation (CorEx) learning algorithm and clinical Patient Health Questionnaire (PHQ) lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. In this article, we propose a CorExQ9 algorithm that integrates Correlation Explanation (CorEx) learning algorithm and clinical PHQ lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. We assessed the level of stress expressed in COVID-19 related tweets by integrating a lexicon-based method derived from established clinical assessment questionnaire PHQ-9 [46] . The CorEx algorithm combined with clinical stress measure index (PHQ-9) helped to minimize human interventions and human language ambiguity in social media data mining for stress detection and provided accurate stress symptom measures of Twitter users related to the COVID-19 pandemic.
cord-320591-re99v1qt	2020	Particularly, these studies mostly focused on the antioxidant and anticancer activities of broccoli sprouts and microgreens owing to the functions of glucosinolates and phenolic compounds (Tables 4 and 5 ). Particularly, these studies mostly focused on the antioxidant and anticancer activities of broccoli sprouts and microgreens owing to the functions of glucosinolates and phenolic compounds (Tables 4 and 5 ). In summary, previous studies showed that broccoli sprout extracts rich in vitamins, carotenoids, and phenolic compounds showed very high antioxidant activity in both in vitro and in vivo tests (Table 4) . Moreover, the previous studies have focused on several biological activities of broccoli seedlings, such as antioxidant, anticancer, antimicrobial, and anti-inflammatory, as well as the potentially beneficial effects for patients with cancers, diabetes, and obesity.
cord-321000-3jd2gn73	2020	title: A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female Hemophagocytic lymphohistiocytosis (HLH) is a rare, potentially life-threatening syndrome caused by excessive immune activation and cytokine storm [1, 2] . We describe a case of acquired HLH secondary to Mediterranean spotted fever (MSF) caused by Rickettsia conorii in a 29-year-old healthy female in the North of Israel. previously reported that in 4 out of 7 reviewed cases of secondary HLH, a diagnosis of sepsis was initially presumed [7] . An excellent outcome has been reported in MSF-associated HLH, in most cases without additional treatment other than antibiotics [17] [18] [19] [20] [21] [22] [23] . Hemophagocytic lymphohistiocytosis secondary to Ehrlichia chaffeensis infection: a case report Diagnosis and treatment of hemophagocytic lymphohistiocytosis in an adult patient with ehrlichiosis
cord-322756-ouvn71r9	2020	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) .
cord-324823-bw2x9h45	2020	Methods and Materials With standard statistical survival models, and based on a systematic literature review, we re-analyzed thirteen radiobiological animal datasets published in 1937-1973 in which animals (guinea pigs/dogs/cats/rats/mice) received radiation before or after bacterial/viral inoculation, and assessing various health endpoints (mortality/pneumonia morbidity). It is the purpose of this paper to report reanalysis of the data abstracted from the original publications so far as that is achievable, using standard statistical survival models in order to assess modification of pneumonia morbidity or mortality risk by radiation exposure before or after inoculation. Each study demonstrated some measure of support for the hypothesis that X-ray treatment could reduce the effects of the pneumonia induced by bacteria or viruses." Manifestly this is not the entirety of the literature relating to post-inoculation radiation exposure (Tables 1, 2) , and a review of our results (Table 2) demonstrates that there is little evidence overall of reduction of morbidity or mortality with increasing radiation dose.
cord-328562-g5i838b3	2020	Respondents experiencing household food insecurity during COVID-19 (both newly and consistently food insecure) were significantly more likely (p < 0.001 comparison across all groups) to express higher levels of concern and worry about a variety of potential situations related to food access and COVID-19 ( Figure 2 , Table A7 ). Respondents experiencing household food insecurity during COVID-19 (both newly and consistently food insecure) were significantly more likely (p < 0.001 comparison across all groups) to express higher levels of concern and worry about a variety of potential situations related to food access and COVID-19 ( Figure 2 , Table A7 ). Compared to food secure households, new and consistently food insecure households were significantly more likely (p < 0.001) to find strategies to address physical or economic food access challenges helpful during COVID-19 (Table A11) .
cord-329890-wg23sa1u	2007	
cord-329999-flzqm3wh	2020	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.
cord-333631-vk3h2qau	2020	
cord-336119-8g37xsys	2020	Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 .
cord-336420-1a2u9p4t	2016	
cord-337481-cxrjzva4	2020	Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. Based on the KEGG database, GO classification, and the suggested biosynthesis pathways, we used a combined method of homolog searching and functional annotation thaliana GB boundaries were derived from a previous study 34 to identify candidate genes for the biosynthesis of three types of active compounds, namely, terpenoids, phenylpropanoids, and indoles, in I. Based on the KEGG maps and previously suggested pathways 25,54,55 , we identified 32 genes that encoded 11 enzymes involved in the biosynthesis of indole alkaloids (Fig. 3c and Supplementary Table S16). Based on homolog searching and functional annotation in our high-quality genome, we further identified candidate genes for the biosynthesis of three main classes of active compounds in I.
cord-338487-jcueu1xh	2020	This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This proposed phased approach is intended to help guide efficient allocation of mental health resources to those most in need of assistance at the time that they need it at the level that they need it (e.g., self-directed versus brief intervention with some support versus traditional treatment sessions with a provider).
cord-338750-6jfw49y7	2020	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] .
cord-339039-6gyo9rya	2018	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] .
cord-340125-il35gs97	2006	
cord-341063-3rqnu5bu	2018	Procacitonin (PCT) emerges as a possible predictive tool in cardiothoracic intensive care unit (CTICU).We aim at testing the predictive power of PCT for early morbidity, prolonged ventilation, ICU and hospital stay, in patients developing early fever after cardiac surgery Methods: A retrospective descriptive study done in tertiary cardiac center, enrolling patients who stayed for more than 24 hours post-operatively in the CTICU Risk stratification included additive Euro score and PCT immunoluminometricaly prior to surgery and every 48 hours in response to onset of fever. Prognostic accuracy of quick sequential organ failure assessment (qSOFA) score for mortality: systematic review and meta-analysis Introduction: The purpose of this study was to summarize the evidence assessing the qSOFA [1] , calculated in admission of the patient in emergency department (ED) or intensive care unit (ICU), as a predictor of mortality.
cord-342012-1w3x0g42	2020	For a completely novel pathogen, especially one with a high (say, >2) basic reproductive number (the expected number of secondary cases generated by a primary case in a completely susceptible population) relative to other recently emergent and seasonal directly transmissible respiratory pathogens 4 , assuming homogeneous mixing and mass action dynamics, the majority of the population will be infected eventually unless drastic public health interventions are applied over prolonged periods and/or vaccines become available sufficiently quickly. We therefore extended our previously published transmission dynamics model 4 , updated with real-time input data and enriched with additional new data sources, to infer a preliminary set of clinical severity estimates that could guide clinical and public health decision-making as the epidemic continues to spread globally. Given that we have parameterized the model using death rates inferred from projected case numbers (from traveler data) and observed death numbers in Wuhan, the precise fatality risk estimates may not be generalizable to those outside the original epicenter, especially during subsequent phases of the epidemic.
cord-343090-dsjq98ks	2020	
cord-343963-99rd3o79	2014	13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production.
cord-344960-m1spgpyu	2020	MiR-122 overexpression appears to exacerbate the angiotensin II-mediated loss of autophagy and increased inflammation, apoptosis, extracellular matrix deposition, cardiovascular fibrosis and dysfunction by modulating the SIRT6-Elabela-ACE2, LGR4-β-catenin, TGFβ-CTGF and PTEN-PI3K-Akt signaling pathways. We previously demonstrated that miR-122 overexpression exacerbated the loss of autophagy and increased cellular migration, apoptosis, extracellular matrix deposition mediated by angiotensin II by modulating the SIRT6-ELA-ACE2, leucine-rich repeat-containing G-protein-coupled receptors 4 (LGR4)-β-catenin, and TGFβ-CTGF signaling pathways (Table 1 ; Fig. 3 ) [1, 6] , indicating that miR-122 inhibition is a promising therapeutic strategy for cardiac fibrosis and dysfunction. Our previous study demonstrated that administration of a miR-122 inhibitor effectively prevented the loss of autophagy and increased cellular proliferation, migration, apoptosis and cardiovascular fibrosis induced by Ang II via modulation of the SIRT6-ELA-ACE2, LGR4/β-catenin and TGFβ1-CTGF-NFAT5 signaling pathways (Table 1 ; Fig. 3 ) [1, 6] .
cord-345373-ulsz1d85	2020	From 6 July to 22 July 2020, the period when the survey was conducted, the following regulations were in force in the country: nose-and-mouth coverings in confined public areas; closure of primary and secondary schools, and institutions of higher education; food and drink establishments were operational with enhanced sanitary measures in place (nose-and-mouth coverings required when not at the table, disinfecting tables, keeping a minimum distance of 1.5 m between patrons); gyms and swimming pools were reopened on 6 June 2020; individuals were allowed to socialise indoors in small groups; in most places, access to specialist medical care was provided at outpatient clinics [3] . Consumption of selected food products during the COVID-19 pandemic is presented in Figure 2 and the breakdown by the type of diabetes and gender is included in Supplementary Table S3 . A statistically significant increase in hand sanitiser use by the youngest respondents during the COVID-19 pandemic (p < 0.001) was observed.
cord-346245-o9hvuwvq	2014	Advantages and drawbacks of this approach are critically (Song et al., 2009d) Bacillus anthracis tetrasaccharide with thiol linker MALDI For attachment to a maleimide functionalized Microarray to study of carbohydrate-antibody interactions (Oberli et al., 2010) Glycodendrimers with N 3 group terminating in α-Man, β-GlcNAc or β-Gal TOF Immobilized on an acetylenyl-terminated gold substrate via click chemistry High-mannose glycans -Oxime linked TOF Used to probe binding to malectin MUC1 Glycopeptides TOF Synthesis on an amine-reactive hydrogelcoated microarray glass surface. The non-commercial CGE-on-a-chip assay allowed electrophoretic separation of proteins in the MW range from 14 kDa to 1 MDa. MW assignment was limited to 500 kDa in the case of SDS-PAGE but with the proper matrix (THAP for most glycoproteins, sinapinic acid for a2-macroglobulin) and sample preparation, analysis with a standard MALDI-TOF-MS provided accurate MWs for all high MW proteins up to 1 MDa. Three methods for N-glycan characterization, namely MALDI-MS of glycopeptides from tryptic digestion, negativeion ESI-MS/MS of released N-glycans, and normal-phase HPLC of fluorescently labeled glycans, in combination with exoglycosidase sequencing, have been evaluated for glycan identification using monoclonal antibodies expressed in tobacco plants as model compounds (Triguero et al., 2010) .
cord-346265-jx4kspen	2020	
cord-350229-56rt4wga	2020	
cord-350286-n7ylgqfu	2020	The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) .
cord-350892-qz6ef05y	2020	The hydrocortisone productivity was further enhanced to ~ 223 mg/L day upon tuning the expression level and the ratio among CYP5311B2, CPR and CYB5 in the engineered yeast strain, then to ~ 268 mg/L day through overexpression of steroid transporter CDR4 from Cochliobolus lunatus, and ultimately towards ~ 677 mg/L day by increasing the cell density to OD 600 ~ 180. As discussed in this session, different yeast strains have been utilized for the production of various steroids through biotransformation strategy and generally with good conversion efficiency. Third, many steroids that can be potentially synthesized in yeast require highly complex synthetic pathways (e.g., brassinolide [83] , tomatidine [84] ), which is a general challenge in engineering de novo synthesis of complex structures in microbial hosts and has been carefully discussed in several recent reviews [81, 85, 86] . The various sterol-producing yeast strains have also been widely used to characterize enzyme activity and elucidate the biosynthesis of specialized steroids from various species.
cord-352016-d2dvdzb1	2020	Abstract Local Government Financing Vehicles (LGFVs) and state-owned enterprises (SOEs) provide implicit guarantee during the issuing of bonds, thereby reducing their funding cost. This paper provides strong evidence that the implicit government guarantee does exist and -3-reduces the funding costs by exploring bonds'' credit spreads. In this period, the government tightened the regulations on LGFVs. Figure 2 shows the revolution of the tightening regulation on China''s LGFVs. As the non-standard municipal corporate crisis happened in 2011, and the first SOE bond Baoding Tianwei defaulted in April 2015, the market began to explore the value of implicit government guarantee (Jin et al. Column (3) shows that the coefficient of ImGovGuarantee is significantly negative, which proves that the spread of state-owned corporate bonds with implicit government guarantees is averagely 1.074% lower. We find strong evidence that government guarantee reduces the funding cost by examining the credit spread of corporate bonds in China.
cord-352080-3rcqbgl7	2020	
cord-352990-0uglwvid	2020	title: Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 In this case, for imperfect lockdown, the basic reproduction number does not rep-90 resent the required elimination effort; rather, the effort at the turning point is described The paper is organized as follows: Our proposed mathematical model which incorporates 108 the lockdown of susceptible individuals and imperfect lockdown efficacy is described in 109 Section 2. backward bifurcation phenomenon, where two stable equilibria, namely the disease-free 387 equilibrium and an endemic equilibrium coexist when the corresponding basic number 388 of reproduction is less than unity. We have 394 seen that the disease-free equilibrium is globally asymptotically stable whenever the as-395 sociated basic reproduction number is less than unity for the perfect lockdown model.
cord-353965-0bb729sp	2016	There was a statistically significant positive correlation between mortality and old age (r =0.633), obesity (r =0.712), diabetes mellitus (r =0.685), renal failure (r =0.705), chronic heart diseases (0.591), COPD (r =0.523), malignancy (r =0.692), kidney transplantation (r =0.644) and liver cirrhosis (r =0.525) (P <0.05). Our study showed that most of the expired patients presented with bilateral pulmonary infiltrates or unilateral infiltrates, but most of the survivors presented with normal radiology or increased bronchovascular markings, and this difference in the results was statistically highly significant (P < 0.01) ( Table 2) . Also, old age, current smoking, smoking severity, presence of associated co-morbidities like obesity, diabetes mellitus, chronic heart diseases, COPD, malignancy, renal failure, renal transplantation and liver cirrhosis associated with a poor outcome of ICU admitted MERS corona virus infected patients. Also, old age, current smoking, smoking severity, presence of associated co-morbidities like obesity, diabetes mellitus, chronic heart diseases, COPD, malignancy, renal failure, renal transplantation and liver cirrhosis associated with a poor outcome of ICU admitted MERS corona virus infected patients.
cord-354651-bxm9yxjm	2020	Chronic consumption of barley β-glucans can decrease fatty liver by increasing small intestinal contents viscosity and improving glucose, lower glycated hemoglobin and relative kidney weights [129] , strengthen the angiogenic ability of ROS-exposed endothelial cells for preventive heart disease [123] , and accelerate the wound closure by promoting the migration and proliferation of human dermal fibroblasts [133] . Therefore, functional ingredients in barley grass and grains are essential for the health contribution of modern human (Homo sapiens), Neanderthals, and early hominids staple food to prevent and treat human chronic diseases. In particular, the healthy effects of functional components of barley grains and grass are the result of longterm continuous evolution of early hominids (fruits/vegetables and leaves rich in polyphenols, K-Ca, and vitamins), Neanderthals (mushrooms and nuts rich in polysaccharides, phytosterols, and linoleic acids), and Homo sapiens (grasses and seeds rich in GABA, enzymes, and resistant starch), which associate with modern humans originating in the progenitor of African Homo sapiens with cognitive hominin, especially after interbreeding between Homo sapiens and Neanderthals that took place in the Middle East.