Miracle-dz/UniFAR-FTUs huggingface dataset:
Coping and violence perpetration in a residential substance use disorder treatment sample

ABSTRACT Background: Individuals in substance use disorder treatment report high rates of violence against partners and non-partners. There is growing interest in integrated coping-oriented treatment approaches for violence and substance use concerns, yet little is known about the relationship between specific coping responses and perpetration of partner and non-partner violence. Objective: This cross-sectional study evaluated relationships between coping responses and partner and non-partner physical assault perpetration in a substance use disorder treatment sample. Methods: Participants included 343 men (76%) and women (24%) who completed self-report survey measures of coping responses, violence perpetration, and substance use as part of screening for a randomized trial. Negative binomial regression was used to examine relationships between coping strategies and partner and non-partner violence perpetration, when accounting for substance use and demographic factors. Results: About one-third of participants reported partner violence perpetration (30%) and non-partner violence perpetration (34%). Frequency of partner violence and non-partner violence were both associated with more use of avoidant and emotion-focused strategies and less use of problem-focused coping in adjusted models. Discussion: Continued research is warranted to determine whether coping-oriented interventions decrease violence among people in substance use disorder treatment.
17p13.3 quadruplication: a prenatal and postpartum clinical characterization of a copy number variant

Prenatal genetic testing has advanced rapidly in the past decade. However, not all results, including variants, are well understood. We report the finding of a 2.5-Mb gene region quadruplication of Chromosome 17p13.3. This region is well characterized for the deletion leading to Miller–Dieker syndrome but has an unclear replication phenotype. Invasive testing performed after ultrasound abnormalities were seen revealed the quadruplication sequence as well as a short segment (850 kb) with x5 copy number variation. This region has previously been reported in a collection of duplications with shared phenotype; our quadruplication suggests similarities in phenotype. This raises the hypothesis of a potential spectrum or copy number variant–based phenotype.
Relative age effect and left-handedness in world class water polo male and female players

ABSTRACT Most studies of the relative age effect (RAE) refer to popular sports. In contrast, we examined to what extent the RAE is present in elite water polo players, as well as the association between handedness and RAE. For these purposes, laterality, anthropometry, month of birth, performance and playing position of participants in the 2011, 2013 and 2015 World Championships (623 women, 622 men) were analised. No RAE was observed in the total sample. However, the proportion of male left-handed field players born in the first quarter (11%) was lower than those born in the second (35.3%) and fourth quarter (29.4%). Regarding the overall laterality, the amount of left handed players was similar to the general population (10%). Nevertheless, there was a larger amount of left-handed wings than expected both in men (23.7%) and women (34.4%). Left-handed male players performed more shots, shots/minute and also scored more goals than right-handed players. Women left-handed players were younger and they performed more shots/minute. There is no RAE in elite male and female water polo players. However, laterality could be a possible moderator of the RAE particularly in left handed players, which should be taken into account in future studies.
MASE‐sLASER, a short‐TE, matched chemical shift displacement error sequence for single‐voxel spectroscopy at ultrahigh field

B1 inhomogeneity and chemical shift displacement error (CSDE) increase with the main magnetic field strength and are therefore deleterious for magnetic resonance spectroscopy (MRS) at ultrahigh field. A solution is to use adiabatic pulses which operate over a broad range of B1 and thus are insensitive to B1 inhomogeneity. Moreover, adiabatic pulses usually have a relatively higher bandwidth, which makes CSDE low to negligible. The use of exclusively adiabatic pulses for single‐voxel spectroscopy (SVS) typically brings the disadvantage of a long echo time (TE), but the advantage of a low and matched CSDE. Herein, we took advantage of short‐duration, low‐power, matched‐phase adiabatic spin echo (MASE) pulses to implement a matched CSDE semi‐localized by adiabatic selective refocusing (sLASER) sequence capable of attaining short TEs, while CSDE is matched and still comparatively low. We also demonstrate here the feasibility of the direct measurement of the γ‐aminobutyric acid (GABA) resonance at 2.28 ppm well separated from the neighboring glutamate resonance at 7 T using the implemented MASE‐sLASER sequence at TEs of 68 and 136 ms. The shorter duration of MASE pulses also made it possible to implement a Mescher–Garwood‐semi‐localized by adiabatic selective refocusing (MEGA‐sLASER) (with MASE) sequence with TE = 68 ms for editing GABA at 7 T, the results for which are also shown.
Using community-based, ethnographic methods to examine risk perceptions and actions of low-income, first-time mothers in a post-spill environment

Following the 2010 Gulf Oil Spill, area pregnant women were thought to be at-risk for poor health outcomes from the stress of managing health actions in this post-disaster environment. Research directed by an ongoing community–academic partnership sought to explore the specific role of culture in environmental risk protection actions among low-income pregnant women. As a part of the first-phase of a mixed-methods cultural study, community health workers (CHWs) used freelisting methods to survey low-income, first-time mother (n = 20) for the threats in the environment and relevant protective actions. Then, a separate pile sort activity (n = 31) was used to further investigate these cultural topics. Results elicited a diverse range of threats, protective actions, and sources of support across socio-demographic groups. Results also showed a culturally tailored conceptualization of threats in the environment. Exploring beliefs among a diverse population helps to uncover cultural differences in a population. Results will aid in developing culturally tailored policies and interventions, and increase the relevance of such interventions to address community concerns. Moreover, incorporating CHWs into the research process enhanced researcher literacy, and fostered mutual trust between the community and researchers.
A brain-enriched Drp1 isoform associates with lysosomes, late endosomes, and the plasma membrane

Dynamin-related protein 1 (Drp1) constricts mitochondria as a mechanochemical GTPase during mitochondrial division. The Drp1 gene contains several alternative exons and produces multiple isoforms through RNA splicing. Here we performed a systematic analysis of Drp1 transcripts in different mouse tissues and identified a previously uncharacterized isoform that is highly enriched in the brain. This Drp1 isoform is termed Drp1ABCD because it contains four alterative exons: A, B, C, and D. Remarkably, Drp1ABCD is located at lysosomes, late endosomes, and the plasma membrane in addition to mitochondria. Furthermore, Drp1ABCD is concentrated at the interorganelle interface between mitochondria and lysosomes/late endosomes. The localizations of Drp1ABCD at lysosomes, late endosomes, and the plasma membrane require two exons, A and B, that are present in the GTPase domain. Drp1ABCD assembles onto these membranes in a manner that is regulated by its oligomerization and GTP hydrolysis. Experiments using lysosomal inhibitors show that the association of Drp1ABCD with lysosomes/late endosomes depends on lysosomal pH but not their protease activities. Thus, Drp1 may connect mitochondria to endosomal–lysosomal pathways in addition to mitochondrial division.
TWO-LEVEL FOURIER ANALYSIS OF MULTIGRID FOR HIGHER-ORDER FINITE-ELEMENT METHODS∗

In this paper, we employ local Fourier analysis (LFA) to analyze the convergence properties of multigrid methods for higher-order finite-element approximations to the Laplacian problem. We find that the LFA smoothing factor fails to accurately predict the observed multigrid performance. This failure of the LFA smoothing factor is explained, and we propose a modification to the analysis that yields a reasonable prediction to help choose the correct damping parameters for relaxation. Finally, we present two-grid and multigrid experiments, and the corrected parameter choice is shown to yield a significant improvement in the resulting two-grid and multigrid convergence factors.
The contributions of the actin machinery to endocytic membrane bending and vesicle formation

Branched and crosslinked actin networks mediate cellular processes that move and shape membranes. To understand how actin contributes during the different stages of endocytic membrane reshaping, we analysed deletion mutants of yeast actin network components using a hybrid imaging approach that combines live imaging with correlative microscopy. We could thereby temporally dissect the effects of different actin network perturbations, revealing distinct stages of actin-based membrane reshaping. Our data show that initiation of membrane bending requires the actin network to be physically linked to the plasma membrane and to be optimally crosslinked. Once initiated, the membrane invagination process is driven by nucleation and polymerization of new actin filaments, independently of the degree of cross-linking and unaffected by a surplus of actin network components. A key transition occurs 2 seconds before scission when the filament nucleation rate drops. From that time point on, invagination growth and vesicle scission are driven by an expansion of the assembled actin network. The expansion is sensitive to the amount of filamentous actin and its crosslinking. Our results suggest that the mechanism by which actin reshapes the membrane adapts to force requirements that vary during the progress of endocytosis.
Detection and reporting of RB1 promoter hypermethylation in diagnostic screening

ABSTRACT Background: RB1 gene screening aids clinical management and genetic counselling in retinoblastoma families. Here we present epigenetic changes identified during routine molecular RB1 screening of tumor and blood samples. Complications in interpreting RB1 methylation are discussed. Materials and Methods: Screening for RB1 promoter hypermethylation was carried out by Methylation Specific PCR (MS-PCR) after bisulphite modification of DNA. The cohort consisted of 315 tumors, and 204 blood samples, from 497 retinoblastoma patients (22 patients had both blood and tumor screened). Results: 11.4% of retinoblastoma tumors had promoter hypermethylation. It was not routinely detected in blood samples, or in tumors with two other oncogenic RB1 changes. One blood sample had promoter hypermethylation due to an X;13 translocation. One tumor had low level methylation as well as two other oncogenic changes. Histopathological analysis of a small subset of age-matched tumors was similar regardless of promoter hypermethylation status. Conclusions: Promoter hypermethylation was detected in 11.4% of the retinoblastoma tumors and should be tested for in routine RB1 screening programmes. Constitutional samples are not expected to display RB1 hypermethylation. In a small proportion of cases it may not be possible to use this somatic change in patient management.
Fluorescent, Bioluminescent, and Optogenetic Approaches to Study Excitable Physiology in the Single Cardiomyocyte

This review briefly summarizes the single cell application of classical chemical dyes used to visualize cardiomyocyte physiology and their undesirable toxicities which have the potential to confound experimental observations. We will discuss, in detail, the more recent iterative development of fluorescent and bioluminescent protein-based indicators and their emerging application to cardiomyocytes. We will discuss the integration of optical control strategies (optogenetics) to augment the standard imaging approach. This will be done in the context of potential applications, and barriers, of these technologies to disease modelling, drug toxicity, and drug discovery efforts at the single-cell scale.
Multiple traumatisation and subsequent psychopathology in people with intellectual disabilities and DSM‐5 PTSD: a preliminary study

BACKGROUND Individuals with intellectual disability (ID) are at greater risk of exposure to traumatic life events compared with the non-ID population. Yet no study to date has examined the role of multiple traumatisation and subsequent psychopathology in people with ID. The aim of this study was to explore the association between multiple traumatisation and subsequent mental health. METHODS A preliminary cross-sectional study involving 33 participants with DSM-5 post-traumatic stress disorder completed self-report questionnaires on exposure to traumatic life events and post-traumatic stress disorder symptoms, anxiety, depression and general distress. RESULTS A proportion of 42.4% of the sample reported multiple traumatisation, including exposure to life events in both childhood and adulthood. Those who reported exposure to life events in childhood and adulthood reported significantly higher risk of harm, depression and general psychological distress compared with those who reported exposure to life events only in adulthood. CONCLUSIONS Preliminary results indicate that more severe psychopathology is associated with multiple traumatisation in childhood and adulthood compared with trauma experienced solely in adulthood.
Streptococcal Siglec-like adhesins recognize different subsets of human plasma glycoproteins: implications for infective endocarditis

Streptococcus gordonii and Streptococcus sanguinis are typically found among the normal oral microbiota but can also cause infective endocarditis. These organisms express cell surface serine-rich repeat adhesins containing "Siglec-like" binding regions (SLBRs) that mediate attachment to α2-3-linked sialic acids on human glycoproteins. Two known receptors for the Siglec-like adhesins are the salivary mucin MG2/MUC7 and platelet GPIbα, and the interaction of streptococci with these targets may contribute to oral colonization and endocarditis, respectively. The SLBRs display a surprising diversity of preferences for defined glycans, ranging from highly selective to broader specificity. In this report, we characterize the glycoproteins in human plasma recognized by four SLBRs that prefer different α2-3 sialoglycan structures. We found that the SLBRs recognize a surprisingly small subset of plasma proteins that are extensively O-glycosylated. The preferred plasma protein ligands for a sialyl-T antigen-selective SLBR are proteoglycan 4 (lubricin) and inter-alpha-trypsin inhibitor heavy chain H4. Conversely, the preferred ligand for a 3'sialyllactosamine-selective SLBR is glycocalicin (the extracellular portion of platelet GPIbα). All four SLBRs recognize C1 inhibitor but detect distinctly different glycoforms of this key regulator of the complement and kallikrein protease cascades. The four plasma ligands have potential roles in thrombosis and inflammation, and each has been cited as a biomarker for one or more vascular or other diseases. The combined results suggest that the interaction of Siglec-like adhesins with different subsets of plasma glycoproteins could have a significant impact on the propensity of streptococci to establish endocardial infections.
A Survey of Viewpoint Selection Methods for Polygonal Models

Viewpoint selection has been an emerging area in computer graphics for some years, and it is now getting maturity with applications in fields such as scene navigation, scientific visualization, object recognition, mesh simplification, and camera placement. In this survey, we review and compare twenty-two measures to select good views of a polygonal 3D model, classify them using an extension of the categories defined by Secord et al., and evaluate them against the Dutagaci et al. benchmark. Eleven of these measures have not been reviewed in previous surveys. Three out of the five short-listed best viewpoint measures are directly related to information. We also present in which fields the different viewpoint measures have been applied. Finally, we provide a publicly available framework where all the viewpoint selection measures are implemented and can be compared against each other.
Taq1A polymorphism and medication effects on inhibitory action control in Parkinson disease

Dopamine therapy in Parkinson disease (PD) can have differential effects on inhibitory action control, or the ability to inhibit reflexive or impulsive actions. Dopamine agonist (DAAg) medications, which preferentially target D2 and D3 receptors, can either improve or worsen control of impulsive actions in patients with PD. We have reported that the direction of this effect depends on baseline levels of performance on inhibitory control tasks. This observation suggests that there may exist certain biologic determinants that contribute to these patient‐specific differences. We hypothesized that one important factor might be functional polymorphisms in D2‐like receptor genes.
Exacerbated Staphylococcus aureus Foot Infections in Obese/Diabetic Mice Are Associated with Impaired Germinal Center Reactions, Ig Class Switching, and Humoral Immunity

Obese patients with type 2 diabetes (T2D) are at an increased risk of foot infection, with impaired immune function believed to be a critical factor in the infectious process. In this study, we test the hypothesis that humoral immune defects contribute to exacerbated foot infection in a murine model of obesity/T2D. C57BL/6J mice were rendered obese and T2D by a high-fat diet for 3 mo and were compared with controls receiving a low-fat diet. Following injection of Staphylococcus aureus into the footpad, obese/T2D mice had greater foot swelling and reduced S. aureus clearance than controls. Obese/T2D mice also had impaired humoral immune responses as indicated by lower total IgG levels and lower anti–S. aureus Ab production. Within the draining popliteal lymph nodes of obese/T2D mice, germinal center formation was reduced, and the percentage of germinal center T and B cells was decreased by 40–50%. Activation of both T and B lymphocytes was similarly suppressed in obese/T2D mice. Impaired humoral immunity in obesity/T2D was independent of active S. aureus infection, as a similarly impaired humoral immune response was demonstrated when mice were administered an S. aureus digest. Isolated splenic B cells from obese/T2D mice activated normally but had markedly suppressed expression of Aicda, with diminished IgG and IgE responses. These results demonstrate impaired humoral immune responses in obesity/T2D, including B cell–specific defects in Ab production and class-switch recombination. Together, the defects in humoral immunity may contribute to the increased risk of foot infection in obese/T2D patients.
Modelling Natural Language, Programs, and their Intersection

As computers and information grow a more integral part of our world, it is becoming more and more important for humans to be able to interact with their computers in complex ways. One way to do so is by programming, but the ability to understand and generate programming languages is a highly specialized skill. As a result, in the past several years there has been an increasing research interest in methods that focus on the intersection of programming and natural language, allowing users to use natural language to interact with computers in the complex ways that programs allow us to do. In this tutorial, we will focus on machine learning models of programs and natural language focused on making this goal a reality. First, we will discuss the similarities and differences between programming and natural language. Then we will discuss methods that have been designed to cover a variety of tasks in this field, including automatic explanation of programs in natural language (code-to-language), automatic generation of programs from natural language specifications (language-to-code), modeling the natural language elements of source code, and analysis of communication in collaborative programming communities. The tutorial will be aimed at NLP researchers and practitioners, aiming to describe the interesting opportunities that models at the intersection of natural and programming languages provide, and also how their techniques could provide benefit to the practice of software engineering as a whole.
Genome-Wide Association Study of Serum Fructosamine and Glycated Albumin in Adults Without Diagnosed Diabetes: Results From the Atherosclerosis Risk in Communities Study

Fructosamine and glycated albumin are potentially useful alternatives to hemoglobin A1c (HbA1c) as diabetes biomarkers. The genetic determinants of fructosamine and glycated albumin, however, are unknown. We performed genome-wide association studies of fructosamine and glycated albumin among 2,104 black and 7,647 white participants without diabetes in the Atherosclerosis Risk in Communities (ARIC) Study and replicated findings in the Coronary Artery Risk Development in Young Adults (CARDIA) study. Among whites, rs34459162, a novel missense single nucleotide polymorphism (SNP) in RCN3, was associated with fructosamine (P = 5.3 × 10−9) and rs1260236, a known diabetes-related missense mutation in GCKR, was associated with percent glycated albumin (P = 5.9 × 10−9) and replicated in CARDIA. We also found two novel associations among blacks: an intergenic SNP, rs2438321, associated with fructosamine (P = 6.2 × 10−9), and an intronic variant in PRKCA, rs59443763, associated with percent glycated albumin (P = 4.1 × 10−9), but these results did not replicate. Few established fasting glucose or HbA1c SNPs were also associated with fructosamine or glycated albumin. Overall, we found genetic variants associated with the glycemic information captured by fructosamine and glycated albumin as well as with their nonglycemic component. This highlights the importance of examining the genetics of hyperglycemia biomarkers to understand the information they capture, including potential glucose-independent factors.
Mre11-Rad50–dependent activity of ATM/Tel1 at DNA breaks and telomeres in the absence of Nbs1

The Mre11-Rad50-Nbs1 (MRN) protein complex and ATM/Tel1 kinase protect genome integrity through their functions in DNA double-strand break (DSB) repair, checkpoint signaling, and telomere maintenance. Nbs1 has a conserved C-terminal motif that binds ATM/Tel1, but the full extent and significance of ATM/Tel1 interactions with MRN are unknown. Here, we show that Tel1 overexpression bypasses the requirement for Nbs1 in DNA damage signaling and telomere maintenance. These activities require Mre11-Rad50, which localizes to DSBs and bind Tel1 in the absence of Nbs1. Fusion of the Tel1-binding motif of Nbs1 to Mre11 is sufficient to restore Tel1 signaling in nbs1Δ cells. Tel1 overexpression does not restore Tel1 signaling in cells carrying the rad50-I1192W mutation, which impairs the ability of Mre11-Rad50 to form the ATP-bound closed conformation. From these findings, we propose that Tel1 has a high-affinity interaction with the C-terminus of Nbs1 and a low-affinity association with Mre11-Rad50, which together accomplish efficient localization and activation of Tel1 at DSBs and telomeres.