bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outdoor Transmission of SARS-CoV-2 and Other Respiratory Viruses: A Systematic Review
Authors: Bulfone Tommaso Celeste , Malekinejad Mohsen , Rutherford George W , Razani Nooshin 
Published: November 2020

Abstract

Background
While risk of outdoor transmission of respiratory viral infections is hypothesized to be low, there are limited data on SARS-CoV-2 transmission in outdoor compared to indoor settings.

Methods
We conducted a systematic review of peer-reviewed papers indexed in PubMed, EMBASE, and Web of Science and preprints in Europe PMC through 12 August 2020 that described cases of human transmission of SARS-CoV-2. Reports of other respiratory virus transmission were included for reference.

Results
Five identified studies found a low proportion of reported global SARS-CoV-2 infections occurred outdoors (&lt;10%) and the odds of indoor transmission was very high compared to outdoors (18.7 times; 95% confidence interval, 6.0–57.9). Five studies described influenza transmission outdoors and 2 adenovirus transmission outdoors. There was high heterogeneity in study quality and individual definitions of outdoor settings, which limited our ability to draw conclusions about outdoor transmission risks. In general, factors such as duration and frequency of personal contact, lack of personal protective equipment, and occasional indoor gathering during a largely outdoor experience were associated with outdoor reports of infection.

Conclusions
Existing evidence supports the wide-held belief that risk of SARS-CoV-2 transmission is lower outdoors but there are significant gaps in our understanding of specific pathways.
A rare case of acute idiopathic colocolic intussusception in an adult patient
Authors: Seifen Christopher , Herzig Werner , Schlüchter Roger , Schraner Christian 
Published: November 2020

AbstractAdult intussusception is a rare condition that is frequently associated with malignancy and requires surgical approach. Symptoms are often non-specific and of subacute or chronic character. Therefore, computerized tomography (CT) scan is the most commonly used modality for identifying adult intussusception. A 51-year-old female presented with a 1-day history of increasing abdominal pain. Abdominal ultrasound and CT scan revealed intussusception. Intra-operatively, colocolic intussusception was present and laparoscopically reduced. A lead point was found neither intra-operatively nor in post-operative ileocolonoscopy and resection of involved bowel segments was not necessary.
Creation/destruction of ultra-wide binaries in tidal streams
Authors: Peñarrubia Jorge 
Published: November 2020

Abstract
This paper uses statistical and N-body methods to explore a new mechanism to form binary stars with extremely large separations (≳ 0.1 pc), whose origin is poorly understood. Here, ultra-wide binaries arise via chance entrapment of unrelated stars in tidal streams of disrupting clusters. It is shown that (i) the formation of ultra-wide binaries is not limited to the lifetime of a cluster, but continues after the progenitor is fully disrupted, (ii) the formation rate is proportional to the local phase-space density of the tidal tails, (iii) the semimajor axis distribution scales as p(a)da ∼ a1/2da at a ≪ D, where D is the mean interstellar distance, and (vi) the eccentricity distribution is close to thermal, p(e)de = 2ede. Owing to their low binding energies, ultra-wide binaries can be disrupted by both the smooth tidal field and passing substructures. The time-scale on which tidal fluctuations dominate over the mean field is inversely proportional to the local density of compact substructures. Monte-Carlo experiments show that binaries subject to tidal evaporation follow p(a)da ∼ a−1da at a ≳ apeak, known as Öpik’s law, with a peak semi-major axis that contracts with time as apeak ∼ t−3/4. In contrast, a smooth Galactic potential introduces a sharp truncation at the tidal radius, p(a) ∼ 0 at a ≳ rt. The scaling relations of young clusters suggest that most ultra-wide binaries arise from the disruption of low-mass systems. Streams of globular clusters may be the birthplace of hundreds of ultra-wide binaries, making them ideal laboratories to probe clumpiness in the Galactic halo.
Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression
Authors: Givechian Kevin B , Garner Chad , Benz Steve , Rabizadeh Shahrooz , Soon-Shiong Patrick 
Published: November 2020

Abstract

Background
The interplay between glycolysis and immunosuppression in cancer has recently emerged as an intriguing area of research. The aim of this study was to elucidate a potential epigenetic link between glycolysis, isocitrate hydrogenase (IDH) status, and immune checkpoint expression in human lower-grade glioma (LGG).

Methods
Genomic analysis was conducted on 507 LGG samples from The Cancer Genome Atlas (TCGA). Data types analyzed included RNA-seq (IlluminaHiSeq) and DNA methylation (Methylation450K). Unsupervised clustering grouped samples according to glycolytic expression level and IDH status. Global promoter methylation patterns were examined, as well as methylation levels of LDHA/LDHB and immune checkpoint genes. Methylation data from a knock-in IDH1R132H/WT allele in HCT116 cells and ChIP-seq data from immortalized human astrocytes using an inducible IDH1R132H mutation were also assessed.

Results
Glycolytic expression distinguished a tumor cluster enriched for wild-type IDH and poorer overall survival (P &lt; .0001). This cluster showed lower levels of LDHA promoter methylation and a higher LDHA/LDHB expression ratio. These samples also displayed lower PDL1/2 promoter methylation and higher PDL1/2 expression, which was more pronounced for PDL2. IDH1R132H/WT cell line data showed that induced changes in methylation were enriched for genes involved in immune regulation, and ChIP-seq data showed that promoter H3K4me3 decreased for LDHA, PDL2, and PDL1 upon induction of IDH1R132H.

Conclusions
These results suggest a previously unrecognized epigenetic link between glycolysis and immune checkpoint expression in LGG. This work advances our understanding of glioma genomics and provides support for further exploration of the metabolic-immune interface in LGG.
Regulating off-centering distortion maximizes photoluminescence in halide perovskites
Authors: Lü Xujie , Stoumpos Constantinos , Hu Qingyang , Ma Xuedan , Zhang Dongzhou , Guo Songhao , Hoffman Justin , Bu Kejun , Guo Xiaofeng , Wang Yingqi , Ji Cheng , Chen Haijie , Xu Hongwu , Jia Quanxi , Yang Wenge , Kanatzidis Mercouri G , Mao Ho-Kwang 
Published: November 2020

Abstract
Metal halide perovskites possess unique atomic and electronic configurations that endow them with high defect tolerance and enable high-performance photovoltaics and optoelectronics. Perovskite light-emitting diodes have achieved an external quantum efficiency of over 20%. Despite tremendous progress, fundamental questions remain, such as how structural distortion affects the optical properties. Addressing their relationships is considerably challenging due to the scarcity of effective diagnostic tools during structural and property tuning as well as the limited tunability achievable by conventional methods. Here, using pressure and chemical methods to regulate the metal off-centering distortion, we demonstrate the giant tunability of photoluminescence (PL) in both the intensity (&gt;20 times) and wavelength (&gt;180 nm/GPa) in the highly distorted halide perovskites [CH3NH3GeI3, HC(NH2)2GeI3, and CsGeI3]. Using advanced in situ high-pressure probes and first-principles calculations, we quantitatively reveal a universal relationship whereby regulating the level of off-centering distortion towards 0.2 leads to the best PL performance in the halide perovskites. By applying this principle, intense PL can still be induced by substituting CH3NH3+ with Cs+ to control the distortion in (CH3NH3)1-xCsxGeI3, where the chemical substitution plays a similar role as external pressure. The compression of a fully substituted sample of CsGeI3 further tunes the distortion to the optimal value at 0.7 GPa, which maximizes the emission with a 10-fold enhancement. This work not only demonstrates a quantitative relationship between structural distortion and PL property of the halide perovskites but also illustrates the use of knowledge gained from high-pressure research to achieve the desired properties by ambient methods.
Peritoneal Dialysis–Associated Peritonitis Caused by Mycobacterium abscessus in Children—A Case Report
Authors: Imam Omar , Al-Zubaidi Khaled , Janahi Mohammad , Imam Abubakr , Leghrouz Bassil , Dobson Simon , Sundararaju Sathyavathi , Tsui Kin Ming , Hasan Mohammad Rubayet , Perez-Lopez Andres 
Published: November 2020

Abstract
Peritoneal dialysis (PD)–associated peritonitis constitutes a major complication associated with the procedure. PD-associated peritonitis caused by nontuberculous mycobacteria, usually as a result of an infection related to the PD catheter, has been reported in adults and is associated with significant complications and poor outcome. The management of PD-associated peritonitis caused by Mycobacterium abscessus is particularly challenging because this species is resistant to many antimicrobials commonly used to treat mycobacterial species. We present here the second reported case of PD-associated peritonitis caused by M. abscessus in children. Our patient was a 9-year-old boy with end-stage renal disease (ESRD) who presented with suspected peritonitis, and his PD fluid cultures eventually grew M. abscessus. The patient received a 3-week course of triple therapy with clarithromycin, amikacin, and meropenem in addition to PD catheter removal. The infection completely resolved even though a susceptibility report at the end of treatment revealed that the isolate was resistant to clarithromycin and had decreased susceptibility to carbapenems. Our observations suggest that PD catheter removal is important in PD-associated peritonitis caused by M. abscessus in children and that more studies are needed to define the optimal length of treatment.
Sleep duration and mood in adolescents: an experimental study
Authors: Booth Stephen A , Carskadon Mary A , Young Robyn , Short Michelle A 
Published: November 2020

Abstract

Study Objectives
This study examines the relationship between experimentally manipulated sleep duration and mood in adolescents.

Methods
Thirty-four adolescents (20 male), aged 15–17 years, lived in a sleep laboratory for 10 days and 9 nights. They were allocated to one of three sleep “doses” for five consecutive nights for 5, 7.5, or 10 h sleep opportunity per night. Two baseline nights and two recovery nights entailed 10 h sleep opportunity per night. Mood was measured every 3 h during wake using unipolar visual analogue scales measuring the mood states “depressed,” “afraid,” “angry,” “confused,” “anxious,” “happy,” and “energetic.”

Results
Mixed models analyses with post hoc comparisons revealed that participants in the 5-h group, but not the 7.5- or 10-h groups, reported being significantly more depressed, angry, and confused during sleep restriction than at baseline. Adolescents were significantly less happy and energetic during sleep restricted to 5 h and significantly less energetic during sleep restricted to 7.5 h. When adolescents had 10 h sleep opportunities their happiness significantly increased. No statistically significant effects of sleep restriction were found for fear or anxiety, although small-to-moderate effects of sleep restricted to 5 or 7.5 h were found. Two nights of recovery sleep was not sufficient to recover from increased negative mood states for the 5-h group, although recovery occurred for positive mood states.

Conclusions
Given the prevalence of insufficient sleep and the rising incidence of mood disorders and dysregulation in adolescents, these findings highlight the importance of sufficient sleep to mitigate these risks.
Impact of non-pharmaceutical interventions for SARS-CoV-2 on norovirus outbreaks: an analysis of outbreaks reported by 9 US States
Authors: Kraay Alicia N.M. , Han Peichun , Kambhampati Anita K. , Wikswo Mary E. , Mirza Sara A. , Lopman Benjamin A. 
Published: November 2020

AbstractImportanceThe impact of non-pharmaceutical interventions (NPIs) in response to the SARS-CoV-2 pandemic on incidence of other infectious diseases is still being assessed.ObjectiveTo determine if the observed change in reported norovirus outbreaks in the United States was best explained by underreporting, seasonal trends, or reduced exposure due to NPIs. We also aimed to assess if the change in reported norovirus outbreaks varied by setting.DesignAn ecologic, interrupted time series analysis of norovirus outbreaks from nine states reported to the National Outbreak Reporting System (NORS) from July 2012–July 2020.SettingSurveillance data from Massachusetts, Michigan, Minnesota, Ohio, Oregon, South Carolina, Tennessee, Virginia, and Wisconsin were included in the analysis.Participants9,226 reports of acute gastroenteritis outbreaks with norovirus as an epidemiologically suspected or laboratory-confirmed etiology were included in the analysis, resulting in more than 8 years of follow up. Outbreak reports from states that participated in NoroSTAT for at least 4 years were included in the analysis (range: 4–8 years).ExposureThe main exposure of interest was time period: before (July 2012–February 2020) or after (April 2020–July 2020) the start of NPIs in the United StatesMain outcomeThe main outcome of interest was monthly rate of reported norovirus outbreaks. As a secondary outcome, we also examined the average outbreak size.ResultsWe found that the decline in norovirus outbreak reports was significant for all 9 states considered (pooled incidence rate ratio (IRR) comparing April 2020-July 2020 vs. all pre-COVID months for each state= 0.14, 95% CI: 0.098, 0.21; P=<0.0001), even after accounting for typical seasonal decline in incidence during the summer months. These patterns were similar across a variety of settings, including nursing homes, child daycares, healthcare settings, and schools. The average outbreak size was also reduced by 61% (95% CI: 56%, 42.7%; P=<0.0001), suggesting that the decline does not reflect a tendency to report only more severe outbreaks due to strained surveillance systems, but instead reflects a decline in incidence.Conclusions and relevanceWhile NPIs implemented during the spring and summer of 2020 were intended to reduce transmission of SARS-CoV-2, these changes also appear to have impacted the incidence of norovirus, a non-respiratory pathogen. These results suggest that NPIs may provide benefit for preventing transmission of other human pathogens, reducing strain to health systems during the continued SARS-CoV-2 pandemic.DisclaimerThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US Centers for Disease Control and Prevention (CDC).
Transcriptional regulation of structural and functional adaptations in a developing adulthood myocardium
Authors: Sunny Sini , Challa Anil Kumar , Barchue Joseph , Ramamurthy Muralidharan T. , Crossman David K , Pogwizd Steven , Cinghu Senthilkumar , Rajasekaran Namakkal S. 
Published: November 2020

AbstractThe development of the heart follows a synergic action of several signaling pathways during gestational, pre- & postnatal stages. The current study aimed to investigate whether the myocardium experiences transcriptional changes during the transition from post-natal to adult hood stages. Herein, we used C57/Bl6/J mice at 4 (28-days; post-natal/PN) and 20 weeks (adulthood/AH) of ages and employed the next generation RNAseq (NGS) to profile the transcriptome and echocardiography analysis to monitor the structural/functional changes in the heart. NGS-based RNA-seq revealed that 1215 genes were significantly upregulated and 2549 were down regulated in the AH versus PN hearts, indicating a significant transcriptional change during this transition. A synchronized cardiac transcriptional regulation through cell cycle, growth hormones, redox homeostasis and metabolic pathways was noticed in both PN and AH hearts. Echocardiography reveals significant structural and functional (i.e. systolic/diastolic) changes during the transition of PN to adult stage. Particularly, a progressive decline in ejection fraction (EF) and cardiac output was observed in AH hearts. These structural adaptations are in line with critical signaling pathways that drive the maturation of heart during AH. Overall, we have presented a comprehensive transcriptomic analysis along with structural-functional relationship during the myocardial development in adult mice.
Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants
Authors: Sandler George , Wright Stephen I. , Agrawal Aneil F. 
Published: November 2020

AbstractMost empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic datasets, one fromCapsella grandifloraand one fromDrosophila melanogaster.We consider how processes such as drift, admixture, Hill-Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD inC. grandifloradecays faster within genes, compared to between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. InD. melanogasternetworks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intra-network negative synergistic epistasis.
High throughput functional screening for next generation cancer immunotherapy using droplet-based microfluidics
Authors: Wang Yuan , Jin Ruina , Shen Bingqing , Li Na , Zhou He , Wang Wei , Zhao Yingjie , Huang Mengshi , Fang Pan , Wang Shanshan , Mary Pascaline , Wang Ruikun , Ma Peixiang , Li Ruonan , Cao Youjia , Li Fubin , Schweizer Liang , Zhang Hongkai 
Published: November 2020

AbstractCurrently high throughput approaches are lagged for isolation of antibodies whose function goes beyond simple binding, which have prevented the next generation cancer immunotherapeutics, such as bispecific T cell engager antibodies or agonist antibody of costimulatory receptor, from reaching their full potential. Here we developed a highly efficient droplet-based microfluidics platform combining with lentivirus transduction system that enables functional screening of millions of antibodies. To showcase the capacity of the system, functional antibodies for CD40 agonism with low frequency (<0.02%) were identified with 2 rounds of screening. To demonstrate its versatility, an anti-Her2/anti-CD3 bispecific antibody library was established using bispecific T cell Engager (BiTE) platform and functional screening enabled efficient identification of potent anti-Her2/anti-CD3 BiTE antibodies. The platform could revolutionize the next generation cancer immunotherapy drug development and research world.
CICLOP: A Robust, Faster, and Accurate Computational Framework for Protein Inner Cavity Detection
Authors: Garg Parth , Sacher Sukriti , Gautam Prutyay , Mrinal  , Atul  , Ray Arjun 
Published: November 2020

AbstractInternal cavities in proteins are of critical functional importance. They can serve as substrate/ligand binding sites, pave path for movement of bio-molecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately, and reliably characterize the inner cavities of the proteins, a prerequisite for elucidating their functions. We have developed a novel method, CICLOP, that can accurately identify these regions at an atomic resolution. The method is able to accurately detect residues lining the inner cavity, the diameter and volume occupied by the cavity, as well as physicochemical properties of residues lining the cavity such as their hydrophobicity and secondary structure distribution in detail. Additionally, our method also provides an option for computing conservation scores for the residues detected on the inside, allowing for a thorough functional characterization of the cavity.AvailabilityCICLOP is available at http://ciclop.raylab.iiitd.edu.in/. A compiled Linux executable can be downloaded from https://ciclop.raylab.iiitd.edu.in/standalone/
Single-cell transcriptomics of the early developing mouse cerebral cortex disentangles the spatial and temporal components of neuronal fate acquisition
Authors: Moreau Matthieu X. , Saillour Yoann , Cwetsch Andrzej W. , Pierani Alessandra , Causeret Frédéric 
Published: November 2020

AbstractIn the developing cerebral cortex, how progenitors that seemingly display limited diversity end up in producing a vast array of neurons remains a puzzling question. The prevailing model that recently emerged suggests that temporal maturation of these progenitors is a key driver in the diversification of the neuronal output. However, temporal constrains are unlikely to account for all diversity across cortical regions, especially in the ventral and lateral domains where neuronal types significantly differ from their dorsal neocortical counterparts born at the same time. In this study, we implemented single-cell RNAseq to sample the diversity of progenitors and neurons along the dorso-ventral axis of the early developing pallium. We first identified neuronal types, mapped them on the tissue and performed genetic tracing to determine their origin. By characterising progenitor diversity, we disentangled the gene expression modules underlying temporal vs spatial regulations of neuronal specification. Finally, we reconstructed the developmental trajectories followed by ventral and dorsal pallial neurons to identify gene waves specific of each lineage. Our data suggest a model by which discrete neuronal fate acquisition from a continuous gradient of progenitors results from the superimposition of spatial information and temporal maturation.