bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASHLEYS: automated quality control for single-cell Strand-seq data
Authors: Gros Christina , Sanders Ashley D , Korbel Jan O , Marschall Tobias , Ebert Peter 
Published: March 2021

Abstract

Summary
Single-cell DNA template strand sequencing (Strand-seq) enables chromosome length haplotype phasing, construction of phased assemblies, mapping sister-chromatid exchange events and structural variant discovery. The initial quality control of potentially thousands of single-cell libraries is still done manually by domain experts. ASHLEYS automates this tedious task, delivers near-expert performance and labels even large datasets in seconds.

Availability and implementation
github.com/friendsofstrandseq/ashleys-qc, MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
Authors: Zhang Ruoshi , Mirdita Milot , Levy Karin Eli , Norroy Clovis , Galiez Clovis , Söding Johannes 
Published: March 2021

Abstract

Summary
SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.

Availability and implementation
SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer.

Supplementary information
Supplementary data are available at Bioinformatics online.
AASRA: an anchor alignment-based small RNA annotation pipeline†
Authors: Tang Chong , Xie Yeming , Guo Mei , Yan Wei 
Published: March 2021

Abstract
Small noncoding RNAs deep sequencing (sncRNA-Seq) has become a routine for sncRNA detection and quantification. However, the software packages currently available for sncRNA annotation can neither recognize sncRNA variants in the sequencing reads, nor annotate all known sncRNA simultaneously. Here, we report a novel anchor alignment-based small RNA annotation (AASRA) software package (https://github.com/biogramming/AASRA). AASRA represents an all-in-one sncRNA annotation pipeline, which allows for high-speed, simultaneous annotation of all known sncRNA species with the capability to distinguish mature from precursor microRNAs, and to identify novel sncRNA variants in the sncRNA-Seq sequencing reads.
Cortical inflammation and brain signs of high-risk atherosclerosis in a non-human primate model
Authors: Di Cataldo Vanessa , Debatisse Justine , Piraquive Joao , Géloën Alain , Grandin Clément , Verset Michaël , Taborik Fabrice , Labaronne Emmanuel , Loizon Emmanuelle , Millon Antoine , Mury Pauline , Pialoux Vincent , Serusclat André , Lamberton Franck , Ibarrola Danielle , Lavenne Franck , Le Bars Didier , Troalen Thomas , Confais Joachim , Crola Da Silva Claire , Mechtouff Laura , Contamin Hugues , Fayad Zahi A , Canet-Soulas Emmanuelle 
Published: March 2021

AbstractAtherosclerosis is a chronic systemic inflammatory disease, inducing cardiovascular and cerebrovascular acute events. A role of neuroinflammation is suspected, but not yet investigated in the gyrencephalic brain and the related activity at blood−brain interfaces is unknown. A non-human primate model of advanced atherosclerosis was first established using longitudinal blood samples, multimodal imaging and gene analysis in aged animals. Non-human primate carotid lesions were compared with human carotid endarterectomy samples. During the whole-body imaging session, imaging of neuroinflammation and choroid plexus function was performed. Advanced plaques were present in multiple sites, premature deaths occurred and downstream lesions (myocardial fibrosis, lacunar stroke) were present in this model. Vascular lesions were similar to in humans: high plaque activity on PET and MRI imaging and systemic inflammation (high plasma C-reactive protein levels: 42 ± 14 µg/ml). We also found the same gene association (metabolic, inflammatory and anti-inflammatory markers) as in patients with similar histological features. Metabolic imaging localized abnormal brain glucose metabolism in the frontal cortex. It corresponded to cortical neuro-inflammation (PET imaging) that correlated with C-reactive protein level. Multimodal imaging also revealed pronounced choroid plexus function impairment in aging atherosclerotic non-human primates. In conclusion, multimodal whole-body inflammation exploration at the vascular level and blood−brain interfaces identified high-risk aging atherosclerosis. These results open the way for systemic and central inflammation targeting in atherosclerosis in the new era of immunotherapy.
Left ventricular free wall perforation by a right ventricular pacemaker lead: a case report
Authors: Satomi Natsuko , Enta Kenji , Otsuka Masato , Ishii Yasuhiro , Asano Ryota , Sawa Shigeharu 
Published: March 2021

Abstract

Background
Lead perforation is one of the major complications of pacemaker implantation, but cases of right ventricular (RV) lead perforation through the septum and left ventricle are rarely reported. We described a rare case of left ventricular (LV) free wall perforation by an RV lead and the management of this complication.

Case summary
An 84-year-old man was admitted with a dual-chamber pacemaker due to pacing failure caused by an RV lead fracture. New lead implantation was performed on the next day, but pacing failure occurred again on the second post-operative day (POD). We found the lead perforation on the fluoroscopy during temporary pacemaker insertion. Computed tomography scan and transthoracic echocardiogram showed that the added lead perforated through both the septum and LV free wall. A new lead was inserted on the fourth POD, and an off-pump open chest surgery for extraction of the penetrating lead was performed uneventfully on the 20th POD.

Discussion
We considered that some features of the lead (SelectSecure 3830-69, Medtronic) may be related to this complication, as the lead was very thin, had a non-retractable bare screw and was inserted with a dedicated delivery catheter. We have to be careful when performing implantation of this kind of lead to avoid such a rare complication.
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Authors: Keller Cheryl A , Wixom Alexander Q , Heuston Elisabeth F , Giardine Belinda , Hsiung Chris C -S , Long Maria R , Miller Amber , Anderson Stacie M , Cockburn April , Blobel Gerd A , Bodine David M , Hardison Ross C 
Published: March 2021

Abstract
Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low-quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.
Uniform error estimates for artificial neural network approximations for heat equations
Authors: Gonon Lukas , Grohs Philipp , Jentzen Arnulf , Kofler David , Šiška David 
Published: March 2021

Abstract
Recently, artificial neural networks (ANNs) in conjunction with stochastic gradient descent optimization methods have been employed to approximately compute solutions of possibly rather high-dimensional partial differential equations (PDEs). Very recently, there have also been a number of rigorous mathematical results in the scientific literature, which examine the approximation capabilities of such deep learning-based approximation algorithms for PDEs. These mathematical results from the scientific literature prove in part that algorithms based on ANNs are capable of overcoming the curse of dimensionality in the numerical approximation of high-dimensional PDEs. In these mathematical results from the scientific literature, usually the error between the solution of the PDE and the approximating ANN is measured in the $L^p$-sense, with respect to some $p \in [1,\infty )$ and some probability measure. In many applications it is, however, also important to control the error in a uniform $L^\infty $-sense. The key contribution of the main result of this article is to develop the techniques to obtain error estimates between solutions of PDEs and approximating ANNs in the uniform $L^\infty $-sense. In particular, we prove that the number of parameters of an ANN to uniformly approximate the classical solution of the heat equation in a region $ [a,b]^d $ for a fixed time point $ T \in (0,\infty ) $ grows at most polynomially in the dimension $ d \in {\mathbb {N}} $ and the reciprocal of the approximation precision $ \varepsilon&gt; 0 $. This verifies that ANNs can overcome the curse of dimensionality in the numerical approximation of the heat equation when the error is measured in the uniform $L^\infty $-norm.
The Birth of “Religion and International Relations”: Questions of Scale
Authors: Adams Nicholas 
Published: March 2021

AbstractThe field religion and international relations (IR) has been established over the last twenty years within the discipline of IR. It marks a new (largely twenty-first century) set of interdisciplinary engagements, bringing together political science and the sociology of religion. “Religion and IR” and “religious studies” continue to conduct their business independently, in different conferences, journals, and book series, but their interests increasingly overlap. This enquiry interprets religion and IR as a “turn to the local.” This is displayed in its concern with events at the local level that have significance that travels up the scale of levels of analysis to events that have international significance. The turn to the local offers compelling arguments for shifting the focus in IR away from states and on to relations between local, national, and international actors. Engaging here with influential works in religion and IR published over the last fifteen years, I argue that it is the turn to the local that offers the most scope for collaboration between scholars of religion and IR and scholars in religious studies.
Education: An overview from the author of ‘Cefiderocol as rescue therapy for Acinetobacter baumannii and other carbapenem-resistant Gram-negative infections in intensive care unit patients’
Authors: Falcone Marco 
Published: March 2021

Abstract
This video is a presentation from Professor Marco Falcone from the University Hospital Pisa, Italy, originally presented at the BSAC conference ‘Into clinical practice: Meeting the challenges of Gram-negative infection management’ on 14 October 2020. Professor Falcone highlights the cefiderocol compassionate use case series that has been published in Clinical Infectious Diseases (Falcone M, Tiseo G, Nicastro M et al. Cefiderocol as rescue therapy for Acinetobacter baumannii and other carbapenem-resistant Gram-negative infections in intensive care unit patients. Clin Infect Dis 2020; doi: 10.1093/cid/ciaa1410). The prescribing information for cefiderocol is available at: https://shionogi-eu-content.com/gb/fetcroja/pi.
Free-ranging bats alter thermoregulatory behavior in response to reproductive stage, roost type, and weather
Authors: Bergeson Scott M , Brigham R Mark , O’Keefe Joy M 
Published: March 2021

Abstract
Heterotherms vary their use of torpor and choice of refugia to deal with energetic stresses such as reproductive activity and extreme weather. We hypothesized that a temperate-region bat would vary its use of heterothermy in response to air temperature but use of torpor would also be influenced by reproductive stage and roost choice. To test this hypothesis, we collected data on skin temperatures of female Indiana bats (Myotis sodalis) carrying temperature-sensitive radiotransmitters during the summers of 2013–2015. We also measured internal temperatures and external characteristics of roosts used by these bats. We analyzed the influence of daytime air temperature, roost canopy closure, roost type, and bat reproductive stage, on daily heterothermy index and torpor characteristics of 17 bats during 103 full roost days (data collected consistently from when a bat entered its roost in the morning to when it emerged at night). Our data showed that Indiana bat heterothermy was influenced by reproductive stage, roost choice, and weather. Although they used torpor, pregnant bats were the least heterothermic (daily heterothermy index = 3.3 ± 0.6°C SE), followed by juvenile bats (5.6 ± 0.5°C), lactating bats (5.7 ± 0.5°C), and one postlactating bat (13.2 ± 1.6°C). Air temperature also influenced heterothermy of pregnant bats less than bats of other reproductive stages. Thermoregulatory strategies varied on a continuum from use of normothermia in warm roosts to use of long and deep bouts of torpor in cool roosts. The thermoregulatory strategy used seemed to be determined by potential reproductive costs of torpor and energetic consequences of weather. Because Indiana bats used different degrees of heterothermy throughout the summer maternity season, managers should offer maternity colonies an array of refugia to facilitate varying behaviors in response to weather and energetic demands.
Physician-reported barriers and challenges to antibiotic prescribing in surgical prophylaxis: a structured systematic review
Authors: Gillani Syed Wasif , Vippadapu Prasanna , Gulam Shabaz Mohiuddin 
Published: March 2021

Abstract

Objectives
The purpose of the study is to identify and analyse the barriers in surgical procedures where antibiotic dissipation is habitual.

Methods
Extensive literature search is carried out using different electronic databases (PubMed, Europe PMC, PLoS and Google Scholar) between January 2000 and December 2020. The articles were selected purely based on the inclusion criteria. Only qualitative and cross-sectional studies were selected to reduce the risk of bias. The JBI and AXIS checklists were used to assessed the quality of the enrolled articles. Data extractions were done by using a predesigned standardized data collection form.

Key findings
A total of 2067 articles were electronically retrieved but only 14 articles met the eligibility criteria. About 15 902 healthcare professionals (HCPs) with an average response rate of 64.7% were pooled for evidence synthesis. The majority of respondents (50%) discussed different barriers in their practice site for surgical antibiotic prophylaxis (SAP) administration. Barriers were categorized into four themes: lack of guideline availability and knowledge, lack of adherence to guidelines, lack of guideline knowledge and adherence and physician perceptions or off-label practices. A total of 723 (56.3%) out of 1282 HCPs from nine different studies reported a lack of adherence to guidelines during the perioperative process. The majority of respondents in three studies, 318 (82%) out of 386 HCPs, reported that physicians’ perceptions play a crucial role in prescribing SAP during surgeries.

Conclusion
This study concluded that the barriers within the practice site play a decisive role in SAP optimization and therefore all HCPs are recommended to maintain local/standard guidelines and adhere to them while prescribing SAP.
‘Warma Kuyay (Amor de Niño)’ By Josê María Arguedas: A Dialectic Prelude to Liberation Ecotheology
Authors: Park Moisés 
Published: March 2021

Abstract
José María Arguedas’ Peruvian short story ‘Warma Kuyay (Amor de niño)’ culminates with the punishment of a calf, as a result of the white landlord’s sexual violation of Justina, an indigenous woman. This article argues that that theoretical discussions in ecotheology offer fruitful tools for analysing the story, resonating with Andean cosmologies and enabling us to think more seriously about Arguedas’ intersectional theological thoughts. ‘Warma Kuyay’ prefaces theological ecocriticism, foreseeing current developments in liberation theology which do not just emphasise class, but other categories of identity.
Exploring Hong Kong nurses’ decision-making processes around presenteeism
Authors: Andres E B , Lui J N M , Song W , Johnston J M 
Published: March 2021

Abstract

Background
Presenteeism among nurses is the common behaviour of being physically present at work when one should not be due to personal health and well-being, a stressful work environment, lack of work–life balance, or a sense of professional identity or obligation.

Aims
To explore nurses’ decision-making process related to presenteeism in a large Hong Kong public hospital.

Methods
As part of a larger study on nurse presenteeism in Hong Kong, we conducted focus groups with nurses to understand their considerations related to working sick.

Results
Eleven major themes emerged from the focus groups, which we grouped into three organizational domains reflecting nurses’ decision-making process around presenteeism: consideration for colleagues, organizational factors and professional identity.

Conclusions
Presenteeism was a familiar behaviour among Hong Kong nurses in our study. We found both overlap and divergence with prior presenteeism research in the domains and themes identified. Loyalty to colleagues, written and unwritten rules and professional identity as nurses all seemed to encourage presenteeism among Hong Kong nurses. Organizations seeking to discourage presenteeism should evaluate policies such as sick leave certificates, ensure appropriate coverage for all nurse ranks and address subcultural norms encouraging presenteeism.
Early Empirical Tuberculosis Treatment in HIV-Positive Patients Admitted to Hospital in South Africa: An Observational Cohort Study
Authors: Bresges Carolin , Wilson Douglas , Fielding Katherine , Corbett Elizabeth L , Del-Greco Fabrizia , Grint Daniel , Peters Jurgens , Gupta-Wright Ankur 
Published: March 2021

Abstract

Background
Empirical tuberculosis (TB) treatment in human immunodeficiency virus (HIV)–positive inpatients is common and may undermine the impact of new diagnostics. We sought to describe empirical TB treatment and compare characteristics and outcomes with patients treated for TB after screening.

Methods
This was a retrospective observational cohort study of HIV-positive inpatients treated empirically for TB prior to TB screening. Data on clinical characteristics, investigations, and outcomes were collected from medical records. Comparison cohorts with microbiologically confirmed or empirical TB treatment after TB screening with Xpert MTB/RIF and urine lipoarabinomannan assays were taken from South African Screening for Tuberculosis to Reduce AIDS-Related Mortality in Hospitalized Patients in Africa (STAMP) trial site. In-hospital mortality was compared using a competing-risks analysis adjusted for age, sex, and CD4 cell count.

Results
Between January 2016 and September 2017, 100 patients excluded from STAMP were treated for TB empirically prior to TB screening. After enrollment in STAMP and TB screening, 240 of 1177 (20.4%) patients received TB treatment, of whom 123 had positive TB tests and 117 were treated empirically. Characteristics were similar among early empirically treated patients and those treated after TB screening. 50% of early empirical TB treatment was based on radiological investigations, 22% on cerebrospinal or pleural fluid testing, and 28% on clinical features alone. Only 11 of 100 empirically treated patients had subsequent microbiological confirmation. In-hospital mortality was lower in patients with microbiologically confirmed TB compared to those treated empirically (adjusted subdistribution hazard ratio, 0.5 [95% confidence interval, .3–.9).

Conclusions
Empirical TB treatment remains common in severely ill HIV-positive inpatients. These patients may benefit from TB screening using existing rapid diagnostics, both to improve confirmation of TB disease and reduce overtreatment for TB.
The Ageing Body, Memory-Loss and Suicide in Georgian England
Authors: Sbaraini Ella 
Published: March 2021

Abstract
This article examines why older people were particularly prone to suicide in Georgian England, and argues that their suicidality is best understood through the lens of the ‘ageing body’. By centring on the experiences of the suicidal, it proposes that suicide was not ‘medicalised’ in the way traditionally described in the historiography, being reconceptualised, over the course of the eighteenth century, as a product of lunacy. Instead, it contends that older people often thought that their suicides were a rational response to the struggles of ageing, which included physical decline and embodied memory-loss. To do this, it uses previously unseen coroners’ inquests from across England, in addition to wills and medical writings. It examines these inquests for what they can tell us about the emotional and embodied experiences of older suicidal people, thus contributing to an under-researched aspect of the social history of ageing.
The nature and prevalence of diagnostic testing in mathematics at tertiary-level in Ireland
Authors: Hyland Diarmaid , O’Shea Ann 
Published: March 2021

Abstract
In this study, we conducted a survey of all tertiary level institutions in Ireland to find out how many of them use diagnostic tests, and what kind of mathematical content areas and topics appear on these tests. The information gathered provides an insight into what instructors expect students to know on entry to university and what they expect students to have difficulty with. In total, 12 diagnostic tests from 11 Irish institutions were collected during the study. An item-by-item analysis was carried out on each diagnostic test to determine the content areas and topics that are assessed on the diagnostic tests and to identify any additional knowledge required for successful completion. We compare the tests administered in the university sector and the Institute of Technology (IT) sector of the Irish tertiary level education system. In addition, current diagnostic tests are compared with two tests from the 1980s to see if the level of mathematical preparedness expected of first-year students has changed over time. Our analysis is situated in a discussion of previous research on diagnostic testing both nationally and internationally.