Miracle-dz/UniFAR-FTUs huggingface dataset:
Software Defect Prediction Using Call Graph Based Ranking (CGBR) Framework

Recent research on static code attribute (SCA) based defect prediction suggests that a performance ceiling has been achieved and this barrier can be exceeded by increasing the information content in data. In this research we propose static call graph based ranking (CGBR) framework, which can be applied to any defect prediction model based on SCA. In this framework, we model both intra module properties and inter module relations. Our results show that defect predictors using CGBR framework can detect the same number of defective modules, while yielding significantly lower false alarm rates. On industrial public data, we also show that using CGBR framework can improve testing efforts by 23%.
Ocular iontophoresis of EGP-437 (dexamethasone phosphate) in dry eye patients: results of a randomized clinical trial

Purpose: To assess safety and efficacy of EGP-437 (dexamethasone phosphate 40 mg/mL [DP]) in dry eye patients. Methods: The study employed a prospective, single-center, double-masked design utilizing a Controlled Adverse Environment (CAE). Patients (n = 103) with confirmed signs and symptoms of dry eye syndrome were randomized into 1 of 3 iontophoresis treatment groups: 7.5 mA-min at 2.5 mA (DP 7.5, n = 41); 10.5 mA-min at 3.5 mA (DP 10.5, n = 37); or 10.5 mA-min at 3.5 mA (placebo, n = 25). Three CAE visits and 4 follow-up visits occurred over 3 weeks. Patients meeting enrollment criteria received iontophoresis in both eyes after the second CAE exposure (visit 3) and before the third CAE exposure (visit 5). Primary efficacy endpoints were corneal staining and ocular discomfort. Secondary endpoints included tear film break-up time, ocular protection index (OPI), and symptomatology. Results: The DP 7.5 and DP 10.5 treatment groups showed statistically significant improvements in signs and symptoms of dry eye at various time points; however, the primary endpoints were not achieved. The DP 7.5 treatment group exhibited statistically significant improvements in corneal staining (when comparing the differences between study entry and exit, 3 weeks, P = 0.039), OPI (immediately following the second treatment, P = 0.048) and ocular discomfort at follow-up visits (a week after the first treatment, P = 0.032; 24 hours after the second treatment, P = 0.0032). Treatment-emergent adverse events (AEs) were experienced by 87% of patients and were consistent across all treatment groups. Most AEs were mild and no severe AEs were observed. Conclusion: Ocular iontophoresis of EGP-437 demonstrated statistically and clinically significant improvements in signs and symptoms of dry eye syndrome within a CAE model.
Reduced interhemispheric resting‐state functional connectivity in unmedicated bipolar II disorder

Abnormalities in structural and functional brain connectivity have been increasingly reported in patients with bipolar disorder (BD) by recent neuroimaging studies. However, relatively little is known about the changes in functional interaction between the cerebral hemispheres in BD. The present study aimed to examine the interhemispheric functional connectivity of the whole brain in patients with BD II during resting state.
Identifying Evidence-Based Interventions for Children and Adolescents Using the Range of Possible Changes Model

The article discusses a study involving a framework (range of possible changes [RPC] Model) developed and applied to identify patterns in consistent and inconsistent intervention outcomes effects by informant, measurement method, and method of statistical analysis to the meta-analytic study of trials testing two evidence-based interventions for children and adolescents (youth-focused cognitive-behavioral treatment for child anxiety problems; parent-focused behavioral parent training for childhood conduct problems). This article illustrates how findings gleaned from applying the RPC Model allow for unique opportunities for hypothesis generation based on the patterns of consistent outcomes effects. Based on the RPC Model, studies can be closely examined to identify the specific instances in which interventions yield robust effects, and the authors illustrate how examining effects in this way can lead to new understandings of interventions and the outcomes they produce. Findings suggest that researchers can employ previously underutilized patterns of consistencies and inconsistencies in outcomes effects as new resources for identifying evidence-based interventions.
Pattern of Distribution of Calcitonin Gene–Related Peptide in the Dorsal Root Ganglion of Animal Models of Diabetes Mellitus

Abstract: This article examined the pattern of distribution of calcitonin gene–related peptide (CGRP) in the dorsal root ganglion (DRG) of normal and diabetic Wistar, Zucker lean, and Goto‐Kakizaki (GK) rats to determine whether there are changes in the number and pattern of distribution of CGRP‐positive neurons after the onset of latent or overt diabetes. Type 1 diabetes mellitus was induced in Wistar rats by a single dose of streptozotocin (STZ) given intraperitoneally (60 mg/kg body weight). Four weeks after the induction of diabetes mellitus, diabetic (n= 6) and normal (n= 6), Zucker lean (n= 6), and GK (n= 6) rats were anesthetized with chloral hydrate and their DRGs were removed and processed for immunohistochemistry. CGRP‐positive neurons were observed in the DRG of normal and diabetic Wistar, Zucker lean (nondiabetic), and GK (animal model of type 2 diabetes) rats. CGRP was present in small‐, medium‐, and large‐sized neurons of the DRG in these three animal models. Only a small percentage of large‐sized neurons contains CGRP. The number of CGRP‐positive neurons was significantly (P < 0.05) reduced in STZ‐induced diabetic Wistar and GK rats compared to normal Wistar and Zucker lean rats. Moreover, the quantity of CGRP‐containing varicose nerves was less in diabetic Wistar and GK rats compared to control Wistar and Zucker lean rats. The reduced number of CGRP‐positive neurons in the DRG of GK rats indicated that subjects with latent diabetes may already have dysfunctional CGRP metabolism and thus diabetic neuropathy.
nab-Paclitaxel as a potential partner with checkpoint inhibitors in solid tumors

Tumors recognized by the host immune system are associated with better survival. However, the immune system is often suppressed in patients with established tumor burden. Stimulating the immune system to detect and kill tumor cells has been a challenge in cancer therapy for some time. Recently, novel cancer immunotherapies, such as immune checkpoint inhibitors, monoclonal antibodies, and vaccine therapies, have emerged as promising therapeutic approaches for many solid tumors. However, for some tumors, immunotherapy alone has not provided significant benefits, and some may even be fully resistant to immunotherapy. It has been suggested that the immune system may require “priming” before an immunotherapy can elicit an immune response. Although chemotherapies are believed to be immunosuppressive, when given at the right dose and sequence these agents may provide this “priming” effect for the immune system. In addition to direct cytotoxic killing of tumor cells, standard chemotherapeutic agents can elicit immunogenicity through various mechanisms. This review highlights the general immunomodulatory properties of chemotherapy agents. It also provides a rationale for combined therapy with nab-paclitaxel and immune checkpoint inhibitors. Recent clinical trial data with these combination regimens in solid tumors are presented, along with a summary of ongoing trials.
Stability of blood homocysteine and other thiols: EDTA or acidic citrate?

Homocysteine (Hcy), a thiol-containing amino acid resulting from demethylation of methionine (Met), is relevant to the risk of vascular diseases (1). In plasma, total homocysteine (tHcy) includes the free reduced and oxidized forms as well as the Hcy bound by disulfide bonds in proteins. tHcy is frequently increased in patients with coronary, cerebrovascular, or peripheral arterial diseases; the association is independent of most other risk factors for atherosclerosis (2). The simultaneous measurement of other thiols is of interest because most of them are metabolically related and disturbances of their concentrations can correspond to disorders of metabolism. Hcy may either be catabolized to cysteine (Cys) or remethylated to Met (3). In addition, Cys and γ-glutamylcysteine are precursors to glutathione (GSH), and cysteinylglycine (CysGly) is a breakdown product of GSH; this latter plays a major role in defense against oxidative and free radical-mediated cell injury, and its measurement permits the evaluation of oxidative status of cells and tissues (4). It should be expected that less rigorous blood sampling and treatment conditions are needed than those involved for thiol redox status evaluation (5). For plasma, storage conditions have little influence on tHcy values: tHcy in plasma is stable at −20 °C for at least 3 months and after nine freeze/thaw cycles (6). In contrast, in whole blood, an increase of tHcy is observed after collection because of ongoing metabolism and time-dependent release from erythrocytes (7). The artificial increase in plasma tHcy occurs at a rate of 1 μmol/L per hour at room temperature (6)(7). In most studies, blood is drawn in tubes containing potassium EDTA, which are put immediately in crushed ice and centrifuged “as soon as possible”, and then the plasma is frozen. These conditions prevent increases in tHcy in whole blood after collection, but they are not always …
Variants in ANGPTL4 and the Risk of Coronary Artery Disease.

n engl j med 375;23 nejm.org December 8, 2016 2303 1. Antic NA, Heeley E, Anderson CS, et al. The Sleep Apnea cardioVascular Endpoints (SAVE) trial: rationale, ethics, design, and progress. Sleep 2015; 38: 1247-57. 2. Weaver TE, Grunstein RR. Adherence to continuous positive airway pressure therapy: the challenge to effective treatment. Proc Am Thorac Soc 2008; 5: 173-8. 3. Kritikou I, Basta M, Tappouni R, et al. Sleep apnoea and visceral adiposity in middle-aged male and female subjects. Eur Respir J 2013; 41: 601-9. 4. Kim AM, Keenan BT, Jackson N, et al. Tongue fat and its relationship to obstructive sleep apnea. Sleep 2014; 37: 163948. 5. Woodward M, Patel A, Zoungas S, et al. Does glycemic control offer similar benefits among patients with diabetes in different regions of the world? Results from the ADVANCE trial. Diabetes Care 2011; 34: 2491-5.
The Importance of the Biological Impact of Exposure to the Concept of the Exposome

Background: The term “exposome” was originally coined in 2005 and defined as the totality of exposures throughout the lifetime. The exposome provides an excellent scientific framework for studying human health and disease. Recently, it has been suggested that how exposures affect our biology and how our bodies respond to such exposures should be part of the exposome. Objectives: The authors describe the biological impact of the exposome and outline many of the targets and processes that can be assessed as part of a comprehensive analysis of the exposome. Discussion: The processes that occur downstream from the initial interactions with exogenous and endogenous compounds determine the biological impact of exposures. If the effects are not considered in the same context as the exposures, it will be difficult to determine cause and effect. The exposome and biology are interactive—changes in biology due to the environment change one’s vulnerability to subsequent exposures. Additionally, highly resilient individuals are able to withstand environmental exposures with minimal effects to their health. We expect that the vast majority of exposures are transient, and chemicals underlying exposures that occurred weeks, months, or years ago are long gone from the body. However, these past chemical exposures often leave molecular fingerprints that may be able to provide information on these past exposures. Conclusions: Through linking exposures to specific biological responses, exposome research could serve to improve understanding of the mechanistic connections between exposures and health to help mitigate adverse health outcomes across the lifespan. Citation: Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner S, Miller GW. 2016. The importance of the biological impact of exposure to the concept of the exposome. Environ Health Perspect 124:1504–1510; http://dx.doi. org/10.1289/EHP140
Intranasal Glucagon for Treatment of Insulin-Induced Hypoglycemia in Adults With Type 1 Diabetes: A Randomized Crossover Noninferiority Study

OBJECTIVE Treatment of severe hypoglycemia with loss of consciousness or seizure outside of the hospital setting is presently limited to intramuscular glucagon requiring reconstitution immediately prior to injection, a process prone to error or omission. A needle-free intranasal glucagon preparation was compared with intramuscular glucagon for treatment of insulin-induced hypoglycemia. RESEARCH DESIGN AND METHODS At eight clinical centers, a randomized crossover noninferiority trial was conducted involving 75 adults with type 1 diabetes (mean age, 33 ± 12 years; median diabetes duration, 18 years) to compare intranasal (3 mg) versus intramuscular (1 mg) glucagon for treatment of hypoglycemia induced by intravenous insulin. Success was defined as an increase in plasma glucose to ≥70 mg/dL or ≥20 mg/dL from the glucose nadir within 30 min after receiving glucagon. RESULTS Mean plasma glucose at time of glucagon administration was 48 ± 8 and 49 ± 8 mg/dL at the intranasal and intramuscular visits, respectively. Success criteria were met at all but one intranasal visit and at all intramuscular visits (98.7% vs. 100%; difference 1.3%, upper end of 1-sided 97.5% CI 4.0%). Mean time to success was 16 min for intranasal and 13 min for intramuscular (P < 0.001). Head/facial discomfort was reported during 25% of intranasal and 9% of intramuscular dosing visits; nausea (with or without vomiting) occurred with 35% and 38% of visits, respectively. CONCLUSIONS Intranasal glucagon was highly effective in treating insulin-induced hypoglycemia in adults with type 1 diabetes. Although the trial was conducted in a controlled setting, the results are applicable to real-world management of severe hypoglycemia, which occurs owing to excessive therapeutic insulin relative to the impaired or absent endogenous glucagon response.
Analyzing and Modeling Temporal Patterns of Human Contacts in Cellular Networks

As the usage of wireless devices rapidly increases, mobile phones have become an important aid for people to maintain social relationships. Analysis on cellular networks through mobile communication records, especially when such records contain temporal and spatial information, can potentially unveil fundamental laws that govern the dynamics of social networks. In this paper, we use call detail records (CDRs) collected from a nation-wide cellular network in North America for more than one month. We analyze contact patterns over one million pairs of people using real call data as looking into pairwise call records for each pair. First, we investigate the impacts of social relationships on contacts and discover that family members show different characteristics from non-family pairs in terms of contact regularity or duration. Next, we characterize inter-contact time and contact duration using finite mixture models of Gaussian, Lognormal, and Gamma distributions for each pair. Our mixture models for pairwise communication patterns of cellular users capture and demonstrate burstiness, periodicity, and inhomogeneity of human communication.
Minimum Makespan Scheduling with Low Rank Processing Times

We investigate approximation algorithms for the classical minimum makespan scheduling problem, focusing on instances where the rank of the matrix describing the processing times of the jobs is bounded. A bounded rank matrix arises naturally when the processing time of a job on machine depends upon a bounded set of resources. A bounded rank matrix also shows up when jobs have varying degrees of parallelizability and the machines have multiple cores. We are interested in studying the tractability of the problem as a function of the (positive) rank of the processing-time matrix. At one extreme is the case of unit rank, also known as related machines, which admits a PTAS [7], and at the other extreme is the full rank case (unrelated machines), which is NP-hard to approximate within a factor better than 3/2 [8]. Our main technical contribution is in showing that the approximability of the problem is not smooth with the rank of the matrix. From the inapproximability side, we show that the problem becomes APX-hard, even for rank four matrices. For rank seven matrices, we prove that it is hard to approximate to a factor 3/2, matching the inapproximability result for general unrelated machines. From the algorithmic side, we obtain a quasi-polynomial approximation scheme (i.e., a (1 + e) approximation in time npoly(1/e,log n)) for the rank two case. This implies that the problem is not APX-hard in this case, unless NP has quasi-polynomial algorithms. Our algorithm is a subtle dynamic program which runs in polynomial time in some interesting special cases. The classification of the three dimensional problem remains open.
Is Volunteering Rewarding in Itself?

Volunteering constitutes one of the most important pro-social activities. Following Aristotle, helping others is the way to higher individual wellbeing. This view contrasts with the selfish utility maximizer, who avoids helping others. The two rival views are studied empirically. We find robust evidence that volunteers are more satisfied with their life than non-volunteers. The issue of causality is studied from the basis of the collapse of East Germany and its infrastructure of volunteering. People who lost their opportunities for volunteering are compared with people who experienced no change in their volunteer status.
Identification of Real and Artifactual Moderators of Effect Size in Meta-Analysis

This article argues that while meta-analytic studies are widely used in psychological literature, heterogeneity and the potential for confounding remain major problems in the interpretation of meta-analytic study results. The article demonstrates the use of exploratory analysis including graphical methods prior to meta-analysis, and introduces a methodology to screen for artifactual effects. These procedures are illustrated on effect size data comparing depression treatment outcome from psychotherapy versus pharmacotherapy. Results support prior findings of a nonsignificant difference in effect size between the two treatments. They also support findings that treatment type accounts for only a very small proportion of outcome variance. However, the results indicate that some previously reported covariates of depression treatment outcome may be artifactual.
Efficacy of Highly Active Antiretroviral Therapy in HIV-1–Infected Children in Kenya

OBJECTIVE. Few studies have investigated the efficacy of antiretroviral therapy among HIV-infected children in resource-poor settings. This observational, retrospective analysis describes the clinical, immunologic, and virologic effects of highly active antiretroviral therapy in treatment-naive, HIV-infected children in Mombasa, Kenya. In keeping with a public health approach, all children were treated by using a simplified, nationally approved, triple-drug regimen. METHODS. Clinical data and stored plasma samples from 29 children who were followed prospectively between April 2003 and October 2004 were analyzed. All children received generic formulations of nevirapine, zidovudine, and lamivudine and were evaluated at baseline and at 3, 6, 9, 12, and 15 months. At each visit, weight and CD4 lymphocyte counts were measured and plasma samples were stored for analysis. HIV RNA load was determined retrospectively at baseline and 9 months after initiation of therapy. RESULTS. The mean age of the children was 8.5 years (range: 2–16 years). At baseline, the mean CD4 count (±SD) was 182.3 × 106 cells per μL (±145.6). On treatment, CD4 counts increased step-wise by a mean of 187 × 106 cells per μL at 3 months, 293 cells per μL at 6 months, 308 cells per μL at 9 months, 334 cells per μL at 12 months, and 363 cells per μL at 15 months. The mean plasma viral load decreased from a baseline level of 622 712 to 35369 copies per mL, and at 9 months was undetectable in 55% of the patients. Mean z scores for weight for age increased from a baseline of −1.61 to −1.12 at 12 months into therapy. CONCLUSIONS. A public health approach using 1 treatment regimen in generic form showed excellent efficacy among treatment-naive, HIV-infected children in a resource-limited country. Clinical and immunologic improvement occurred in all patients, but 9 months after the start of therapy, only 55% of the children had an undetectable viral load.
Extracellular signal fluctuations in shark electrosensors

We examine the roll of an extracellular gel in the functioning of the electrosensors of elasmobranchs (sharks, skates, and rays). Here we focus on physical characteristics of the gel and their mechanistic relevance to the observed functioning of the electrosensors. The electrosensitive organs show sharp transient responses to both tiny electrical fluctuations and temperature fluctuations. We present a thermoelectric characterization of the gel. The data suggest a gel-mediated mechanism of transducing thermal fluctuations to electrical fluctuations in the electrosensor, independent of the sensing cells. We also present frequency-dependent electrical properties of the gel collected using electrical impedance spectroscopy. From these measurements we try to extract characteristic relaxation times. We analyze these results within the context of the electrosensors’ bandwidth, as demonstrated in previous behavioral experiments.
Segmentation of sows in farrowing pens

The correct segmentation of a foreground object in video recordings is an important task for many surveillance systems. The development of an effective and practical algorithm to segment sows in grayscale video recordings captured under commercial production conditions is described. The segmentation algorithm combines a modified adaptive Gaussian mixture model for background subtraction with the boundaries of foreground objects, which is obtained by using dyadic wavelet transform. This algorithm can accurately extract the shapes of a sow under complex environments, such as dynamic background and illumination changes as well as motionless foreground objects. About 97% of the segmented binary images in the validation data sets can be used to track sow behaviours, such as position, orientation and movement. The experimental results demonstrate that the proposed algorithm is able to provide a basis to detect and classify the sow behaviours in farrowing pens.
Investment Cycles and Sovereign Debt Overhang

We characterize optimal taxation of foreign capital and optimal sovereign debt policy in a small open economy where the government cannot commit to policy and seeks to insure a risk averse domestic constituency. The expected tax on capital is shown to vary with the state of the economy, generating cyclicality in investment and debt in an environment where the first best capital stock is a constant. The government's lack of commitment induces a negative correlation between investment and the stock of government debt, a "debt overhang'' effect. If the government discounts the future at a rate higher than the market, then capital oscillates indefinitely at a level strictly below the first best. Debt relief is never Pareto improving and cannot affect the long-run level of investment. Further, restricting the government to a balanced budget can eliminate the cyclical distortion of investment.