Miracle-dz/UniFAR-FTUs huggingface dataset:
Test particle acceleration in turbulent reconnecting magnetic fields

The induced electric field produced by magnetohydrodynamic processes can accelerate test particles very efficiently under certain circumstances. Numerical experiments indicate that particles are accelerated to very high energy by the magnetohydrodynamic fields accompanying reconnection that is triggered by finite amplitude turbulent fluctuations. This turbulent neutral point mechanism includes both coherent and stochastic components of acceleration. Turbulence appears to influence the acceleration in two ways: It enhances the reconnection electric field while producing a stochastic electric field that gives rise to momentum diffusion; it also produces magnetic “bubbles” and other irregularities that can temporarily trap test particles in the strong reconnection electric field for times comparable to the magnetofluid characteristic time. We propose a scaling of the acceleration process to parameter regimes of interest which indicates that this type of acceleration may be an important factor in space physics and astrophysics.
Influence of substrate structure on the growth of CdTe thin films

We report on a high-resolution transmission electron microscopy and energy-dispersive x-ray spectroscopy study of the microstructure of CdTe thin films epitaxially grown on single-crystal hexagonal CdS and cubic CdTe substrates. We find that the different structures of the substrates do not make a great structural difference on the grown CdTe films; i.e., on both substrates, the grown CdTe films have a cubic structure and high density of planar defects near the interface regions. At the CdTe/CdS interface, interdiffusion occurs, forming CdTe1−xSx and CdS1−xTex alloys. These alloys lead to significantly reduced mismatch at the interface.
Validation of the Lee‐Jones theoretical model of fear of cancer recurrence among breast cancer survivors using a structural equation modeling approach

The Lee‐Jones model posits that antecedent individual and interpersonal factors predicate the development of fear of cancer recurrence (FCR) through cognitive and emotional processing, which further to behavioral, emotional, and/or physiological responses. We analyzed data from FoRtitude, a FCR intervention grounded in the Lee‐Jones FCR model, to evaluate associations between FCR antecedents, resources (e.g., breast cancer self‐efficacy, BCSE) and psychological and behavioral consequences.
Low genetic diversity and population structuring of Amblyomma hebraeum and Rickettsia africae from coastal and inland regions in the Eastern Cape Province of South Africa

Amblyomma hebraeum is the main vector of Rickettsia africae, the causative agent of African tick bite fever in southern Africa. Because pathogen dispersal is known to be influenced by tick adaptations to climate or host species, this study aimed to analyse the genetic diversity of A. hebraeum and R. africae infection of ticks collected from cattle in the Eastern Cape province of South Africa. DNA was extracted, amplified, and sequenced for the COI and ITS2 markers from A. hebraeum samples and the 17 kDa and ompA genes for rickettsial detection. Between six and ten haplotypes were identified from 40 COI and 31 ITS2 sequences; however, no population structuring was observed among sites (ΦST = 0.22, p < 0.05). All A. hebraeum isolates clustered with southern Africa GenBank isolates. Rickettsia africae was detected in 46.92% (95% CI = 41%–53%, n = 260) of ticks. All R. africae isolates clustered with strain PELE and Chucks, which were reported previously from South Africa. These results confirm that A. hebraeum populations are undergoing a recent population expansion driven by cattle movement, facilitating local and long dispersal events across the Eastern Cape province.
Ideal models of good inpatient care for adults with intellectual disability: Lessons from England

Background: In recent years, a significant proportion of inpatient facilities for people with intellectual disabilities and/or autism has been de-commissioned in England, This has resulted in individuals with intellectual disabilities being sent to distant hospitals far away from their families and carers leading to challenges in follow-up, community care and interventions. The impact of de-institutionalisation, has often caused patient trauma, family distress and subsequent discharge difficulties. Not every individual with intellectual disabilities and/or autism requires inpatient care but inpatient care when needed has to be local, adequate and appropriate. Aims: To evaluate current evidence of utility of inpatient models for people with intellectual disabilities and outline best clinical practice. Method: PubMed, CINAHL, EMBASE, Cochrane Library, Scopus, Web of Science were searched with key search terms. The search was conducted by the information specialist and identified abstracts screened further for inclusion criteria, methodological issues, and other appropriate characteristics. Twenty-three papers were included in the rapid review. Papers shortlisted had the inclusion criteria applied against the full text version independently by two reviewers. Disagreements regarding eligibility of studies was resolved by discussion and consensus within the project team. Key data related to in-patient models of care was extracted from the included papers, which included year of study, design, study objectives, target population, method/s tested, outcomes reported, country of study/studies, and results. Data extraction was performed by two reviewers and reviewed by the project team. Results: From the review of services for people with intellectual disabilities, we came across four broad models/frameworks/approaches. Evidence on what worked for inpatient service provision tended to be based on models developed and implemented locally. Conclusions: We make recommendations for the best clinical practice and standards. Both clinical service providers and policymakers need to be aware of specific needs of individuals with intellectual disability and/or autism.
Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.
Exact solution of a boundary-value problem for a rectangular checkerboard field

A class of two-phase composite materials with a biperiodic structure is investigated by the methods of complex analysis. Two interface conditions -continuity of normal component of a desired vector w and tangential component of ρ̂w at the contact boundary as well as the double-periodicity condition - are involved in rigorous form. The exact analytic solution of the corresponding generalized Riemann boundary-value problem is obtained. The explicit values of the effective parameters, namely effective resistivity and dissipation of energy of an elementary cell and resistivities along the symmetry axes are calculated in closed analytic form. The coincidence of our formulae with the well-known effective resistivity (conductivity) formula of Keller (1964), Dykhne (1970) and Mendelson (1975) and the dissipation formula of Dykhne (1970) is shown in the case of square checkerboard field. The Keller (1963) identity is generalized for the heterogeneous structure studied.
Mind your heart to bear the weight: Cardiac interoception predicts action-related visual perception when wearing a heavy backpack

Visual perception can be modulated by the physiological potential for action. For instance, it was famously shown that a geographical slant appears steeper when wearing a heavy backpack than not wearing any. However, those results are not always replicated. In the present exploratory study, we test the hypothesis that the backpack weight’s effect on perception relies on the ability of the cognitive system to integrate the physiological constraint’s change rather than the change itself. Young adults (n = 54) wore an electrocardiogram monitor and completed a computerised task in which photographs of real geographical slants were displayed on a screen while wearing a heavy versus light backpack. The activity of the vagus nerve, as an index of physiological adaptability, was recorded as a proxy of the physiological state during the task. The participants also completed an interoception task assessing one’s ability to detect his or her own heartbeat as the index of integration ability of the cognitive system. While Bayesian analyses revealed no difference in angle estimation between carrying a heavy versus light backpack, the results indicated that interoception predicted less accurate angle estimation only when wearing a heavy backpack. In contrast, there was anecdotal evidence that vagal activity changes predicted visual perception. Interoception might thus play a crucial role in the interplay between the physiological potential for action and action-related visual perception.
The Econometrics of Piecewise-Linear Budget Constraints: A Monte Carlo Study

This article presents a Monte Carlo evaluation of some alternative estimators for a demand model when the budget constraint is piecewise-linear and the budget set is convex. We examine the performance of two maximum likelihood (ML) estimators and an ordinary least squares (OLS) estimator under varying sample sizes and error variances. A simple log-linear demand function, with income and price as the explanatory variables, is specified. Although I find that the OLS bias decreases as the error variance decreases, the ML results are far superior. Furthermore, statistical tests based on the OLS results lead to erroneous conclusions regarding the structure.
An Analysis of PubMed Abstracts From 1946 to 2021 to Identify Organizational Affiliations in Epidemiological Criminology: Descriptive Study

Background Epidemiological criminology refers to health issues affecting incarcerated and nonincarcerated offender populations, a group recognized as being challenging to conduct research with. Notwithstanding this, an urgent need exists for new knowledge and interventions to improve health, justice, and social outcomes for this marginalized population. Objective To better understand research outputs in the field of epidemiological criminology, we examined the lead author’s affiliation by analyzing peer-reviewed published outputs to determine countries and organizations (eg, universities, governmental and nongovernmental organizations) responsible for peer-reviewed publications. Methods We used a semiautomated approach to examine the first-author affiliations of 23,904 PubMed epidemiological studies related to incarcerated and offender populations published in English between 1946 and 2021. We also mapped research outputs to the World Justice Project Rule of Law Index to better understand whether there was a relationship between research outputs and the overall standard of a country’s justice system. Results Nordic countries (Sweden, Norway, Finland, and Denmark) had the highest research outputs proportional to their incarcerated population, followed by Australia. University-affiliated first authors comprised 73.3% of published articles, with the Karolinska Institute (Sweden) being the most published, followed by the University of New South Wales (Australia). Government-affiliated first authors were on 8.9% of published outputs, and prison-affiliated groups were on 1%. Countries with the lowest research outputs also had the lowest scores on the Rule of Law Index. Conclusions This study provides important information on who is publishing research in the epidemiological criminology field. This has implications for promoting research diversity, independence, funding equity, and partnerships between universities and government departments that control access to incarcerated and offending populations.
Light scattering of double wall carbon nanotubes under hydrostatic pressure: pressure effects on the internal and external tubes

We report high‐pressure Raman light scattering studies up to 10 GPa on double walled carbon nanotubes using two pressure transmitting media. In alcohol, a clear splitting of the G band is observed up to 10 GPa. This splitting is evidence for both discontinuous tangential stress and continuous radial stress. A structural distortion seems to be present at 3 GPa, revealed by a spectroscopic signature at 1480 cm–1. With argon as the pressure transmitting medium, the nanotubes bundles show a transition at 6 GPa which corresponds to a collapse to a flattened structure and removes the splitting. The comparison of the pressure coefficients before the transition for the two pressure transmitting media shows that the ratio of the two coefficients associated with internal and external tubes, is the same but the absolute values are different. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Marinobacter: A case study in bioelectrochemical chassis evaluation

The junction of bioelectrochemical systems and synthetic biology opens the door to many potentially groundbreaking technologies. When developing these possibilities, choosing the correct chassis organism can save a great deal of engineering effort and, indeed, can mean the difference between success and failure. Choosing the correct chassis for a specific application requires a knowledge of the metabolic potential of the candidate organisms, as well as a clear delineation of the traits, required in the application. In this review, we will explore the metabolic and electrochemical potential of a single genus, Marinobacter. We will cover its strengths, (salt tolerance, biofilm formation and electrochemical potential) and weaknesses (insufficient characterization of many strains and a less developed toolbox for genetic manipulation) in potential synthetic electromicrobiology applications. In doing so, we will provide a roadmap for choosing a chassis organism for bioelectrochemical systems.
Effects of Face Masks on the Multiple Dimensions and Neurophysiological Mechanisms of Exertional Dyspnea

ABSTRACT Introduction During the coronavirus disease 2019 pandemic, public health officials widely adopted the use of face masks (FM) to minimize infections. Despite consistent evidence that FMs increase dyspnea, no studies have examined the multidimensional components of dyspnea or their underlying physiological mechanisms. Methods In a randomized crossover design, 16 healthy individuals (n = 9 women, 25 ± 3 yr) completed incremental cycling tests over three visits, where visits 2 and 3 were randomized to either surgical FM or no mask control. Dyspnea intensity and unpleasantness were assessed throughout exercise (0–10 Borg scale), and the Multidimensional Dyspnea Profile was administered immediately after exercise. Crural diaphragmatic EMG and esophageal pressure were measured using a catheter to estimate neural respiratory drive and respiratory muscle effort, respectively. Results Dyspnea unpleasantness was significantly greater with the FM at the highest equivalent submaximal work rate achieved by a given participant in both conditions (iso-work; 5.9 ± 1.7 vs 3.9 ± 2.9 Borg 0–10 units, P = 0.007) and at peak exercise (7.8 ± 2.1 vs 5.9 ± 3.4 Borg 0–10 units, P = 0.01) with no differences in dyspnea intensity ratings throughout exercise compared with control. There were significant increases in the sensory quality of “smothering/air hunger” (P = 0.01) and the emotional response of “anxiousness” (P = 0.04) in the FM condition. There were significant increases in diaphragmatic EMG and esophageal pressure at select submaximal work rates, but no differences in heart rate, pulse oximetry–derived arterial oxygen saturation, or breathing frequency throughout exercise with FMs compared with control. FMs significantly reduced peak work rate and exercise duration (both P = 0.02). Conclusions FMs negatively impact the affective domain of dyspnea and increase neural respiratory drive and respiratory muscle effort during exercise, although the impact on other cardiorespiratory responses are minimal.
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data

Abstract Motivation Whole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Results Here, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment. Availability and implementation TransFlow is free available at https://github.com/cvn001/transflow. Supplementary information Supplementary data are available at Bioinformatics online.
DREADD‐inactivation of dorsal CA1 pyramidal neurons in mice impairs retrieval of object and spatial memories

The hippocampus, a medial temporal lobe brain region, is critical for the consolidation of information from short‐term memory into long‐term episodic memory and for spatial memory that enables navigation. Hippocampal damage in humans has been linked to amnesia and memory loss, characteristic of Alzheimer's disease and other dementias. Numerous studies indicate that the rodent hippocampus contributes significantly to long‐term memory for spatial and nonspatial information. For example, muscimol‐induced depression of CA1 neuronal activity in the dorsal hippocampus impairs the encoding, consolidation, and retrieval of nonspatial object memory in mice. Here, a chemogenetic designer receptor exclusively activated by designer drugs (DREADDs) approach was used to test the selective involvement of CA1 pyramidal neurons in memory retrieval for objects and for spatial location in a cohort of male C57BL/6J mice. Activation of the inhibitory (hM4Di) DREADDs receptor expressed in CA1 neurons significantly impaired the retrieval of object memory in the spontaneous object recognition task and of spatial memory in the Morris water maze. Silencing of CA1 neuronal activity in hM4Di‐expressing mice was confirmed by comparing Fos expression in vehicle‐ and clozapine‐N‐oxide‐treated mice after exploration of a novel environment. Histological analyses revealed that expression of the hM4Di receptor was limited to CA1 neurons of the dorsal hippocampus. These results suggest that a common subset of CA1 neurons (i.e., those expressing hM4Di receptors) in mouse hippocampus contributed to the retrieval of long‐term memory for nonspatial and spatial information. Our findings support the view that the contribution of the rodent hippocampus is like that of the primate hippocampus, specifically essential for global memory. Our results further validate mice as a suitable model system to study the neurobiological mechanisms of human episodic memory, but also in developing treatments and understanding the underlying causes of diseases affecting long‐term memory, such as Alzheimer's disease.
Targeted Protein Degradation: Design Considerations for PROTAC Development

Targeted protein degradation has recently gained widespread interest as both a novel therapeutic strategy and a useful tool in biomedical research. Targeted protein degraders are often sub‐stoichiometric and do not require strong binding affinity for their targets, enabling access to previously inaccessible targets. Proteolysis‐targeting chimeras (PROTACs) are one class of targeted protein degraders that promote degradation by recruiting a target protein to an E3‐ligase complex via a heterobifunctional molecule. The modular nature of PROTACs allows for their rational design and systematic optimization. Here we suggest resources and methodologies for developing PROTAC degraders for researchers that may be new to the field. © 2022 Wiley Periodicals LLC.
Moving towards the cold region or the hot region? Thermocapillary migration of a droplet attached on a horizontal substrate

We study computationally thermocapillary migration of a two-dimensional droplet attached on a horizontal substrate with a constant temperature gradient. A level-set approach is employed to track the droplet interface and a Navier slip boundary condition is imposed to alleviate a stress singularity at the moving contact lines. The present numerical model allows us to consider droplets with large contact angles and to take into account effects of the fluid outside the droplet, both have not been well studied so far. In the limits of a zero contact angle hysteresis and a small viscosity ratio of the fluids outside and inside the droplet (μout/μin ⩽ 0.1), we find the droplet finally migrates towards the cold region, and both the steady migration speed and the velocity field inside the droplet obtained from numerical simulation agree very well with the lubrication theory of Ford and Nadim [“Thermocapillary migration of an attached drop on a solid surface,” Phys. Fluids 6, 3183–3185 (1994)] when the contact ang.