bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary patterns of the formation abrasion-accumulative jumpers in the bays entrance gates of the lake area of the Volgograd Reservoir
Authors: Baranova M S , Kochetkova A I , Bryzgalina E S , Ob“edkova O A , Leont‘ev D A 
Published: September 2021

Abstract
The article contents preliminary process patterns. They were obtained as a result of a researching of some representative bays of the Volgograd reservoir in 2019-2020, as well as an analysis of archival materials, maps and satellite images. The bays separation process depends on the primary volume, morphological features, lithological composition of the coasts, the speed and direction of wave, the frequency and repeatability of storms, and the anthropogenic factor. There are some differences in the formation of the abrasion-accumulative jumpers on the right and left coasts of the reservoir. It was previously established that current’s speeds formative jumpers are 0.48-0.62, 0.63-0.78, 2.83-2.89, 3.60-3.64 m/s. The spatiotemporal dynamics of the formation and development of bays estuarine abrasion-accumulative jumpers of the Volgograd reservoir was revealed by our researching.
Water bodies on the surface of the earth (reservoirs and lakes) and their influence on the long-term changes in the regulated rivers’ runoff. A comparative study
Authors: Dobrovolski S G , Istomina M N , Lebedeva I P , Sokolova O V , Solomonova I V , Yu Vyruchalkina T 
Published: September 2021

Abstract
Archives of data on the most important reservoirs and flowing lakes of the world, and on long-term changes in the flow of rivers regulated by them have been formed. The features of the parameters of artificially regulated rivers and lacustrine rivers and the dependence of these parameters on the characteristics of reservoirs and lakes were analysed. A phenomenon of «monotonous» and «intermittent» nonstationarity are described. The possible role of reservoirs and lakes in their formation has been assessed.
Sedimentation in the Volga Cascade reservoirs in the 21st century
Authors: Zakonnov V V 
Published: September 2021

Abstract
The complex surveys of sediments in the Volga River reservoir has begun in the 20th century and continued in the 21st century providing the basis for a modern quantitative assessment of the impact of bottom sediments on functioning of freshwater ecosystems. The results may be used in modelling of the multi-factor components in the water-bottom sediments-biota system, prediction, creating of object-oriented, special and thematic maps as well as for making decisions on elimination the negative consequences associated with water quality.
Modelling the response of the Ivankovo Reservoir ecosystem to changes in the external chemical load
Authors: Datsenko Y S , Puklakov V V 
Published: September 2021

Abstract
A two-dimensional hydroecological model is used to analyse changes in water quality indicators in the Ivankovo Reservoir due to the response of the reservoir to the doubling of their concentrations in the main tributaries of the reservoir set in the model in the average water content year.
Features of the impact of thermal power plants on the environment on the example of the Uy River Basin
Authors: Vtorova A I , Myakisheva N V 
Published: September 2021

Abstract
The probabilistic analysis of intra-annual and interannual variability of river flow in the Uy river basin is carried out using the theory of random processes. The results of the analysis are summarized in terms of a probabilistic model. The regulatory capacity of the catchment area and man-made structures is estimated. Materials of observations made it possible to assess the hydrological structure of flowing water bodies and the impact of waste water from thermal power plants. Analysis of the hydrological and hydrochemical regime of reservoirs has shown that dynamic mixing plays a significant role in the regime of water bodies.
Calculation of the radiated power in WEST
Authors: Devynck P , Fedorczak N , Mao R , Vartanian S 
Published: September 2021

Abstract
The WEST tokamak is currently equipped with a set of horizontal bolometers to estimate the radiation level of plasma scenarios. The exact relation between bolometer signal and radiating power is derived, highlighting the approximations required to express a proportionality between bolometer signal and radiation level. Further approximations are needed to correct for overlapping lines of sights. They are done via a truncated trapeze approximation. To test the robustness of all these approximations and uncertainties, a synthetic diagnostic basis is constructed coupled to a Monte Carlo ray-tracing tool, and applied to a large set of emissivity phantoms representative of WEST plasma geometries and radiation distributions. It results that the approximations are valid, with uncertainty levels bounded by 5% to 10% depending on the plasma geometry. Application to WEST plasmas shows that the radiated power fraction (related to total power) is about 50% in the first experimental campaigns. A finite radiation level originates from the divertor together with finite radiations from the core. It suggests a detrimental mixture of light impurities and tungsten in the plasma, possibly caused by poor chamber conditioning.
Sequential Projected Newton method for regularization of nonlinear least squares problems
Authors: Cornelis J , Vanroose W 
Published: September 2021

Abstract
We develop a computationally efficient algorithm for the automatic regularization of nonlinear inverse problems based on the discrepancy principle. We formulate the problem as an equality constrained optimization problem, where the constraint is given by a least squares data fidelity term and expresses the discrepancy principle. The objective function is a convex regularization function that incorporates some prior knowledge, such as the total variation regularization function. Using the Jacobian matrix of the nonlinear forward model, we consider a sequence of quadratically constrained optimization problems that can all be solved using the Projected Newton method. We show that the solution of such a quadratically constrained sub-problem results in a descent direction for an exact merit function. This merit function can then be used to describe a formal line-search method. We also formulate a slightly more heuristic approach that simplifies the algorithm and allows for an inexact solution of the sequence of sub-problems. We illustrate the behavior of the algorithm using a number of numerical experiments, with Talbot-Lau x-ray phase contrast imaging as the main application. The numerical experiments confirm that the quadratically constrained sub-problems need not be solved with high accuracy in early iterations to make sufficient progress towards the solution. In addition, we show that the proposed method is able to produce reconstructions of similar quality compared to other state-of-the-art approaches with a significant reduction in computational time.
FRETraj: integrating single-molecule spectroscopy with molecular dynamics
Authors: Steffen Fabio D , Sigel Roland K O , Börner Richard 
Published: September 2021

Abstract

Summary
Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here, we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes.

Availability and implementation
FRETraj is implemented as a cross-platform Python package available under the GPL-3.0 on Github (https://github.com/RNA-FRETools/fretraj) and is documented at https://RNA-FRETools.github.io/fretraj.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deep Subspace Mutual Learning for cancer subtypes prediction
Authors: Yang Bo , Xin Ting-Ting , Pang Shan-Min , Wang Meng , Wang Yi-Jie 
Published: September 2021

Abstract

Motivation
Precise prediction of cancer subtypes is of significant importance in cancer diagnosis and treatment. Disease etiology is complicated existing at different omics levels; hence integrative analysis provides a very effective way to improve our understanding of cancer.

Results
We propose a novel computational framework, named Deep Subspace Mutual Learning (DSML). DSML has the capability to simultaneously learn the subspace structures in each available omics data and in overall multi-omics data by adopting deep neural networks, which thereby facilitates the subtype’s prediction via clustering on multi-level, single-level and partial-level omics data. Extensive experiments are performed in five different cancers on three levels of omics data from The Cancer Genome Atlas. The experimental analysis demonstrates that DSML delivers comparable or even better results than many state-of-the-art integrative methods.

Availability and implementation
An implementation and documentation of the DSML is publicly available at https://github.com/polytechnicXTT/Deep-Subspace-Mutual-Learning.git.
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis
Authors: Stirling David R , Carpenter Anne E , Cimini Beth A 
Published: September 2021

Abstract

Summary
Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration of quantitative image-derived data and the training of machine learning classifiers with an intuitive user interface. We have now released CellProfiler Analyst 3.0, which in addition to enhanced performance adds support for neural network classifiers, identifying rare object subsets, and direct transfer of objects of interest from visualization tools into the Classifier tool for use as training data. This release also increases interoperability with the recently released CellProfiler 4, making it easier for users to detect and measure particular classes of objects in their analyses.

Availability
CellProfiler Analyst binaries for Windows and MacOS are freely available for download at https://cellprofileranalyst.org/. Source code is implemented in Python 3 and is available at https://github.com/CellProfiler/CellProfiler-Analyst/. A sample dataset is available at https://cellprofileranalyst.org/examples, based on images freely available from the Broad Bioimage Benchmark Collection.
Homozygous missense WIPI2 variants cause a congenital disorder of autophagy with neurodevelopmental impairments of variable clinical severity and disease course
Authors: Maroofian Reza , Gubas Andrea , Kaiyrzhanov Rauan , Scala Marcello , Hundallah Khalid , Severino Mariasavina , Abdel-Hamid Mohamed S , Rosenfeld Jill A , Ebrahimi-Fakhari Darius , Ali Zahir , Rahim Fazal , Houlden Henry , Tooze Sharon A , Alsaleh Norah S , Zaki Maha S 
Published: September 2021

Abstract
WIPI2 is a member of the human WIPI protein family (seven-bladed b-propeller proteins binding phosphatidylinositols, PROPPINs), which play a pivotal role in autophagy and has been implicated in the pathogenesis of several neurological conditions. The homozygous WIPI2 variant c.745G&gt;A; p.(Val249Met) (NM_015610.4) has recently been associated with a neurodevelopmental disorder in a single family. Using exome sequencing and Sanger segregation analysis, here, two novel homozygous WIPI2 variants [c.551T&gt;G; p.(Val184Gly) and c.724C&gt;T; p.(Arg242Trp) (NM_015610.4)] were identified in four individuals of two consanguineous families. Additionally, follow-up clinical data were sought from the previously reported family. Three non-ambulant affected siblings of the first family harbouring the p.(Val184Gly) missense variant presented with microcephaly, profound global developmental delay/intellectual disability, refractory infantile/childhood-onset epilepsy, progressive tetraplegia with joint contractures and dyskinesia. In contrast, the proband of the second family carrying the p.(Arg242Trp) missense variant, similar to the initially reported WIPI2 cases, presented with a milder phenotype, encompassing moderate intellectual disability, speech and visual impairment, autistic features, and an ataxic gait. Brain MR imaging in five patients showed prominent white matter involvement with a global reduction in volume, posterior corpus callosum hypoplasia, abnormal dentate nuclei and hypoplasia of the inferior cerebellar vermis. To investigate the functional impact of these novel WIPI2 variants, we overexpressed both in WIPI2-knockout HEK293A cells. In comparison to wildtype, expression of the Val166Gly WIPI2b mutant resulted in a deficient rescue of LC3 lipidation whereas Arg224Trp mutant increased LC3 lipidation, in line with the previously reported Val231Met variant. These findings support a dysregulation of the early steps of the autophagy pathway. Collectively, our findings provide evidence that biallelic WIPI2 variants cause a neurodevelopmental disorder of variable severity and disease course. Our report expands the clinical spectrum and establishes WIPI2-related disorder as a congenital disorders of autophagy.
Association of renin–angiotensin system blockers with COVID-19 diagnosis and prognosis in patients with hypertension: a population-based study
Authors: Soler María José , Ribera Aida , Marsal Josep R , Mendez Ana Belen , Andres Mireia , Azancot Maria Antonia , Oristrell Gerard , Méndez-Boo Leonardo , Cohen Jordana , Barrabés Jose A , Ferreira-González Ignacio ,   Vall d’Hebron COVID-19 Working Group
Published: September 2021

ABSTRACTBackgroundThe effect of renin–angiotensin system (RAS) blockade either by angiotensin-converting enzyme inhibitors (ACEis) or angiotensin-receptor blockers (ARBs) on coronavirus disease 2019 (COVID-19) susceptibility, mortality and severity is inadequately described. We examined the association between RAS blockade and COVID-19 diagnosis and prognosis in a large population-based cohort of patients with hypertension (HTN).MethodsThis is a cohort study using regional health records. We identified all individuals aged 18–95 years from 87 healthcare reference areas of the main health provider in Catalonia (Spain), with a history of HTN from primary care records. Data were linked to COVID-19 test results, hospital, pharmacy and mortality records from 1 March 2020 to 14 August 2020. We defined exposure to RAS blockers as the dispensation of ACEi/ARBs during the 3 months before COVID-19 diagnosis or 1 March 2020. Primary outcomes were: COVID-19 infection and severe progression in hospitalized patients with COVID-19 (the composite of need for invasive respiratory support or death). For both outcomes and for each exposure of interest (RAS blockade, ACEi or ARB) we estimated associations in age-, sex-, healthcare area- and propensity score-matched samples.ResultsFrom a cohort of 1 365 215 inhabitants we identified 305 972 patients with HTN history. Recent use of ACEi/ARBs in patients with HTN was associated with a lower 6-month cumulative incidence of COVID-19 diagnosis {3.78% [95% confidence interval (CI) 3.69–3.86%] versus 4.53% (95% CI 4.40–4.65%); P &lt; 0.001}. In the 12 344 patients with COVID-19 infection, the use of ACEi/ARBs was not associated with a higher risk of hospitalization with need for invasive respiratory support or death [OR = 0.91 (0.71–1.15); P = 0.426].ConclusionsRAS blockade in patients with HTN is not associated with higher risk of COVID-19 infection or with a worse progression of the disease.
Patients with varying courses of single coronary artery: case series
Authors: Sheng Calvin C , Ghobrial Joanna , Cho Leslie 
Published: September 2021

Abstract

Background
Single coronary artery (SCA) is a rare congenital anomaly where blood to the heart is supplied through a common trunk. Identifying these abnormalities is important because some variants can compromise myocardial blood flow and increase risk of sudden cardiac death.

Case summary
We present five patients with varying Lipton Group I and Group II SCA subtypes, corroborated on multi-imaging modalities and evaluated with comprehensive non-invasive as well as invasive testing. Their clinical presentations also vary from a spectrum of asymptomatic finding to angina equivalent. The decision for definitive surgical intervention involving unroofing of the involved vessel depends largely on symptoms and evidence of myocardial ischaemia.

Discussion
While SCA findings are often incidental and benign, understanding the origin, branching pattern, and course of the anomalous artery has implications in prognosis and treatment. This usually involves a combination of anatomic assessment with imaging such as coronary Computed Tomography Angiography (CTA), Magnetic Resonance Angiography (MRA), and/or coronary angiography as well as functional assessment with invasive testing using tools like instantaneous wave-free ratio and intravascular ultrasound both at rest and with stress. Individualized treatment plans can then be made through a multidisciplinary approach involving adult congenital heart disease specialists and congenital cardiothoracic surgeons.
Cardiac perforation due to delayed migration of a chronic dialysis catheter: a case report
Authors: Jahnke Charlotte , Hoxha Elion , Söffker Gerold , Seiffert Moritz 
Published: September 2021

Abstract

Background
Tunnelled haemodialysis catheters are commonly used to perform haemodialysis. Rare complications of these catheters include perforations of major blood vessels or the heart. Albeit rare, these complications can lead to significant morbidity and mortality.

Case summary
We present a case of late migration of a tunnelled haemodialysis catheter causing a right atrial perforation with subsequent pericardial tamponade, haemodynamic shock, and cardiac arrest. A 51-year-old female patient with end-stage renal disease presented with hypotension and lactate acidosis, indicating circulatory shock, during ambulatory intermittent haemodialysis. Dialysis was performed through a tunnelled haemodialysis catheter that had been implanted more than 1 year ago. Upon admission to the hospital, initial diagnostics, including transthoracic echocardiography and computed tomography scan, showed a circumferential pericardial effusion which was not haemodynamically significant and no other pathological findings. After being transferred to the intensive care unit, the patient again showed signs of haemodynamic shock at the start of another dialysis session which deteriorated to cardiac arrest. Ultimately, using multi-modality imaging, migration of the catheter tip through the right atrial wall into the pericardial space was diagnosed. Emergency sternotomy and surgical extraction of the tunnelled haemodialysis catheter were performed and the patient recovered completely.

Discussion
Migration and perforation of a tunnelled haemodialysis catheter can occur late after implantation and lead to circulatory shock, thus requiring immediate diagnostic workup and surgical therapy. Routine diagnostic procedures may be insufficient for making a correct diagnosis. More specific approaches, such as multi-modality imaging including contrast echocardiography, should be implemented upon clinical suspicion.
Estimation of genetic variance contributed by a quantitative trait locus: correcting the bias associated with significance tests
Authors: Xie Fangjie , Wang Shibo , Beavis William D , Xu Shizhong 
Published: September 2021

Abstract
The Beavis effect in quantitative trait locus (QTL) mapping describes a phenomenon that the estimated effect size of a statistically significant QTL (measured by the QTL variance) is greater than the true effect size of the QTL if the sample size is not sufficiently large. This is a typical example of the Winners’ curse applied to molecular quantitative genetics. Theoretical evaluation and correction for the Winners’ curse have been studied for interval mapping. However, similar technologies have not been available for current models of QTL mapping and genome-wide association studies where a polygene is often included in the linear mixed models to control the genetic background effect. In this study, we developed the theory of the Beavis effect in a linear mixed model using a truncated noncentral Chi-square distribution. We equated the observed Wald test statistic of a significant QTL to the expectation of a truncated noncentral Chi-square distribution to obtain a bias-corrected estimate of the QTL variance. The results are validated from replicated Monte Carlo simulation experiments. We applied the new method to the grain width (GW) trait of a rice population consisting of 524 homozygous varieties with over 300 k single nucleotide polymorphism markers. Two loci were identified and the estimated QTL heritability were corrected for the Beavis effect. Bias correction for the larger QTL on chromosome 5 (GW5) with an estimated heritability of 12% did not change the QTL heritability due to the extremely large test score and estimated QTL effect. The smaller QTL on chromosome 9 (GW9) had an estimated QTL heritability of 9% reduced to 6% after the bias-correction.
Dynamic sampling bias and overdispersion induced by skewed offspring distributions
Authors: Okada Takashi , Hallatschek Oskar 
Published: September 2021

AbstractNatural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions. The resulting allele-frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the forward-in-time dynamics, especially with selection. Here, we employ an asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele-frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law.