bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Location of Substitutions and Bacterial Genome Arrangements
Authors: Lato Daniella F , Golding G Brian 
Published: December 2020

AbstractIncreasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, whereas substitution rates usually increase with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and the distance from the origin of replication is significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), whereas others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS, and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.
Understanding the Molecular Drivers of Disease Heterogeneity in Crohn’s Disease Using Multi-omic Data Integration and Network Analysis
Authors: Sudhakar Padhmanand , Verstockt Bram , Cremer Jonathan , Verstockt Sare , Sabino João , Ferrante Marc , Vermeire Séverine 
Published: December 2020

Abstract
Crohn’s disease (CD), a form of inflammatory bowel disease (IBD), is characterized by heterogeneity along multiple clinical axes, which in turn impacts disease progression and treatment modalities. Using advanced data integration approaches and systems biology tools, we studied the contribution of CD susceptibility variants and gene expression in distinct peripheral immune cell subsets (CD14+ monocytes and CD4+ T cells) to relevant clinical traits. Our analyses revealed that most clinical traits capturing CD heterogeneity could be associated with CD14+ and CD4+ gene expression rather than disease susceptibility variants. By disentangling the sources of variation, we identified molecular features that could potentially be driving the heterogeneity of various clinical traits of CD patients. Further downstream analyses identified contextual hub proteins such as genes encoding barrier functions, antimicrobial peptides, chemokines, and their receptors, which are either targeted by drugs used in CD or other inflammatory diseases or are relevant to the biological functions implicated in disease pathology. These hubs could be used as cell type–specific targets to treat specific subtypes of CD patients in a more individualized approach based on the underlying biology driving their disease subtypes. Our study highlights the importance of data integration and systems approaches to investigate complex and heterogeneous diseases such as IBD.
Simulation of McKean–Vlasov SDEs with super-linear growth
Authors: dos Reis Gonçalo , Engelhardt Stefan , Smith Greig 
Published: December 2020

Abstract
We present two fully probabilistic Euler schemes, one explicit and one implicit, for the simulation of McKean–Vlasov Stochastic Differential Equations (MV-SDEs) with drifts of super-linear growth and random initial condition. We provide a pathwise propagation of chaos result and show strong convergence for both schemes on the consequent particle system. The explicit scheme attains the standard $1/2$ rate in stepsize. From a technical point of view, we successfully use stopping times to prove the convergence of the implicit method; although we avoid them altogether for the explicit one. The combination of particle interactions and random initial condition makes the proofs technically more involved. Numerical tests recover the theoretical convergence rates and illustrate a computational complexity advantage of the explicit over the implicit scheme. Comparative analysis is carried out on a stylized non-Lipschitz MV-SDE and a mean-field model for FitzHugh–Nagumo neurons. We provide numerical tests illustrating particle corruption effect where one single particle diverging can ‘corrupt’ the whole particle system. Moreover, the more particles in the system the more likely this divergence is to occur.
Natural History of Coronavirus Disease 2019: Risk Factors for Hospitalizations and Deaths Among &gt;26 Million US Medicare Beneficiaries
Authors: Izurieta Hector S , Graham David J , Jiao Yixin , Hu Mao , Lu Yun , Wu Yue , Chillarige Yoganand , Wernecke Michael , Menis Mikhail , Pratt Douglas , Kelman Jeffrey , Forshee Richard 
Published: December 2020

AbstractBackgroundThe current study was performed to evaluate risk factors for severe coronavirus disease 2019 (COVID-19) outcomes among Medicare beneficiaries during the pandemic’s early phase.MethodsIn a retrospective cohort study covering Medicare fee-for-service beneficiaries, we separated out elderly residents in nursing homes (NHs) and those with end-stage renal disease (ESRD) from the primary study population of individuals age ≥65 years. Outcomes included COVID-19 hospital encounters and COVID-19-associated deaths. We estimated adjusted odds ratios (ORs) using logistic regression.ResultsWe analyzed 25 333 329 elderly non-NH beneficiaries without ESRD, 653 966 elderly NH residents, and 292 302 patients with ESRD. COVID-related death rates (per 10 000) were much higher among elderly NH residents (275.7) and patients with ESRD (60.8) than in the primary study population (5.0). Regression-adjusted clinical predictors of death among the primary population included immunocompromised status (OR, 1.43), frailty index conditions such as cognitive impairment (3.16), and other comorbid conditions, including congestive heart failure (1.30). Demographic-related risk factors included male sex (OR, 1.77), older age (3.09 for 80- vs 65-year-olds), Medicaid dual-eligibility status (2.17), and racial/ethnic minority. Compared with whites, ORs were higher for blacks (2.47), Hispanics (3.11), and Native Americans (5.82). Results for COVID-19 hospital encounters were consistent.ConclusionsFrailty, comorbid conditions, and race/ethnicity were strong risk factors for COVID-19 hospitalization and death among the US elderly.
Advancement in predicting interactions between drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources
Authors: Patrick Matthew T , Bardhi Redina , Raja Kalpana , He Kevin , Tsoi Lam C 
Published: December 2020

Abstract

Objective
Drug–drug interactions (DDIs) can result in adverse and potentially life-threatening health consequences; however, it is challenging to predict potential DDIs in advance. We introduce a new computational approach to comprehensively assess the drug pairs which may be involved in specific DDI types by combining information from large-scale gene expression (984 transcriptomic datasets), molecular structure (2159 drugs), and medical claims (150 million patients).

Materials and Methods
Features were integrated using ensemble machine learning techniques, and we evaluated the DDIs predicted with a large hospital-based medical records dataset. Our pipeline integrates information from &gt;30 different resources, including &gt;10 000 drugs and &gt;1.7 million drug–gene pairs. We applied our technique to predict interactions between 37 611 drug pairs used to treat psoriasis and its comorbidities.

Results
Our approach achieves &gt;0.9 area under the receiver operator curve (AUROC) for differentiating 11 861 known DDIs from 25 750 non-DDI drug pairs. Significantly, we demonstrate that the novel DDIs we predict can be confirmed through independent data sources and supported using clinical medical records.

Conclusions
By applying machine learning and taking advantage of molecular, genomic, and health record data, we are able to accurately predict potential new DDIs that can have an impact on public health.
Spot the difference: comparing results of analyses from real patient data and synthetic derivatives
Authors: Foraker Randi E , Yu Sean C , Gupta Aditi , Michelson Andrew P , Pineda Soto Jose A , Colvin Ryan , Loh Francis , Kollef Marin H , Maddox Thomas , Evanoff Bradley , Dror Hovav , Zamstein Noa , Lai Albert M , Payne Philip R O 
Published: December 2020

Abstract

Background
Synthetic data may provide a solution to researchers who wish to generate and share data in support of precision healthcare. Recent advances in data synthesis enable the creation and analysis of synthetic derivatives as if they were the original data; this process has significant advantages over data deidentification.

Objectives
To assess a big-data platform with data-synthesizing capabilities (MDClone Ltd., Beer Sheva, Israel) for its ability to produce data that can be used for research purposes while obviating privacy and confidentiality concerns.

Methods
We explored three use cases and tested the robustness of synthetic data by comparing the results of analyses using synthetic derivatives to analyses using the original data using traditional statistics, machine learning approaches, and spatial representations of the data. We designed these use cases with the purpose of conducting analyses at the observation level (Use Case 1), patient cohorts (Use Case 2), and population-level data (Use Case 3).

Results
For each use case, the results of the analyses were sufficiently statistically similar (P &gt; 0.05) between the synthetic derivative and the real data to draw the same conclusions.

Discussion and conclusion
This article presents the results of each use case and outlines key considerations for the use of synthetic data, examining their role in clinical research for faster insights and improved data sharing in support of precision healthcare.
CFD analysis for airflow distribution of a conventional building plan for different wind directions
Authors: Kummitha Obula Reddy , Kumar R Vijay , Krishna V Murali 
Published: December 2020

Abstract
Computational fluid dynamics analysis of a building plan has been investigated with predominant wind velocity for different wind directions. The flow properties’ variation in the computational domain has been modeled by solving the Reynolds-Averaged Navier–Stokes (RANS) equations with the finite volume second-order discretization scheme. The turbulence of airflow distribution in and around the building has been modeled with the Shear Stress Transport (SST) k–ω turbulence model from the analysis of different turbulence models. Numerical results are analysed by evaluating and comparing the various flow properties at different building plan locations with different wind directions. The development of pressure coefficients, wind-driven driving force, and air change per hour are studied for different wind directions. From the analysis of numerical results, it is identified that better ventilation with sufficient airflow distribution has existed when the wind is coming from the west direction.
Disseminated Toxoplasmosis in a Child Following Allogeneic Hematopoietic Cell Transplantation
Authors: Boutzoukas Angelique E , Kussman Ashleigh , Bajwa Rajinder P S , Ouellette Christopher P 
Published: December 2020

Abstract
A 23-month old female with hypoplastic myelodysplastic syndrome underwent allogenic hematopoietic cell transplantation (HCT), complicated by development of acute exotropia. Bilateral chorioretinal scars and a ring enhancing brain lesion were identified in further workup. Disseminated toxoplasmosis post-allogeneic HCT was subsequently confirmed by serologic and polymerase chain reaction testing results.
No More “Little Jews without Beards”: Insights into Yiddish Children’s Literature in Eastern Europe Prior to World War I1
Authors: Cohen Nathan 
Published: December 2020

Abstract
The first modern publications in Yiddish which were intended for young readers in Eastern Europe—either original works or translations from foreign languages—appeared at the turn of the twentieth century as the sporadic initiatives of a few writers. A more systematic literature for children in Yiddish started relatively late, and was linked to the developing Yiddish school system. A growing number of writers and cultural activists, including Sholem Aleichem and Y. L. Peretz, became gradually aware of the importance and need for appropriate literature for children. Within less than a decade, the Yiddish book market was enriched with a variety of publications focused upon young readers whose ages ranged between 5 and 12 years. These publications included many translations (or adaptations) from foreign languages—either directly or indirectly—as well as original works by known Yiddish writers. The first Yiddish periodicals for youngsters, as well as textbooks, also appeared then, prior to World War I. Yiddishists and publishers established publishing companies for this purpose and initiated pretentious projects of which few were realized, or even partly realized. The current article will review and examine the first initiatives for publishing Yiddish children’s literature and periodicals, who the initiators were and what their purpose was. Also, to what extent these publications were accepted, and their contribution to modern Yiddish literature.
A β Cephei pulsator and a changing orbital inclination in the high-mass eclipsing binary system VV Orionis
Authors: Southworth John , Bowman D M , Pavlovski K 
Published: December 2020

ABSTRACT
We present an analysis of the high-mass eclipsing binary system VV Ori based on photometry from the TESS satellite. The primary star (B1 V, 9.5 $\, {\rm M}_\odot$) shows β Cephei pulsations and the secondary (B7 V, 3.8 $\, {\rm M}_\odot$) is possibly a slowly pulsating B star. We detect 51 significant oscillation frequencies, including two multiplets with separations equal to the orbital frequency, indicating that the pulsations are tidally perturbed. We analyse the TESS light curve and published radial velocities to determine the physical properties of the system. Both stars are only the second of their pulsation type with a precisely measured mass. The orbital inclination is also currently decreasing, likely due to gravitational interactions with a third body.
Runaway stars masquerading as star formation in galactic outskirts
Authors: Andersson Eric P , Renaud Florent , Agertz Oscar 
Published: December 2020

ABSTRACT
In the outskirts of nearby spiral galaxies, star formation is observed in extremely low gas surface densities. Star formation in these regions, where the interstellar medium is dominated by diffuse atomic hydrogen, is difficult to explain with classic star formation theories. In this letter, we introduce runaway stars as an explanation for this observation. Runaway stars, produced by collisional dynamics in young stellar clusters, can travel kiloparsecs during their main-sequence lifetime. Using galactic-scale hydrodynamic simulations including a treatment of individual stars, we demonstrate that this mechanism enables the ejection of young massive stars into environments where the gas is not dense enough to trigger star formation. This results in the appearance of star formation in regions where it ought to be impossible. We conclude that runaway stars are a contributing, if not dominant, factor to the observations of star formation in the outskirts of spiral galaxies.
Normal observers show no evidence for blindsight in facial emotion perception
Authors: Rajananda Sivananda , Zhu Jeanette , Peters Megan A K 
Published: December 2020

Abstract
Some researchers have argued that normal human observers can exhibit “blindsight-like” behavior: the ability to discriminate or identify a stimulus without being aware of it. However, we recently used a bias-free task to show that what looks like blindsight may in fact be an artifact of typical experimental paradigms’ susceptibility to response bias. While those findings challenge previous reports of blindsight in normal observers, they do not rule out the possibility that different stimuli or techniques could still reveal perception without awareness. One intriguing candidate is emotion processing, since processing of emotional stimuli (e.g. fearful/happy faces) has been reported to potentially bypass conscious visual circuits. Here we used the bias-free blindsight paradigm to investigate whether emotion processing might reveal “featural blindsight,” i.e. ability to identify a face’s emotion without introspective access to the task-relevant features that led to the discrimination decision. However, we saw no evidence for emotion processing “featural blindsight”: as before, whenever participants could identify a face’s emotion they displayed introspective access to the task-relevant features, matching predictions of a Bayesian ideal observer. These results add to the growing body of evidence that perceptual discrimination ability without introspective access may not be possible for neurologically intact observers.
Psychological correlates of arbovirus preventive health behaviour
Authors: Mayi Bindu S , Sternglanz R Weylin , Aldana Nathalia , Menon Madhavi 
Published: December 2020

Abstract

Background
Current arbovirus preventive health interventions do not take social and personality variables into account. Social cognition models posit that people engage in preventive health behaviour (PHB) after an assessment of the perceived risk of disease, an analysis of potential consequences and an evaluation of self-efficacy.

Methods
In a sample of 385 undergraduate and medical students, we examined the association between social relationships, conscientiousness and mosquito repellent use. Data were analysed in a series of stepwise regression analyses.

Results
Social relationships influenced the association between conscientiousness and mosquito repellent use. As expected, perceptions of positive social relationships and conscientiousness are positively linked with mosquito repellent use. Conversely, perceptions of negative social relationships are linked to an inverse association between conscientiousness and mosquito repellent use.

Conclusions
Future interventions designed to increase perceptions of social relationships might be helpful in increasing arbovirus preventive health behaviour such as using mosquito repellents. Since the present study was concurrent correlational in nature, future research would benefit from experimental interventions designed to directly examine the effect of enhancing positive relations and social support on arbovirus preventive health behaviour.
Influencing factors of lung cancer in nonsmoking women: systematic review and meta-analysis
Authors: Huang Jinxin , Yue Na , Shi Naiyang , Wang Qiang , Cui Tingting , Ying Hongyan , Wang Zhijian , Leng Jianqiang , Sui Zhixiang , Xu Yanjuan , Wei Bingyuan , Jin Hui 
Published: December 2020

AbstractBackgroundEpidemiological studies have shown that some factors other than smoking may affect the risk of lung cancer in women, but the results are controversial. We conducted a meta-analysis to summarize the influencing factors of lung cancer in nonsmoking women.MethodsBoth English and Chinese databases were searched for publications from 1990 to 2020. All included studies were assessed according to the Newcastle-Ottawa Scale (NOS). The pooled odds ratios (ORs) and 95% confidence interval (CI) of influential factors were analyzed using the meta-analysis method, and the publication bias and sensitivity were analyzed.ResultsAmong the five categories, the pooled OR of cooking factors category was the highest. Among 42 influencing factors, there were frequent fried food (OR = 2.42, 95% CI: 1.73–3.38) and long menstrual cycle (0.54, 95% CI: 0.39–0.75). A positive association of history of lung diseases/family lung/all cancer with lung cancer among Asian nonsmoking women (1.82, 95% CI: 1.60–2.07). Unlike other regions, cooking factors were the main risk factor for lung cancer in Asian.ConclusionThe meta-analysis suggests that cooking habits, diet, passive smoking, history of cancer and lung disease, and female reproduction are related to lung cancer in nonsmoking women. However, additional studies are warranted to extend this finding.
Anticipatory grieving and loss during the COVID-19 pandemic
Authors: Yap John Federick C , Garcia Louiegi L , Alfaro Ramilyn A , Sarmiento Philip Joseph D 
Published: December 2020

Abstract
Recent correspondence shows that death and burial practices deem significant in understanding the meaning and acceptance of the untimely and unexpected death of a family member afflicted with the coronavirus (COVID-19) disease. These, in turn, raise the need to address the anticipatory grieving process of the family. This paper examines the importance of anticipatory grieving that ultimately affects the lives of the family of the bereaved.
Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses
Authors: Chiba Yuto , Oiki Sayoko , Yaguchi Takashi , Urayama Syun-ichi , Hagiwara Daisuke 
Published: December 2020

Abstract
By identifying variations in viral RNA genomes, cutting-edge metagenome technology has potential to reshape current concepts about the evolution of RNA viruses. This technology, however, cannot process low-homology genomic regions properly, leaving the true diversity of RNA viruses unappreciated. To overcome this technological limitation, we applied an advanced method, Fragmented and Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses from 155 fungal isolates, which allowed us to obtain complete viral genomes in a homology-independent manner. We created a high-quality catalog of 19 RNA viruses (12 viral species) that infect Aspergillus isolates. Among them, nine viruses were not detectable by the conventional methodology involving agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections. Segmented genome structures were determined in 42 per cent of the viruses. Some RNA viruses had novel genome architectures; one contained a dual methyltransferase domain and another had a separated RNA-dependent RNA polymerase (RdRp) gene. A virus from a different fungal taxon (Pyricularia) had an RdRp sequence that was separated on different segments, suggesting that a divided RdRp is widely present among fungal viruses, despite the belief that all RNA viruses encode RdRp as a single gene. These findings illustrate the previously hidden diversity and evolution of RNA viruses, and prompt reconsideration of the structural plasticity of RdRp.