bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute Herpes Simplex Virus Hepatitis in Pregnancy
Authors: Calix R.X. , Loeliger K.B. , Burn M.S. , Campbell K.H. 
Published: November 2020

(Obstet Gynecol. 2020;135:396–400)
Genital herpes simplex virus (HSV) infection is one of the most common sexually transmitted infections and poses risks to both pregnant women and their fetuses and newborns. In rare cases, HSV infection can cause severe maternal disease, including viral sepsis, encephalitis, and hepatitis. Although rare, HSV hepatitis can cause acute liver failure or death, and delaying or missing a diagnosis of HSV hepatitis can have serious consequences. This case study described an atypical case of HSV-1 hepatitis to demonstrate the diagnostic challenges associated with this disease as well as the necessity for early treatment.
Primary Cutaneous Desmoplastic Melanoma With Collagen Rosettes and Pseudoglandular Features
Authors: Donati Michele , Nožička Jan , Kastnerova Liubov , Hajkova Veronika , Persichetti Paolo , Michal Michal , Kazakov Dmitry V. 
Published: November 2020

Abstract:
Primary cutaneous desmoplastic melanoma (DM) is a group of rare melanocytic tumors arising on severely sun-damaged skin, histologically characterized by the proliferation of spindled melanocytes in a prominent desmoplastic stroma, with a range of morphological presentations. In this article, we report a unique case of primary cutaneous DM composed of a nodular proliferation of highly pleomorphic spindled and epithelioid cells, pseudoglandular structures, clear cell change, and unusual collagen rosettes. Immunohistochemical analysis showed a strong and diffuse positivity for S-100 protein, SOX-10, nestin, p75 (nerve growth factor receptor), WT1, and p53. Molecular analysis detected a mutation in the NF1 gene [c.4084C > T, p.(Arg1362Ter)], 2 different pathogenic mutations in TP53 [c.742C > T, p.(Arg248Trp), AF:12%, COSM1640831 and c.528C > G, p.(Cys176Trp), AF:12%, COSM11114], and a mutation in GNAS [c.601C > T, p.(Arg201Cys), AF: 9%, COSM123397]. To the best of our knowledge, this is the first case reporting collagen rosettes and pseudoglandular features in primary cutaneous DM.
Adding Insult to Injury: Levator Ani Avulsion in Women With Obstetric Anal Sphincter Injuries
Authors: Heliker Bhumy Davé , Kenton Kimberly , Leader-Cramer Alix , Brown Oluwateniola , Bochenska Katarzyna , Geynisman-Tan Julia , Mueller Margaret , Lewicky-Gaupp Christina 
Published: November 2020

Objective
In women with obstetric anal sphincter injuries, we compared the rate of major levator ani avulsion after forceps-assisted delivery versus spontaneous vaginal delivery.

Methods
Prospective cohort of primiparous women with obstetric anal sphincter injuries. The primary outcome was the rate of major levator ani avulsion as measured by 3-dimensional transvaginal ultrasonography performed between 1 and 2 weeks postpartum. Secondary outcomes included ultrasonographic anteroposterior hiatal diameter, levator hiatal area, and levator-urethra gap, and differences in validated pelvic disorder questionnaires scores at 1 to 2 and 13 weeks postpartum.

Results
Sixty-two women (30 spontaneous deliveries, 32 forceps deliveries) were included in the final analysis. After controlling for delivery variables, women who underwent forceps-assisted delivery were more likely to experience a major avulsion as compared with those who underwent spontaneous delivery (21/32, [65.6%] vs 8/30 [26.7%]; odds ratio, 5.9; 95% confidence interval, 1.5–24.5; P = 0.014). They were also more likely to have larger levator-urethra gaps bilaterally (P = 0.012, 0.016). After controlling for potential confounders, levator ani avulsion was independently associated with persistent anal incontinence symptoms at 13 weeks postpartum (P = 0.02).

Conclusions
In women with obstetric anal sphincter injuries, the risk of levator ani avulsion is almost 6 times higher after forceps-assisted vaginal delivery as compared with spontaneous vaginal delivery. In those with avulsion, recovery of anal continence is compromised, suggesting that adding insult (avulsion) to injury (obstetric anal sphincter injury) may have negative functional consequences.
Genetic Liability to Cannabis Use Disorder and COVID-19 Hospitalization
Authors: Hatoum Alexander S. , Morrison Claire L. , Winiger Evan A. , Johnson Emma C. , Agrawal Arpana , Bogdan Ryan 
Published: November 2020

AbstractBehavioral and life style factors plausibly play a role in likelihood of being hospitalized for COVID-19. Genetic vulnerability to hospitalization after SARS-CoV2 infection may partially relate to comorbid behavioral risk factors, especially the use of combustible psychoactive substances. Paralleling the COVID-19 crisis has been increasingly permissive laws for recreational cannabis use. Cannabis Use Disorder (CUD) is a psychiatric disorder that is heritable and genetically correlated with respiratory disease, independent of tobacco smoking. By leveraging genome-wide association summary statistics of CUD and COVID-19, we find that at least 1/3rd of the genetic vulnerability to COVID-19 overlaps with genomic liability to CUD (rg=.34, p=0.0003). Genetic causality as a potential mechanism of risk could not be excluded. The association between CUD and COVID-19 remained when accounting for genetics of trying marijuana, tobacco smoking (ever smoking regularly, cigarettes per day, smoking cessation, age of smoking initiation), BMI, fasting glucose, forced expiration volume, education attainment, and Townsend deprivation index. Heavy problematic cannabis use may increase chances of hospitalization due to COVID-19 respiratory complications. Curbing excessive cannabis use may be an essential strategy in COVID-19 mitigation.
The effects of hypertension as an existing comorbidity on mortality rate in patients with COVID-19 A systematic review and meta-analysis
Authors: Whiteman Elena 
Published: November 2020

AbstractIntroductionCoronavirus has spread throughout the world rapidly, and there is a growing need to identify host risk factors to identify those most at risk. There is a growing body of evidence suggesting a close link exists between an increased risk of infection and an increased severity of lung injury and mortality, in patients infected with COVID-19 who have existing hypertension. This is thought to be due to the possible involvement of the virus target receptor, ACE2, in the renin-angiotensin-aldosterone blood pressure management system.ObjectiveTo investigate the association between hypertension as an existing comorbidity and mortality in hospitalized patients with confirmed coronavirus disease 2019 (COVID-19).MethodsA systematic literature search in several databases was performed to identify studies that comment on hypertension as an existing comorbidity, and its effect on mortality in hospitalized patients with confirmed COVID-19 infection. The results of these studies were then pooled, and a meta-analysis was peformed to assess the overall effect of hypertension as an existing comorbidity on risk of mortality in hospitalized COVID-19 positive patients.ResultsA total of 12243 hospitalised patients were pooled from 19 studies. All studies demonstrated a higher fatality rate in hypertensive COVID-19 patients when compared to non-hypertensive patients. Meta-analysis of the pooled studies also demonstrated that hypertension was associated with increased mortality in hospitalized patients with confirmed COVID-19 infection (risk ratio (RR) 2.57 (95% confidence interval (CI) 2.10, 3.14), p < 0.001;I2=74.98%).ConclusionHypertension is associated with 157% increased risk of mortality in hospitalized COVID-19 positive patients. These results have not been adjusted for age, and a meta-regression of covariates including age is required to make these findings more conclusive.SummaryRisk of mortality is considerably higher in hospitalised COVID-19 patients who have hypertension as an existing comorbidity prior to admission.
Designing Efficient Contact Tracing Through Risk-Based Quarantining
Authors: Perrault Andrew , Charpignon Marie , Gruber Jonathan , Tambe Milind , Majumder Maimuna S. 
Published: November 2020

AbstractContact tracing for COVID-19 is especially challenging because transmission often occurs in the absence of symptoms and because a purported 20% of cases cause 80% of infections, resulting in a small risk of infection for some contacts and a high risk for others. Here, we introduce risk-based quarantine, a system for contact tracing where each cluster (a group of individuals with a common source of exposure) is observed for symptoms when tracing begins, and clusters that do not display them are released from quarantine. We show that, under our assumptions, risk-based quarantine reduces the amount of quarantine time served by more than 30%, while achieving a reduction in transmission similar to standard contact tracing policies where all contacts are quarantined for two weeks. We compare our proposed risk-based quarantine approach against test-driven release policies, which fail to achieve a comparable level of transmission reduction due to the inability of tests to detect exposed people who are not yet infectious but will eventually become so. Additionally, test-based release policies are expensive, limiting their effectiveness in low-resource environments, whereas the costs imposed by risk-based quarantine are primarily in terms of labor and organization.
Risk factors for fecal carriage of multidrug-resistantEscherichia coliin a college community: a penalized regression model
Authors: Hu Yuan , Rubin Julia , Mussio Kaitlyn , Riley Lee W. 
Published: November 2020

AbstractBackgroundBacterial antimicrobial resistance is a serious global public health threat. Intestinal commensal drug-resistant bacteria have been suggested as an important reservoir of antimicrobial resistant genes (ARGs), which may be acquired via food. We aimed to identify risk factors associated with fecal carriage of drug-resistant commensalEscherichia coli (E. coli)among healthy adults focused on their dietary habit.MethodsWe conducted a cross-sectional study targeting healthy adult volunteers in a college community. Fecal samples and questionnaires were obtained from 113 volunteers. We conducted backward elimination logistic regression and least absolute shrinkage and selection (LASSO) methods to identify risk factors.ResultsWe analyzed responses from 81 of 113 volunteers who completed the questionnaire. The logistic regression and LASSO methods identified red meat consumption to be associated with increased risk (OR = 6.13 [1.83-24.2] and 1.82, respectively) and fish consumption with reduced risk (OR = 0.27 [0.08-0.85] and 0.82) for the carriage of multidrug-resistantE. coli, adjusted for gender, employment status, frequently-used supermarket, and previous travel.ConclusionsDietary habits are associated with the risk of fecal carriage of multidrug-resistantE. coli. This study supports the growing evidence that food may be an important source of ARGs present in human commensalE. coli.
The total number and mass of SARS-CoV-2 virions
Authors: Sender Ron , Bar-On Yinon M. , Gleizer Shmuel , Bernsthein Biana , Flamholz Avi , Phillips Rob , Milo Ron 
Published: November 2020

AbstractQuantitatively describing the time course of the SARS-CoV-2 infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109-1011virions during peak infection, with a total mass in the range of 1-100 μg, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1-10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.SignificanceKnowing the absolute numbers of virions in an infection promotes better understanding of the disease dynamics and the response of the immune system. Here we use the best current knowledge on the concentrations of virions in infected individuals to estimate the total number and mass of SARS-CoV-2 virions in an infected person. Although each infected person carries an estimated 1-100 billion virions during peak infection, their total mass is no more than 0.1 mg. This curiously implies that all SARS-CoV-2 virions currently in all human hosts have a mass of between 100 gram and 10 kilogram. Combining the known mutation rate and our estimate of the number of infectious virions we quantify the formation rate of genetic variants.
Maternal perception of child weight and concern about child overweight mediates the relationship between child weight and non-responsive feeding practices
Authors: Wang Jian , Zhu Daqiao , Cheng Xuwen , LiuZhou Yicong , Zhu Bingqian , Montgomery Scott , Cao Yang 
Published: November 2020

AbstractWe aimed to examine the mediating effects of maternal perception of child weight (weight perception) and concern about overweight (weight concern) on the paths between child weight and non-responsive feeding practices. We recruited a convenience sample of 1164 mothers who were primary caregivers of preschool children. Child body mass index (BMI) Z-score was calculated to assess child weight. The Chinese version of the Child Feeding Questionnaire (C-CFQ) was used to measure four common non-responsive feeding practices, weight perception and weight concern. Structural equation modeling (SEM) was used to examine the associations between child BMI Z-scores, maternal feeding practices, and other covariates. Sixty percent of the mothers perceived their overweight/obese children as normal weight or even underweight. The disagreement between actual child weight and maternal weight perception was statistically significant (Kappa = 0.212,P< 0.001). SEM indicated that weight perception fully mediated the relationship between child BMI Z-scores and pressure to eat. Weight concern fully mediated the relationships between child BMI Z-scores and the other three feeding practices. The serial mediating effects of weight perception and concern were statistically significant for the paths between child BMI Z-score and monitoring (β = 0.035,P< 0.001), restriction (β = 0.022,P< 0.001), and food as a reward (β = -0.017,P< 0.05).ConclusionChild weight may influence maternal feeding practices through weight perception and concern. Thus, interventions are needed to increase the accuracy of weight perception, which may influence several maternal feeding practices and thereby contribute to child health.What is KnownNon-responsive feeding practices may contribute to childhood obesity or eating disorders.Relationships between maternal weight perception and concern, child weight, and feeding practices have been mixed.What is NewChild weight may influence maternal non-responsive feeding practices through maternal weight perception and concern.Interventions are needed to increase the accuracy of caregivers’ perception of child weight which may influence maternal feeding practices and thereby contribute to child health.
Phenotyping of Indian Polycystic Ovarian Syndrome on the basis of Biochemical Parameters: A retrospective analysis via Hierarchical Cluster Classification
Authors: Moorthy Janani Dakshina , Ayyappan Rajapriya , Usha B 
Published: November 2020

ABSTRACTObjectiveWe aimed to phenotype the Indian PCOS population based on their etiology for an effective treatment regimen.DesignRetrospective analysis of biochemical data.SettingPCOS clinics in Tamil Nadu, IndiaPopulation or SampleGirls and women in age group 18 to 30 diagnosed as PCOS by RC.MethodThe statistical analysis was done using two-way cluster analysis function of SPSS v.22 to identify the phenotypes and the resolving biochemical parameter. Also, the population was segregated into three cohorts based on their age for further analysis.Main outcome measureEndocrine parameters like LH, FSH, estradiol, testosterone and thyroid profile. Biochemical parameters like complete lipid profile, blood glucose and insulin fasting. Body Mass Index (BMI).ResultsThe statistical analysis reported two phenotypes among the Indian PCOS population, segregated based on their LH: FSH ratio. The phenotype with LH: FSH >2, had a hormonal imbalance and may have its etiology from Hypothalamus – Pituitary - Ovarian axis. The phenotype with LH: FSH < 2 had significant markers indicating the incidence of metabolic syndrome and may follow an insulin – dependent pathway for PCOS manifestation.ConclusionThe PCOS population needs a comprehensive screening before deciding on a treatment regimen. All the PCOS patients need to be recommended to follow an active lifestyle since 80% of them are predisposed to a metabolic syndrome in their later ages.
Celda: A Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data
Authors: Wang Zhe , Yang Shiyi , Koga Yusuke , Corbett Sean E. , Johnson W. Evan , Yajima Masanao , Campbell Joshua D. 
Published: November 2020

AbstractSingle-cell RNA-seq (scRNA-seq) has emerged as a powerful technique to quantify gene expression in individual cells and elucidate the molecular and cellular building blocks of complex tissues. We developed a novel Bayesian hierarchical model called Cellular Latent Dirichlet Allocation (Celda) to perform simultaneous co-clustering of genes into transcriptional modules and cells into subpopulations. Celda can quantify the probabilistic contribution of each gene to each module, each module to each cell population, and each cell population to each sample. We used Celda to identify transcriptional modules and cell subpopulations in a publicly available peripheral blood mononuclear cell (PBMC) dataset. Celda identified a population of proliferating T cells and a single plasma cell which were missed by two other clustering methods. Celda identified transcriptional modules that highlighted unique and shared biological programs across cell types. Celda also outperformed a PCA-based approach for gene clustering on simulated data. Overall, Celda presents a novel statistically principled approach towards characterizing transcriptional programs and cellular heterogeneity in single-cell RNA-seq data.
Molecular evidence indicates the existence of multiple lineages ofSperata speciesin Indian Rivers
Authors: Yadav Prabhaker , Kumar Ajit , Yadav Neha , Bisht Mansi , Hussain Syed Ainul , Gupta Sandeep Kumar 
Published: November 2020

AbstractSperata seenghala(Giant river-catfish) andSperata aor(Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of theSperataspecies are morphologically close and well adapted to the same habitat. In this study, we have assessed the level of genetic diversity and differentiation ofS. seenghalaandS. aorin the Ganga River based on the mitochondrial DNA (mtDNA) control region and compared with the other major Indian rivers. We found high haplotypes diversity for both the species in the Ganga. However, it was comparatively low forS. seenghalain Mahanadi and Brahmaputra populations. The phylogenetic and median-joining network strongly indicated the presence of two distinct maternal lineages ofS. seenghalafrom the Ganga river. Interestingly, the genetic differentiation betweenS. seenghalaof Ganga-Brahmaputra was much higher (~25.3%) than theS. seenghalaandS. aor(~17%), whereas it was comparatively low between Ganges-Mahanadi (~8.0%). Our finding provided evidence that all the three rivers: Ganga, Mahanadi, and the Brahmaputra sustain a highly diverse and genetically distinct stock of giant river catfish; therefore, all populations should be considered as a different management unit for the protection of stocks. Our findings indicated that Brahmaputra lineages qualify the species level variations. This study can be further used as a reference database for proper lineage identification ofS. seenghalaandS. aorthat could formulate the appropriate conservation and management plans.
Looking for the needle in a downsized haystack: Whole-exome sequencing unravels how selection and gene flow have shaped climatic adaptation in Douglas-fir (Pseudotsuga menziesii)
Authors: George Jan-Peter , Schueler Silvio , Grabner Michael , Karanitsch-Ackerl Sandra , Mayer Konrad , Stierschneider Michael , Weissenbacher Lambert , van Loo Marcela 
Published: November 2020

AbstractThe widespread Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) occurs along a steep gradient of diverse climates throughout its natural range, which is expected to result in spatially varying selection to local climate conditions. However, phenotypic signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Here, we present phenotypic and genotypic data from a common garden experiment showing a putative signal of adaptation to climate after trees have been growing for 40 years in a common environment. Sixteen Douglas-fir provenances originating from a North-to-South gradient of approx. 1,000 km were analyzed and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FSToutlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs and found that a relatively small proportion of the exome showed a truely adaptive signal (0.01-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationship with climate at provenance origins which strongly suggests that they have most likely featured adaption in Douglas-fir across a steep climatic gradient. Two SNPs were independently found by three of the employed algorithms and one could be assigned with high probability to aPicea abieshomolog gene involved in circadian clock control as was also found inPopulus balsamifera.