Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Bug Report Field Reassignment and Refinement Prediction

Bug fixing is one of the most important activities in software development and maintenance. Bugs are reported, recorded, and managed in bug tracking systems such as Bugzilla. In general, a bug report contains many fields, such as product, component, severity, priority, fixer, operating system (OS), and platform, which provide important information for the bug triaging and fixing process. Our previous study finds that approximately 80% of bug reports have their fields reassigned and refined at least once, and bugs with reassigned and refined fields take more time to fix than bugs with no reassigned and refined fields. Thus, automatically predicting which bug report fields get reassigned and refined could help developers to save bug fixing time. Considering that a bug report could have multiple field reassignments and refinements (e.g., the product, component, fixer, and other fields of a bug report can get reassigned and refined), in this paper, we propose a multi-label learning algorithm to predict which bug report fields might be reassigned and refined. We note that the number of bug reports with some types of reassignment and refinement (e.g., bugs whose severity fields gets reassigned and refined) is a small proportion of the whole bug report collection, indicating the class imbalance problem. Thus, we propose imbalanced ML.KNN (Im-ML.KNN), which extends ML.KNN, one of the state-of-the-art multi-label learning algorithms, to achieve better performance. Im-ML.KNN is a composite model that combines 3 multi-label classifiers built using different types of features (i.e., meta, textual, and mixed features). We evaluate our solution on 4 large bug report datasets including OpenOffice, Netbeans, Eclipse, and Mozilla containing a total of 190,558 bug reports. We show that Im-ML.KNN can achieve an average F-measure score of 0.56-0.62. We also compare Im-ML.KNN with other state-of-art methods, such as the method proposed by Lamkanfi , ML.KNN, and HOMER-NB. The results show that Im-ML.KNN, on average, improves the average F-measure scores of Lamkanfi 's method, ML.KNN, and HOMER-NB by 119.69%, 9.11%, and 161.08%, respectively.
A meta-analysis of adiponectin gene rs22411766 T>G polymorphism and ischemic stroke susceptibility

Abstract Several studies have investigated the correlation between adiponectin gene rs22411766 T>G polymorphism and ischemic stroke risk. However, the results were not conclusive with each other. Therefore, to overcome this obstacle, we performed this meta-analysis to further explicate the adiponectin gene rs22411766 T>G polymorphism and ischemic stroke susceptibility. Case-control or cohort studies focused on adiponectin gene rs22411766 T>G polymorphism and ischemic stroke risk were electronic searched in the databases of Medline, Pubmed, Cochrane library, Excerpta Medica database(EMBASE) and China National Knowledge Infrastructure (CNKI). All the potentially relevant studies were included in this meta-analysis. The association between adiponectin gene rs22411766 T>G polymorphism and ischemic stroke was expressed by odds ratio with its confidence interval. Publication bias has been assessed by begg’s funnel plot. All the analyses have been performed by Revman 5.1 statistical software. Finally, a total of six studies with 1,345 cases and 1,421 controls were included in this meta-analysis. Our results demonstrated that there was a significant association between adiponectin gene rs22411766 T>G polymorphism and ischemic stroke risk (p<0.05). People with G single nucleotide of adiponectin gene have the increased risk of developing ischemic stroke compared to T single nucleotide.
Screening Detects a High Proportion of Celiac Disease in Young HLA-genotyped Children

Background and Aims: Celiac disease is associated with tissue transglutaminase autoantibodies (tTGAb) and the human leukocyte antigen (HLA)–risk alleles DQB1*02 and DQB1*0302. The aim was to estimate the proportion of undiagnosed celiac disease in children with HLA risk at 3 years of age. Patients and Methods: From a population-based HLA-DQ screening study of newborns born between June 2001 and August 2004 in the southern part of Sweden, 6206 children with HLA-risk alleles were identified and asked to participate at a mean 3.3 ± 0.4 years of age. As controls, 7654 children with HLA-nonrisk alleles were asked to participate. In all, 1620 (26.1%) children with HLA risk and 1815 (23.7%) controls were screened for tTGAb using radioligand-binding assays. Celiac disease was established by intestinal biopsy in children with a confirmed positive tTGAb test. Results: Twenty-three children reported already having clinically diagnosed celiac disease and did not participate further. In children with HLA-risk genotypes, 73 of 1620 (4.5%, 95% CI 3.5%–5.5%) were tTGAb-positive compared with none of 1815 from the controls (P < 0.0001). Seventy-one children underwent biopsy (1 refused biopsy and 1 biopsy failed), of whom 56 of 1618 (3.5%, 95% CI 2.6%–4.4%) had damaged intestinal mucosa classified as celiac disease. The ratio between clinically and screening detected celiac disease in this study was 1:2.4 (23:56). Conclusions: The proportion of clinically undetected celiac disease may be particularly high among 3-year-old children with HLA-DQB1*02 and DQB1*0302 in Sweden, where these 2 HLA-risk alleles frequently occur.
Revisiting the security of speaker verification systems against imposture using synthetic speech

In this paper, we investigate imposture using synthetic speech. Although this problem was first examined over a decade ago, dramatic improvements in both speaker verification (SV) and speech synthesis have renewed interest in this problem. We use a HMM-based speech synthesizer which creates synthetic speech for a targeted speaker through adaptation of a background model. We use two SV systems: standard GMM-UBM-based and a newer SVM-based. Our results show when the systems are tested with human speech, there are zero false acceptances and zero false rejections. However, when the systems are tested with synthesized speech, all claims for the targeted speaker are accepted while all other claims are rejected. We propose a two-step process for detection of synthesized speech in order to prevent this imposture. Overall, while SV systems have impressive accuracy, even with the proposed detector, high-quality synthetic speech will lead to an unacceptably high false acceptance rate.
Biological properties of dehydrated human amnion/chorion composite graft: implications for chronic wound healing

Human amnion/chorion tissue derived from the placenta is rich in cytokines and growth factors known to promote wound healing; however, preservation of the biological activities of therapeutic allografts during processing remains a challenge. In this study, PURION® (MiMedx, Marietta, GA) processed dehydrated human amnion/chorion tissue allografts (dHACM, EpiFix®, MiMedx) were evaluated for the presence of growth factors, interleukins (ILs) and tissue inhibitors of metalloproteinases (TIMPs). Enzyme‐linked immunosorbent assays (ELISA) were performed on samples of dHACM and showed quantifiable levels of the following growth factors: platelet‐derived growth factor‐AA (PDGF‐AA), PDGF‐BB, transforming growth factor α (TGFα), TGFβ1, basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), placental growth factor (PLGF) and granulocyte colony‐stimulating factor (GCSF). The ELISA assays also confirmed the presence of IL‐4, 6, 8 and 10, and TIMP 1, 2 and 4. Moreover, the relative elution of growth factors into saline from the allograft ranged from 4% to 62%, indicating that there are bound and unbound fractions of these compounds within the allograft. dHACM retained biological activities that cause human dermal fibroblast proliferation and migration of human mesenchymal stem cells (MSCs) in vitro. An in vivo mouse model showed that dHACM when tested in a skin flap model caused mesenchymal progenitor cell recruitment to the site of implantation. The results from both the in vitro and in vivo experiments clearly established that dHACM contains one or more soluble factors capable of stimulating MSC migration and recruitment. In summary, PURION® processed dHACM retains its biological activities related to wound healing, including the potential to positively affect four distinct and pivotal physiological processes intimately involved in wound healing: cell proliferation, inflammation, metalloproteinase activity and recruitment of progenitor cells. This suggests a paracrine mechanism of action for dHACM when used for wound healing applications.
The pathogenesis of liver disease in the setting of HIV–hepatitis B virus coinfection

There are many potential reasons for increased liver-related mortality in HIV–hepatitis B virus (HBV) coinfection compared with either infection alone. HIV infects multiple cells in the liver and might potentially alter the life cycle of HBV, although evidence to date is limited. Unique mutations in HBV have been defined in HIV–HBV-coinfected individuals and might directly alter pathogenesis. In addition, an impaired HBV- specific T-cell immune response is likely to be important. The roles of microbial translocation, immune activation and increased hepatic stellate cell activation will be important areas for future study.
Magnesium, Iron, and Zinc Supplementation for the Treatment of Attention Deficit Hyperactivity Disorder: A Systematic Review on the Recent Literature

Background: The etiology of attention deficit hyperactivity disorder (ADHD) is not exactly known and its etiology is multifactorial. The usual treatment for these children is based on pharmacotherapy treatment, although the pharmacotherapy has a high effectiveness in ADHD treatment, it often causes different side effects. Existing evidence suggests that children who receive mineral supplement without considering their age and supplement formula may perform better on different behavioral tests compared with those receiving placebo. Methods: In this study, we tried to review the previous evidence regarding the effects of minerals in prevention and management of ADHD. We searched PubMed/Medline, Google Scholar, Ovid, Scopus, and ISI web of science up to June 2013. “iron,” “iron supplementation,” “magnesium,” “magnesium supplementation,” “zinc,” “zinc supplementation,” “attention deficit hyperactivity disorder” were used as the keywords. Totally 11 randomized controlled trials were eligible to be included in the systematic review. Results: Our review showed that we don’t have any predominant evidence about using mineral supplementation on children with ADHD. Conclusions: We need more evidence for indicating the effect of zinc, magnesium, and iron supplementation in the treatment of ADHD among children.
Self-organized annealing in laterally inhibited neural networks shows power law decay

In this paper we present a method which assigns to each layer of a multilayer neural network, whose network dynamics is governed by a noisy winner-take-all mechanism, a neural temperature. This neural temperature is obtained by a least mean square fit of the probability distribution of the noisy winner-take-all mechanism to the distribution of a softmax mechanism, which has a well defined temperature as free parameter. We call this approximated temperature resulting from the optimization step the neural temperature. We apply this method to a multilayer neural network during learning the XOR-problem with a Hebb-like learning rule and show that after a transient the neural temperature decreases in each layer according to a power law. This indicates a self-organized annealing behavior induced by the learning rule itself instead of an external adjustment of a control parameter as in physically motivated optimization methods e.g. simulated annealing.
Specification of Mixed Logit Models Using an Optimization Approach

iii ACKNOWLEDGMENT. iv DEDICATION . v TABLE OF CONTENTS . vi LIST OF TABLES . viii LIST OF FIGURES . ix CHAPTER 1: INTRODUCTION . 1 CHAPTER 2: LITERATURE REVIEW . 6 CHAPTER 3: METHODOLOGY . 9 Mathematical Programming Problem Formulation . 9 Solution Algorithm.11 CHAPTER 4: EXPERIMENTS . 15 Experiment 1 and 2 . 15 Experiment 3 . 17 CHAPTER 5: RESULTS . 18 Experiment 1 and 2 . 18 Experiment 3 . 22 CHAPTER 6: CONCLUSIONS . 26 APPENDIX A: INSTRUCTIONS TO EXECUTE ALGORITHM . 29 Requirements . 29 Steps . 29
Reproductive capacity of free-roaming domestic cats and kitten survival rate.

OBJECTIVE To determine reproductive capacity of naturally breeding free-roaming domestic cats and kitten survival rate. DESIGN Prospective cohort and retrospective cross-sectional study. ANIMALS 2,332 female cats brought to a trap-neuter-return clinic for neutering and 71 female cats and 171 kittens comprising 50 litters from a cohort study of feral cats in managed colonies. PROCEDURE Data collected for all cats included pregnancy, lactation, and estrus status and number of fetuses for pregnant cats. Additional data collected for feral cats in managed colonies included numbers of litters per year and kittens per litter, date of birth, kitten survival rate, and causes of death. RESULTS Pregnant cats were observed in all months of the year, but the percentage of cats found to be pregnant was highest in March, April, and May. Cats produced a mean of 1.4 litters/y, with a median of 3 kittens/litter (range, 1 to 6). Overall, 127 of 169 (75%) kittens died or disappeared before 6 months of age. Trauma was the most common cause of death. CONCLUSIONS AND CLINICAL RELEVANCE Results illustrate the high reproductive capacity of free-roaming domestic cats. Realistic estimates of the reproductive capacity of female cats may be useful in assessing the effectiveness of population control strategies.
Cell surface antigens of human renal cancer defined by autologous typing

Sera from 28 patients with renal cancer were tested for reactivity with surface antigens of cultured autologous renal cancer cells. Four serological assays were used to survey sera for autologous antibody. Immune adherence, protein A, and C3-mixed hemadsorption assays detected reactivity in a high percentage of patients (80-100%), whereas mixed hemadsorption assays were negative with sera from all but one patient. Reactive sera from six patients were analyzed by absorption tests with autologous, allogeneic, and restricted to autologous renal cancer cells; class 2 antigens, present on certain allogeneic renal and nonrenal cancer cells; and class 3 antigens, found on a wide variety of normal and malignant cell types. The sera of one patient detected class 1, 2, and 3 antigens, the sera of three patients detected class 2 antigens, and the sera of two patients detected class 3 antigens. This analysis of renal cancer, with the recognition of three classes of surface antigens recognized by autologous sera, resembles the results of autologous typing of three other human malignancies: malignant melanoma, acute leukemia, and astrocytoma. Evidence provided by autologous typing of these cancers indicates that class 1 and class 2 antigens are tumor-restricted and that under certain circumstances these antigens are immunogenic for the autologous host.
Brownian motion of a self-propelled particle.

Overdamped Brownian motion of a self-propelled particle is studied by solving the Langevin equation analytically. On top of translational and rotational diffusion, in the context of the presented model, the 'active' particle is driven along its internal orientation axis. We calculate the first four moments of the probability distribution function for displacements as a function of time for a spherical particle with isotropic translational diffusion, as well as for an anisotropic ellipsoidal particle. In both cases the translational and rotational motion is either unconfined or confined to one or two dimensions. A significant non-Gaussian behaviour at finite times t is signalled by a non-vanishing kurtosis γ(t). To delimit the super-diffusive regime, which occurs at intermediate times, two timescales are identified. For certain model situations a characteristic t3 behaviour of the mean-square displacement is observed. Comparing the dynamics of real and artificial microswimmers, like bacteria or catalytically driven Janus particles, to our analytical expressions reveals whether their motion is Brownian or not.
Tuberculous Granulomas Are Hypoxic in Guinea Pigs, Rabbits, and Nonhuman Primates

ABSTRACT Understanding the physical characteristics of the local microenvironment in which Mycobacterium tuberculosis resides is an important goal that may allow the targeting of metabolic processes to shorten drug regimens. Pimonidazole hydrochloride (Hypoxyprobe) is an imaging agent that is bioreductively activated only under hypoxic conditions in mammalian tissue. We employed this probe to evaluate the oxygen tension in tuberculous granulomas in four animal models of disease: mouse, guinea pig, rabbit, and nonhuman primate. Following infusion of pimonidazole into animals with established infections, lung tissues from the guinea pig, rabbit, and nonhuman primate showed discrete areas of pimonidazole adduct formation surrounding necrotic and caseous regions of pulmonary granulomas by immunohistochemical staining. This labeling could be substantially reduced by housing the animal under an atmosphere of 95% O2. Direct measurement of tissue oxygen partial pressure by surgical insertion of a fiber optic oxygen probe into granulomas in the lungs of living infected rabbits demonstrated that even small (3-mm) pulmonary lesions were severely hypoxic (1.6 ± 0.7 mm Hg). Finally, metronidazole, which has potent bactericidal activity in vitro only under low-oxygen culture conditions, was highly effective at reducing total-lung bacterial burdens in infected rabbits. Thus, three independent lines of evidence support the hypothesis that hypoxic microenvironments are an important feature of some lesions in these animal models of tuberculosis.
Dimension of the speech space

Defines a statistic for estimating the intrinsic dimension of a finite set of points on the assumption that they lie on a smoothly embedded manifold, when of course, the dimension is an integer, The authors test the method on finite sets drawn from known manifolds and show that it is robust. They also apply it to the Lorenz attractor. Finally they apply it to speech data of the type used by Tattersal et al (1983). It is concluded that the speech space is not discernibly a low-dimensional manifold at all, and that a more plausible hypothesis is that the space is an open subset of the enclosing space. A measure is constructed of the extent to which the surface that the Kohonen algorithm fits to the speech space is buckled or crinkled related to the mean absolute curvature. The speech space can be approximated with a low-dimensional manifold, but it has dimension greater than two.
Physical exercise and internet-based cognitive–behavioural therapy in the treatment of depression: Randomised controlled trial

Background Depression is common and tends to be recurrent. Alternative treatments are needed that are non-stigmatising, accessible and can be prescribed by general medical practitioners. Aims To compare the effectiveness of three interventions for depression: physical exercise, internet-based cognitive–behavioural therapy (ICBT) and treatment as usual (TAU). A secondary aim was to assess changes in self-rated work capacity. Method A total of 946 patients diagnosed with mild to moderate depression were recruited through primary healthcare centres across Sweden and randomly assigned to one of three 12-week interventions (trail registry: KCTR study ID: KT20110063). Patients were reassessed at 3 months (response rate 78%). Results Patients in the exercise and ICBT groups reported larger improvements in depressive symptoms compared with TAU. Work capacity improved over time in all three groups (no significant differences). Conclusions Exercise and ICBT were more effective than TAU by a general medical practitioner, and both represent promising non-stigmatising treatment alternatives for patients with mild to moderate depression.
Runtime analysis for maximizing population diversity in single-objective optimization

Recently Ulrich and Thiele [14] have introduced evolutionary algorithms for the mixed multi-objective problem of maximizing fitness as well as diversity in the decision space. Such an approach allows to generate a diverse set of solutions which are all of good quality. With this paper, we contribute to the theoretical understanding of evolutionary algorithms for maximizing the diversity in a population that contains several solutions of high quality. We study how evolutionary algorithms maximize the diversity of a population where each individual has to have fitness beyond a given threshold value. We present a first runtime analysis in this area and study the classical problems called \emph{\OM} and \emph{\LO}. Our results give first rigorous insights on how evolutionary algorithms can be used to produce a maximal diverse set of solutions in which all solutions have quality above a certain threshold value.
Lipoprotein Apheresis for Lipoprotein(a)-Associated Cardiovascular Disease: Prospective 5 Years of Follow-Up and Apolipoprotein(a) Characterization.

OBJECTIVE Lipoprotein(a)-hyperlipoproteinemia (Lp(a)-HLP) along with progressive cardiovascular disease has been approved as indication for regular lipoprotein apheresis (LA) in Germany since 2008. We aimed to study the long-term preventive effect of LA and to assess hypothetical clinical correlations of apolipoprotein(a) (apo(a)) by analyzing genotypes and phenotypes. APPROACH AND RESULTS This prospective observational multicenter study included 170 patients with Lp(a)-HLP and progressive cardiovascular disease (48.9 years median age at diagnosis) despite other cardiovascular risk factors, including low-density lipoprotein cholesterol had maximally been treated (mean baseline low-density lipoprotein cholesterol: measured, 2.56 mmol/L [98.9 mg/dL] and corrected, 1.72 mmol/L [66.3 mg/dL]). Patients were prospectively investigated during a 5-year period about annual incidence rates of cardiovascular events. In addition, apo(a) isoforms and polymorphisms at the apo(a) gene (LPA) were characterized. One hundred fifty-four patients (90.6%) completed 5 years of follow-up. Mean Lp(a) concentration before commencing regular LA was 108.1 mg/dL. This was reduced by a single LA treatment by 68.1% on average. Significant decline of the mean annual cardiovascular event rate was observed from 0.58±0.53 2 years before regular LA to 0.11±0.15 thereafter (P<0.0001); 95.3% of patients expressed at least 1 small apo(a) isoform. Small apo(a) isoform (35.2%) carrying phenotypes were not tagged by single-nucleotide polymorphisms rs10455872 or rs3798220. CONCLUSIONS Results of 5 years of prospective follow-up confirm that LA has a lasting effect on prevention of cardiovascular events in patients with Lp(a)-HLP. Patients clinically selected by progressive cardiovascular disease were characterized by a highly frequent expression of small apo(a) isoforms. Only Lp(a) concentration seemed to comprehensively reflect Lp(a)-associated cardiovascular risk, however.