An open-source natural language processing toolkit to support software development: addressing automatic bug detection, code summarisation and code search.

This paper aims to introduce the innovative work carried out in the Horizon 2020 DECODER project - acronym for "DEveloper COmpanion for Documented and annotatEd code Reference" - (Grant Agreement no. 824231) by linking the fields of natural language processing (NLP) and software engineering. The project as a whole addresses the development of a framework, namely the Persistent Knowledge Monitor (PKM), that acts as a central infrastructure to store, access, and trace all the data, information and knowledge related to a given software or ecosystem.

A personalized medicine approach identifies enasidenib as an efficient treatment for IDH2 mutant chondrosarcoma.

Background: Sarcomas represent an extensive group of malignant diseases affecting mesodermal tissues. Among sarcomas, the clinical management of chondrosarcomas remains a complex challenge, as high-grade tumours do not respond to current therapies. Mutations in the isocitrate dehydrogenase (IDH) 1 and 2 genes are among the most common mutations detected in chondrosarcomas and may represent a therapeutic opportunity.

Community Exercise Program Participation and Mental Well-Being in the U.S. Texas-Mexico Border Region.

Hispanics are disproportionately affected by low rates of physical activity and high rates of chronic diseases. Hispanics generally and Mexican Americans specifically are underrepresented in research on physical activity and its impact on mental well-being. Some community-based interventions have been effective in increasing physical activity among Hispanics.

CD44 Modulates Cell Migration and Invasion in Ewing Sarcoma Cells.

The chimeric EWSR1::FLI1 transcription factor is the main oncogenic event in Ewing sarcoma. Recently, it has been proposed that EWSR1::FLI1 levels can fluctuate in Ewing sarcoma cells, giving rise to two cell populations. EWSR1::FLI1 cells present a migratory and invasive phenotype, while EWSR1::FLI1 cells are more proliferative.

The subjective perception of the happiness of older adult residents in Colombia.

Introduction: Happiness is understood as the perception of subjective well-being, it can be a quality, a result, or a state characterized by well-being or satisfaction that every person wants to achieve. In older adults, this satisfaction is a sum of lifelong achievements and triumphs; However, some factors influence this ideal.

Objective: Analyze demographic, family, social, personal, and health factors associated with the subjective perception of happiness in older adults, using data from a study conducted in five cities in Colombia, in order to make a theoretical contribution in the search for improvement of their physical, mental and social health.

Perceived barriers and facilitators for adhering to COVID-19 preventive measures in Chile: a qualitative study in three large cities.

Background: Globally, it has been reported that different social determinants of health -structural, sociodemographic, economic, living conditions and cultural factors- may affect opportunities to adhere to prevention measures against SARS-CoV-2. The objective of this study was to explore the perceptions around barriers and facilitators for adherence to COVID-19 prevention measures among the adult population residing in three large cities in Chile from a social determinants of health perspective.

Methods: Qualitative paradigm, multiple case-study design.

Factors associated with meeting physical activity guidelines during the COVID-19 pandemic.

Introduction: The COVID-19 pandemic impacted individual physical activity levels. Less is known regarding how factors such as sociodemographic and built environment were associated with physical activity engagement during the pandemic. Understanding these factors is critical to informing future infectious disease mitigation policies that promote, rather than hinder physical activity.

Social Connectedness, Physical Distancing, and Anxiety in Complying with Shelter-In-Place Orders and Advisories during the Once-In-A-Century COVID-19 Pandemic in the US: A Study of Social Media and Internet Users.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease (COVID-19), was first identified in Wuhan, China, in December 2019. As of 20 October 2020, the virus had infected 8,202,552 people, with 220,061 deaths in US, and in countries around the world, over 38 million people have become infected and over one million have died. The virus usually spreads via respiratory droplets from an infected person.

Changes in Antimicrobial Resistance and Etiology of Blood Culture Isolates: Results of a Decade (2010-2019) of Surveillance in a Northern Region of Colombia.

Background: Bloodstream infections (BSI) are important causes of morbidity and mortality worldwide. Antimicrobial surveillance is essential for identifying emerging resistance and generating empirical treatment guides, the purpose of this study is to analyze trends in antimicrobial susceptibility of BSI from 2010 to 2019 in healthcare institutions from Medellin and nearby towns in Colombia.

Methods: A Whonet database was analyzed from the GERMEN antimicrobial surveillance network; frequency and antibiotic susceptibility trends were calculated on more frequent microorganisms using Mann Kendall and Sen's Slope Estimator Test.

Factors Contributing to SARS-CoV-2 Vaccine Hesitancy of Hispanic Population in Rio Grande Valley.

Hispanic communities have been disproportionately affected by economic disparities. These inequalities have put Hispanics at an increased risk for preventable health conditions. In addition, the CDC reports Hispanics to have 1.

Assessing urinary phenol and paraben mixtures in pregnant women with and without gestational diabetes mellitus: A case-control study.

Prior studies have identified the associations between environmental phenol and paraben exposures and increased risk of gestational diabetes mellitus (GDM), but no study addressed these exposures as mixtures. As methods have emerged to better assess exposures to multiple chemicals, our study aimed to apply Bayesian kernel machine regression (BKMR) to evaluate the association between phenol and paraben mixtures and GDM. This study included 64 GDM cases and 237 obstetric patient controls from the University of Oklahoma Medical Center.

Intentional Storytelling to Sustain Low-cost/Free Breast Cancer Services: A Latina Example of Community-driven Advocacy.

Background: Community-based public health advocacy efforts are crucial to sustaining the low-cost/free breast cancer services that support underserved populations.

Objectives: We introduce two ways in which narrative theory may be a useful tool for developing advocacy materials and provide an example, using a community-academic partnership to promote Latina breast health in Chicago, Illinois.

Methods: Community and academic partners 1) engaged 25 Spanish-speaking Latinas in an advocacy workshop, 2) leveraged narrative theory to develop multi-media advocacy materials, and 3) disseminated materials to policymakers.

[From theory to practice: the discourse of healthy lifestyles and its application to the daily lives of low-income Chilean women].

The discourse on healthy lifestyles (HLS) states that a population will remain healthy by adopting such lifestyles, modifying unhealthy and thus morally incorrect individual behaviors. The HLS discourse has been hegemonic in Public Health since the late 20th century. It assumes freedom of choice by individuals, who purportedly make rational decisions, seeking the lowest cost and maximum individual benefit, the neoliberal model's basic premise.

Comparing Different Interventions' Effects on Latinas' Screening Mammography Attainment and Participant-Driven Information Diffusion.

Evaluation of multiple community-based approaches to improve Latinas' breast cancer (BC) screening utilization has resulted in inconsistent findings. Factors contributing to this variation include heterogeneity in approaches (e.g.

Comparison of Dosing Schemes for Thyroid Hormone Replacement Therapy After Thyroidectomy.

Background: Current thyroid hormone replacement therapy (THRT) is built on weight-based standard calculation of dose. A novel Poisson regression model, which accounts for seven clinical variables, was recently proposed to improve accuracy of THRT. We aimed to compare the accuracy of estimated THRT dose to reach euthyroid and the difference in predicted dose between the Poisson (scheme A) and the weight-based standard (scheme B) in patients following total thyroidectomy for benign disease.

Urinary total arsenic and arsenic methylation capacity in pregnancy and gestational diabetes mellitus: A case-control study.

Previous studies suggest arsenic exposure may increase the risk of gestational diabetes mellitus (GDM). However, prior assessments of total arsenic concentrations have not distinguished between toxic and nontoxic species. Our study aimed to investigate the relationships between inorganic arsenic exposure, arsenic methylation capacity, and GDM.

Clinical, biological, and prognostic implications of SF3B1 co-occurrence mutations in very low/low- and intermediate-risk MDS patients.

SF3B1 is a highly mutated gene in myelodysplastic syndrome (MDS) patients, related to a specific subtype and parameters of good prognosis in MDS without excess blasts. More than 40% of MDS patients carry at least two myeloid-related gene mutations but little is known about the impact of concurrent mutations on the outcome of MDS patients. In applying next-generation sequencing (NGS) with a 117 myeloid gene custom panel, we analyzed the co-occurrence of SF3B1 with other mutations to reveal their clinical, biological, and prognostic implications in very low/low- and intermediate-risk MDS patients.

Examining the Gap Between Medical School Matriculation and Graduation Rates Amongst Self-Identified Minorities.

Purpose: Despite increasing diversity, data indicates that there is a gap between the matriculation or admission of and graduation rates amongst medical students who identify with racial or ethnic minority groups. The purpose of this study was to identify barriers experienced by minority medical students that may account for this gap.

Methods: An IRB approved online survey was created, and distributed electronically to minority medical students, residents, and practicing physicians.

Helpful Criteria When Implementing NGS Panels in Childhood Lymphoblastic Leukemia.

The development of Next-Generation Sequencing (NGS) has provided useful diagnostic, prognostic, and therapeutic strategies for individualized management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Consequently, NGS is rapidly being established in clinical practice. However, the technology's complexity, bioinformatics analysis, and the different available options difficult a broad consensus between different laboratories in its daily routine introduction.

Integrated Genomic Analysis of Chromosomal Alterations and Mutations in B-Cell Acute Lymphoblastic Leukemia Reveals Distinct Genetic Profiles at Relapse.

The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis-relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse.

Frequency of low-level and high-level mosaicism in sporadic retinoblastoma: genotype-phenotype relationships.

Somatic mutational mosaicism is a common feature of monogenic genetic disorders, particularly in diseases such as retinoblastoma, with high rates of de novo mutations. The detection and quantification of mosaicism is particularly relevant in these diseases, since it has important implications for genetic counseling, patient management, and probably also on disease onset and progression. In order to assess the rate of somatic mosaicism (high- and low-level mosaicism) in sporadic retinoblastoma patients, we analyzed a cohort of 153 patients with sporadic retinoblastoma using ultra deep next-generation sequencing.

Obstetric and neonatal complications among women with autoimmune disease.

Background: The impact of autoimmune diseases on pregnancy remains understudied on a population level. Examination of obstetric and neonatal outcomes among women with autoimmune disease and their infants can provide important insights for clinical management.

Methods: Autoimmune diseases and outcomes were identified using medical records.

Reduction in FSH Throughout the Menstrual Cycle After Omega-3 Fatty Acid Supplementation in Young Normal Weight but not Obese Women.

Dietary fish oil restores ovarian function in subfertile rats, which is thought to be associated with decreased transcription of follicle-stimulating hormone (FSH) β-subunit. We have previously demonstrated a reduction in early follicular serum FSH levels in normal weight but not obese women after treatment with omega-3 polyunsaturated fatty acids (PUFA). Herein, we report the effect of supplementation with omega-3 PUFA on urinary reproductive hormones across the whole menstrual cycle.

[Evaluation Exercise Vaccination status inquiry and hierarchy of prevention and health education opportunities. Experience in a Pediatric Residency using the Mini-Clinical Evaluation Exercise].

Introduction: The Mini-Clinical Evaluation Exercise (Mini-CEX) is a formative tool with two descriptors assessing the inquiry of vaccination status and the hierarchy of prevention opportunities. Objectives. Determine the prevalence of both items in pediatric controls and spontaneous demands.