Miracle-dz/UniFAR-FTUs huggingface dataset:
Depression among patients with tuberculosis: determinants, course and impact on pathways to care and treatment outcomes in a primary care setting in southern Ethiopia—a study protocol

Introduction Depression is commonly comorbid with chronic physical illnesses and is associated with a range of adverse clinical outcomes. Currently, the literature on the role of depression in determining the course and outcome of tuberculosis (TB) is very limited. Aim Our aim is to examine the relationship between depression and TB among people newly diagnosed and accessing care for TB in a rural Ethiopian setting. Our objectives are to investigate: the prevalence and determinants of probable depression, the role of depression in influencing pathways to treatment of TB, the incidence of depression during treatment, the impact of anti-TB treatment on the prognosis of depression and the impact of depression on the outcomes of TB treatment. Methods and analysis We will use a prospective cohort design. 703 newly diagnosed cases of TB (469 without depression and 234 with depression) will be consecutively recruited from primary care health centres. Data collection will take place at baseline, 2 and 6 months after treatment initiation. The primary exposure variable is probable depression measured using the Patient Health Questionnaire-9. Outcome variables include: pathways to treatment, classical outcomes for anti-TB treatment quality of life and disability. Descriptive statistics, logistic regression and multilevel mixed-effect analysis will be used to test the study hypotheses. Ethics and dissemination Ethical approval has been obtained from the Institutional Review Board (IRB) of the College of Health Sciences, Addis Ababa University. Findings will be disseminated through scientific publications, conference presentations, community meetings and policy briefs. Anticipated impact Findings will contribute to a sparse evidence base on comorbidity of depression and TB. We hope the dissemination of findings will raise awareness of comorbidity among clinicians and service providers, and contribute to ongoing debates regarding the delivery of mental healthcare in primary care in Ethiopia.
Comparing Different Models of the Development of Verb Inflection in Early Child Spanish

How children acquire knowledge of verb inflection is a long-standing question in language acquisition research. In the present study, we test the predictions of some current constructivist and generativist accounts of the development of verb inflection by focusing on data from two Spanish-speaking children between the ages of 2;0 and 2;6. The constructivist claim that children’s early knowledge of verb inflection is only partially productive is tested by comparing the average number of different inflections per verb in matched samples of child and adult speech. The generativist claim that children’s early use of verb inflection is essentially error-free is tested by investigating the rate at which the children made subject-verb agreement errors in different parts of the present tense paradigm. Our results show: 1) that, although even adults’ use of verb inflection in Spanish tends to look somewhat lexically restricted, both children’s use of verb inflection was significantly less flexible than that of their caregivers, and 2) that, although the rate at which the two children produced subject-verb agreement errors in their speech was very low, this overall error rate hid a consistent pattern of error in which error rates were substantially higher in low frequency than in high frequency contexts, and substantially higher for low frequency than for high frequency verbs. These results undermine the claim that children’s use of verb inflection is fully productive from the earliest observable stages, and are consistent with the constructivist claim that knowledge of verb inflection develops only gradually.
Sustained and Incomplete Recovery of Naive CD8+ T Cell Precursors after Sepsis Contributes to Impaired CD8+ T Cell Responses to Infection

Patients who survive severe sepsis often display compromised immune function with impairment in innate and adaptive immune responses. These septic patients are highly susceptible to “secondary” infections with intracellular pathogens that are usually controlled by CD8+ T cells. It is not known when and if this observed immunoparalysis of CD8+ T cell immunity recovers, and the long-term consequences of sepsis on the ability of naive CD8+ T cells to respond to subsequent infections are poorly understood. In this study, using the cecal-ligation and puncture mouse model of sepsis, we show that sepsis induces a rapid loss of naive CD8+ T cells. However, IL-15–dependent numerical recovery is observed a month after initial septic insult. Numerical recovery is accompanied by IL-15–dependent phenotypic changes where a substantial proportion of naive (Ag-inexperienced) CD8+ T cells display a “memory-like” phenotype (CD44hi/CD11ahi). Importantly, the impairment of naive CD8+ T cells to respond to viral and bacterial infection was sustained for month(s) after sepsis induction. Incomplete recovery of naive CD8+ T cell precursors was observed in septic mice, suggesting that the availability of naive precursors contributes to the sustained impairment in primary CD8+ T cell responses. Thus, sepsis can result in substantial and long-lasting changes in the available CD8+ T cell repertoire affecting the capacity of the host to respond to new infections.
Spironolactone reduces fibrosis of dilated atria during heart failure in rats with myocardial infarction.

AIMS Congestive heart failure (CHF) is associated with severe structural changes of atria, contributing to impaired atrial function and the risk of arrhythmia. This study investigated the effects of CHF treatments on atrial remodelling. METHODS AND RESULTS Three months after myocardial infarction (MI), rats were treated for 1 month with spironolactone, lisinopril, or atenolol alone or in combination. Echocardiography-Doppler tissue imaging, haemodynamic measurements, and 24-h Holter monitoring were used to characterize the cardiomyopathy. Atrial fibrosis was quantified with Picrosirius Red staining. Left atrial diameter was increased (5.8+/-0.6 mm in MI vs. 3.6+/-0.3 mm in sham; P<0.0001), as was atrial fibrosis (26.7+/-3.8% in MI vs. 10.5+/-2.2% in sham; P<0.0001), which correlated with left ventricular (LV) dysfunction after 3 months of MI. P-wave duration was also increased and premature atrial beats were frequent on the 24-h electrocardiogram. Similar improvements in LV dysfunction were observed after 1 month of spironolactone, ACE-inhibitor, or beta-blocker therapy alone or in combination. Atrial hyperexcitability was reduced by all the treatments, but only spironolactone attenuated atrial fibrosis and reduced P-wave duration. CONCLUSION Atrial fibrosis caused by chronic CHF is reduced by spironolactone.
Respectability, morality and disgust in the night‐time economy: exploring reactions to ‘lap dance’ clubs in England and Wales

The night-time economy is often described as repelling consumers fearful of the ‘undesirable Others’ imagined dominant within such time-spaces. In this paper we explore this by describing attitudes towards, and reactions to, one particularly contentious site: the ‘lap dance’ club. Often targeted by campaigners in England and Wales as a source of criminality and anti-sociality, in this paper we shift the focus from fear to disgust, and argue that Sexual Entertainment Venues (SEVs) are opposed on the basis of moral judgments that reflect distinctions of both class and gender. Drawing on documentary analysis, survey results and interview data collected during guided walks, we detail the concerns voiced by those anxious about the presence of lap dance or striptease clubs in their town or city, particularly the notion that they ‘lower the tone’ of particular streets or neighbourhoods. Our conclusion is that the opposition expressed to lap dance clubs is part of an attempt to police the boundaries of respectable masculinities and femininities, marginalizing the producers and consumers of sexual entertainment through ‘speech acts’ which identify such entertainment as unruly, vulgar and uncivilized. These findings are considered in the light of ongoing debates concerning the relations of morality, respectability and disgust.
Effects of Insulin on the Metabolic Control of Hepatic Gluconeogenesis In Vivo

OBJECTIVE Insulin represses the expression of gluconeogenic genes at the mRNA level, but the hormone appears to have only weak inhibitory effects in vivo. The aims of this study were 1) to determine the maximal physiologic effect of insulin, 2) to determine the relative importance of its effects on gluconeogenic regulatory sites, and 3) to correlate those changes with alterations at the cellular level. RESEARCH DESIGN AND METHODS Conscious 60-h fasted canines were studied at three insulin levels (near basal, 4×, or 16×) during a 5-h euglycemic clamp. Pancreatic hormones were controlled using somatostatin with portal insulin and glucagon infusions. Glucose metabolism was assessed using the arteriovenous difference technique, and molecular signals were assessed. RESULTS Insulin reduced gluconeogenic flux to glucose-6-phosphate (G6P) but only at the near-maximal physiological level (16× basal). The effect was modest compared with its inhibitory effect on net hepatic glycogenolysis, occurred within 30 min, and was associated with a marked decrease in hepatic fat oxidation, increased liver fructose 2,6-bisphosphate level, and reductions in lactate, glycerol, and amino acid extraction. No further diminution in gluconeogenic flux to G6P occurred over the remaining 4.5 h of the study, despite a marked decrease in PEPCK content, suggesting poor control strength for this enzyme in gluconeogenic regulation in canines. CONCLUSIONS Gluconeogenic flux can be rapidly inhibited by high insulin levels in canines. Initially decreased hepatic lactate extraction is important, and later reduced gluconeogenic precursor availability plays a role. Changes in PEPCK appear to have little or no acute effect on gluconeogenic flux.
Visualization Analysis of Flow Behavior During Weld-line Formation in Injection Molding Process

This paper presents a quantitative visualization analysis of flow behavior that was carried out to study flow behavior during weld-line formation. A visual mold with an obstacle pin in a plate-shaped cavity was designed, and weld-line formation was recorded for post-analysis. The main focus was on the motion behavior of the two adjacent flows originated by the obstacle pin. A particle tracking technique was used to track the melt and quantify its motion at the merging front to investigate flow behavior in orientation point of view. A micro-photography study on the cross-section of the weld-line was also carried out.
Functional genomics of the evolution of increased resistance to parasitism in Drosophila

Individual hosts normally respond to parasite attack by launching an acute immune response (a phenotypic plastic response), while host populations can respond in the longer term by evolving higher level of defence against parasites. Little is known about the genetics of the evolved response: the identity and number of genes involved and whether it involves a pre‐activation of the regulatory systems governing the plastic response. We explored these questions by surveying transcriptional changes in a Drosophila melanogaster strain artificially selected for resistance against the hymenopteran endoparasitoid Asobara tabida. Using micro‐arrays, we profiled gene expression at seven time points during development (from the egg to the second instar larva) and found a large number of genes (almost 900) with altered expression levels. Bioinformatic analysis showed that some were involved in immunity or defence‐associated functions but many were not. Previously, we had defined a set of genes whose level of expression changed after parasitoid attack and a comparison with the present set showed a significant though comparatively small overlap. This suggests that the evolutionary response to parasitism is not a simple pre‐activation of the plastic, acute response. We also found overlap in the genes involved in the evolutionary response to parasitism and to other biotic and abiotic stressors, perhaps suggesting a ‘module’ of genes involved in a generalized stress response as has been found in other organisms.
Viral Decay Kinetics in the Highly Active Antiretroviral Therapy-Treated Rhesus Macaque Model of AIDS

To prevent progression to AIDS, persons infected with human immunodeficiency virus type 1 (HIV-1) must remain on highly active antiretroviral therapy (HAART) indefinitely since this modality does not eradicate the virus. The mechanisms involved in viral persistence during HAART are poorly understood, but an animal model of HAART could help elucidate these mechanisms and enable studies of HIV-1 eradication strategies. Due to the specificity of non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) for HIV-1, we have used RT-SHIV, a chimeric virus of simian immunodeficiency virus with RT from HIV-1. This virus is susceptible to NNRTIs and causes an AIDS-like disease in rhesus macaques. In this study, two groups of HAART-treated, RT-SHIV-infected macaques were analyzed to determine viral decay kinetics. In the first group, viral loads were monitored with a standard TaqMan RT-PCR assay with a limit of detection of 50 viral RNA copies per mL. Upon initiation of HAART, viremia decayed in a bi-phasic manner with half-lives of 1.7 and 8.5 days, respectively. A third phase was observed with little further decay. In the second group, the macaques were followed longitudinally with a more sensitive assay utilizing ultracentrifugation to concentrate virus from plasma. Bi-phasic decay of viral RNA was also observed in these animals with half-lives of 1.8 and 5.8 days. Viral loads in these animals during a third phase ranged from 2–58 RNA copies/mL, with little decay over time. The viral decay kinetics observed in these macaques are similar to those reported for HIV-1 infected humans. These results demonstrate that low-level viremia persists in RT-SHIV-infected macaques despite a HAART regimen commonly used in humans.
Skin Cancer Detection and Tracking using Data Synthesis and Deep Learning

Dense object detection and temporal tracking are needed across applications domains ranging from people-tracking to analysis of satellite imagery over time. The detection and tracking of malignant skin cancers and benign moles poses a particularly challenging problem due to the general uniformity of large skin patches, the fact that skin lesions vary little in their appearance, and the relatively small amount of data available. Here we introduce a novel data synthesis technique that merges images of individual skin lesions with full-body images and heavily augments them to generate significant amounts of data. We build a convolutional neural network (CNN) based system, trained on this synthetic data, and demonstrate superior performance to traditional detection and tracking techniques. Additionally, we compare our system to humans trained with simple criteria. Our system is intended for potential clinical use to augment the capabilities of healthcare providers. While domain-specific, we believe the methods invoked in this work will be useful in applying CNNs across domains that suffer from limited data availability.
Peptide YY is secreted after oral glucose administration in a gender-specific manner.

CONTEXT Previous studies with small numbers of subjects showed a negative correlation between plasma peptide YY (PYY) levels and obesity. If correct, this would imply that low PYY levels might be involved in the pathogenesis of obesity. OBJECTIVE Our objective was to investigate whether plasma PYY levels were correlated with sex and body mass index (BMI). DESIGN, SETTING, AND PATIENTS We conducted a cross-sectional study of 151 normal volunteers (19-90 yr of age) in the Baltimore Longitudinal Study of Aging. INTERVENTIONS All subjects had an oral glucose tolerance test (75 g) performed. MAIN OUTCOME MEASURES Immunostaining of human duodenum, BMI, hemoglobin A1c, plasma glucose, insulin, PYY, glucagon like peptide-1 (GLP-1), ghrelin, and leptin were the main outcome measures. RESULTS PYY and GLP-1 colocalized in the same cells in human duodenum. Both hormones reached peak plasma levels by 20 min and had similar secretory patterns. The incremental increases in PYY and GLP-1 during that first 20 min were significantly correlated (r2 = 0.388; P < 0.0001). The areas under the curve from 0-120 min for PYY and GLP-1 were similar in both obese and lean participants. Female participants across the range of BMI had significantly higher PYY area under the curve (17,464 +/- 1,240 vs. 14,120 +/- 806 pmol/liter x min, female vs. male; P < 0.05) compared with male participants. CONCLUSIONS Our findings show that PYY and GLP-1 are colocalized and cosecreted from L cells and that total secretion of PYY is higher in females than in males, but fasting PYY levels and PYY secretion in response to oral glucose were not in any way correlated with BMI.
A Combined Measure of Procedural Volume and Outcome to Assess Hospital Quality of Colorectal Cancer Surgery, a Secondary Analysis of Clinical Audit Data

Objective To identify, on the basis of past performance, those hospitals that demonstrate good outcomes in sufficient numbers to make it likely that they will provide adequate quality of care in the future, using a combined measure of volume and outcome (CM-V&O). To compare this CM-V&O with measures using outcome-only (O-O) or volume-only (V-O), and verify 2010-quality of care assessment on 2011 data. Design Secondary analysis of clinical audit data. Setting The Dutch Surgical Colorectal Audit database of 2010 and 2011, the Netherlands. Participants 8911 patients (test population, treated in 2010) and 9212 patients (verification population, treated in 2011) who underwent a resection of primary colorectal cancer in 89 Dutch hospitals. Main Outcome Measures Outcome was measured by Observed/Expected (O/E) postoperative mortality and morbidity. CM-V&O states 2 criteria; 1) outcome is not significantly worse than average, and 2) outcome is significantly better than substandard, with ‘substandard care’ being defined as an unacceptably high O/E threshold for mortality and/or morbidity (which we set at 2 and 1.5 respectively). Results Average mortality and morbidity in 2010 were 4.1 and 24.3% respectively. 84 (94%) hospitals performed ‘not worse than average’ for mortality, but only 21 (24%) of those were able to prove they were also ‘better than substandard’ (O/E<2). For morbidity, 42 hospitals (47%) met the CM-V&O. Morbidity in 2011 was significantly lower in these hospitals (19.8 vs. 22.8% p<0.01). No relationship was found between hospitals' 2010 performance on O-O en V-O, and the quality of their care in 2011. Conclusion CM-V&O for morbidity can be used to identify hospitals that provide adequate quality and is associated with better outcomes in the subsequent year.
Disability, anxiety and depression in patients with medication‐overuse headache in primary care – the BIMOH study

Medication‐overuse headache (MOH) is common in the general population. Detoxification is the general treatment principle for MOH. The present paper is based on a study of a brief intervention (BI) for MOH in primary care. New data on headache disability and the Hospital Anxiety and Depression Scale (HADS) for MOH patients compared to population controls with and without chronic headache are presented and compared to previously published main outcome data.
Differential gene expression in notochord and nerve cord fate segregation in the Ciona intestinalis embryo

During early embryogenesis, embryonic cells gradually restrict their developmental potential and are eventually destined to give rise to one type of cells. Molecular mechanisms underlying developmental fate restriction are one of the major research subjects within developmental biology. In this article, this subject was addressed by combining blastomere isolation with microarray analysis. During the 6th cleavage of the Ciona intestinalis embryo, from the 32‐cell to the 64‐cell stage, four mother cells divide into daughter cells with two distinct fates, one giving rise to notochord precursor cells and the other to nerve cord precursors. Approximately 2,200 each of notochord and nerve cord precursor cells were isolated, and their mRNA expression profiles were compared by microarray. This analysis identified 106 and 68 genes, respectively, that are differentially expressed in notochord and nerve cord precursor cells. These included not only genes for transcription factors and signaling molecules but also those with generalized functions observed in many types of cells. In addition, whole‐mount in situ hybridization showed dynamic spatial expression profiles of these genes during segregation of the two fates: partitioning of transcripts present in the mother cells into either type of daughter cells, and initiation of preferential gene expression in either type of cells. genesis 51:647–659. © 2013 Wiley Periodicals, Inc.
A validity and reliability study of the coping self-efficacy scale.

OBJECTIVES Investigate the psychometric characteristics of the coping self-efficacy (CSE) scale, a 26-item measure of one's confidence in performing coping behaviors when faced with life challenges. DESIGN Data came from two randomized clinical trials (N1=149, N2=199) evaluating a theory-based Coping Effectiveness Training (CET) intervention in reducing psychological distress and increasing positive mood in persons coping with chronic illness. METHODS The 348 participants were HIV-seropositive men with depressed mood who have sex with men. Participants were randomly assigned to intervention and comparison conditions and assessed pre- and post-intervention. Outcome variables included the CSE scale, ways of coping, and measures of social support and psychological distress and well-being. RESULTS Exploratory (EFA) and confirmatory factor analyses (CFA) revealed a 13-item reduced form of the CSE scale with three factors: Use problem-focused coping (6 items, alpha=.91), stop unpleasant emotions and thoughts (4 items, alpha=.91), and get support from friends and family (3 items, alpha=.80). Internal consistency and test-retest reliability are strong for all three factors. Concurrent validity analyses showed these factors assess self-efficacy for different types of coping. Predictive validity analyses showed that residualized change scores in using problem- and emotion-focused coping skills were predictive of reduced psychological distress and increased psychological well-being over time. CONCLUSIONS The CSE scale provides a measure of a person's perceived ability to cope effectively with life challenges, as well as a way to assess changes in CSE over time in intervention research.
A Step-indexed Semantics of Imperative Objects

Step-indexed semantic interpretations of types were proposed as an alternative to purely syntactic proofs of type safety using subject reduction. The types are interpreted as sets of values indexed by the number of computation steps for which these values are guaranteed to behave like proper elements of the type. Building on work by Ahmed, Appel and others, we introduce a step-indexed semantics for the imperative object calculus of Abadi and Cardelli. Providing a semantic account of this calculus using more `traditional', domain-theoretic approaches has proved challenging due to the combination of dynamically allocated objects, higher-order store, and an expressive type system. Here we show that, using step-indexing, one can interpret a rich type discipline with object types, subtyping, recursive and bounded quantified types in the presence of state.