bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of nearly isothermal, adiabatic shock waves
Authors: Coughlin Eric R 
Published: May 2020

ABSTRACT
An explosively generated shock wave with time-dependent radius R(t) is characterized by a phase in which the shocked gas becomes radiative with an effective adiabatic index γ ≃ 1. Using the result that the post-shock gas is compressed into a shell of width ΔR/R ≃ δ, where δ = γ − 1, we show that a choice of self-similar variable that exploits this compressive behaviour in the limit that γ → 1 naturally leads to a series expansion of the post-shock fluid density, pressure, and velocity in the small quantity δ. We demonstrate that the leading-order (in δ) solutions, which are increasingly accurate as γ → 1, can be written in simple, closed forms when the fluid is still approximated to be in the energy-conserving regime (i.e. the Sedov–Taylor limit), and that the density declines exponentially rapidly with distance behind the shock. We also analyse the solutions for the bubble surrounding a stellar or galactic wind that interacts with its surroundings, and derive expressions for the location of the contact discontinuity that separates the shocked ambient gas from the shocked wind. We discuss the implications of our findings in the context of the dynamical stability of nearly isothermal shocks.
Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications
Authors: Touceda-Suárez María , Kita Elizabeth M , Acemel Rafael D , Firbas Panos N , Magri Marta S , Naranjo Silvia , Tena Juan J , Gómez-Skarmeta Jose Luis , Maeso Ignacio , Irimia Manuel 
Published: May 2020

Abstract
We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic regulatory blocks, GRBs). We showed that the majority of GRBs identified in the last common ancestor of chordates have been maintained as a single copy in humans. We found evidence that dismantling of the duplicated GRB copies occurred early in vertebrate evolution often through the differential retention of the regulatory gene but loss of the bystander gene’s exonic sequences. Despite the large evolutionary scale, the presence of duplicated highly conserved noncoding regions provided unambiguous proof for this scenario for multiple ancient GRBs. Remarkably, the dismantling of ancient GRB duplicates has contributed to the creation of large gene deserts associated with regulatory genes in vertebrates, providing a potentially widespread mechanism for the origin of these enigmatic genomic traits.
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe
Authors: Iqbal Sumaiya , Hoksza David , Pérez-Palma Eduardo , May Patrick , Jespersen Jakob B , Ahmed Shehab S , Rifat Zaara T , Heyne Henrike O , Rahman M Sohel , Cottrell Jeffrey R , Wagner Florence F , Daly Mark J , Campbell Arthur J , Lal Dennis 
Published: May 2020

AbstractHuman genome sequencing efforts have greatly expanded, and a plethora of missense variants identified both in patients and in the general population is now publicly accessible. Interpretation of the molecular-level effect of missense variants, however, remains challenging and requires a particular investigation of amino acid substitutions in the context of protein structure and function. Answers to questions like ‘Is a variant perturbing a site involved in key macromolecular interactions and/or cellular signaling?’, or ‘Is a variant changing an amino acid located at the protein core or part of a cluster of known pathogenic mutations in 3D?’ are crucial. Motivated by these needs, we developed MISCAST (missense variant to protein structure analysis web suite; http://miscast.broadinstitute.org/). MISCAST is an interactive and user-friendly web server to visualize and analyze missense variants in protein sequence and structure space. Additionally, a comprehensive set of protein structural and functional features have been aggregated in MISCAST from multiple databases, and displayed on structures alongside the variants to provide users with the biological context of the variant location in an integrated platform. We further made the annotated data and protein structures readily downloadable from MISCAST to foster advanced offline analysis of missense variants by a wide biological community.
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
Authors: Xu Yifei , Yang-Turner Fan , Volk Denis , Crook Derrick 
Published: May 2020

Abstract
Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission. We implement NanoSPC using Nextflow manager within Docker images to allow reproducibility and portability of the analysis. Moreover, we deploy NanoSPC to our scalable pathogen pipeline platform, enabling elastic computing for high throughput Nanopore data on HPC cluster as well as multiple cloud platforms, such as Google Cloud, Amazon Elastic Computing Cloud, Microsoft Azure and OpenStack. Users could either access our web interface (https://nanospc.mmmoxford.uk) to run cloud-based analysis, monitor process, and visualize results, as well as download Docker images and run command line to analyse data locally.
Macrophage development and activation involve coordinated intron retention in key inflammatory regulators
Authors: Green Immanuel D , Pinello Natalia , Song Renhua , Lee Quintin , Halstead James M , Kwok Chau-To , Wong Alex C H , Nair Shalima S , Clark Susan J , Roediger Ben , Schmitz Ulf , Larance Mark , Hayashi Rippei , Rasko John E J , Wong Justin J-L 
Published: May 2020

Abstract
Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.
Large shift of the Pacific Walker Circulation across the Cenozoic
Authors: Yan Qing , Korty Robert , Zhang Zhongshi , Brierley Chris , Li Xiangyu , Wang Huijun 
Published: May 2020

AbstractFluctuations in the Pacific Walker Circulation (PWC), a zonally oriented overturning cell across the tropical Pacific, can cause widespread climatic and biogeochemical perturbations. It remains unknown how the PWC developed during the Cenozoic era, with its substantial changes in greenhouse gases and continental positions. Through a suite of coupled model simulations on tectonic timescales, we demonstrate that the PWC was ∼38° broader and ∼5% more intense during the Early Eocene relative to present. As the climate cooled from the Early Eocene to the Late Miocene, the width of the PWC shrank, accompanied by an increase in intensity that was tied to the enhanced Pacific zonal temperature gradient. However, the locations of the western and eastern branches behave differently from the Early Eocene to the Late Miocene, with the western edge remaining steady with time due to the relatively stable geography of the western tropical Pacific; the eastern edge migrates westward with time as the South American continent moves northwest. A transition occurs in the PWC between the Late Miocene and Late Pliocene, manifested by an eastward shift (both the western and eastern edges migrate eastward by &gt;12°) and weakening (by ∼22%), which we show here is linked with the closure of the tropical seaways. Moreover, our results suggest that rising CO2 favors a weaker PWC under the same land-sea configurations, a robust feature across the large spread of Cenozoic climates considered here, supporting a weakening of the PWC in a warmer future.
Pater Knows Best: Withdrawal of Medical Treatment from Infants in Scotland
Authors: Brown Jonathan , Christie Sarah 
Published: May 2020

Abstract
The cases of Charlie Gard and Alfie Evans placed the withdrawal of treatment from terminally ill infants at the forefront of medical law and ethics. In the medico-legal context, Scottish court procedures materially differ from those in England. This article considers these differences in light of the possibility that a similar case might soon be called before the Scottish courts. The Court of Session would then be required to consider whether to utilise its parens patriae jurisdiction to consent to the withdrawal of treatment as if it were the parent of the infant. The operation of this jurisdiction is such that the outcome of any Scottish case cannot be said to be certain, as the Scottish courts are bound to pay more heed to parental autonomy than their English counterparts do.
Multispecies Diffusion of Yttrium, Rare Earth Elements and Hafnium in Garnet
Authors: Bloch E M , Jollands M C , Devoir A , Bouvier A -S , Ibañez-Mejia M , Baumgartner L P 
Published: May 2020

AbstractWe report experimental data for Y, La, Lu and Hf diffusion in garnet, in which diffusant concentrations and silica activity have been systematically varied. Experiments were conducted at 950 and 1050 °C, at 1 atm pressure and oxygen fugacity corresponding to the quartz–fayalite–magnetite buffer. At Y and REE concentrations below several hundred ppm we observe both slow and fast diffusion mechanisms, which operate simultaneously and correspond to relatively high and low concentrations, respectively. Diffusivity of Y and REE is independent of silica activity over the studied range. General formulae for REE diffusion in garnet, incorporating data from this and previous studies, are  logDREE(f)(m2 s−1)=−10·24(±0·21)−221057(±4284)2·303RT(K) for the ‘fast’ REE diffusion mechanism at 1 atm pressure, and  logDREE(s)(m2 s−1)=−9·28(±0·65)−265200(±38540)+10800(±2600)×P(GPa)2·303RT(K) for the ‘slow’ REE diffusion mechanism. These slow and fast diffusion mechanisms are in agreement with previous, apparently conflicting, datasets for REE diffusion in garnet. Comparison with high-pressure experiments suggests that at high pressures (&gt;∼1 GPa minimum) the fast diffusion mechanism no longer operates to a significant degree. When Y and/or REE surface concentrations are greater than several hundred ppm, complex concentration profiles develop. These profiles are consistent with a multi-site diffusion–reaction model, whereby Y and REE cations diffuse through, and exchange between, different crystallographic sites. Diffusion profiles of Hf do not exhibit any of the complexities observed for Y and REE profiles, and can be modeled using a standard (i.e. single mechanism) solution to the diffusion equation. Hafnium diffusion in garnet shows a negative dependence on silica activity, and is described by  logDHf(m2 s−1)=−8·85(±0·38)−299344(±15136)+12500(±900)×P(GPa)2·303RT(K)−0·52(±0·09)×log⁡10aSiO2. In many natural garnets, diffusion of both Lu and Hf would be sufficiently slow that the Lu–Hf system can be reliably used to date garnet growth. In cases in which significant Lu diffusion does occur, preferential retention of 176Hf/177Hf relative to 176Lu/177Hf will skew isochron relationships such that their apparent ages may not correspond to anything meaningful (e.g. garnet growth, peak temperature or the closure temperature of Lu or Hf). Late-stage reheating events are capable of causing larger degrees of preferential retention of 176Hf/177Hf relative to 176Lu/177Hf and partial to full resetting of the Sm–Nd system within garnet, thus increasing the separation between garnet Lu–Hf and Sm–Nd isochron dates, owing to the fact that these systems are more significantly disturbed through diffusion as more radiogenic 176Hf and 143Nd have accumulated.
A Qualitative Exploratory Study of the Knowledge, Forensic, and Legal Challenges from the Perspective of Police Cybercrime Specialists
Authors: De Paoli Stefano , Johnstone Jason , Coull Natalie , Ferguson Ian , Sinclair Georgina , Tomkins Patrick , Brown Maureen , Martin Rebecca 
Published: May 2020

AbstractThe extant literature has demonstrated that there is a need for more empirical research on the subject of policing cybercrime. This article makes a contribution and offers a qualitative exploration of the problem of policing cybercrime from an international perspective. It structures the analysis around three main challenges: the knowledge, forensic, and legal challenges. A literature review supports the evidence that these issues are core challenges when policing cybercrime. Through 13 semi-structured interviews with cybercrime specialists from 8 countries, these three challenges are further investigated. A thematic analysis of the interviews, whilst confirming some of the previous literature findings, also outlines novel findings. Interview analysis shows that in some areas little recent progress has been made, in particular the recording of cybercrime. However, in other areas new creative solutions have been implemented, including filling the policing skills gap with civilian specialists. The article concludes by offering recommendations for addressing some of the challenges for policing cybercrime.
Global, regional, and national burden of other musculoskeletal disorders 1990–2017: results from the Global Burden of Disease Study 2017
Authors: Safiri Saeid , Kolahi Ali Asghar , Cross Marita , Carson-Chahhoud Kristin , Almasi-Hashiani Amir , Kaufman Jay , Mansournia Mohammad Ali , Sepidarkish Mahdi , Ashrafi-Asgarabad Ahad , Hoy Damian , Collins Gary , Woolf Anthony D , March Lyn , Smith Emma 
Published: May 2020

Abstract

Objectives
To describe the level and trends of point prevalence, deaths and disability-adjusted life years (DALYs) for other musculoskeletal (MSK) disorders, i.e. those not covered by specific estimates generated for RA, OA, low back pain, neck pain and gout, from 1990 to 2017 by age, sex and sociodemographic index.

Methods
Publicly available modelled estimates from the Global Burden of Disease (GBD) 2017 study were extracted and reported as counts and age-standardized rates per 100 000 population for 195 countries and territories between 1990 and 2017.

Results
Globally, the age-standardized point prevalence estimates and deaths rates of other MSK disorders in 2017 were 4151.1 and 1.0 per 100 000. This was an increase of 3.4% and 7.2%, respectively. The age-standardized DALY rate in 2017 was 380.2, an increase of 3.4%. The point prevalence estimate was higher among females and increased with age. This peaked in the 65–69 year age group for both females and males in 2017, followed by a decreasing trend for both sexes. At the national level, the highest age-standardized point prevalence estimates in 2017 were seen in Bangladesh, India and Nepal. The largest increases in age-standardized point prevalence estimates were observed in Romania, Croatia and Armenia.

Conclusion
The burden of other MSK disorders is proven to be substantial and increasing worldwide, with a notable intercountry variation. Data pertaining to specific diseases within this overarching category are required for future GBD MSK estimates. This would enable policymakers to better allocate resources and provide interventions appropriately.
Acute encephalopathy in children in Muzaffarpur, India: a review of aetiopathogenesis
Authors: Sarkar Abhirup , Datta Debatri , Datta Sudip Kumar , John T Jacob 
Published: May 2020

AbstractThe acute encephalopathy occurring in children in Muzaffarpur, India, also recognised in other litchi-cultivating areas of India, Bangladesh, Vietnam and China, had previously been linked to litchi consumption. Recently, it has been identified as hypoglycaemic encephalopathy of an unusual aetiology with three key factors: undernutrition, prolonged fasting and litchi consumption. A second set of investigators has independently reconfirmed the diagnosis and the three-factor aetiology. Skipping the evening meal with an intake of large amounts of litchi in undernourished children is causative. Early-morning hypoglycaemia with an inadequate glycogen store leads to initiation of gluconeogenesis and fatty acid β-oxidation, but methylene cyclopropyl alanine and glycine present in the litchi aril block the fatty acid β-oxidation cycle. The outcomes are uncorrected hypoglycaemia and encephalopathy due to the entry of metabolic intermediates that cross the blood-brain barrier and affect neuronal function. Suggested measures include early 10% dextrose infusion. Awareness about the disease is of prime importance. The diagnosis and aetiopathogenesis are still under question from a part of the scientific community. This review was undertaken to present a comprehensive view of hypoglycaemic encephalopathy and to remove some of the lingering doubts.
A Furosemide Excretion Stress Test Predicts Mortality in Mice After Sepsis and Outperforms the Furosemide Stress Test During Vasopressin Administration
Authors: Street Jonathan M. , Bellomo Tiffany R. , Koritzinsky Erik H. , Kojima Hiroshi , Yuen Peter S. T. , Star Robert A. 
Published: May 2020

Objectives:
The furosemide stress test measures the volume of urine produced after a furosemide challenge. Furosemide stress test has previously demonstrated sensitive and specific prediction of progression to Kidney Disease: Improving Global Outcomes guideline defined acute kidney injury stage III in the ICU. Furosemide is actively excreted into the nephron lumen where it inhibits the sodium-potassium-chloride cotransporter, causing diuresis. We hypothesize that furosemide excretion is a more direct measure of tubule health than diuresis.

Design:
We developed a furosemide excretion stress test to evaluate this hypothesis in a murine model of septic-acute kidney injury.

Setting:
Basic science laboratory.

Subjects:
Male and female 8-week old CD-1 mice.

Interventions:
Sepsis was induced by cecal ligation and puncture in male and female mice. Furosemide stress test/furosemide excretion stress test started 42 hours post-cecal ligation and puncture with a 1 mg/kg furosemide bolus and urine was collected for 12 hours. The mice were then euthanized or monitored until 7 days post-cecal ligation and puncture. In another cohort, mice were treated with vasopressin, which decreases urine volume. Furosemide concentration was determined by high performance liquid chromatography.

Measurements and Main Results:
Urine production during the 12-hour collection varied from 0.08 to 2.62 mL. Both urine production (furosemide stress test) and furosemide excretion (furosemide excretion stress test) predicted mortality (area under the receiver operating characteristic curve = 0.925 and 0.916) and time of death (R
2 = 0.26 and 0.74). Male and female mice demonstrated consistent results. Following vasopressin treatment, furosemide stress test specificity fell to 33% (p = 0.016) but furosemide excretion stress test specificity was maintained.

Conclusions:
The furosemide stress test and furosemide excretion stress test performed similarly in predicting mortality; however, furosemide excretion stress test was superior in predicting time to death and maintained performance when challenged with vasopressin treatment in a mouse sepsis model.
Extracorporeal Membrane Oxygenation for Poisonings Reported to U.S. Poison Centers from 2000 to 2018: An Analysis of the National Poison Data System*
Authors: Cole Jon B. , Olives Travis D. , Ulici Alexandru , Litell John M. , Bangh Stacey A. , Arens Ann M. , Puskarich Michael A. , Prekker Matthew E. 
Published: May 2020

Objectives:
To assess trends in the use of extracorporeal membrane oxygenation for poisoning in the United States.

Design:
Retrospective cohort study.

Setting:
The National Poison Data System, the databased owned and managed by the American Association of Poison Control Centers, the organization that supports and accredits all 55 U.S. Poison Centers, 2000–2018.

Patients:
All patients reported to National Poison Data System treated with extracorporeal membrane oxygenation.

Interventions:
None.

Measurements and Main Results:
In total, 407 patients met final inclusion criteria (332 adults, 75 children). Median age was 27 years (interquartile range, 15–39 yr); 52.5% were male. Median number of ingested substances was three (interquartile range, 2–4); 51.5% were single-substance exposures. Extracorporeal membrane oxygenation use in poisoned patients in the United States has significantly increased over time (z = 3.18; p = 0.001) in both adults (age > 12 yr) and children (age ≤ 12 yr), increasing by 9–100% per year since 2008. Increase in use occurred more commonly in adults. We found substantial geographical variation in extracorporeal membrane oxygenation use by geospatially mapping the ZIP code associated with the initial call, with large, primarily rural areas of the United States reporting no cases. Overall survival was 70% and did not vary significantly over the study period for children or adults. Patients with metabolic and hematologic poisonings were less likely to survive following extracorporeal membrane oxygenation than those with other poisonings (49% vs 72%; p = 0.004).

Conclusions:
The use of extracorporeal membrane oxygenation to support critically ill, poisoned patients in the United States is increasing, driven primarily by increased use in patients greater than 12 years old. We observed no trends in survival over time. Mortality was higher when extracorporeal membrane oxygenation was used for metabolic or hematologic poisonings. Large, predominantly rural regions of the United States reported no cases of extracorporeal membrane oxygenation for poisoning. Further research should focus on refining criteria for the use of extracorporeal membrane oxygenation in poisoning.