bluuebunny/crossref_metadata_2025 huggingface dataset:
A stochastic two-dimensional intelligent driver car-following model with vehicular dynamics
Authors: Qi Hong-Sheng , Ying Yu-Yan
Published: September 2022

The law of vehicle movement has long been studied under the umbrella of microscopic traffic flow models, especially the car-following (CF) models. These models of the movement of vehicles serve as the backbone of traffic flow analysis, simulation, autonomous vehicle development, etc. Two-dimensional (2D) vehicular movement is basically stochastic and is the result of interactions between a driver’s behavior and a vehicle’s characteristics. Current microscopic models either neglect 2D noise, or overlook vehicle dynamics. The modeling capabilities, thus, are limited, so that stochastic lateral movement cannot be reproduced. The present research extends an intelligent driver model (IDM) by explicitly considering both vehicle dynamics and 2D noises to formulate a stochastic 2D IDM model, with vehicle dynamics based on the stochastic differential equation (SDE) theory. Control inputs from the vehicle include the steer rate and longitudinal acceleration, both of which are developed based on an idea from a traditional intelligent driver model. The stochastic stability condition is analyzed on the basis of Lyapunov theory. Numerical analysis is used to assess the two cases: (i) when a vehicle accelerates from a standstill and (ii) when a platoon of vehicles follow a leader with a stop-and-go speed profile, the formation of congestion and subsequent dispersion are simulated. The results show that the model can reproduce the stochastic 2D trajectories of the vehicle and the marginal distribution of lateral movement. The proposed model can be used in both a simulation platform and a behavioral analysis of a human driver in traffic flow.
Mapping of Compositional Diversity and Chronological Ages of Lunar Farside Multiring Mare Moscoviense Basin: Implications to the Middle Imbrian Mare Basalts
Authors: Karthi A. , Arivazhagan S. , Sharma Manish
Published: September 2022

The Mare Moscoviense is an astonishing rare flatland multi-ring basin and one of the recognizable mare regions on the Moon’s farside. The mineralogical, chronological, topographical and morphological studies of the maria surface of the Moon provide a primary understanding of the origin and evolution of the mare provinces. In this study, the Chandrayaan-1 M3data have been employed to prepare optical maturity index, FeO and TiO2concentration, and standard band ratio map to detect the mafic indexes like olivine and pyroxene minerals. The crater size frequency distribution method has been applied to LROC WAC data to obtain the absolute model ages of the Moscoviense basin. The four geological unit ages were observed as 3.57 Ga (U-2), 3.65 Ga (U-1), 3.8 Ga (U-3) and 3.92 Ga (U-4), which could have been formed between the Imbrian and Nectarian epochs. The M3imaging and reflectance spectral parameters were used to reveal the minerals like pyroxene, olivine, ilmenite, plagioclase, orthopyroxene-olivine-spinel lithology, and olivine-pyroxene mixtures present in the gabbroic basalt, anorthositic and massive ilmenite rocks, and validated with the existing database. The results show that the Moscoviense basin is dominated by intermediate TiO2basalts that derived from olivine-ilmenite-pyroxene cumulate depths ranging from 200 to 500 km between 3.5 Ga and 3.6 Ga.
The Spin-up of a Star Gaining Mass in a Close Binary System on the Thermal Time Scale
Authors: Staritsin Evgeny
Published: September 2022

We investigate the exchange of mass in a binary system as a channel through which a Be star can receive a rapid rotation. The mass-transfer phase in a massive close binary system in the Hertzsprung-gap is accompanied by the spinning up of the accreting component. We consider a case when the mass of the accreting component increases by 1.5 times. The component acquires mass and angular momentum while in a state of critical rotation. The angular momentum of the component increases by 50 times. Meridional circulation effectively transports angular momentum inside the component during the mass-transfer phase and during the thermal timescale after the end of the mass-transfer phase. As a result of mass transfer, the component acquires the rotation typical of classical Be stars.
Evaluation of different general V(λ) mismatch indices of photometers for LED-based light sources in general lighting applications
Authors: Krüger Udo , Ferrero Alejandro , Mantela Ville , Thorseth Anders , Trampert Klaus , Pellegrino Olivier , Sperling Armin
Published: September 2022

The general V(λ) mismatch index,

f

1

′

, of a photometer quantifies the deviation between its determined relative spectral responsivity,

s

rel

λ

, and its nominal responsivity, the spectral luminous efficiency function for photopic vision, V(λ). LED-based light sources now dominate in general lighting, displacing incandescent and fluorescent lamps. Furthermore, the calibration of photometers will very likely see the replacement of the reference CIE standard illuminant A with CIE reference spectrum L41. The article evaluates the consequences. Should we also change the definition of the general V(λ) mismatch index? Based on performance criteria, the individual indices are evaluated using various datasets with the help of statistical analyses. As a result, the authors can conclude that the current definition works very well even under changed calibration and application conditions and does not need to be changed. Other evaluated indices for a new index definition perform only slightly better in some cases, but do not generate generally better properties.
Stabilization of double tearing mode growth by resonant magnetic perturbations
Authors: Yu Q.
Published: September 2022

It is well known that for non-monotonic profiles of the safety factor q with two q = m/n resonant surfaces inside the plasma (m/n being the poloidal/toroidal mode numbers), the low-m double tearing modes (DTMs) are usually unstable, especially for plasmas with a high bootstrap current fraction as required for the steady operation of advanced scenarios. The effect of applied resonant magnetic perturbations (RMPs) on the m/n = 2/1 DTM growth is investigated numerically in this paper using two-fluid equations. The DTM growth is found to be stabilized by moderate static m/n = 2/1, 4/2 or 6/3 RMPs below their penetration threshold if the distance between the two resonant surfaces and the local plasma rotation velocity at the outer resonant surface are sufficiently large. The outer magnetic island is stabilized due to the change of the local plasma current density gradient around the outer resonant surface caused by RMPs, while the inner island growth is stabilized by the bootstrap current perturbation in the negative magnetic shear region. The mode stabilization is more effective for a higher electron temperature, indicating a possible method to improve the DTM stability in a fusion reactor.
Simulation of the TAEs’ saturation phase in the Large Helical Device: MHD burst
Authors: Varela J. , Spong D.A. , Todo Y. , Garcia L. , Ghai Y. , Ortiz J. , Seki R.
Published: September 2022

The aim of the present study is to analyze the saturation regime of the toroidal Alfven eigenmodes (TAE) in the Large Helical Device plasma, particularly the MHD burst. The linear and nonlinear evolution of the TAEs are simulated by the FAR3d code that uses a reduced MHD model for the thermal plasma coupled with a gyrofluid model for the energetic particle (EP) species. The linear simulations indicate the overlapping of 1/2 − 1/1, 2/3–2/4 and 3/5–3/6 TAEs in the inner-middle plasma region and frequency range of 45–75 kHz, triggered by EPs with an energy of T

f
= 45 keV and EP β = 0.022. The nonlinear simulations show that 2/3–2/4 and 3/4–3/5 TAEs are further destabilized due to the energy transfer from the 1/1–1/2 TAE, leading to broad TAE radial overlapping and triggering of the MHD burst. The energy of the 1/1–1/2 TAE is also nonlinearly transferred to the thermal plasma destabilizing the 0/0 and 0/1 modes, inducing the generation of shear flows and zonal currents, as well as large deformations in the thermal pressure and EP density radial profiles. The nonlinear simulation reproduces the same succession of instabilities and the same frequency range with respect to the experiment. The instability propagates outward during the bursting phase, showing a large decrease of the EP density profile between the middle-outer plasma, indicating the loss of part of the EP population that explains the decrease in the plasma heating efficiency observed during the MHD burst.
Development of titanium diaphragms for space propellant tank
Authors: Zhang Hai , Gu Sendong , Zhang Jianjun , Ouyang Ruijie , Yu Bin , Yang Wenbo , Zhang Xiao
Published: September 2022

The fundamental structure of the space propellant tank is introduced. The design flow and the numerical simulation method of a typical metal diaphragm are proposed. Then, a range of 237mm diameter titanium diaphragms with different bottom fillet radiuses are designed. Based on the arc-length method, a series of finite element models of the reversal process of these titanium diaphragms are developed. With the aid of the models, this paper analyzes the effect of bottom fillet radius on pressures differential to roll the titanium diaphragms. The results show that the critical pressure increases with the decrease of the bottom fillet radius. A near linear increase is found, which indicated that the bottom fillet radius has a certain effect on the critical pressure. The maximum equivalent von mises stress increases with the decrease of the bottom fillet radius. The increase leads to the increase of the critical pressure. In addition, the deformation of the diaphragms becomes more and more instable with the decrease the bottom fillet radius.
Adaptive sampling strategy of five-axis inspection for free-form surface reconstruction
Authors: Zhang Wenze , Shen Yijun , Zhang Yaqi , Zhang Jun , Zhang Yang
Published: September 2022

Five-axis inspection is widely used for measuring free-form surfaces, which require high-precision surface reconstruction for quality analysis, remanufacturing and so on. Nevertheless, existing sampling strategies for five-axis inspection neither make full use of surface characteristics nor are they able to pre-calculate the number of paths based on the required surface reconstruction error. To solve these problems, we propose an adaptive sampling strategy aiming at improving the precision of surface reconstruction without affecting the inspection efficiency. The proposed algorithm uses the chord height of corresponding points between two adjacent sampling paths as a criterion to determine the distribution and shape adjustment of the sampling paths. Experiments proved that the proposed algorithm can improve the surface reconstruction by 26.3% in terms of the maximum error and 19.5% in terms of the mean error compared with two traditional sampling algorithms.
High subsonic and low reynolds number airfoil optimization of high-altitude propeller
Authors: Li Dichen , Yang Long , Wei Chuang
Published: September 2022

This paper presents an airfoil optimization at high subsonic and low Reynolds number condition, to improve the efficiency of an E387-based HALE UAV propeller at cruising condition. The optimization design method is based on surrogate model coupled with validated RANS simulation. The optimal airfoil shape is flat and sharp leading-edged, which remarkably differs from the original and resembles a very thin airfoil in reversed configuration. Significant increment of lift-to-drag ratio and aerodynamical independency of Mach and Reynolds number were observed due to expanded supersonic flow region, weakened shock wave, and considerably reduced flow separation. By applying the optimized airfoil to propeller outboard, the new propeller’s efficiency increased more than 2%, while maintained required thrust, as proved by both Blade Element Theory and CFD simulation.
A moving target trajectory prediction method based on neighborhood fitting
Authors: He Sihua , Liu Chenghao , Li Junhua
Published: September 2022

In order to solve the influence of time delay and data frame loss on the tracking accuracy of high mobility target, a moving target trajectory prediction method based on neighborhood fitting is proposed. The influence of neighborhood width, polynomial order and prediction steps on prediction accuracy are analyzed, and suggestions on parameter selection are given. Four typical moving target trajectories, such as parabola, climb line, spiral line and gyratory line are predicted. The experimental results show that the trajectory prediction method has high accuracy and good stability, and can meet the requirements of moving target tracking.
Optimal guidance method based on conjugate gradient method and pseudospectral method
Authors: Li Yang , Chen Wanchun , Yang Liang
Published: September 2022

This paper aims to propose a method to solve the nonlinear optimal guidance problems with various performance indexes. First, the conjugate gradient method is derived based on the performance indexes of general form and specified form, and the execution steps of the optimal guidance method are obtained. Secondly, the pseudospectral collocation scheme is used to solve some intermediate variables in the algorithm, and the differential equations are transformed into algebraic equations, so as to improve the computational efficiency. Finally, the proposed method is applied to the air-to-ground missile guidance problem. By comparing with the simulation results of GPOPS-II, the optimality of the proposed method is verified. Additionally, the high computational efficiency of the algorithm is also verified.
Cost-Effectiveness analysis model for civil aircraft flight tests
Authors: Sun Mingming , Duan Xinyu , Liu Qingling , Sun Changtai , Song Hao
Published: September 2022

Flight tests for civil transport aircraft are a necessary condition for acquiring airworthiness type certification (TC) for new types of aircraft to enter the market. For commercial aircraft, cost control is an important consideration for aircraft development because flight tests are highly complex, time consuming and expensive. As a large and complex system, it is important to evaluate the cost-effectiveness of civil aircraft flight tests. However, due to the large number of and complex relationship between the factors involved in the project, it is extremely difficult to conduct a reasonable cost-effectiveness evaluation. Based upon the characteristics of the flight test mission, this paper analyzes the key indicators which have an important influence on the flight test project during the test, and proposes an operable and reasonable cost-effectiveness evaluation model, which provides the basis for the scientific decision-making of flight test planning.
Research on condition monitoring and fault diagnosis technology of dynamometer in aero-engine test bed
Authors: Lu Weirong , Wang Chaoyu , Gao Fan
Published: September 2022

In the process of engine development, production, improvement and renewal, engine bench test is an indispensable and important link, dynamometer is the main component of the test bed, in the test process the dynamometer will bear a large load, so it will produce violent vibration, easy to produce mechanical failure. The implementation of engine test bed condition monitoring and fault diagnosis can evaluate the health status of mechanical transmission components of the bend and the dynamic performance of the engine under test. This paper implements monitoring and diagnosis of key mechanical parts, through comprehensive analysis of time domain, amplitude domain, frequency domain characteristic information under no-load, low load, high load and other operating conditions to determine the health / unhealthy condition, fault type and fault severity, validity and accuracy of diagnostic conclusions such as rotor imbalance, bearing outer ring failure were verified by the equipment open and maintenance. This case provides practical guidance for the status monitoring and accurate fault location of aero-engine test bed.
Is flood to drip irrigation a solution to groundwater depletion in the Indo-Gangetic plain?
Authors: Joseph Jisha , Scheidegger Johanna M , Jackson Christopher R , Barik Beas , Ghosh Subimal
Published: September 2022

Indian river basins are intensively managed with country-specific agricultural practices of cultivating submerged paddy and uncontrolled groundwater (GW) irrigation. Numerical experiments with the state-of-the-art land surface models, such as variable infiltration capacity (VIC), without incorporating region-specific practices, could be misleading. Here, we coupled VIC with 2D GW model AMBHAS, incorporating India-specific irrigation practices and crop practices, including submerged paddy fields. We performed numerical experiments to understand the causal factors of GW depletion in the northwest Indo-Gangetic plain (IGP). We identify widespread flood irrigation and cultivation of water-intensive paddy as critical drivers of the declining GW scenario. Our numerical experiments suggest that the introduction of drip irrigation reduces GW depletion in the northwest, but does not change the sign of GW level trends. The GW levels in the non-paddy fields of the middle IGP are less sensitive to irrigation practices due to the high return flow to GW for flood irrigation.
Formal stability in Hamiltonian fluid models for plasmas
Authors: Tassi E
Published: September 2022

We review the progress made, during the last decade, on the analysis of formal stability for Hamiltonian fluid models for plasmas, carried out by means of the energy-Casimir (EC) method. The review begins with a tutorial section describing the essential concepts on the Hamiltonian formalism for fluid models and on the EC method, which will be frequently used in the article. Subsequently, a nonlinear stability analysis applied to reduced magnetohydrodynamics (MHD) is described, as paradigmatic example for the application of the EC method. The review of the recent results begins with the equilibrium and formal stability analysis of MHD with general helical symmetry, followed by the treatment of extended MHD. Applications of the EC method to a hybrid MHD-Vlasov model with pressure coupling and to a reduced fluid model accounting for electron temperature anisotropy are described next. The formal stability analysis of compressible reduced MHD is then presented and used to show the connection between the EC method and the classicalδWmethod for MHD stability. The concept of negative energy mode (NEM) is also briefly reviewed and applied to a model for electron temperature gradient (ETG) instability. In the context of the search for equilibria by a variational procedure, which is part of the EC method, we discuss a recent interpretation of the classical tearing modes in terms of singular equilibria of MHD linearized about Beltrami equilibria. Finally, we mention some possible directions for future developments.
i-scope: a compact automated fluorescence microscope for cell counting applications in low resource settings
Authors: Tyagi Arti , Khaware Neha , Tripathi Bramha , Jeet Tushar , Balasubramanian Prabhu , Elangovan Ravikrishnan
Published: September 2022

Fluorescence microscopy has widespread applications across biological sciences. It has been routinely used for cell counting, which provides a preliminary diagnostic test for many infectious diseases. Conventional fluorescence microscopes are bulky, expensive, time-intensive and laborious. They often require trained operators to acquire and analyze data. We report a compact automated digital fluorescence microscopy system, i-scope, for cell counting applications. The i-scope employs a total internal reflection fluorescence (TIRF) mode of sample illumination, along with a brightfield mode. It has a magnification of 30X, an optical resolution of ∼0.2 μm/pixel and offers sample scanning over 20 mm × 20 mm. A custom-written program enables automated image acquisition and analysis, thereby enhancing ease of operation. It has a compact form-factor and has been developed into a standalone system with a processing unit, screen, and other accessories to offer a portable and economic point-of-care diagnostic solution in low-resource settings. We analysed the performance of the i-scope for milk somatic cell enumeration and benchmarked it against that of a conventional fluorescence microscope.
Encapsulated layer induces boundary effect and twist angle adjust absorption in h-BN/graphene/h-BN heterostructure
Authors: Miao Wenjing , Gai Xinwen , Yu Jing , Jin Ying , Wang Jingang
Published: September 2022

This work studied the optical absorption properties and electronic properties of graphene nanosheets encapsulated in h-BN at different twisted angles based on first principles. UV–Vis spectrum shows that compared with the monolayer graphene nanosheets, the absorption’s peak of the encapsulated graphene nanosheets show a red shift and its molar absorption coefficient decreased significantly. The molar absorption coefficients of h-BN/graphene/h-BN heterostructures show an increasing trend when the graphene nanosheets are twisted relative to the packaging layer (twisted angles are 0°, 15°, 21.8°, 27.8° and 30°, respectively). More curiously, charge density difference (CDD) indicates that the region of electron aggregation in excited state mainly occurs at the centre of graphene nanosheets due to the introduction of h-BN packaging layer. The smoothed isosurface diagram of electron hole pairs shows that the distribution breadth of electron hole pair density decreases compared with that before encapsulation, and the distribution breadth of electron increase is larger than that of hole. With the increase of twisted angles, the distribution breadth of electron hole pair density increases gradually. Both CDD and smoothed isosurface diagram show that the system has strong boundary effect. This provides a method to adjust the photoelectric properties of graphene nanosheets by using different twisted angles, and provides a theoretical basis for its application in the field of micro-nano optoelectronics.
Pressure induced band gap shifting from ultra-violet to visible region of RbSrCl3 perovskite
Authors: Asfia Md Borhanul , Jaman Sahadat , Abdur Rashid Mohammad
Published: September 2022

Metal halide perovskites that do not contain lead are non-toxic and offer a wide range of uses in low-cost photovoltaic and optoelectronic systems. In this report, density functional theory is used to explore the influence of pressure (0–150 GPa) on the structural, electronic and optical characteristics of RbSrCl3 perovskite metal halide. At 0 GPa, RbSrCl3 was found to be an indirect wide-bandgap semiconductor. Under pressure, the electronic band gap transforms to visible range direct band gap which is suitable for optoelectronic devices. Higher absorption for RbSrCl3 was found in the ultraviolet region under the influence of different pressures. As the pressure on the halide perovskite increased, absorption peak is shifted to higher energy range. The optical conductivity, reflectivity and extinction coefficient were significantly changed due to induced pressures. The results suggest that under uniform pressure RbSrCl3 can be used in optoelectronic applications.
The Brief Alcohol Use Disorder Severity Scale: An Initial Validation Evaluation
Authors: Donato Suzanna , Nieto Steven , Ray Lara A
Published: September 2022

Aims

The goal of this study was to develop a standard measure of AUD severity that includes multiple dimensions and can be used in clinical settings to inform treatment selection.

Methods

A large sample (n = 1939) of moderate to heavy drinkers was amassed from six psychopharmacology studies. The severity factor was comprised of four dimensions: withdrawal, craving, AUD symptoms and alcohol-related consequences. First, a confirmatory factor analysis (CFA) was conducted to examine model fit. Next, a comprehensive item list from the four measures (i.e. CIWA, DrinC, PACs and SCID-5 AUD criteria) was reduced through exploratory factor analysis (EFA). Once the final items were merged into a preliminary assessment, an EFA was run to observe the factor structure. Initial validation of the measure was obtained via associations with clinical endpoints.

Results

The chi-square test statistic (${\chi}^2(2)=2.432\ P=0.297$) for a single-factor model of severity demonstrated good fit. Additional goodness-of-fit indices from the CFA revealed similar support for the single-factor model of severity (i.e. SRMSR = 0.011; RMSEA = 0.011; CFI = 0.999). Next, nine items from the individual EFAs were selected based on factor loading. The final EFA conducted on the 9-item scale demonstrated that a single factor model of severity best fit the data. Analysis of the psychometric properties revealed good internal consistency ($\alpha$= 0.79).

Conclusions

The current study extends upon the measurement of severity and supports a brief severity measure. This brief 9-item scale can be leveraged in future studies as a screening instrument and as a tool for personalized medicine.
Neuropsychological and Structural Neuroimaging Outcomes in LGI1-Limbic Encephalitis: A Case Study
Authors: Joshi Jarod , Patel Ronak , Figley Chase R , Figley Teresa D , Salter Jennifer , Bernstein Charles N , Marrie Ruth Ann
Published: September 2022

Objective

Anti-leucine-rich glioma-inactivated 1 limbic encephalitis (LGI1-LE) is a rare autoimmune condition that affects the structural integrity and functioning of the brain’s limbic system. Little is known about its impact on long-term neuropsychological functioning and the structural integrity of the medial temporal lobe. Here we examined the long-term neuropsychological and neuroanatomical outcomes of a 68-year-old male who acquired LGI1-LE.

Methods

Our case patient underwent standardized neuropsychological testing at two time points. Volumetric analyses of T1-weighted images were undertaken at four separate time points and qualitatively compared with a group of age-matched healthy controls.

Results

At the time of initial assessment, our case study exhibited focal impairments in verbal and visual episodic memory and these impairments continued to persist after undergoing a course of immunotherapy. Furthermore, in reference to an age-matched healthy control group, over the course of 11 months, volumetric brain imaging analyses revealed that areas of the medial temporal lobe including specific hippocampal subfields (e.g., CA1 and dentate gyrus) underwent a subacute period of volumetric enlargement followed by a chronic period of volumetric reduction in the same regions.

Conclusions

In patients with persisting neurocognitive deficits, LGI1-LE may produce chronic volume loss in specific areas of the medial temporal lobe; however, this appears to follow a subacute period of volume enlargement possibly driven by neuro-inflammatory processes.
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information
Authors: Li Haoyang , Li Hanmin , Zhou Juexiao , Gao Xin
Published: September 2022

Motivation

Unveiling the heterogeneity in the tissues is crucial to explore cell–cell interactions and cellular targets of human diseases. Spatial transcriptomics (ST) supplies spatial gene expression profile which has revolutionized our biological understanding, but variations in cell-type proportions of each spot with dozens of cells would confound downstream analysis. Therefore, deconvolution of ST has been an indispensable step and a technical challenge toward the higher-resolution panorama of tissues.

Results

Here, we propose a novel ST deconvolution method called SD2 integrating spatial information of ST data and embracing an important characteristic, dropout, which is traditionally considered as an obstruction in single-cell RNA sequencing data (scRNA-seq) analysis. First, we extract the dropout-based genes as informative features from ST and scRNA-seq data by fitting a Michaelis–Menten function. After synthesizing pseudo-ST spots by randomly composing cells from scRNA-seq data, auto-encoder is applied to discover low-dimensional and non-linear representation of the real- and pseudo-ST spots. Next, we create a graph containing embedded profiles as nodes, and edges determined by transcriptional similarity and spatial relationship. Given the graph, a graph convolutional neural network is used to predict the cell-type compositions for real-ST spots. We benchmark the performance of SD2 on the simulated seqFISH+ dataset with different resolutions and measurements which show superior performance compared with the state-of-the-art methods. SD2 is further validated on three real-world datasets with different ST technologies and demonstrates the capability to localize cell-type composition accurately with quantitative evidence. Finally, ablation study is conducted to verify the contribution of different modules proposed in SD2.

Availability and implementation

The SD2 is freely available in github (https://github.com/leihouyeung/SD2) and Zenodo (https://doi.org/10.5281/zenodo.7024684).

Supplementary information

Supplementary data are available at Bioinformatics online.
Systematic replication enables normalization of high-throughput imaging assays
Authors: Hunt Gregory J , Dane Mark A , Korkola James E , Heiser Laura M , Gagnon-Bartsch Johann A
Published: September 2022

Motivation

High-throughput fluorescent microscopy is a popular class of techniques for studying tissues and cells through automated imaging and feature extraction of hundreds to thousands of samples. Like other high-throughput assays, these approaches can suffer from unwanted noise and technical artifacts that obscure the biological signal. In this work, we consider how an experimental design incorporating multiple levels of replication enables the removal of technical artifacts from such image-based platforms.

Results

We develop a general approach to remove technical artifacts from high-throughput image data that leverages an experimental design with multiple levels of replication. To illustrate the methods, we consider microenvironment microarrays (MEMAs), a high-throughput platform designed to study cellular responses to microenvironmental perturbations. In application to MEMAs, our approach removes unwanted spatial artifacts and thereby enhances the biological signal. This approach has broad applicability to diverse biological assays.

Availability and implementation

Raw data are on synapse (syn2862345), analysis code is on github: gjhunt/mema_norm, a reproducible Docker image is available on dockerhub: gjhunt/mema_norm.

Supplementary information

Supplementary data are available at Bioinformatics online.
TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning
Authors: Yang Hai , Chen Rui , Wang Quan , Wei Qiang , Ji Ying , Zhong Xue , Li Bingshan
Published: September 2022

Motivation

Analysis of whole-genome sequencing (WGS) for genetics is still a challenge due to the lack of accurate functional annotation of non-coding variants, especially the rare ones. As eQTLs have been extensively implicated in the genetics of human diseases, we hypothesize that rare non-coding variants discovered in WGS play a regulatory role in predisposing disease risk.

Results

With thousands of tissue- and cell-type-specific epigenomic features, we propose TVAR. This multi-label learning-based deep neural network predicts the functionality of non-coding variants in the genome based on eQTLs across 49 human tissues in the GTEx project. TVAR learns the relationships between high-dimensional epigenomics and eQTLs across tissues, taking the correlation among tissues into account to understand shared and tissue-specific eQTL effects. As a result, TVAR outputs tissue-specific annotations, with an average AUROC of 0.77 across these tissues. We evaluate TVAR’s performance on four complex diseases (coronary artery disease, breast cancer, Type 2 diabetes and Schizophrenia), using TVAR’s tissue-specific annotations, and observe its superior performance in predicting functional variants for both common and rare variants, compared with five existing state-of-the-art tools. We further evaluate TVAR’s G-score, a scoring scheme across all tissues, on ClinVar, fine-mapped GWAS loci, Massive Parallel Reporter Assay (MPRA) validated variants and observe the consistently better performance of TVAR compared with other competing tools.

Availability and implementation

The TVAR source code and its scores on the ClinVar catalog, fine mapped GWAS Loci, high confidence eQTLs from GTEx dataset, and MPRA validated functional variants are available at https://github.com/haiyang1986/TVAR.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Role of Digital Data on Citizens in Social Work Research: A Literature Review
Authors: Andersen Lars Bo , Christensen Michael , Danholt Peter , Lauritsen Peter
Published: September 2022

This article presents a scoping review of the existing research on the use of digital data in social work. This review focuses on research that includes empirical investigations of digital data on citizens in social work practices. The purpose of this review is to map the emerging field of research and contribute knowledge of the role of digital data on citizens in social work. This review includes twenty-eight articles published between 2013 and 2020, and concludes that data pervade almost every aspect of social work and that there is a variety of research on the use of data in social work. However, detailed analyses of data that describe and conceptualise the production, circulation and utilisation of data are few. In consequence, this article introduces and discusses concepts from other data-laden fields of research, and calls for further research that addresses the challenges presented by digital data used in social work.
Impairment in social interaction and hippocampal long-term potentiation at perforant pathway-dentate gyrus synapses in a prenatal valproic acid-induced rat model of autism
Authors: Mohammadkhani Reihaneh , Ghahremani Reza , Salehi Iraj , Safari Samaneh , Karimi Seyed Asaad , Zarei Mohammad
Published: September 2022

It is well established that prenatal valproic acid exposure in rats leads to autism-like behaviours and social deficits. Long-term potentiation changes in the brain have been proposed as a potential mechanism in the development of autistic behaviour. However, there are controversies regarding the effect of in utero valproic acid exposure on long-term potentiation. This study examined the social interaction and long-term potentiation induction in perforant pathway-dentate gyrus synapses in male offspring of a rat model of autism induced by prenatal exposure to valproic acid. On Embryonic Day 12.5, the pregnant dams received an injection of 500 mg/kg valproic acid (intraperitoneal) to produce the autism model. The sociability test was performed between Postnatal Days 37 and 40. The offsprings were urethane-anaesthetized and placed into a stereotaxic apparatus for surgery, electrode implantation and field potential recording on Postnatal Days 45–55. In the dentate gyrus region, excitatory postsynaptic potential slope and population spike amplitude were measured. Valproic acid-exposed offspring showed significantly impaired social interaction. The birth weight in valproic acid-exposed rats was significantly lower than in control rats. The ability of dentate gyrus synapses to induce long-term potentiation was hampered by valproic acid exposure. The decreasing excitatory postsynaptic potential slope and population spike amplitude of long-term potentiation provide evidence in favour of this notion. It is widely supposed that the hippocampus plays a central role in the process of learning and memory as well as social interaction and social memory. Therefore, deficiencies in hippocampal synaptic plasticity may be responsible, at least in part, for the social interaction deficits in valproic acid-exposed rats.
Age-stratified effects of coronary artery calcification on cardiovascular and non-cardiovascular mortality in Korean adults
Authors: Kang Jeonggyu , Kim Seolhye , Chang Yoosoo , Kim Yejin , Jung Hyun-Suk , Ryu Seungho
Published: September 2022

Aims

The role of coronary artery calcium score (CACS) in predicting cardiovascular disease (CVD) and non-CVD mortality in young adults is unclear. We investigated the association of CACS with CVD and non-CVD mortality in young and older individuals.

Methods and results

CVD-free Koreans (n = 160 821; mean age, 41.4 years; 73.2% young individuals aged <45 years) who underwent cardiac tomography estimation of CACS (69.7% one-time measurement), were followed-up for a median of 5.6 years. The vital status and cause of death were ascertained from the national death records. Sub-distribution hazard ratios (SHR) and 95% confidence intervals (CIs) for cause-specific mortality were estimated using the Fine and Gray proportional hazards models. Overall, a higher CACS was strongly associated with an increased risk of CVD mortality. Among young individuals, multivariable-adjusted SHR (95% CIs) for CVD mortality comparing a CACS of 1–100, 101–300, and >300 to 0 CACS were 5.67 (2.33–13.78), 22.34 (5.72–87.19), and 74.1 (18.98–239.3), respectively, and among older individuals, corresponding SHR were 1.51 (0.60–3.84), 8.57 (3.05–24.06), and 6.41 (1.98–20.74). The addition of CACS to Framingham risk score significantly but modestly improved risk prediction for CVD mortality in young individuals. Conversely, CACS was significantly associated with non-CVD mortality only in older individuals.

Conclusions

Strong associations of CACS with CVD mortality, but not non-CVD mortality, were observed in young individuals, beginning in the low CACS category. Our findings reaffirm the need for early intervention for young adults even with low CACS to reduce CVD mortality.
Primary cardiac sarcoma presenting with easy bruising: a case report
Authors: Mishra Rina , Shemmeri Ealaf , Pani Saroj , Tribble Matthew
Published: September 2022

Background

Primary cardiac sarcomas are rare, aggressive types of malignancies with poor prognoses and can rarely present with thrombocytopenia. Sarcomas account for 65% of primary malignant cardiac tumours. Clinical symptoms often present with constitutional symptoms such as shortness of breath, weight loss, and fatigue. In addition, the tumour’s location determines treatment options and prognosis. Multimodal imaging facilitates the detection and assessment of cardiovascular tumours. This case study presents a rare primary right heart cardiac sarcoma presenting with thrombocytopenia.

Case summary

An 80-year-old male presented to the emergency department with complaints of worsening dyspnoea, ease of bruising, and chest pain. An extensive investigation into the cause of thrombocytopenia was performed. A transthoracic echocardiogram, computed tomography scan, and cardiac magnetic resonance (CMR) image revealed a large mass affecting the right atrium and right ventricle. Myocardial biopsy showed high-grade angiosarcoma. Due to his advanced age and intraventricular septal involvement of the mass, the multidisciplinary team decided to proceed with palliative chemotherapy.

Discussion

Many cardiac tumours remain asymptomatic, and the diagnosis is made at an advanced stage of the disease. Differential diagnoses of the intramural masses include haemangiomas, lipomas, rhabdomyomas, lymphomas, and sarcomas. Multiple treatment options should be considered to address thrombocytopenia. Tumour diagnosis and identification consist of laboratory tests and multimodal imaging. Complete surgical resection with neoadjuvant and adjuvant purposes is the mainstay of cardiac sarcoma therapy. A multidisciplinary, individualized care approach should be performed.
Snare and track (SNACK) technique: a novel approach for successful placement of an intracardiac echocardiogram catheter in the left atrium: a case report
Authors: Kawsara Akram , Raybuck Bryan
Published: September 2022

Background

Placing an intracardiac echocardiogram (ICE) catheter in the left atrium allows for excellent visualization of the left atrial appendage to guide left atrial (LA) appendage occlusion (LAAO). Nonetheless, it requires a separate septal puncture or a unique set of skills to navigate the ICE through a previously prepared septal puncture, which can be challenging.

Case summary

This report describes a novel method to insert an ICE in the left atrium through a single septal puncture utilizing a snare technique. A 76-year-old male underwent LAAO by ICE guidance. After obtaining a standard atrial septal puncture, we were unable to advance the ICE into the left atrium. Therefore, we used a loop snare to grasp the ICE catheter-tip in the right atrium and direct it into the left atrium via the prepared septal puncture by tracking a pigtail wire that we routinely place as part of the procedure. Afterward, the left atrial appendage was successfully occluded with a Watchman device (Boston Scientific, Galway, Ireland), and the patient was discharged home without complications.

Discussion

The described technique could be a helpful tool for ICE placement to the left atrium in a controlled fashion, especially when challenging anatomy is encountered.
Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa
Authors: Sottolano Christopher J , Revaitis Nicole T , Geneva Anthony J , Yakoby Nir
Published: September 2022

The diversity among Drosophila species presents an opportunity to study the molecular mechanisms underlying the evolution of biological phenomena. A challenge to investigating these species is that, unlike the plethora of molecular and genetics tools available for D. melanogaster research, many other species do not have sequenced genomes; a requirement for employing these tools. Selecting transgenic flies through white (w) complementation has been commonly practiced in numerous Drosophila species. While tolerated, the disruption of w is associated with impaired vision, among other effects in D. melanogaster. The D. nebulosa fly has a unique mating behavior which requires vision, and is thus unable to successfully mate in dark conditions. Here, we hypothesized that the disruption of w will impede mating success. As a first step, using PacBio long-read sequencing, we assembled a high-quality annotated genome of D. nebulosa. Using these data, we employed CRISPR/Cas9 to successfully disrupt the w gene. As expected, D. nebulosa males null for w did not court females, unlike several other mutant strains of Drosophila species whose w gene has been disrupted. In the absence of mating, no females became homozygous null for w. We conclude that gene disruption via CRISPR/Cas9 genome engineering is a successful tool in D. nebulosa, and that the w gene is necessary for mating. Thus, an alternative selectable marker unrelated to vision is desirable.
Sexual Motives, Stress, and Depressive Symptoms Among Midlife Different-Sex and Same-Sex Couples
Authors: Chai Hye Won , Mernitz Sara E , Umberson Debra J
Published: September 2022

Background and Objectives

Within relationships, sexual motives and stress are independent determinants of psychological health, with notable gendered patterns. However, previous research largely focuses on young adults and different-sex couples. Both sexual motives and levels of stress may be uniquely important to psychological health in midlife, and in potentially different ways for same-sex and different-sex couples. This study examined how the associations between sexual motives, stress, and depressive symptoms differ for midlife men and women in same-sex and different-sex marriages.

Research Design and Methods

Using dyadic data from same-sex and different-sex midlife married couples (N = 830 individuals; 415 couples), we examined the associations of intrinsic (e.g., sex for enjoyment and pleasure) and extrinsic (e.g., sex to please one’s spouse) motives for having sex with depressive symptoms and tested whether these associations differed by levels of stress for same-sex and different-sex spouses.

Results

Intrinsic sexual motives were associated with fewer depressive symptoms only for same-sex married couples under high stress. Extrinsic sexual motives were related to greater depressive symptoms for women in low-stress conditions and men in high-stress conditions, and this did not differ for same-sex compared to different-sex marriages.

Discussion and Implications

Results show that the interplay between sexual motives and stress varies for men and women in same-sex and different-sex marriages. These findings underscore the importance of considering both gender and sexuality in studying sexual motives in midlife and suggest sexual motives as a useful treatment focus for protecting the psychological health of midlife married couples.
Pushing the boundaries of minimally invasive repair of pectus excavatum: first experience with a 4-bar technique
Authors: Yüksel Mustafa , Ersöz Hasan
Published: September 2022

Several modifications to minimally invasive repair of pectus excavatum have been reported to date. Of these, the use of multiple bars was a major development. At present, there are 2 established techniques: cross-bar and parallel bar placement. We used a combination of both parallel and cross-bar techniques in a 25-year-old male patient with deep, Grand-Canyon type pectus excavatum, placing a total of 4 bars and 4 stabilizers. The patient had no complications during the 7 months of postoperative follow-up. We share this case report as the first experience using this modified technique in the literature.
Child malnutrition in Afghanistan amid a deepening humanitarian crisis
Authors: Rahmat Zainab Syyeda , Rafi Hania Mansoor , Nadeem Arsalan , Salman Yumna , Nawaz Faisal A , Essar Mohammad Yasir
Published: September 2022

Decades of political turmoil and stifling war, among other issues, has turned Afghanistan into the world's largest humanitarian crisis. Just 4 months after the Taliban seized control, the majority of the Afghan population face starvation, with >3.3 million children unable to afford basic food resources, leading to dozens of deaths every week. Restrictions on humanitarian assistance, withholding of vital food supplies and inadequate medical care play a major role in exacerbating the rates of malnutrition in the vulnerable paediatric population. Global interference is warranted to avoid unfathomable consequences in mitigating this public health catastrophe.
Integrating traditional medicine into the Ghanaian health system: perceptions and experiences of traditional medicine practitioners in the Ashanti region
Authors: Ampomah Irene G , Malau-Aduli Bunmi S , Seidu Abdul-Aziz , Malau-Aduli Aduli E O , Emeto Theophilus I
Published: September 2022

Background

Traditional medicine (TM) plays a vital role in the Ghanaian health system by serving as an alternative healthcare delivery system for the majority of people. However, the quality of practice and level of TM practitioners’ involvement in the integration of TM into the health system have not been fully investigated.

Methods

This study employed a phenomenological qualitative study design to explore the perceptions, experiences and recommendations of TM practitioners in the Ashanti region regarding TM integration. Data were collected through individual interviews with 17 participants.

Results

Participants had knowledge about TM integration. They cited effective alternative healthcare delivery and improved patient outcomes as the key benefits of TM integration. However, they reported a shortage of approved TM products, poor visibility of TM integration and poor relational coordination of care as factors hampering the integration. Participants recommended improved interprofessional relationships, provision of financial support and improved publicity of TM as possible strategies to enhance TM integration in Ghana.

Conclusions

The findings of the study clearly demonstrate that the Ghanaian health system is currently operating a consumer-led, tolerant health system with a parallel (between orthodox and TM practitioners) healthcare delivery model. Successful implementation of an effective TM integration would require improved integrative collaborative coordination of care between orthodox and TM practitioners in Ghana.