Miracle-dz/UniFAR-FTUs huggingface dataset:
Mental disorders in chronic obstructive pulmonary diseases

PURPOSE Anxiety and depression are underdiagnosed in chronic obstructive pulmonary disease (COPD) patients. Few studies have tried to identify their association with hospitalization (severe exacerbation). The objective of this study was to determine whether the anxiety/depression was associated with severe exacerbation. DESIGN AND METHODS A prospective cohort study, based on a sample of 512 patients diagnosed with COPD originating from primary care in a rural area in Lleida (Spain) and monitored between November 1, 2012 and October 31, 2014. For each patient, variables of interest were recorded; they were administered the HADS (Hospital Anxiety and Depression Scale) test to determine the possible presence of anxiety/depression, and its association with severe exacerbation was analyzed using a logistic regression model. FINDINGS Initially, the prevalence of anxiety/depression was 15.6%. The incidence of global hospitalization in the first year was 8.2% and 11.3% in the second year. In patients with anxiety/depression, it increased to 17.5% in the first year and 18.8% in the second year. In the multivariate regression model, the diagnosis of anxiety/depression almost doubled the risk of hospitalization (OR = 1.94) (p < .041). PRACTICE IMPLICATIONS Anxiety and depression are associated with an increased risk of hospitalization. Intervention studies are needed to evaluate the effects of anxiety/depression in the hospitalization.
LES on unstructured deforming meshes: Towards reciprocating IC engines

A variable explicit/implicit characteristics-based advection scheme that is second-order accurate in space and time has been developed recently for unstructured deforming meshes (O'Rourke & Sahota 1996a). To explore the suitability of this methodology for Large-Eddy Simulation (LES), three subgrid-scale turbulence models have been implemented in the CHAD CFD code (O'Rourke & Sahota 1996b): a constant-coefficient Smagorinsky model, a dynamic Smagorinsky model for flows having one or more directions of statistical homogeneity, and a Lagrangian dynamic Smagorinsky model for flows having no spatial or temporal homogeneity (Meneveau et al. 1996). Computations have been made for three canonical flows, progressing towards the intended application of in-cylinder flow in a reciprocating engine. Grid sizes were selected to be comparable to the coarsest meshes used in earlier spectral LES studies. Quantitative results are reported for decaying homogeneous isotropic turbulence, and for a planar channel flow. Computations are compared to experimental measurements, to Direct-Numerical Simulation (DNS) data, and to Rapid-Distortion Theory (RDT) where appropriate. Generally satisfactory evolution of first and second moments is found on these coarse meshes; deviations are attributed to insufficient mesh resolution. Issues include mesh resolution and computational requirements for a specified level of accuracy, analytic characterization of the filtering implied by the numerical method, wall treatment, and inflow boundary conditions. To resolve these issues, finer-mesh simulations and computations of a simplified axisymmetric reciprocating piston-cylinder assembly are in progress.
Assessment of health, functioning and disability of a population aged 60-70 in south-eastern Poland using the WHO Disability Assessment Schedule (WHODAS 2.0).

INTRODUCTION There is a growing number of older people in Poland. This phenomenon results in the need to assess their problems related with functioning in everyday life. This is the first study conducted in Polish society which evaluates the prevalence of disability and limitations in functioning by means of WHODAS 2.0 questionnaire. OBJECTIVE Evaluation of the health, functioning and disability of people aged 60-70 years living in south-eastern Poland. MATERIAL AND METHODS The researched material was a randomly- selected sample of 1,000 inhabitants of south-eastern Poland. The study was conducted by use of direct interviews applying the WHODAS 2.0. For the purpose of statistical analysis, measures of descriptive statistics and non-parametric tests of significance were used. RESULTS Limitations in functioning were reported by 67.00% of participants aged 60-70 years, including 46.20% with a mild disability, 14.50% - moderate, 6.30% - significant and extremely large disability. The highest level of disability occurred in areas related to participation in social life (mean = 20.77), performing activities of daily living (mean = 17.42) and mobility (mean = 17.23). A significantly higher level of disability (p <0.0001)was observed among unmarried people, the elderly and those with a greater number of chronic diseases. Higher level of physical activity was associated with lower disability level in the studied population (p<0.009). CONCLUSIONS Regarding the studied population, it was found that many health problems become worse over the years. The state of health that deteriorates with age causes limitations in daily functioning, which lead to disability, activity limitations and participation in everyday life. The progressive ageing of the Polish population will cause an increasing demand for medical care and on the social services.
Polyamines Are Not Required for Aerobic Growth of Escherichia coli: Preparation of a Strain with Deletions in All of the Genes for Polyamine Biosynthesis

ABSTRACT A strain of Escherichia coli was constructed in which all of the genes involved in polyamine biosynthesis—speA (arginine decarboxylase), speB (agmatine ureohydrolase), speC (ornithine decarboxylase), spe D (adenosylmethionine decarboxylase), speE (spermidine synthase), speF (inducible ornithine decarboxylase), cadA (lysine decarboxylase), and ldcC (lysine decarboxylase)—had been deleted. Despite the complete absence of all of the polyamines, the strain grew indefinitely in air in amine-free medium, albeit at a slightly (ca. 40 to 50%) reduced growth rate. Even though this strain grew well in the absence of the amines in air, it was still sensitive to oxygen stress in the absence of added spermidine. In contrast to the ability to grow in air in the absence of polyamines, this strain, surprisingly, showed a requirement for polyamines for growth under strictly anaerobic conditions.
Coffee Consumption and Coronary Artery Calcium Score: Cross‐Sectional Results of ELSA‐Brasil (Brazilian Longitudinal Study of Adult Health)

Background Available evidence for the relationship between coffee intake and subclinical atherosclerosis is limited and inconsistent. This study aimed to evaluate the association between coffee consumption and coronary artery calcium (CAC) in ELSA‐Brasil (Brazilian Longitudinal Study of Adult Health). Methods and Results This cross‐sectional study is based on baseline data from participants of the ELSA‐Brasil cohort. Only participants living in São Paulo, Brazil, who underwent a CAC measurement (n=4426) were included. Coffee consumption was collected using a food frequency questionnaire. CAC was detected with computed tomography and expressed as Agatston units. CAC was further categorized as an Agatson score ≥100 (CAC ≥100). In multiple logistic regression analysis considering intake of coffee and smoking status interaction, significant inverse associations were observed between coffee consumption (>3 cups/d) and CAC≥100 (odds ratio [OR]: 0.85 [95% confidence interval, 0.58–1.24] for ≤1 cup/d; OR: 0.73 [95% confidence interval, 0.51–1.05] for 1–3 cups/d; OR: 0.33 [95% confidence interval, 0.17–0.65] for >3 cups/d). Moreover, there was a statistically significant interaction effect for coffee consumption and smoking status (P=0.028 for interaction). After stratification by smoking status, the analysis revealed a lower OR of coronary calcification in never smokers drinking >3 cups/d (OR: 0.37 [95% confidence interval, 0.15–0.91]), whereas among current and former smokers, the intake of coffee was not significantly associated with coronary calcification. Conclusions Habitual consumption of >3 cups/d of coffee decreased odds of subclinical atherosclerosis among never smokers. The consumption of coffee could exert a potential beneficial effect against coronary calcification, particularly in nonsmokers.
Electronic health records-driven phenotyping: challenges, recent advances, and perspectives.

With the completion of the Human Genome Project1 as well as recent advances in genomic science and comparative biological studies, a new era of individualized medicine is evolving where novel biomedical discoveries are leading to more effective prevention, treatment, and diagnosis of disease. Although altered phenotypes are one of the most reliable manifestations of altered gene functions, research in extracting, representing, and analyzing phenotype–genotype relationships is still evolving. This has led to the emergence of a trans-discipline field, called ‘Phenomics,’2 that aims to capitalize on high-throughput computation and informatics technologies for the systematic study of phenotypes and how they might influence personal genomics.3 Many comparative phenomics studies in the recent past4 ,5 have demonstrated the power of positively correlating phenotypes with several measures of gene functions. However, despite the advances, research in phenomics is presented with various challenges, including (i) developing approaches for high-throughput extraction and representation of phenotypes, (ii) building techniques for storing, integrating, and querying phenotype data, and (iii) advancing phenotypic-driven analysis to derive phenotype–genotype associations. A significant barrier in the discovery of new genetic variants is the requirement to obtain the large sample sizes needed for an effective study (since variants may be rare within a population) leading to time-consuming and onerous sample collection efforts. Electronic health records (EHRs) can accelerate clinical research and genomic medicine, but are hindered by the limited number of validated processes and tools to enable accurate and rapid phenotype extraction.6 EHRs are increasing in ubiquity, functionality, and comprehensiveness across the USA, in part due to Meaningful Use standards7 implemented as part of the Health Information Technology for Economic and Clinical Health (HITECH) Act. One recent advance has been the coupling of DNA biorepositories to EHR data,8–13 combined with advances in informatics techniques, … Correspondence to Dr Jyotishman Pathak, Department of Biomedical Statistics and Informatics, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA; pathak.jyotishman{at}mayo.edu
A Systematic Literature Review on Combining Ontology with Bayesian Network to Support Logical and Probabilistic Reasoning

Reasoning in ontology is currently limited to logical reasoning. It is because ontology does not have a standard for probabilistic reasoning. Various approaches have been made by researchers to add the ability for ontological reasoner to do probabilistic reasoning. The approach is done by combining ontology with Bayesian network that does have probabilistic reasoning abilities. This study mapped out various approaches performed in combining ontologies with Bayesian networks to realize logical and probabilistic reasoning simultaneously. We use a systematic literature review method to identify the primary studies on combining ontology with Bayesian network following a predefined review protocol. We searched from four indexing services (SCOPUS, IEEE Xplore, ACM Digital Library, and SpringerLink) and got the result of 74 papers accepted for the review. We extracted properties from these studies and found 8 motivations of the studies, 5 contexts, 4 factors involved, and 5 techniques used in combining ontology with Bayesian network. The aim and the context are clearly stated in most of the studies, while most of the authors did not completely discuss the threats in their papers. As for the method and findings, most of the studies describe and discuss it moderately.
Standardized Reporting System Use During Handoffs Reduces Patient Length of Stay in the Emergency Department

Background Emergency department (ED) shift handoffs are potential sources of delay in care. We aimed to determine the impact that using standardized reporting tool and process may have on throughput metrics for patients undergoing a transition of care at shift change. Methods We performed a prospective, pre- and post-intervention quality improvement study from September 1 to November 30, 2015. A handoff procedure intervention, including a mandatory workshop and personnel training on a standard reporting system template, was implemented. The primary endpoint was patient length of stay (LOS). A comparative analysis of differences between patient LOS and various handoff communication methods were assessed pre- and post-intervention. Communication methods were entered a multivariable logistic regression model independently as risk factors for patient LOS. Results The final analysis included 1,006 patients, with 327 comprising the pre-intervention and 679 comprising the post-intervention populations. Bedside rounding occurred 45% of the time without a standard reporting during pre-intervention and increased to 85% of the time with the use of a standard reporting system in the post-intervention period (P < 0.001). Provider time (provider-initiated care to patient care completed) in the pre-intervention period averaged 297 min, but decreased to 265 min in the post-intervention period (P < 0.001). After adjusting for other communication methods, the use of a standard reporting system during handoff was associated with shortened ED LOS (OR = 0.60, 95% CI 0.40 - 0.90, P < 0.05). Conclusions Standard reporting system use during emergency physician handoffs at shift change improves ED throughput efficiency and is associated with shorter ED LOS.
Synthesis and in vitro anticancer activity of some organotin(IV) benzoate compounds

We have prepared a series of dibutyl-, diphenyl- and triphenyltin(IV) benzoate compounds by the reaction of the dibutyltin(IV) dichloride, diphenyltin(IV) dichloride and triphenyltin(IV) chloride respectively via the dibutyltin(IV) oxide, diphenyltin(IV) dihydroxide and triphenyltin(IV) hydroxide with benzoic acid. The compounds synthesized were characterized by 1 H and 13 C NMR, IR and UV-Vis spectroscopies, and are based on the microanalytical data. The in vitro activity showed that triphenyltin(IV) benzoate synthesized exhibit higher antitumor than those of dibutyltin(IV) and diphenyltin(IV) analogous.
Histone octamer trans-transfer: a signature mechanism of ATP-dependent chromatin remodelling unravelled in wheat nuclear extract.

BACKGROUND AND SCOPE In eukaryotes, chromatin remodelling complexes are shown to be responsible for nucleosome mobility, leading to increased accessibility of DNA for DNA binding proteins. Although the existence of such complexes in plants has been surmised mainly at the genetic level from bioinformatics studies and analysis of mutants, the biochemical existence of such complexes has remained unexplored. METHODS Histone H1-depleted donor chromatin was prepared by micrococcal nuclease digestion of wheat nuclei and fractionation by exclusion chromatography. Nuclear extract was partially purified by cellulose phosphate ion exchange chromatography. Histone octamer trans-transfer activity was analysed using the synthetic nucleosome positioning sequence in the absence and presence of ATP and its analogues. ATPase activity was measured as (32)Pi released using liquid scintillation counting. KEY RESULTS ATP-dependent histone octamer trans-transfer activity, partially purified from wheat nuclei using cellulose phosphate, showed ATP-dependent octamer displacement in trans from the H1-depleted native donor chromatin of wheat to the labelled synthetic nucleosome positioning sequence. It also showed nucleosome-dependent ATPase activity. Substitution of ATP by ATP analogues, namely ATPγS, AMP-PNP and ADP abolished the octamer trans-transfer, indicating the requirement of ATP hydrolysis for this activity. CONCLUSIONS ATP-dependent histone octamer transfer in trans is a recognized activity of chromatin remodelling complexes required for chromatin structure dynamics in non-plant species. Our results suggested that wheat nuclei also possess a typical chromatin remodelling activity, similar to that in other eukaryotes. This is the first report on chromatin remodelling activity in vitro from plants.
Evaluation of potential mechanisms of atrazine‐induced reproductive impairment in fathead minnow (Pimephales promelas) and Japanese medaka (Oryzias latipes)

Atrazine has been implicated in reproductive dysfunction of exposed organisms, and previous studies documented decreased egg production in Japanese medaka (Oryzias latipes) and fathead minnows (Pimephales promelas) during 30‐d to 38‐d exposures to 0.5 µg/L, 5 µg/L, and 50 µg/L atrazine. The authors evaluated possible mechanisms underlying the reduction in egg production. Gene expression in steroidogenesis pathways and the hypothalamus–pituitary–gonad axis of male and female fish was measured. Atrazine did not significantly induce gonad aromatase (cyp19a1a) expression. An atrazine‐induced shift in the number of females in an active reproductive state was observed. Expression of the egg maturation genes vitellogenin 1 (vtg1) and zona pellucida glycoprotein 3.1 (zp3.1) in medaka females was correlated and had a bimodal distribution. In both species, females with low vtg1 or zp3.1 expression also had low expression of steroidogenesis genes in the gonad, estrogen receptor in the liver, and gonadotropins in the brain. In the medaka, the number of females per tank that had high expression of zp3.1 was significantly correlated with egg production per tank. The number of medaka females with low expression of zp3.1 increased significantly with atrazine exposure. Thus, the decline in egg production observed in response to atrazine exposure may be the result of a coordinated downregulation of genes required for reproduction in a subset of females. Environ Toxicol Chem 2016;35:2230–2238. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Application of finite-state transducers to the acquisition of verb subcategorization information

This paper presents the design and implementation of a finite-state syntactic grammar of Basque that has been used with the objective of extracting information about verb subcategorization instances from newspaper texts. After a partial parser has built basic syntactic units such as noun phrases, prepositional phrases, and sentential complements, a finite-state parser performs syntactic disambiguation, determination of clause boundaries and filtering of the results, in order to obtain a verb occurrence together with its associated syntactic components, either complements or adjuncts. The set of occurrences for each verb is then filtered by statistical measures that distinguish arguments from adjuncts.
Perspectives of school-work transitions among youth with spina bifida, their parents and health care providers

Abstract Purpose Youth with disabilities encounter many challenges in finding employment and transitioning to post-secondary education. In this article, we explore the nature of school-work transitions for youth with spina bifida, which few studies have previously addressed. Method We conducted in-depth interviews with 44 participants (nine youth and 12 young adults with spina bifida, 11 parents and 12 clinicians). We analyzed our data using a qualitative content analysis approach. Results We identified several enablers to school-work transitions, including professional support, social support and school accommodations. Lacking such support created several challenges for youth with spina bifida. We also identified several barriers to school-work transitions, including lack of education and information on finances, housing and transportation; discrimination and stigma; and challenges coping with spina bifida at school and work. Conclusions Although some supports are available, youth with spina bifida encounter many challenges in transitioning to post-secondary education and employment. With clinicians at the helm, efforts should be put in place within the health and social services system to better prepare youth, as they transition to adulthood, to become connected to appropriate information and resources to help them to succeed in their school and employment goals. Implications for Rehabilitation Youth with spina bifida encounter many challenges in transitioning to post-secondary education or work. Clinicians, educators and parents should continue to support youth with spina bifida in choosing their vocations, setting career goals and developing career plans. Starting from a young age, parents, clinicians and educators should help youth with spina bifida prepare for school work transitions by fostering their independence, life skills and self-management of spina bifida-related symptoms. Clinicians and educators should help connect youth with spina bifida to appropriate information and resources to support their school-work transitions, including information on finances, housing, transportation, school accommodations and employment supports.
Thermal Cycling Damage Mechanisms of C/SiC Composites in Displacement Constraint and Oxidizing Atmosphere

A constraint stress of 62.5 MPa is created on a three-dimensional C/SiC composite specimen whose both ends are fixed when temperature is cycled between 900° and 1200°C. The cyclic stress results in a maximum damage strain of 0.06% within 50 cycles owing to coating and matrix cracking, fiber debonding, sliding, and breaking in the composite. This constrained specimen elongation also leads to a final compressive stress of 14 MPa on the composite through a decrease in the baseline constraint stress. Wet oxygen atmosphere at a high cyclic temperature, concomitant with stresses, can aggravate the damage situation by alternate oxidation between internal and external fibers in composites.
A dual-axis rotation rule for updating the head direction cell reference frame during movement in three dimensions

In the mammalian brain, allocentric (Earth-referenced) head direction, called azimuth, is encoded by head direction (HD) cells, which fire according to the facing direction of the animal’s head. On a horizontal surface, rotations of the head around the dorsoventral (D-V) axis, called yaw, correspond to changes in azimuth and elicit appropriate updating of the HD “compass” signal to enable large-scale navigation. However, if the animal moves through three-dimensional (3D) space then there is no longer a simple relationship between yaw rotations and azimuth changes, and so processing of 3D rotations is needed. Construction of a global 3D compass would require complex integration of 3D rotations, and also a large neuronal population, most neurons of which would be silent most of the time since animals rarely sample all available 3D orientations. We propose that, instead, the HD system treats the 3D space as a set of interrelated 2D surfaces. It could do this by updating activity according to both yaw rotations around the D-V axis and rotations of the D-V axis around the gravity-defined vertical axis. We present preliminary data to suggest that this rule operates when rats move between walls of opposing orientations. This dual-axis rule, which we show is straightforward to implement using the classic one-dimensional “attractor” architecture, allows consistent representation of azimuth even in volumetric space and thus may be a general feature of mammalian directional computations even for animals that swim or fly. NEW & NOTEWORTHY Maintaining a sense of direction is complicated when moving in three-dimensional (3D) space. Head direction cells, which update the direction sense based on head rotations, may accommodate 3D movement by processing both rotations of the head around the axis of the animal’s body and rotations of the head/body around gravity. With modeling we show that this dual-axis rule works in principle, and we present preliminary data to support its operation in rats.