bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Expert Witnesses in the Adjudication of Religious and Culture-based Asylum Claims in the United Kingdom: the Case Study of ‘Witchcraft’ Persecution
Authors: BIANCHINI KATIA 
Published: February 2021

Abstract
This article examines the role of cultural expertise in asylum judicial decisions in the UK by focusing on witchcraft-based persecution. The case study highlights multiple challenges to decision-making created by religious and cultural diversity, and the ensuing problems of assessing unfamiliar facts and beliefs against the often lack of corroborating evidence. Drawing on legal sources and a small number of anthropological studies, as well as analyses of judicial decisions, the article discusses how the unique characteristics of witchcraft cases, with their unfamiliar paradigms, are illustrative of the need to analyse and understand asylum claims within their broad cultural, historical, economic, and political contexts. The article exposes how cultural expertise assists judges in appreciating specific contexts and curbing their Eurocentric understanding of culture and religion, and shapes the final outcome of cases.
Acute severe asthma
Authors: Nyman Andrew , Durward Andrew 
Published: February 2021

Abstract
Children with acute severe asthma requiring invasive ventilation are among the most difficult to manage in the Intensive Care Unit (ICU). This chapter begins by explaining the pathophysiology of asthma before examining the approaches to its management on the ICU—starting with the evidence for the use of non-invasive ventilation and bronchodilators. Indications for invasive ventilation in acute severe asthma are discussed and important considerations in the conduct of induction of anaesthesia and intubation in this patient group. Ventilation strategies are explored, with particular reference to the concepts of airway resistance, driving pressure, inspiratory flow limitation, and auto-positive end expiratory pressure (PEEP). The use of the mucolytic therapy intratracheal DNAse is discussed, and indications for the use of extracorporeal membrane oxygenation in refractory cases. Finally, the chapter reports on outcomes for children with acute severe asthma and factors associated with higher risk of mortality.
Traumatic brain injury
Authors: DelSignore Lisa A. , Tasker Robert C. 
Published: February 2021

Abstract
Chapter 7 covers the definition, epidemiology, pathophysiology, and management of traumatic brain injury (TBI). It explains the fundamental concepts of brain physiology: intracranial compliance; intracranial hypertension; cerebral perfusion pressure; cerebral blood flow; and autoregulation. Medical management of TBI is detailed, including hyperosmolar therapy and nutritional support. Neuromonitoring of patients with TBI in the intensive care unit is discussed, including the evidence base for seizure monitoring and antiepileptic drug prophylaxis. Patients with severe TBI and refractory intracranial hypertension may need escalation to second-tier therapies, which are evaluated, including the evidence for decompressive craniectomy. A concise summary of the different therapies is included.
Ophthalmology
Authors: Denniston Alastair , Mathewson Priscilla 
Published: February 2021

AbstractThis chapter in the Oxford Handbook of Clinical Specialties explores the specialty of ophthalmology. Starting with an ophthalmic glossary, it describes in depth how to assess the eyes and flags some key points to remember. Eye conditions such as acute glaucoma, acute anterior uveitis, episcleritis, corneal ulcers, ophthalmic shingles, conjunctivitis, and allergic eye disease are investigated. Tears and lacrimation are explored, along with blepharospasm, hemifacial spasm, and orbital swelling. Retinal problems such as retinoblastoma, loss of vision, primary open-angle glaucoma, cataract, macular degeneration, and retinal detachment are described, moving on to visual field defects, squint, and pupil problems. Systemic disease and diabetes mellitus are explored, as well as ocular disease in pregnancy, the effect of drugs on the eye, and tropical eye disease. A look at vision rounds off the chapter, with refraction, contact lenses, refractive procedures, and blindness, before a glimpse of the possible future for the eye.
Anaesthesia
Authors: Hjelde Nina 
Published: February 2021

AbstractThis chapter in the Oxford Handbook of Clinical Specialties explores the specialty of anaesthesia. It reviews preoperative assessment, sedation, drugs used to induce anaesthesia, inhalational anaesthetic agents, intravenous anaesthetic agents, and muscle relaxants. It explores the practical conduct of anaesthesia, Difficult Airway Society (DAS) guidelines, maintaining and monitoring, rapid sequence induction aspiration, and intubation technique. It examines some complications of anaesthesia, end of anaesthesia, recovery, pain, and postoperative nausea and vomiting, and describes regional anaesthesia, including peripheral nerve blocks and neuraxial anaesthesia.
Spectropolarimetry of low redshift quasars: origin of the polarization and implications for black hole mass estimates
Authors: Capetti Alessandro , Laor Ari , Baldi Ranieri D , Robinson Andrew , Marconi Alessandro 
Published: February 2021

ABSTRACT
We present the results of high signal-to-noise ratio VLT spectropolarimetry of a representative sample of 25 bright type 1 AGN at z &lt; 0.37, of which nine are radio-loud. The sample covers uniformly the 5100 Å optical luminosity at L5100 ∼ 1044−1046 erg s−1, and H α width at FWHM ∼ 1000−10 000 $\rm {\, km \, s}^{-1}$. We derive the continuum and the H α polarization amplitude, polarization angle, and angle swing across the line, together with the radio properties. We find the following: (1) The broad line region (BLR) and continuum polarization are both produced by a single scattering medium. (2) The scattering medium is equatorial and at right angle to the system axis. (3) The scattering medium is located at or just outside the BLR. The continuum polarization and the H α polarization angle swing, can both serve as an inclination indicator. The observed line width is found to be affected by inclination, which can lead to an underestimate of the black hole mass by a factor of ∼5 for a close-to face-on view. The line width measured in the polarized flux overcomes the inclination bias and provides a close-to equatorial view of the BLR in all AGN, which allows to reduce the inclination bias in the BLR based black hole mass estimates.
Top1-PARP1 association and beyond: from DNA topology to break repair
Authors: Chowdhuri Srijita Paul , Das Benu Brata 
Published: February 2021

Abstract
Selective trapping of human topoisomerase 1 (Top1) on the DNA (Top1 cleavage complexes; Top1cc) by specific Top1-poisons triggers DNA breaks and cell death. Poly(ADP-ribose) polymerase 1 (PARP1) is an early nick sensor for trapped Top1cc. New mechanistic insights have been developed in recent years to rationalize the importance of PARP1 beyond the repair of Top1-induced DNA breaks. This review summarizes the progress in the molecular mechanisms of trapped Top1cc-induced DNA damage, PARP1 activation at DNA damage sites, PAR-dependent regulation of Top1 nuclear dynamics, and PARP1-associated molecular network for Top1cc repair. Finally, we have discussed the rationale behind the synergy between the combination of Top1 poison and PARP inhibitors in cancer chemotherapies, which is independent of the ‘PARP trapping’ phenomenon.
ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules
Authors: Xu Peng , chen Yu , Gao Min , Chong Zechen 
Published: February 2021

Abstract
Structural variation (SV), which consists of genomic variation from 50 to millions of base pairs, confers considerable impacts on human diseases, complex traits and evolution. Accurately detecting SV is a fundamental step to characterize the features of individual genomes. Currently, several methods have been proposed to detect SVs using the next-generation sequencing (NGS) platform. However, due to the short length of sequencing reads and the complexity of SV content, the SV-detecting tools are still limited by low sensitivity, especially for insertion detection. In this study, we developed a novel tool, ClipSV, to improve SV discovery. ClipSV utilizes a read extension and spliced alignment approach to overcoming the limitation of read length. By reconstructing long sequences from SV-associated short reads, ClipSV discovers deletions and short insertions from the long sequence alignments. To comprehensively characterize insertions, ClipSV implements tree-based decision rules that can efficiently utilize SV-containing reads. Based on the evaluations of both simulated and real sequencing data, ClipSV exhibited an overall better performance compared to currently popular tools, especially for insertion detection. As NGS platform represents the mainstream sequencing capacity for routine genomic applications, we anticipate ClipSV will serve as an important tool for SV characterization in future genomic studies.
Interpretable detection of novel human viruses from genome sequencing data
Authors: Bartoszewicz Jakub M , Seidel Anja , Renard Bernhard Y 
Published: February 2021

AbstractViruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example, the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages not only enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.
Bi-directional electron transfer between H2 and NADPH mitigates light fluctuation responses in green algae
Authors: Milrad Yuval , Schweitzer Shira , Feldman Yael , Yacoby Iftach 
Published: February 2021

Abstract
The metabolism of green algae has been the focus of much research over the last century. These photosynthetic organisms can thrive under various conditions and adapt quickly to changing environments by concomitant usage of several metabolic apparatuses. The main electron coordinator in their chloroplasts, nicotinamide adenine dinucleotide phosphate (NADPH), participates in many enzymatic activities and is also responsible for inter-organellar communication. Under anaerobic conditions, green algae also accumulate molecular hydrogen (H2), a promising alternative for fossil fuels. However, to scale-up its accumulation, a firm understanding of its integration in the photosynthetic apparatus is still required. While it is generally accepted that NADPH metabolism correlates to H2 accumulation, the mechanism of this collaboration is still vague and relies on indirect measurements. Here, we investigated this connection in Chlamydomonas reinhardtii using simultaneous measurements of both dissolved gases concentration, NADPH fluorescence and electrochromic shifts at 520–546 nm. Our results indicate that energy transfer between H2 and NADPH is bi-directional and crucial for the maintenance of redox balance under light fluctuations. At light onset, NADPH consumption initially eventuates in H2 evolution, which initiates the photosynthetic electron flow. Later on, as illumination continues the majority of NADPH is diverted to the Calvin–Benson–Bassham cycle. Dark onset triggers re-assimilation of H2, which produces NADPH and so, enables initiation of dark fermentative metabolism.
A Systematic Review of Clinical Practice Guidelines for Physical Therapist Management of Patellofemoral Pain
Authors: Wallis Jason A , Roddy Leanne , Bottrell Judy , Parslow Sue , Taylor Nicholas F 
Published: February 2021

Abstract

Objective
The purpose of this study was to conduct a systematic review to evaluate clinical practice guidelines for the physical therapist management of patellofemoral pain.

Methods
Five electronic databases (CINAHL, Embase, Medline, Psychinfo, Cochrane Library) were searched from January 2013 to October 2019. Additional search methods included searching websites that publish clinical practice guidelines containing recommendations for physical therapist management of patellofemoral pain. Characteristics of the guidelines were extracted, including recommendations for examination, interventions, and evaluation applicable to physical therapist practice. Quality assessment was conducted using the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument, applicability of recommendations to physical therapist practice was examined using the AGREE Recommendation Excellence instrument, and convergence of recommendations across guidelines was assessed.

Results
Four clinical practice guidelines were included. One guideline evaluated as higher quality provided the most clinically applicable set of recommendations for examination, interventions, and evaluation processes to assess the effectiveness of interventions. Guideline-recommended interventions were consistent for exercise therapy, foot orthoses, patellar taping, patient education, and combined interventions and did not recommend the use of electrotherapeutic modalities. Two guidelines evaluated as higher quality did not recommend using manual therapy (in isolation), dry needling, and patellar bracing.

Conclusion
Recommendations from higher-quality clinical practice guidelines may conflict with routine physical therapist management of patellofemoral pain. This review provides guidance for clinicians to deliver high-value physical therapist management of patellofemoral pain.

Impact
This review addresses an important gap between evidence and practice in the physical therapist management of patellofemoral pain.

Lay Summary
If you have kneecap pain, this review offers guidance for your physical therapist to provide examination processes, treatments, and evaluation processes that are recommended by high-quality guidelines.
Developing Functional Network Connectivity of the Dorsal Anterior Cingulate Cortex Mediates Externalizing Psychopathology in Adolescents with Child Neglect
Authors: Silveira Sarita , Boney Simone , Tapert Susan F. , Mishra Jyoti 
Published: February 2021

AbstractChildhood adversity in form of child abuse and neglect is associated with elevated risk for psychopathologies. We investigated whether development of functional brain networks important for executive function (EF) could serve as potential mediators of this association. We analyzed data of 475 adolescents, a subsample of the multisite longitudinal NCANDA (National Consortium on Alcohol and Neurodevelopment in Adolescence) cohort with completed measures of childhood trauma, resting-state functional brain connectivity data, and internalizing/externalizing psychopathological syndrome data at baseline and follow-up years 1-4. Using parallel process latent growth models, we found that childhood adversity was associated with increased risk for externalizing/internalizing behaviors. We specifically investigated whether functional connectivity of the dorsal anterior cingulate cortex (dACC) to brain regions within the cingulo-opercular (CO) network, a well-known EF network that underlies control of attention and self-regulation, mediates the association between adversity and psychopathological behaviors. We found that childhood adversity, specifically neglect was negatively associated with functional connectivity of the dACC within the CO network, and that this connectivity mediated the association between child neglect and externalizing behaviors. Our study advances a mechanistic understanding of how childhood adversity may impact the development of psychopathology, highlighting the relevance of dACC functional networks particularly for externalizing psychopathology.
Emergence of first strains of SARS-CoV-2 lineage B.1.1.7 in Romania
Authors: Lobiuc Andrei , Dimian Mihai , Sturdza Olga , Filip Roxana , Covasa Mihai 
Published: February 2021

AbstractUnited Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant B.1.1.7. that rapidly spread to other contries. The impact of this new mutation that occurs in the S protein, on infectivity, virulence and current vaccine effectiveness is still under evaluation. We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the UK region where the new variant was originally sequenced. Mutations in the Nsp3 protein, N844S and D455N and L15F in Orf3a were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. These results indicate, for the first time, the presence and characteristics of the new variant B.1.1.7 in Romania and underscore the need for increased genomic sequencing in confirmed COVID-19 patients.
Clearing spheroids for 3D fluorescent microscopy: combining safe and soft chemicals with deep convolutional neural network
Authors: Ahmad Ali , Goodarzi Saba , Frindel Carole , Recher Gaëlle , Riviere Charlotte , Rousseau David 
Published: February 2021

AbstractIn life sciences, there are increasing interest in 3D culture models to better reproduce the 3D environment encountered in-vivo. Imaging of such 3D culture models is instrumental for drug discovery, but face several issues before its use becomes widespread. Extensive microscopic investigation of these 3D cell models faces the challenge of light penetration in depth in opaque biological tissues. To overcome this limit, diverse clearing techniques have emerged over the past decades. However, it is not straightforward to choose the best clearing protocols, and assess quantitatively their clearing efficiency. Focusing on spheroids, we propose a combination of fast and cost-effective clearing procedure for such medium-sized samples. A generic method with local contrast metrics and deep convolutional neural network-based segmentation of nuclei is proposed to quantify the efficiency of clearing. We challenged this method by testing the possibility to transfer segmentation knowledge from a clearing protocol to another. The later results support the pertinence of training deep learning algorithms on cleared samples to further use the segmentation pipeline on non-cleared ones. This second step of the protocol gives access to digital clearing possibilities applicable to live and high-throughput optical imaging.
Environmentally-induced mdig is a major contributor to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism
Authors: Zhang Qian , Thakur Chitra , Fu Yao , Bi Zhuoyue , Qiu Yiran , Wadgaonkar Priya , Xu Liping , Almutairy Bandar , Zhang Wenxuan , Stemmer Paul , Chen Fei 
Published: February 2021

AbstractThe novel β-coronavirus, SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has infected more than 101 million people and resulted in 2.2 million death worldwide. Recent epidemiological studies suggested that some environmental factors, such as air pollution, might be the important contributors to the mortality of COVID-19. However, how environmental exposure enhances the severity of COVID-19 remains to be fully understood. In the present report, we provide evidence showing that mdig, a previously reported environmentally-induced oncogene that antagonizes repressive trimethylation of histone proteins, is a master regulator for SARS-CoV-2 receptors neuropilin-1 (NRP1) and NRP2, cathepsins, glycan metabolism and inflammation, key determinants for viral infection and cytokine storm of the patients. Depletion of mdig in bronchial epithelial cells by CRISPR-Cas-9 gene editing resulted in a decreased expression of NRP1, NRP2, cathepsins, and genes involved in protein glycosylation and inflammation, largely due to a substantial enrichment of lysine 9 and/or lysine 27 trimethylation of histone H3 (H3K9me3/H3K27me3) on these genes as determined by ChIP-seq. These data, accordingly, suggest that mdig is a key mediator for the severity of COVID-19 in response to environmental exposure and targeting mdig may be one of the effective strategies in ameliorating the symptom and reducing the mortality of COVID-19.
Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury
Authors: Trairatphisan Panuwat , de Souza Terezinha Maria , Kleinjans Jos , Jennen Danyel , Saez-Rodriguez Julio 
Published: February 2021

AbstractToxicogenomics studies typically reveal a group of genes relevant to the pathophysiology of drug-induced organ injury. In recent years, network-based methods have become an attractive analytical approach as they can capture not only the global changes of regulatory gene networks but also the relationships between their components. Among them, a causal reasoning approach additionally depicts the mechanisms of regulation that connect upstream regulators in signaling networks towards their downstream gene targets.In this work, we applied CARNIVAL, a causal network contextualisation tool, to infer upstream regulatory signaling networks based on gene expression microarray data from the TG-GATEs database. We focussed on six compounds that induce observable histopathologies linked to drug-induced liver injury (DILI) from repeated dosing experiments in rats. We compared responsesin vitroandin vivoto identify potential cross-platform concordances in rats as well as network preservations between rat and human. Our results showed similarities of enriched pathways and network motifs between compounds. These pathways and motifs induce the same pathology in rats but not in humans. In particular, the causal interactions “LCK activates SOCS3, which in turn inhibits TFDP1” was commonly identified as a regulatory path among the fibrosis-inducing compounds. This potential pathology-inducing regulation illustrates the value of our approach to generate hypotheses that can be further validated experimentally.
Cannabinoids is a “No-Go” While a Cancer Patient is on Immunotherapy; but is It Safe to Use Psychedelics During Cancer Immunotherapy?
Authors: Romach E. Amit , Nachliely M. , Moran O. , Brami M. , Lamensdorf I. 
Published: February 2021

AbstractThe use of Psychedelics by patients with cancer to relieve anxiety and depression has increased in the past few years. Since Psychedelics have immunomodulatory effects, their consumption among cancer patients should be carefully considered due to their potential negative effects on the tumor immune stroma, especially in view of the increase in the utilization of therapeutic approaches that are based on immune activation such as treatment with immune checkpoint inhibitors (ICIs). Preclinical data provided in this report indicate a potentially negative impact on tumor growth as a result of Psychedelics consumption during treatment with ICIs. Furthermore, our research suggests that the use of psychedelic agents (Lysergic acid diethylamide [LSD] or Psylocibin) might diminish the beneficial therapeutic benefits of ICIs.It might be necessary to expend this line of research in order to validate these findings, in view of the increase use of cannabinoids and psychedelics among cancer patients, some of them being treated with immune-based modalities.