bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-ray and optical emission from large superbubbles including the stellar photoionization
Authors: Schneiter E M , Reyes-Iturbide J , Velázquez P F , Esquivel A 
Published: January 2022

ABSTRACT
N70 is a giant superbubble (SB) produced by the stellar cluster LH 114. The dynamic of the stellar SB can be explained with hydrodynamic simulations. However, the explanation of the observed X-ray luminosity is still a matter of debate. Observations show that this kind of superbubbles exhibits X-ray luminosities of the order of 1035 erg s−1, which cannot be explained by only considering the mechanical luminosity of the stellar components. Instead, theoretical models predict luminosities one order of magnitude lower. In this work, we attempt to answer this discrepancy by including a core-collapse supernova explosion (SN) and the photons emitted by each of the stars involved. We find that a core-collapse SN, with an initial mass of 10 M⊙, can explain the missing X-ray emission, lasting approximately 1000 yr. Also, the radiation produces an enhancement of the filamentary superbubble morphology and it increases the SB radius by $\sim 23{{\ \rm per\ cent}}$ with respect to the pure hydrodynamic case.
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses
Authors: Lin Ping , Shen Guanwang , Guo Kai , Qin Shugang , Pu Qinqin , Wang Zhihan , Gao Pan , Xia Zhenwei , Khan Nadeem , Jiang Jianxin , Xia Qingyou , Wu Min 
Published: January 2022

Abstract
Gene-editing technologies, including the widespread usage of CRISPR endonucleases, have the potential for clinical treatments of various human diseases. Due to the rapid mutations of SARS-CoV-2, specific and effective prevention and treatment by CRISPR toolkits for coronavirus disease 2019 (COVID-19) are urgently needed to control the current pandemic spread. Here, we designed Type III CRISPR endonuclease antivirals for coronaviruses (TEAR-CoV) as a therapeutic to combat SARS-CoV-2 infection. We provided a proof of principle demonstration that TEAR-CoV-based RNA engineering approach leads to RNA-guided transcript degradation both in vitro and in eukaryotic cells, which could be used to broadly target RNA viruses. We report that TEAR-CoV not only cleaves SARS-CoV-2 genome and mRNA transcripts, but also degrades live influenza A virus (IAV), impeding viral replication in cells and in mice. Moreover, bioinformatics screening of gRNAs along RNA sequences reveals that a group of five gRNAs (hCoV-gRNAs) could potentially target 99.98% of human coronaviruses. TEAR-CoV also exerted specific targeting and cleavage of common human coronaviruses. The fast design and broad targeting of TEAR-CoV may represent a versatile antiviral approach for SARS-CoV-2 or potentially other emerging human coronaviruses.
SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural sources
Authors: Borges Rafael J , Salvador Guilherme H M , Pimenta Daniel C , dos Santos Lucilene D , Fontes Marcos R M , Usón Isabel 
Published: January 2022

Abstract
Proteins isolated from natural sources can be composed of a mixture of isoforms with similar physicochemical properties that coexist in the final steps of purification. Yet, even where unverified, the assumed sequence is enforced throughout the structural studies. Herein, we propose a novel perspective to address the usually neglected sequence heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER. The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data, and the genetic information relating sequence conservation is integrated into this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MS de novo sequencing with genomic-based algorithms to detect point mutations. We calibrated SLIDER with Gallus gallus lysozyme, whose sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterize a metalloproteinase and a phospholipase A2-like protein from the venom of Bothrops moojeni and a crotoxin from Crotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural sources.
CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells
Authors: Lin-Shiao Enrique , Pfeifer Wolfgang G , Shy Brian R , Saffari Doost Mohammad , Chen Evelyn , Vykunta Vivasvan S , Hamilton Jennifer R , Stahl Elizabeth C , Lopez Diana M , Sandoval Espinoza Cindy R , Deyanov Alexander E , Lew Rachel J , Poirer Michael G , Marson Alexander , Castro Carlos E , Doudna Jennifer A 
Published: January 2022

Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
Acute kidney injury increases risk of kidney stones—a retrospective propensity score matched cohort study
Authors: Cheikh Hassan Hicham I , Murali Karumathil , Lambert Kelly , Lonergan Maureen , McAlister Brendan , Suesse Thomas , Mullan Judy 
Published: January 2022

ABSTRACT

Background
Acute kidney injury (AKI) is common. An episode of AKI may modify the risk of developing kidney stones by potential long-term effects on urine composition. We aimed to investigate the association between AKI and the risk of kidney stone presentations.

Methods
The retrospective cohort study used patient data (1 January 2008–31 December 2017), from an Australian Local Health District, which included AKI diagnosis, demographics, comorbidities and kidney stone admissions. Time-varying Cox proportional hazards and propensity-matched analysis were used to determine the impact of AKI on the risk of kidney stones. To address possible population inhomogeneity in comparisons between no AKI and hospitalized AKI, sub-group analysis was done comparing inpatient and outpatient AKI versus no AKI, to assess consistency of association with future stones. Sensitivity analysis was undertaken to capture the impact of a known AKI status and AKI severity.

Results
Out of 137 635 patients, 23 001 (17%) had an AKI diagnosis and 2295 (2%) had kidney stone presentations. In the unadjusted analysis, AKI was associated with kidney stones, with AKI used as a time-varying exposure, [hazard ratio (HR) 1.32, 95% confidence interval (CI) 1.16–1.50)]. Both inpatient-AKI (HR 1.19, 95% CI 1.01–1.39) and outpatient-AKI (HR 1.59, 95% CI 1.30–1.94) were significantly associated with future stones compared to no AKI subjects. This association persisted in the adjusted analysis (HR 1.45, 95% CI 1.26–1.66), propensity-matched dataset (HR 1.67, 95% CI 1.40–1.99) and sensitivity analysis. There was a dose-response relationship with higher stages of AKI being associated with a greater risk of kidney stones.

Conclusions
In a large cohort of patients, AKI is associated with a greater risk of kidney stones, which increases with higher stages of AKI. This association should be examined in other cohorts and populations for verification.
The cyclicality of job search effort in matching models
Authors: Çenesiz M Alper , Guimarães Luís 
Published: January 2022

Abstract
The canonical matching model is the workhorse model of the labour market but lacks a proper amplification mechanism for productivity shocks. One way to amplify the effects of shocks is to allow workers to endogenously adjust their job search effort: as search effort is procyclical in the canonical model, volatilities increase. Yet, the empirical literature points against procyclical search effort, raising doubts of how acyclical (or countercyclical) search effort can coincide with volatile labour market variables in matching models. We show that they can coincide in a model with procyclical value of leisure and alternating-offer wage bargaining.
Genomic Analysis of Community Transmission Networks for MRSA Among Females Entering a Large Inner-city Jail
Authors: Popovich Kyle J , Thiede Stephanie N , Zawitz Chad , Payne Darjai , Aroutcheva Alla , Schoeny Michael , Green Stefan J , Snitkin Evan S , Weinstein Robert A 
Published: January 2022

Abstract

Background
It is unclear if there are differences in methicillin-resistant Staphylococcus aureus (MRSA) risk between sexes in high-risk populations.

Methods
Females incarcerated at the Cook County Jail were enrolled within 72 hours of intake. Surveillance cultures (nares, throat, groin) were collected to determine the prevalence of MRSA colonization. A survey was administered to identify colonization predictors. Univariate and multivariate analyses were performed to identify predictors of colonization at intake. Genomic sequencing was performed on MRSA colonization and archived clinical isolates.

Results
Two hundred fifty women were enrolled (70% African American, 15% Hispanic), with 70% previously in jail. The prevalence of MRSA colonization at intake was 20%, with 42% of those colonized solely in the throat or groin. Univariate predictors of MRSA colonization at entrance were illicit drug use, unstable housing, engaging in anal sex, recent exchange of sex for drugs/money, and a higher number of recent sexual partners. With multivariate adjustment for race/ethnicity, use of needles for illicit drugs was a significant predictor of MRSA. Use of illicit drugs was also associated with inclusion in a genomic cluster. Nares colonization was significantly associated with not being in a genomic cluster (18.8% vs 78.6%; P &lt; .001), whereas exclusive extranasal colonization was associated (odds ratio, 15.89; P &lt; .001).

Conclusions
We found that a high proportion (20%) of females entered jail colonized with MRSA, suggesting that previously reported sex disparities of a lower risk in women may not apply to high-risk populations. Our findings suggest high-risk activities or venues in the community for MRSA, with potential for directing sex-specific interventions.
Three Issues in the Law of Contractual Discretion
Authors: Varuhas Jason N E 
Published: January 2022

Abstract
The new law of contractual discretion is developing apace. This article addresses three major issues in this dynamic field. First, the article propounds an analytical framework for understanding the nature and practice of reasonableness review in the contractual setting, based on doctrinal exegesis of the full run of cases on contractual discretion. Significantly, the analysis demonstrates that review of contractual discretion is characterised by a ‘variable intensity’ approach: the intensity with which courts scrutinise exercises of discretion is dependent on a series of contextual factors. Second, the article analyses the genus of the implied term, which imposes legal constraints on contractual decision-makers, arguing that the term is properly conceptualised as a term implied in law. Third, the article addresses the remedial consequences of non-compliance with implied fetters, identifying three different remedial models in the case law. The article challenges the common assertion that damages are the invariable remedy, arguing that an impugned exercise of discretion may be void or voidable.
Investigation of buckling of rectilinear beams with additional constraint at an arbitrary internal point
Authors: Ryzhak E I 
Published: January 2022

Summary
The problems of stability and instability (buckling) of compressed rectilinear beams are considered. The beams are treated as one-dimensional elastic bodies possessing stiffnesses of two kinds: the stiffness with respect to extension–compression and the stiffness with respect to bending. The ends of beams are hinged, but along with traditional setting of a problem, characterized by one movable hinge and a given compressive load, the problem with both immovable end hinges fixing the ends of a beam in a compressed state, is considered. In addition to the ends, the beams are assumed to be constrained in a certain way at some internal point located at an arbitrary specified distance from one of the ends. These constraints are supposed to prohibit either lateral displacements with free rotation (a hinge), or rotation with free lateral displacements. Analytical solutions for all four types of problems regarding the onset of instability are obtained and examined with respect to the position of additional constraint. It turned out that results for the cases of one movable end hinge with given compressive load and of fixed end hinges, coincide. In the case of additional hinge, its middle position provides maximal value of the critical force, whereas its limiting end position corresponds to its minimal value. As for the case of additional constraint prohibiting rotation, its middle position corresponds to minimal value of the critical force, whereas its maximal value is attained at a certain internal point of a beam located approximately at the distance of one-sixth of its length from one of the ends.
Kawasaki Disease with Peripheral Gangrene in Children: A Case Series and Review of Literature
Authors: Sidharth   , Mahajan Akanksha , Maheshwari Anu , Meena Himanshu , Mahto Deonath , Mukherjee Sharmila Banerjee , Seth Anju 
Published: January 2022

Abstract
Kawasaki disease (KD) is a medium vessel vasculitis of childhood particularly affecting the coronary arteries and leads to aneurysms in 15–25% of untreated patients. It is a rare cause of peripheral limb gangrene in children under 5 years. Most of the cases in literature are reported during infancy. The median age of KD in patients with gangrene is 3 months and the median time for onset of signs of ischaemic necrosis is 2–4 weeks after the diagnosis and often leads to amputation of the affected limb. Even with early treatment, salvaging the limb is difficult and often not successful. There is an acute risk of mortality and long-term morbidity if the underlying inflammatory process is not identified and treated in a timely manner. We present four cases of KD, who had peripheral limb gangrene at the time of presentation. Initial workup for infective aetiology and pro-coagulant state were negative. Diagnosis of peripheral limb gangrene secondary to atypical KD was made on the basis of echocardiography and laboratory findings.
The GacA-GacS Type Two-Component System Modulates the Pathogenicity of Dickeya oryzae EC1 Mainly by Regulating the Production of Zeamines
Authors: Chen Yufan , Li Yanchang , Zhu Minya , Lv Mingfa , Liu Zhiqing , Chen Zhongqiao , Huang Ying , Gu Weihan , Liang Zhibin , Chang Changqing , Zhou Jianuan , Zhang Lian-Hui , Liu Qiongguang 
Published: January 2022

The GacS-GacA type two-component system (TCS) positively regulates pathogenicity-related phenotypes in many plant pathogens. In addition, Dickeya oryzae EC1, the causative agent of soft rot disease, produces antibiotic‐like toxins called zeamines as one of the major virulence factors that inhibit the germination of rice seeds. The present study identified a GacS-GacA type TCS, named TzpS-TzpA, that positively controls the virulence of EC1, mainly by regulating production of the toxin zeamines. RNA-seq analysis of strain EC1 and its tzpA mutant showed that the TCS regulated a wide range of virulence genes, especially those encoding zeamines. Protein-protein interaction was detected between TzpS and TzpA through the bacterial two-hybrid system and pull-down assay. In trans expression of tzpA failed to rescue the defective phenotypes in both the ΔtzpS and ΔtzpSΔtzpA mutants. Furthermore, TzpA controls target gene expression by direct binding to DNA promoters that contain a Gac-box motif, including a regulatory RNA rsmB and the vfm quorum-sensing system regulator vfmE. These findings therefore suggested that the EC1 TzpS-TzpA TCS system mediates the pathogenicity of Dickeya oryzae EC1 mainly by regulating the production of zeamines. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Applying ALARA Principles in the Design of New Radiological Facilities
Authors: Baker Samuel I. , Kamboj Sunita 
Published: January 2022

Abstract
The application of ALARA (as low as reasonably achievable) principles to the design of new radiological facilities at Argonne National Laboratory provides a consistent radiation safety basis for future facility operations. This paper discusses the criteria for controlling radiation exposure and the techniques applied to meet those criteria for two new facilities. Argonne is a US Department of Energy (US DOE) laboratory, and the criteria are specified in the DOE Rule found at 10 CFR 835. The worst case radionuclides and their source strengths are chosen. Local shielding is specified to reduce dose rates to less than 50 μSv h−1at 30 cm from the shielding, thus avoiding the creation of a radiation area. Version 6 of the Los Alamos National Laboratory radiation transport code MCNP is then used to calculate the dose rates elsewhere. Based on the results of the calculations, design modifications are made to meet the design objectives criteria.
Association of Gallbladder Volume and Wall Thickness With Acute Appendicitis in Pediatric Patients
Authors: Yalcin Ahmet , Demir Berrin , Demir Muhammed , Firinci Binali , Polat Gokhan , Pirimoglu Berhan , Sade Recep 
Published: January 2022

Objectives
Ultrasonography in a child with suspected appendicitis is primarily performed to detect inflamed appendix, whereas secondary findings are important in patients with a nonvisualized appendix. The aim of this study is to evaluate the gallbladder wall thickness and volume in patients with suspected appendicitis and search an association between these parameters and appendicitis.

Methods
Between January 2018 and August 2018, 113 patients with suspected appendicitis were included in this prospective study. Gallbladder and right lower quadrant were evaluated in separate sessions by different radiologists. The wall thickness along with the width, length, and height of the gallbladder was measured and recorded for each patient. Assessment of the appendix was classified as acute appendicitis, normal, and equivocal. Statistically significant association was sought between the thickness of the gallbladder wall and diagnosis of appendicitis.

Results
Gallbladder wall thickness was significantly higher in patients without appendicitis (P = 0.017), whereas significantly increased gallbladder volume was observed in patients with appendicitis (P = 0.004). Receiver operating characteristic analysis showed gallbladder wall thickness threshold of 0.5 mm with a sensitivity of 83.3, specificity of 93.9, and volume threshold of 41.6 mL with a sensitivity of 100 and a specificity of 0.69.

Conclusions
Gallbladder wall thickness and volume measurements were associated with the diagnosis of appendicitis in pediatric patients.
Child Abuse Imaging and Findings in the Time of COVID-19
Authors: Henry M. Katherine , Wood Joanne N. , Bennett Colleen E. , Chaiyachati Barbara H. , Egbe Teniola I. , Otero Hansel J. 
Published: January 2022

Objective
To assess the impact of the COVID-19 pandemic on physical abuse in young children, we compared the following before and during the pandemic: (1) skeletal survey volume, (2) percent of skeletal surveys revealing clinically unsuspected (occult) fractures, and (3) clinical severity of presentation. We hypothesized that during the pandemic, children with minor abusive injuries would be less likely to present for care, but severely injured children would present at a comparable rate to prepandemic times. We expected that during the pandemic, the volume of skeletal surveys would decrease but the percentage revealing occult fractures would increase and that injury severity would increase.

Methods
We conducted a retrospective study of children younger than 2 years undergoing skeletal surveys because of concern for physical abuse at a tertiary children's hospital. Subjects were identified by querying a radiology database during the March 15, 2019–October 15, 2019 (pre–COVID-19) period and the March 15, 2020–October 15, 2020 (COVID-19) period, followed by chart review to refine our population and abstract clinical and imaging data.

Results
Pre–COVID-19, 160 skeletal surveys were performed meeting the inclusion criteria, compared with 125 during COVID-19, representing a 22% decrease. No change was observed in identification of occult fractures (6.9% pre-COVID vs 6.4% COVID, P = 0.87). Clinical severity of presentation did not change, and child protective services involvement/referral decreased during COVID.

Conclusions
Despite a >20% decrease in skeletal survey performance early in the pandemic, the percent of skeletal surveys revealing occult fractures did not increase. Our results suggest that decreases in medical evaluations for abuse did not stem from decreased presentation of less severely injured children.