Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive churn metrics

A central part of software quality is finding bugs. One method of finding bugs is by measuring important aspects of the software product and the development process. In recent history, researchers have discovered evidence of a "code churn" effect whereby the degree to which a given source code file has changed over time is correlated with faults and vulnerabilities. Computing the code churn metric comes from counting source code differences in version control repositories. However, code churn does not take into account a critical factor of any software development team: the human factor, specifically who is making the changes. In this paper, we introduce a new class of human-centered metrics, "interactive churn metrics" as variants of code churn. Using the git blame tool, we identify the most recent developer who changed a given line of code in a file prior to a given revision. Then, for each line changed in a given revision, determined if the revision author was changing his or her own code ("self churn"), or the author was changing code last modified by somebody else ("interactive churn"). We derive and present several metrics from this concept. Finally, we conducted an empirical analysis of these metrics on the PHP programming language and its post-release vulnerabilities. We found that our interactive churn metrics are statistically correlated with post-release vulnerabilities and only weakly correlated with code churn metrics and source lines of code. The results indicate that interactive churn metrics are associated with software quality and are different from the code churn and source lines of code.
Depressive Symptomatology, Exercise Adherence, and Fitness Are Associated With Reduced Cognitive Performance in Heart Failure

Objective: Depression is common in heart failure (HF) and associated with reduced cognitive function. The current study used Structrual Equation Modeling to examine whether depression adversely impacts cognitive function in HF through its adverse affects on exercise adherence and cardiovascular fitness. Method: 158 HF patients completed neuropsychological testing, physical fitness test, Beck Depression Inventory-II (BDI-II), and measures assessing exercise adherence and physical exertion. Results: The model demonstrated excellent model fit and increased scores on the BDI-II negatively affected exercise adherence and cardiovascular fitness. There was a strong inverse association between cardiovascular fitness and cognitive function. Sobel test showed a significant indirect pathway between the BDI-II and cognitive function through cardiovascular fitness. Discussion: This study suggests depression in HF may adversely impact cognitive function through reduced cardiovascular fitness. Prospective studies are needed to determine whether treatment of depression can lead to better lifestyle behaviors and ultimately improve neurocognitive outcomes in HF.
An Essential Role for Tumor Necrosis Factor in Natural Killer Cell–mediated Tumor Rejection in the Peritoneum

Natural killer (NK) cells are thought to provide the first line of defence against tumors, particularly major histocompatibility complex (MHC) class I− variants. We have confirmed in C57BL/6 (B6) mice lacking perforin that peritoneal growth of MHC class I− RMA-S tumor cells in unprimed mice is controlled by perforin-dependent cytotoxicity mediated by CD3− NK1.1+ cells. Furthermore, we demonstrate that B6 mice lacking tumor necrosis factor (TNF) are also significantly defective in their rejection of RMA-S, despite the fact that RMA-S is insensitive to TNF in vitro and that spleen NK cells from B6 and TNF-deficient mice are equally lytic towards RMA-S. NK cell recruitment into the peritoneum was abrogated in TNF-deficient mice challenged with RMA-S or RM-1, a B6 MHC class I− prostate carcinoma, compared with B6 or perforin-deficient mice. The reduced NK cell migration to the peritoneum of TNF-deficient mice correlated with the defective NK cell response to tumor in these mice. By contrast, a lack of TNF did not affect peptide-specific cytotoxic T lymphocyte–mediated rejection of tumor from the peritoneum of preimmunized mice. Overall, these data show that NK cells delivering perforin are the major effectors of class I− tumor rejection in the peritoneum, and that TNF is specifically critical for their recruitment to the peritoneum.
Comment on: “Dulaglutide treatment results in effective glycaemic control in latent autoimmune diabetes in adults (LADA): A post‐hoc analysis of the AWARD‐2, −4 and −5 trials”

We note with interest Pozzilli et al recent investigation of Dulaglutide treatment response in Latent Autoimmune Diabetes in Adults (LADA) in the AWARD -2, -4 and -5 trials. Pozzilli and colleagues reported no association between GAD islet autoantibody positivity and Dulaglutide response in their combined cohort population [1] . This is in contrast to our previously published findings in a prospective observational cohort of participants receiving other GLP-1 receptor agonists, where glycaemic response in GAD positive participants was reduced [2].
Phylogenetic Analysis and Antimicrobial Profiles of Cultured Emerging Opportunistic Pathogens (Phyla Actinobacteria and Proteobacteria) Identified in Hot Springs

Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial resistance of culturable emerging and opportunistic bacterial pathogens, in water and sediment of hot springs located in Limpopo, South Africa. Aerobic bacteria were cultured and identified using 16S ribosomal DNA (rDNA) gene sequencing. The presence of Legionella spp. was investigated using real-time polymerase chain reaction. Isolates were tested for resistance to ten antibiotics representing six different classes: β-lactam (carbenicillin), aminoglycosides (gentamycin, kanamycin, streptomycin), tetracycline, amphenicols (chloramphenicol, ceftriaxone), sulphonamides (co-trimoxazole) and quinolones (nalidixic acid, norfloxacin). Gram-positive Kocuria sp. and Arthrobacter sp. and gram-negative Cupriavidus sp. , Ralstonia sp. , Cronobacter sp. , Tepidimonas sp. , Hafnia sp. and Sphingomonas sp. were isolated, all recognised as emerging food-borne pathogens. Legionella spp. was not detected throughout the study. Isolates of Kocuria, Arthrobacter and Hafnia and an unknown species of the class Gammaproteobacteria were resistant to two antibiotics in different combinations of carbenicillin, ceftriaxone, nalidixic acid and chloramphenicol. Cronobacter sp. was sensitive to all ten antibiotics. This study suggests that hot springs are potential reservoirs for emerging opportunistic pathogens, including multiple antibiotic resistant strains, and highlights the presence of unknown populations of emerging and potential waterborne opportunistic pathogens in the environment.
Socio-economic position and subjective health and well-being among older people in Europe: a systematic narrative review

Objectives: Previous studies of older European populations have established that disability and morbidity vary with indicators of socio-economic position (SEP). We undertook a systematic narrative review of the literature to ascertain to what extent there is evidence of similar inequalities in the subjective health and well-being of older people in Europe. Method: Relevant original research articles were searched for using Medline, Global Health, Embase, Social Policy and Practice, Cinahl, Web of Science and International Bibliography of the Social Sciences (IBSS). We included studies of SEP and indicators of subjective health and well-being (self-rated health; life satisfaction; quality of life) conducted since 1991 using population-based samples of older people in Europe and published 1995–2013. Results: A total of 71 studies were identified. Poorer SEP was associated with poorer subjective health and well-being. Associations varied somewhat depending on the SEP measure and subjective health and well-being outcome used. Associations were weaker when social support and health-related behaviours were adjusted for suggesting that these factors mediate the relationship between SEP and subjective health and well-being. Associations tended to be weaker in the oldest age groups. The patterns of associations by gender were not consistent and tended to diminish after adjusting for indicators of health and life circumstances. Conclusion: The results of this systematic narrative review of the literature demonstrate the importance of social influences on later life subjective health and well-being and indicate areas which need further investigation, such as more studies from Eastern Europe, more longitudinal studies and more research on the role of mediating factors.
Th1/Th17 Cell Induction and Corresponding Reduction in ATP Consumption following Vaccination with the Novel Mycobacterium tuberculosis Vaccine MVA85A

Vaccination with Bacille Calmette-Guérin (BCG) has traditionally been used for protection against disease caused by the bacterium Mycobacterium tuberculosis (M.tb). The efficacy of BCG, especially against pulmonary tuberculosis (TB) is variable. The best protection is conferred in temperate climates and there is close to zero protection in many tropical areas with a high prevalence of both tuberculous and non-tuberculous mycobacterial species. Although interferon (IFN)-γ is known to be important in protection against TB disease, data is emerging on a possible role for interleukin (IL)-17 as a key cytokine in both murine and bovine TB vaccine studies, as well as in humans. Modified Vaccinia virus Ankara expressing Antigen 85A (MVA85A) is a novel TB vaccine designed to enhance responses induced by BCG. Antigen-specific IFN-γ production has already been shown to peak one week post-MVA85A vaccination, and an inverse relationship between IL-17-producing cells and regulatory T cells expressing the ectonucleosidease CD39, which metabolises pro-inflammatory extracellular ATP has previously been described. This paper explores this relationship and finds that consumption of extracellular ATP by peripheral blood mononuclear cells from MVA85A-vaccinated subjects drops two weeks post-vaccination, corresponding to a drop in the percentage of a regulatory T cell subset expressing the ectonucleosidase CD39. Also at this time point, we report a peak in co-production of IL-17 and IFN-γ by CD4+ T cells. These results suggest a relationship between extracellular ATP and effector responses and unveil a possible pathway that could be targeted during vaccine design.
Indications, complications, and outcome of horses undergoing repeated celiotomy within 14 days after the first colic surgery: 95 cases (2005-2013).

OBJECTIVE To examine factors associated with short- and long-term prognosis for horses undergoing repeated celiotomy within 14 days after the first colic surgery. DESIGN Retrospective case series. ANIMALS 95 horses that had undergone 2 celiotomies within a 14-day period between 2005 and 2013 at 3 equine referral hospitals. PROCEDURES Historical, clinical, and laboratory data were compared between horses that did not survive and horses that did survive to hospital discharge (short-term survival rate) and to > 3 and > 6 months after hospital discharge (long-term survival rates). RESULTS Strangulating small intestinal lesions were the most common finding during the first celiotomy (60/95 [63.2%]), and persistent gastric reflux was the most common reason for the second celiotomy (56/95 [58.9%]). Reasons for a second celiotomy were not associated with survival rate. For horses that had long-term follow-up, 22 of 92 (23.9%) survived > 6 months after hospital discharge. Two of 13 horses with intestinal resections during both surgeries survived to > 6 months after hospital discharge. Compared with horses not undergoing intestinal resection, significantly fewer horses requiring resection during 1 or both surgeries survived to hospital discharge and to > 3 and > 6 months after hospital discharge. Incisional infections occurred in 68.4% (26/38) of horses that survived to hospital discharge, and 31.6% (12/38) developed incisional hernias or dehiscence. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that the prognosis for horses undergoing repeated celiotomy is guarded, and intestinal resection negatively affects the long-term survival rate.
Molecular characterization of the Cenxi classical three-buff chicken (Gallus gallus domesticus) based on mitochondrial DNA

Abstract The complete mitochondrial genome sequence of the Cenxi classical three-buff chicken was measured by PCR-based methods and analyzed in detail. Our research findings reveal that the entire mitochondrial genome of the Cenxi classical three-buff chicken is a circular molecule consisting of 16,786 bp (GenBank accession number: KM433666). The contents of A, T, C, and G in the mitochondrial genome were found to be 30.27%, 23.75%, 32.49% and 13.49%, respectively. The complete mitochondrial genome of the Cenxi classical three-buff chicken contains a typical structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (D-loop region). This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Gallus gallus domesticus mitochondrial genomes.
NSCLC Patients Harbouring Rare or Complex EGFR Mutations Are More Often Smokers and Might Not Benefit from First-Line Tyrosine Kinase Inhibitor Therapy

Background: Generally, tyrosine kinase inhibitor (TKI) therapy is recommended in first-line treatment of patients with advanced non-small cell lung cancer (NSCLC) harbouring a classic epidermal growth factor receptor (EGFR) mutation. However, the response of patients with rare or complex EGFR mutations to TKI treatment is not predictable, nor is the prognosis for such patients. Objectives: In cases of rare or complex EGFR mutations, the right approach to therapy remains challenging. That is why we sought to analyse the characteristics as well as the prognosis and the response to TKI treatment of patients with rare or complex EGFR mutations. Patients and Methods: 343 NSCLC patients tested for EGFR mutation at a German lung cancer centre were analysed for age, gender, and smoking status as well as for the mutation status. For 12 patients with rare and complex mutations, response to TKI treatment was described. Results: 282 of all patients had a wild-type EGFR, whereas 61 harboured an EGFR mutation. 32 of these were classic mutations, followed by 16 rare and 7 complex mutations. EGFR mutations were significantly more frequent in women. Patients with rare or complex mutations were significantly more often smokers compared to those with classic EGFR mutations. Furthermore, rare and complex mutations were less responsive to TKI therapy. Conclusion: Patients with rare or complex EGFR mutations differ from those with classic mutations in terms of smoking status and response to TKIs. As these mutations may not respond well to TKI therapy, first-line TKIs should not be automatically chosen based on the sole presence of an EGFR mutation.
Increasing seed size and quality by manipulating BIG SEEDS1 in legume species

Significance One of the most important agronomic traits in crop breeding is yield, which includes increased seed size and weight in grain crops and leaf biomass in forage crops. In this work, we demonstrate that a transcription regulator encoded by the BIG SEEDS1 (BS1) gene from the model legume Medicago truncatula, negatively regulates primary cell proliferation in plants. The deletion of this gene in M. truncatula and down-regulation of its orthologs in soybean (Glycine max) lead to significant increases in the size of plant organs, including leaf and seed. Understanding the BS1 gene function and its regulatory mechanism offers an opportunity for increasing plant yield in legumes and other grain crops. Plant organs, such as seeds, are primary sources of food for both humans and animals. Seed size is one of the major agronomic traits that have been selected in crop plants during their domestication. Legume seeds are a major source of dietary proteins and oils. Here, we report a conserved role for the BIG SEEDS1 (BS1) gene in the control of seed size and weight in the model legume Medicago truncatula and the grain legume soybean (Glycine max). BS1 encodes a plant-specific transcription regulator and plays a key role in the control of the size of plant organs, including seeds, seed pods, and leaves, through a regulatory module that targets primary cell proliferation. Importantly, down-regulation of BS1 orthologs in soybean by an artificial microRNA significantly increased soybean seed size, weight, and amino acid content. Our results provide a strategy for the increase in yield and seed quality in legumes.
Multivariate Statistics and Supervised Learning for Predictive Detection of Unintentional Islanding in Grid-Tied Solar PV Systems

Integration of solar photovoltaic PV generation with power distribution networks leads to many operational challenges and complexities. Unintentional islanding is one of them which is of rising concern given the steady increase in grid-connected PV power. This paper builds up on an exploratory study of unintentional islanding on a modeled radial feeder having large PV penetration. Dynamic simulations, also run in real time, resulted in exploration of unique potential causes of creation of accidental islands. The resulting voltage and current data underwent dimensionality reduction using principal component analysis PCA which formed the basis for the application of Q statistic control charts for detecting the anomalous currents that could island the system. For reducing the false alarm rate of anomaly detection, Kullback-Leibler K-L divergence was applied on the principal component projections which concluded that Q statistic based approach alone is not reliable for detection of the symptoms liable to cause unintentional islanding. The obtained data was labeled and a K-nearest neighbor K-NN binomial classifier was then trained for identification and classification of potential islanding precursors from other power system transients. The three-phase short-circuit fault case was successfully identified as statistically different from islanding symptoms.
The Structure of the NPC1L1 N-Terminal Domain in a Closed Conformation

Background NPC1L1 is the molecular target of the cholesterol lowering drug Ezetimibe and mediates the intestinal absorption of cholesterol. Inhibition or deletion of NPC1L1 reduces intestinal cholesterol absorption, resulting in reduction of plasma cholesterol levels. Principal Findings Here we present the 2.8 Å crystal structure of the N-terminal domain (NTD) of NPC1L1 in the absence of cholesterol. The structure, combined with biochemical data, reveals the mechanism of cholesterol selectivity of NPC1L1. Comparison to the cholesterol free and bound structures of NPC1(NTD) reveals that NPC1L1(NTD) is in a closed conformation and the sterol binding pocket is occluded from solvent. Conclusion The structure of NPC1L1(NTD) reveals a degree of flexibility surrounding the entrance to the sterol binding pocket, suggesting a gating mechanism that relies on multiple movements around the entrance to the sterol binding pocket.
Augmented Metacognition: Exploring Pupil Dilation Sonification to Elicit Metacognitive Awareness

Metacognitive awareness enables people to make conscious decisions about their own cognitions, and adapt to meet task performance goals. Despite the role of metacognition in task performance, technologies that effectively augment metacognition are scarce. We explore a novel approach to augment metacognition based on making the eye's pupil dilations, which associate with a variety of cognitions, audible via sonification in real-time. In this exploratory study, we investigated whether pupil dilation sonification can elicit metacognitive awareness. Our findings suggest that correlations between a variety of cognitions, e.g., attentional focus and depth of thinking, and sounds generated by the sonification can emerge spontaneously and by instruction. This justifies further research into the use of pupil dilation sonification as a means to augment metacognitive abilities.
Intestinal Worm Infestation and Anaemia in Pregnant Women.

INTRODUCTION Severe Anaemia during pregnancy is an important contributor to maternal mortality, as well as to the low birth weight which is in turn an important risk factor for infant mortality. We aim to determine the prevalence of anaemia in the region amongst pregnant women and identify their problems and to easily provide them with the clinical services. METHODS A community based cross sectional study done in PHCRC Chapagaun, Lalitpur from July 17,2011 to September 17,2011. Date from pregnant women presenting at PHCRC, , were filled and analysed using standard guidelines from WHO and Indian council of Medical research. RESULTS Out of 192 pregnant women, the average age of pregnancy was 21-25 years (46.55), mean haemoglobin (Hb) in pregnancy was 11g/dl. Majority pregnant women are Newar (35.4%) ethnicity,67.7% of them housewives and 31.5% have primary level education. Only 24% was found to have their haemoglobin level in anaemic range. Among the pregnant women (n) =192; 48 (25%) had worm infestation, 119 (62%) had negative stool report and 25 (13%) had other than worms were found. Only about one third of the sample has actually taken albendazole. CONCLUSIONS Aanaemia is prevalent in pregnant women of PHCRC, chapagaun and there was a significant correlation between anaemia and worm infestation. However, the relation among the haemoglobin level, iron, folic acid and albendazole was not significant.
Protective Activity of Total Polyphenols from Genista quadriflora Munby and Teucrium polium geyrii Maire in Acetaminophen-Induced Hepatotoxicity in Rats

Oxidative stress is a major cause of drug-induced hepatic diseases and several studies have demonstrated that diet supplementation with plants rich in antioxidant compounds provides a variety of health benefits in these circumstances. Genista quadriflora Munby (Gq) and Teucrium polium geyrii Maire (Tp) are known to possess antioxidant and numerous biological properties and these endemic plants are often used for dietary or medicinal applications. Herein, we evaluated the beneficial effect of rich-polyphenol fractions of Gq and Tp to prevent Acetaminophen-induced liver injury and investigated the mechanisms involved in this protective action. Rats were orally administered polyphenolic extracts from Gq or Tp (300 mg/kg) or N-acetylcysteine (NAC: 200 mg/kg) once daily for ten days prior to the single oral administration of Acetaminophen (APAP: 1 g/kg). The results show that preventive administration of polyphenolic extracts from Gq or Tp exerts a hepatoprotective influence during APAP treatment by improving transaminases leakage and liver histology and stimulating antioxidant defenses. Besides, suppression of liver CYP2E1, GSTpi and TNF-α mRNA levels, with enhancement of mitochondrial bioenergetics may contribute to the observed hepatoprotection induced by Gq and Tp extracts. The effect of Tp extract is significantly higher (1.5–2 fold) than that of Gq extract and NAC regarding the enhancement of mitochondrial functionality. Overall, this study brings the first evidence that pretreatment with these natural extracts display in vivo protective activity against APAP hepatotoxicity through improving mitochondrial bioenergetics, oxidant status, phase I and II enzymes expression and inflammatory processes probably by virtue of their high total polyphenols content.