Miracle-dz/UniFAR-FTUs huggingface dataset:
A Cross-Sectional Study of the Relationship between Previous Military Experience and Mental Health Disorders in Currently Serving Public Safety Personnel in Canada

Objective There is an increased incidence of some mental health disorders such as post-traumatic stress disorder (PTSD) in some members of the military and in some public safety personnel (PSP) such as firefighters, police officers, paramedics, and dispatchers. Upon retirement from the armed forces, many individuals go on to second careers as PSP. Individuals with prior military experience may be at even greater risk than nonveterans for developing mental health disorders. The present study was designed to examine the relationship between prior military service and symptoms of mental health disorders in PSP. Methods This is a cross-sectional, observational study. Data for this study were collected from an anonymous, web-based, self-report survey of PSP in Canada. Invitations to participate were sent to PSP via their professional organizations. Indications of mental disorder(s) and symptom severity were assessed using well-validated self-report screening measures. Results Of the survey respondents who provided this information, 631 (6.8%) had prior armed forces experience; however, not all responses were complete. Ex-military PSP reported significantly more exposure to traumatic events and were approximately 1.5 times more likely to screen positive for indications of PTSD, mood, anxiety, or acute stress disorders and to have contemplated suicide than those without prior armed forces experience. Conclusions In our study, individuals in PSP with prior service experience in the armed forces were more likely to screen positive for indicators of some mental health disorders. Accordingly, mental health practitioners should inquire about previous service in the armed forces when screening, assessing, and treating PSP.
MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

Summary MLDSP-GUI (Machine Learning with Digital Signal Processing) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool with an interactive Graphical User Interface (GUI) for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others. Availability MLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/. Contact grandha8@uwo.ca Supplementary information Supplementary data are available online.
Digital interventions to facilitate patient‐provider communication in cancer care: A systematic review

Patient‐provider communication is a critical component of cancer care. Digital tools have been applied to facilitate cancer care and patient‐provider communication. However, to date, there is no systematic review on this growing body of literature. The objective of this study is to identify the existing digital interventions to improve patient‐provider communication among cancer patients and survivors, summarize their characteristics, and synthesize the outcomes of these interventions.
Enhancers as regulators of antigen receptor loci three-dimensional chromatin structure

ABSTRACT Enhancers are defined as regulatory elements that control transcription in a cell-type and developmental stage-specific manner. They achieve this by physically interacting with their cognate gene promoters. Significantly, these interactions can occur through long genomic distances since enhancers may not be near their cognate promoters. The optimal coordination of enhancer-regulated transcription is essential for the function and identity of the cell. Although great efforts to fully understand the principles of this type of regulation are ongoing, other potential functions of the long-range chromatin interactions (LRCIs) involving enhancers are largely unexplored. We recently uncovered a new role for enhancer elements in determining the three-dimensional (3D) structure of the immunoglobulin kappa (Igκ) light chain receptor locus suggesting a structural function for these DNA elements. This enhancer-mediated locus configuration shapes the resulting Igκ repertoire. We also propose a role for enhancers as critical components of sub-topologically associating domain (subTAD) formation and nuclear spatial localization.
Central Drive to the Paretic Ankle Plantarflexors Affects the Relationship Between Propulsion and Walking Speed After Stroke

Supplemental Digital Content is Available in the Text. Background and Purpose: The ankle plantarflexor muscles are the primary generators of propulsion during walking. Impaired paretic plantarflexion is a key contributor to interlimb propulsion asymmetry after stroke. Poststroke muscle weakness may be the result of a reduced force-generating capacity, reduced central drive, or a combination of these impairments. This study sought to elucidate the relationship between the neuromuscular function of the paretic plantarflexor muscles and propulsion deficits across individuals with different walking speeds. Methods: For 40 individuals poststroke, we used instrumented gait analysis and dynamometry coupled with supramaximal electrostimulation to study the interplay between limb kinematics, the neuromuscular function of the paretic plantarflexors (ie, strength capacity and central drive), propulsion, and walking speed. Results: The strength capacity of the paretic plantarflexors was not independently related to paretic propulsion. Reduced central drive to the paretic plantarflexors independently contributed to paretic propulsion deficits. An interaction between walking speed and plantarflexor central drive was observed. Individuals with slower speeds and lower paretic plantarflexor central drive presented with the largest propulsion impairments. Some study participants with low paretic plantarflexor central drive presented with similarly fast speeds as those with near-normal central drive by leveraging a compensatory reliance on nonparetic propulsion. The final model accounted for 86% of the variance in paretic propulsion (R2 = 0.86, F = 33.10, P < 0.001). Discussion and Conclusions: Individuals poststroke have latent paretic plantarflexion strength that they are not able to voluntarily access. The magnitude of central drive deficit is a strong indicator of propulsion impairment in both slow and fast walkers. Video Abstract available for more insights from the authors (see the Video, Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A298).
Functionalized selenium nanoparticles for targeted siRNA delivery silence Derlin1 and promote antitumor efficacy against cervical cancer

Abstract Small interfering RNA (siRNA) exhibits great potential as a novel therapeutic option due to its highly sequence-specific ability to silence genes. However, efficient and safe delivery carriers are required for developing novel therapeutic paradigms. Thus, the successful development of efficient delivery platforms for siRNA is a crucial issue for the development of siRNA-based drugs in cancer treatments. In this study, biocompatible selenium nanoparticles (SeNPs) were loaded with RGDfC peptide to fabricate tumor-targeting gene delivery vehicle RGDfC-SeNPs. Subsequently, RGDfC-SeNPs were loaded with Derlin1-siRNA to fabricate RGDfC-Se@siRNA, which are functionalized selenium nanoparticles. RGDfC-Se@siRNA showed greater uptake in HeLa cervical cancer cells in comparison with that in human umbilical vein endothelial cells (HUVECs), verifying the RGDfC-mediated specific uptake of RGDfC-Se@siRNA. RGDfC-Se@siRNA was capable of entering HeLa cells via clathrin-associated endocytosis, and showed faster siRNA release in a cancer cell microenvironment in comparison with a normal physiological environment. qPCR and western blotting assays both indicated that RGDfC-Se@siRNA exhibited an obvious gene silencing efficacy in HeLa cells. RGDfC-Se@siRNA suppressed the invasion, migration and the proliferation of HeLa cells, and triggered HeLa cell apoptosis. Moreover, RGDfC-Se@siRNA induced the disruption of mitochondrial membrane potentials. Meanwhile, RGDfC-Se@siRNA enhanced the generation of reactive oxygen species (ROS) in HeLa cell, suggesting that mitochondrial dysfunction mediated by ROS might play a significant role in RGDfC-Se@siRNA-induced apoptosis. Interestingly, RGDfC-SeNPs@siRNA exhibited significant antitumor activity in a HeLa tumor-bearing mouse model. Additionally, RGDfC-SeNPs@siRNA is nontoxic to main organ of mouse. The above results indicate that RGDfC-Se@siRNA provides a promising potential for cervical cancer therapy.
An Annotated Draft Genome of the Mountain Hare (Lepus timidus)

Abstract Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.
A Volumetric Approach to Point Cloud Compression–Part II: Geometry Compression

Compression of point clouds has so far been confined to coding the positions of a discrete set of points in space and the attributes of those discrete points. We introduce an alternative approach based on volumetric functions, which are functions defined not just on a finite set of points, but throughout space. As in regression analysis, volumetric functions are continuous functions that are able to interpolate values on a finite set of points as linear combinations of continuous basis functions. Using a B-spline wavelet basis, we are able to code volumetric functions representing both geometry and attributes. Attribute compression is addressed in Part I of this paper, while geometry compression is addressed in Part II. Geometry is represented implicitly as the level set of a volumetric function (the signed distance function or similar). Experimental results show that geometry compression using volumetric functions improves over the methods used in the emerging MPEG Point Cloud Compression (G-PCC) standard.
Platform-integrated mRNA isoform quantification

MOTIVATION Accurate estimation of transcript isoform abundance is critical for downstream transcriptome analyses and can lead to precise molecular mechanisms for understanding complex human diseases, such as cancer. Simplex mRNA Sequencing (RNA-Seq) based isoform quantification approaches are facing the challenges of inherent sampling bias and unidentifiable read origins. A large-scale experiment shows that the consistency between RNA-Seq and other mRNA quantification platforms is relatively low at the isoform level compared to the gene level. In this project, we developed a platform-integrated model for transcript quantification (IntMTQ) to improve the performance of RNA-Seq on isoform expression estimation. IntMTQ, which benefits from the mRNA expressions reported by the other platforms, provides more precise RNA-Seq-based isoform quantification and leads to more accurate molecular signatures for disease phenotype prediction. RESULTS In the experiments to assess the quality of isoform expression estimated by IntMTQ, we designed three tasks for clustering and classification of 46 cancer cell lines with four different mRNA quantification platforms, including newly developed NanoString's nCounter technology. The results demonstrate that the isoform expressions learned by IntMTQ consistently provide more and better molecular features for downstream analyses compared with five baseline algorithms which consider RNA-Seq data only. An independent RT-qPCR experiment on seven genes in twelve cancer cell lines showed that the IntMTQ improved overall transcript quantification. The platform-integrated algorithms could be applied to large-scale cancer studies, such as The Cancer Genome Atlas (TCGA), with both RNA-Seq and array-based platforms available. AVAILABILITY Source code is available at: https://github.com/CompbioLabUcf/IntMTQ. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
A Survey of American Thyroid Association Members Regarding the 2015 Adult Thyroid Nodule and Differentiated Thyroid Cancer Clinical Practice Guidelines.

BACKGROUND The 2015 American Thyroid Association (ATA) clinical practice guidelines (CPG) on management of thyroid nodules and differentiated thyroid cancer in adults were developed to inform clinicians, patients, researchers, and health policy makers about the best available evidence, and its limitations, relating to management of these conditions. METHODS We conducted a cross-sectional electronic survey of ATA members' perspectives of these CPG, using a standardized survey (Clinician Guidelines Determinant Questionnaire) developed by the Guidelines International Network. A survey link was electronically mailed to members in February of 2019, with reminders sent to non-respondents 2 and 5 weeks later. Data were descriptively summarized, after excluding missing responses. RESULTS The overall response rate was 19.8% (348/1761). The effective response rate was 20.2% (348/1720), after excluding a recently deceased member and individuals who had either invalid e-mail addresses or whose e-mails were returned. Of the respondents, 37.9% (132/348) were female, 60.4% (209/346) were endocrinologists, 27.5% (95/346) were surgeons, and 3.5% (12/346) were nuclear medicine specialists. The majority of respondents (71.9%; 250/348) were at a mid- or advanced-career level, and more than half were in academia (57.5%; 195/339). The majority (69.8%; 243/348) practiced in North America. The vast majority of respondents indicated that the CPG explained the underlying evidence (92.3%; 298/323) and 92.9% (300/323) agreed or strongly agreed with the content. Most respondents stated that they regularly used the CPG in their practice (83.0%; 268/323). Most respondents (83.0%; 268/323) also agreed or strongly agreed that the recommendations were easy to incorporate in their practice. The most popular CPG format was an electronic desktop file (78.8%; 252/320). Shorter more frequent CPG were favored by 55.0% (176/320) of respondents, and longer traditional CPG were favored by 39.7% (127/320). CONCLUSIONS The clinical content and evidence explanations in the adult thyroid nodule and differentiated thyroid cancer CPG are widely accepted and applied among ATA survey respondents. Future ATA CPG updates need to be optimized to best meet users' preferences regarding format, frequency and length.
Impact of sunshine on the risk of gestational diabetes mellitus in primiparous women

ABSTRACT There is a lack of data about the influence of sunshine hours on the prevalence for gestational diabetes mellitus (GDM). The aim of this study was to evaluate whether the prevalence of GDM varied according to hours of daily sunshine during the first trimester. The study cohort (N = 6189) consists of all primiparous women with a Finnish background who delivered between 2009 and 2015 living in Vantaa city, Finland. Data on births and maternal characteristics were obtained from National Health Registers. Data on sunshine hours were obtained from the Finnish Meteorological Institute. Individual daily sunshine hours during the first trimester of pregnancy were calculated for each woman. Diagnosis of GDM was based on a standard 75-g 2-h glucose tolerance test (OGTT). No relationship was observed between month of conception and GDM. Daily sunshine hours during the first trimester and GDM showed a U-shaped association (adjusted p-value 0.019). In OGTT, a U-shaped association was observed between 0-h glucose value and daily sunshine hours during the first trimester (p = 0.039) as well as with the 1-h glucose value (p = 0.012), respectively. In primiparous women daily sunshine hours during the first trimester showed a U-shaped association with the prevalence of GDM independent of pre-pregnancy risk factors. Abbreviations: BMI: body mass index; GDM: gestational diabetes mellitus; OGTT: standard 75 g 2-h glucose tolerance test; SD: standard deviation
Long-term outcome in patients after treatment for Cushing’s disease in childhood

Introduction Cushing’s disease (CD) is a rare cause of hypercortisolemia presenting a major diagnostic and therapeutic challenge. Data on pituitary function in long-term follow-up after CD treatment in childhood is limited. Aim Long-term assessment of patients of the Children’s Memorial Health Institute (CMHI) after CD treatment in childhood. Materials and methods Retrospective analysis of 29 CD patients, mean age at the time of diagnosis 13.46 yrs. The long-term follow-up (FU) was done by: 1) obtaining the data from a patient’s questionnaire (75% of adult patients); 2) using the data from the last clinic visit for patients who did not respond to the questionnaire and for current CMHI patients. The average long-term FU from transsphenoidal pituitary surgery (TSS) was 10.23 yrs. Results At the latest FU: 18 patients (62%) had long-term disease remission after TSS1, 2 patients (6.9%) after TSS2, 1 patient (3.4%) after the post-TSS radiotherapy (XRT) cycle and 3 patients (10.3%) after bilateral adrenalectomy (BA). One patient (3.4%) died after TSS2 due to postoperative complications, 1 patient (3.4%) had persistent disease at latest FU, in 1 patient (3.4%) the long-term FU was not possible to perform. CD recurrence occurred in 4 out of 28 patients (14%) at an average time 3.6 yrs. from definitive treatment. One patient (3.4%) after BA was operated because of Nelson's syndrome. Two patients (6.9%) were suspected of relapse at latest assessment. At the time of the last evaluation, 17 patients (63%) were on levothyroxine therapy since definitive treatment, 16 patients (59%) were on hydrocortisone treatment, 10 patients (37%) were taking sex hormones replacement, 4 patients (15%)—antidiuretic hormone. Conclusions Relatively large number of patients after CD treatment in childhood have hormonal pituitary deficits as well as mood and cognitive disorders. CD recurrence can occur even after a long time post effective treatment.
Relevance of Sex and Subtype in Patients With IBS: An Exploratory Study of Gene Expression

Background: Psychological state, stress level, and gastrointestinal function are intricately related and relevant to symptom exacerbation in patients with irritable bowel syndrome (IBS), but genetic contributors to this brain–gut connection are not fully understood. The purpose of this exploratory study was to compare gene expression in participants with IBS to that of healthy controls (HC) and to examine patterns of expression in participants with IBS by sex and IBS subtype. Method: Participants were recruited to an ongoing protocol at the National Institutes of Health. Differences in demographic and clinical characteristics were assessed using descriptive statistics and Mann–Whitney U tests. Expression levels of 84 genes were evaluated in peripheral whole blood using Custom RT2 Profiler polymerase chain reaction (PCR) Arrays, and data analysis was performed through GeneGlobe Data Analysis Center. Results: Participants with IBS (n = 27) reported greater levels of perceived stress (p = .037) and differed in expression values of ±2 for the genes ADIPOR1, ADIPOR2, CNR2, COMT, OXTR, and PPARA compared to HC (n = 43). Further analyses by sex and IBS subtype revealed differential patterns of gene expression related to the endocannabinoid system, cytokines, stress, and sex steroid hormones. Conclusions: Diverse yet interconnected processes such as metabolism, inflammation, immunity, social behavior, and pain are associated with differences in gene expression between participants with IBS and HC. These findings lend support for genomic associations with the brain–gut connection in patients with IBS and highlight the relevance of sex and IBS subtype in performing such analyses.
Barriers and Facilitators to Exercise Participation Among Frail Older African American Assisted Living Residents

Despite the well-known health benefits of physical activity, older adults are more sedentary than any other age group. This issue is particularly true for assisted living (AL) residents, which also represents an important and often overlooked aspect of palliative care. Here, we analyze ethnographic and interview data from a longitudinal study aimed at identifying best practices for palliative care in one African American AL community. The aim was to identify the factors that facilitate and constrain resident participation in instructor-led group exercise. Thematic analysis identified several main themes including the quality and location of the exercise program, AL staffing limitations, residents’ health and function, values about exercise, and residents’ interest in recreation and social engagement. We identified facilitators and barriers that shaped residents’ opportunity, desire, and commitment related to attending group exercise. Findings have implications for interventions aimed at increasing resident participation in group exercise, leading to multiple health benefits.
Trait self-control does not predict attentional control: Evidence from a novel attention capture paradigm

To what extent are low-level visual and attentional phenomena related to higher-level personality traits? Trait self-control is thought to modulate behavior via two separate mechanisms: 1) by preventing initial temptation and, 2) by inhibiting temptation when it occurs (disengagement). Similarly, the control of visual attention often entails preventing initial distraction by irrelevant but tempting (goal-similar) objects, and disengaging attention when it has been inappropriately captured. Given these similarities, we examined whether individuals higher versus lower in trait self-control would differ in their susceptibility to attention capture using mouse-tracking as a sensitive, online measure of how attentional dynamics resolve over time and space in response to a distracting visual cue. Using a variety of metrics of attention capture, we found that differences among people in trait self-control did not predict initial selection of visual information nor subsequent disengagement. Overall, these results suggest that trait self-control and attention capture operate via separate mechanisms.