Miracle-dz/UniFAR-FTUs huggingface dataset:
An Empirical Study on Real Bug Fixes

Software bugs can cause significant financial loss and even the loss of human lives. To reduce such loss, developers devote substantial efforts to fixing bugs, which generally requires much expertise and experience. Various approaches have been proposed to aid debugging. An interesting recent research direction is automatic program repair, which achieves promising results, and attracts much academic and industrial attention. However, people also cast doubt on the effectiveness and promise of this direction. A key criticism is to what extent such approaches can fix real bugs. As only research prototypes for these approaches are available, it is infeasible to address the criticism by evaluating them directly on real bugs. Instead, in this paper, we design and develop BUGSTAT, a tool that extracts and analyzes bug fixes. With BUGSTAT's support, we conduct an empirical study on more than 9,000 real-world bug fixes from six popular Java projects. Comparing the nature of manual fixes with automatic program repair, we distill 15 findings, which are further summarized into four insights on the two key ingredients of automatic program repair: fault localization and faulty code fix. In addition, we provide indirect evidence on the size of the search space to fix real bugs and find that bugs may also reside in non-source files. Our results provide useful guidance and insights for improving the state-of-the-art of automatic program repair.
Characterizing and Optimizing Cellular Network Performance During Crowded Events

During crowded events, cellular networks face voice and data traffic volumes that are often orders of magnitude higher than what they face during routine days. Despite the use of portable base stations for temporarily increasing communication capacity and free Wi-Fi access points for offloading Internet traffic from cellular base stations, crowded events still present significant challenges for cellular network operators looking to reduce dropped call events and improve Internet speeds. For an effective cellular network design, management, and optimization, it is crucial to understand how cellular network performance degrades during crowded events, what causes this degradation, and how practical mitigation schemes would perform in real-life crowded events. This paper makes a first step toward this end by characterizing the operational performance of a tier-1 cellular network in the U.S. during two high-profile crowded events in 2012. We illustrate how the changes in population distribution, user behavior, and application workload during crowded events result in significant voice and data performance degradation, including more than two orders of magnitude increase in connection failures. Our findings suggest two mechanisms that can improve performance without resorting to costly infrastructure changes: radio resource allocation tuning and opportunistic connection sharing. Using trace-driven simulations, we show that more aggressive release of radio resources via 1–2 s shorter radio resource control timeouts as compared with routine days helps to achieve better tradeoff between wasted radio resources, energy consumption, and delay during crowded events, and opportunistic connection sharing can reduce connection failures by 95% when employed by a small number of devices in each cell sector.
The HIVdb System for HIV-1 Genotypic Resistance Interpretation

The Stanford HIV Drug Resistance Database hosts a freely available online genotypic resistance interpretation system called HIVdb to help clinicians and laboratories interpret HIV-1 genotypic resistance tests. These tests are designed to assess susceptibility to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTI and NNRTI), protease inhibitors and integrase inhibitors. The HIVdb genotypic resistance interpretation system output consists of (1) a list of penalty scores for each antiretroviral (ARV) resistance mutation in a submitted sequence, (2) estimates of decreased NRTI, NNRTI, protease and integrase inhibitor susceptibility, and (3) comments about each ARV resistance mutation in the submitted sequence. The application’s strengths are its convenience for submitting sequences, its quality control analysis, its transparency and its extensive comments. The Sierra Web service is an extension that enables laboratories analyzing many sequences to individualize the format of their results. The algorithm specification interface compiler makes it possible for HIVdb to provide results using a variety of different HIV-1 genotypic resistance interpretation algorithms.
Dose gradient impact on equivalent dose at 2 Gy for high dose rate interstitial brachytherapy

Purpose To evaluate a new calculation model estimating the equivalent dose at 2 Gy (EQD2) taking into account dose gradient in high dose rate interstitial brachytherapy (HDRIB). Material and methods Forty dose-volume histograms (DVHs) of breast (20 pts) and prostate (20 pts) cancer dose distributions were reviewed. Physical prescribed doses (PPD) were 34 Gy (10f/5d) and 18 Gy (6f/2d) for breast (partial irradiation protocol) and prostate (boost after external irradiation) treatment, respectively. For each DVH, clinical target volume (CTV), V100, V150, V200, D90 and D100 were determined. Based on DVH segmentation, elementary doses (d) delivered to elementary volumes were determined, then multiplied by C (% of CTV receiving d). According to the linear quadratic model, EQD2 was calculated for different α/β ratios. Results For breast implant, median EQD2 (α/β = 4) was 42 Gy and 76 Gy (66-85) without and with dose gradient consideration, respectively. For prostate implant, median EQD2 (α/β = 1.5) was 39 Gy and 98 Gy (90-103) whether dose gradient was not or was taken into account, respectively. Conclusions This study pointed out that for brachytherapy, EQD2 calculation must take into account the dose gradient. Because this model is a mathematical one, it has to be cautiously applied. Nevertheless, it appears as a useful tool for EQD2 comparison between the same PPD delivered through EBRT or brachytherapy regarding trial result interpretation.
Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification

MOTIVATION In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. RESULTS The method was shown to properly account for stratification under various simulated scenari presenting population and/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM. AVAILABILITY The software GLASCOW can be freely downloaded from www.giga. ulg.ac. be/jcms/prod_381171/software. CONTACT francois.guillaume@jouy.inra. fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Congestion Control in Intelligent Networks for Real Time Performance and Profit Optimisation

Current developments in technologies and markets stress the importance of exible and robust performance optimisation and congestion control. In intelligent networks, congestion control has traditionally taken a purely technical view and focused on pro- tecting individual nodes from harmful overloads. We take a profit oriented, network wide view and develop a congestion control mechanism to ensure real time performance under profit maximisation. Numerical studies in a simulator show that the proposed mechanism is robust and, in particular in overloaded states, provides a substantial improvement in comparison to conventional load control mechanisms.
Nitrogen metabolism and urinary excretion of purines in goat kids

1. In Expt 1 three male goat kids of the Swedish Landrace breed were bottle-fed on isoenergetic liquid diets composed of goat’s milk alone or substituted with 200, 400, 600 and 800 ml of a nitrogen-free liqud diet/l. The goat kids were 3 weeks old at the start of the experiment and weighed on average 5.3 (SD 0.22) kg. The experiment lasted for 45 d divided into nine 5 d periods. The goat kids were kept individually in metabolism cages, and faeces and urine were collected daily. 2. In Expt 1 there was a significant (P < 0.001) relation between N intake and N retention, with an estimated (extrapolation) basal N excretion of 21 1 mg N/kg metabolic live weight (W075). While the creatinine excretion remained fairly constant (19.9 mg/Wo75), there was a tendency for both the allantoin and uric acid excretions to change with N intakes. Hypoxanthine showed no consistent excretion pattern, and xanthine could not be detected. 3. In Expt 2 three male goat kids of the Swedish Landrace breed were used to study the effect of level of intake on N and purine metabolism. The first experimental period (period 1) started at 2 weeks of age (5.5 kg live weight) and the second experimental period (period 2) at 9 weeks of age (9.8 kg live weight). The goat kids were bottlefed on goat milk at intended intakes of 400,600,800 and 1000 kJ gross energy/kg W075. Each treatment was given for 7 d with adaptation for 3 d and collections for 4 d. 4. In Expt 2 there were significant (P < 0.001) increases in both live weight and N retention when level of intake was increased. With increasing N intakes both total N and urea-N excretions increased significantly (P < 005). The proportions of urea-N and ammonia-N were fairly constant within periods, and were on average respectively 0.81 and 0.059 in period I and 0.84 and 0.068 in period 2. There was no significant effect of treatment on the urinary excretion of allantoin, hypoxanthine, xanthine and creatinine. In period 2 uric acid excretion was significantly (P < 0.01) affected by the treatments. 5. From the presented findings it is concluded that the endogenous urinary excretion of purine derivatives in a young growing ruminant was only marginally affected by large variations in protein supply, and also by the level of intake of milk.
The Cost Channel in a New Keynesian Model: Evidence and Implications

In the standard new Keynesian framework, an optimizing policy maker does not face at rade-off between stabilizing the gap between actual output and output under flexible prices and stabilizing the inflation rate. An ad hoc, exogenous cost-push shock is typically added to the inflation equation to generate a meaningful policy problem. In this paper, we show that a cost-push shock arises endogenously when a cost channel for monetary policy is introduced into the new Keynesian model. A cost channel arises when firms’ marginal cost depends directly on the nominal rate of interest. Besides providing additional empirical evidence for a cost channel, we explore its implications for monetary policy trade-offs, the objectives of monetary policy, and the effects of shocks on the economy under optimal discretionary and optimal commitment policies. We show that the presence of a cost channel alters the optimal policy problem in important ways. For example, both the output gap and inflation are allowed to fluctuate in response to productivity and fiscal shocks under optimal monetary policy.
A survey of Wireless Sensor Network technologies: research trends and middleware’s role

Wireless Sensor Networks (WSNs) provide a new paradigm for sensing and disseminating information from various environments, with the potential to serve many and diverse applications. Current WSNs typically communicate directly with a centralized controller or satellite. On the other hand, a smart WSN consists of a number of sensors spread across a geographical area; each sensor has wireless communication capability and sufficient intelligence for signal processing and networking of the data. The structure of WSNs are tightly application-dependent, and many services are also dependent on application semantics (e.g. application-specific data processing combined with data routing). Thus, there is no single typical WSN application, and dependency on applications is higher than in traditional distributed applications. The application/middleware layer must provide functions that create effective new capabilities for efficient extraction, manipulation, transport, and representation of information derived from sensor data. In this paper, we report recent trends in wireless sensor network research including an overview of the various categories of WSN, a survey of WSN technologies and a discussion of existing research prototypes and industry applications. We focus on middleware technology, and describe details of some existing research prototypes, then address challenges and future perspectives on the middleware. This study highlights that middleware needs to provide a common interface for various functional components of WSN: detection and data collection, signal processing, data aggregation, and notification. By integrating sensing, signal processing, and communication functions, a WSN provides a natural platform for hierarchical information processing.
Vascular phyllotaxis transition and an evolutionary mechanism of phyllotaxis

Leaves of vascular plants are arranged regularly around stems, a phe- nomenon known as phyllotaxis. A constant angle between two successive leaves is called divergence angle. On the one side, the divergence angle �0 of an initial pattern of leaf primordia at a shoot apex is most commonly an irrational number of about 137.5 degrees, called limit divergence. On the other side, the divergenceof a final pattern of leaf traces in the vascu- lar system of a mature stem is expressed in terms of a sequence of rational 21 , called phyllotactic fractions. The mathematical relationship between the initial divergence �0, the final divergence �, and the number of internodes traversed by the leaf traces nc is investigated by means of a theoretical model of vascular phyllotaxis. It is shown that continuous changes of the trace length nc induce transitions between the fractional or- ders in the vascular structure. The vascular phyllotaxis transition suggests an evolutionary mechanism for the phenomenon of phyllotaxis. To provide supporting evidence for the model and mechanism, available experimental re- sults for fossil remains of Lepidodendron and the vascular structure of Linum and Populus are analyzed with the model.
The changing nature of student engagement during a digital learning task

The construct of student engagement has been useful in understanding student’s motivation in digital learning environments where they are required to show increased autonomy and independence in learning. Increasing clarity around this construct has allowed researchers to more accurately describe the nature of student engagement and the context in which it is being investigated. At a task-level, psychological states of engagement have been shown to be beneficial for student’s positive learning experience, and performance. Despite this, we still lack knowledge of how these engaged states unfold or sustain during a learning task. In this paper we report on a qualitative study that investigated undergraduate student’s experiences of psychological states of engagement in a digital learning task. Findings revealed that the three dimensions of engagement – cognition, affect, and behaviour – changed in intensity, with the subject experiencing both times of engagement and of not being engaged through the course of a digital learning task.
Research Ethics and Intellectual Disability: Broadening the Debates

This article examines the ethical issues surrounding the inclusion of people with intellectual disabilities as research subjects. It explores subject selection, competence, risk and benefits, and authority through three tensions that emerge when considering these concepts in the context of the Disability Rights Movement and critical disability scholarship. These tensions are defined as the double dangers of inclusion and exclusion; the challenges of defining competence and risk in terms of individuals vs. groups; and the conflicts that arise when pursuing the dual goals of amelioration and elimination of disabilities. Though these tensions are not resolved, they underscore the importance of researchers engaging with critical disability perspectives in order to navigate these complex ethical questions.
An internet census taken by an illegal botnet: a qualitative assessment of published measurements

On March 17, 2013, an Internet census data set and an accompanying report were released by an anonymous author or group of authors. It created an immediate media buzz, mainly because of the unorthodox and unethical data collection methodology (i.e., exploiting default passwords to form the Carna botnet), but also because of the alleged unprecedented large scale of this census (even though legitimate census studies of similar and even larger sizes have been performed in the past). Given the unknown source of this released data set, little is known about it. For example, can it be ruled out that the data is faked? Or if it is indeed real, what is the quality of the released data? The purpose of this paper is to shed light on these and related questions and put the contributions of this anonymous Internet census study into perspective. Indeed, our findings suggest that the released data set is real and not faked, but that the measurements suffer from a number of methodological flaws and also lack adequate meta-data information. As a result, we have not been able to verify several claims that the anonymous author(s) made in the published report. In the process, we use this study as an educational example for illustrating how to deal with a large data set of unknown quality, hint at pitfalls in Internet-scale measurement studies, and discuss ethical considerations concerning third-party use of this released data set for publications.
Global Phylogeography of the Widely Introduced North West Pacific Ascidian Styela clava

The solitary ascidian Styela clava Herdman, 1882 is considered to be native to Japan, Korea, northern China and the Russian Federation in the NW Pacific, but it has spread globally over the last 80 years and is now established as an introduced species on the east and west coasts of North America, Europe, Australia and New Zealand. In eastern Canada it reaches sufficient density to be a serious pest to aquaculture concerns. We sequenced a fragment of the cytochrome oxidase subunit I mitochondrial gene (COI) from a total of 554 individuals to examine the genetic relationships of 20 S. clava populations sampled throughout the introduced and native ranges, in order to investigate invasive population characteristics. The data presented here show a moderate level of genetic diversity throughout the northern hemisphere. The southern hemisphere (particularly New Zealand) displays a greater amount of haplotype and nucleotide diversity in comparison. This species, like many other invasive species, shows a range of genetic diversities among introduced populations independent of the age of incursion. The successful establishment of this species appears to be associated with multiple incursions in many locations, while other locations appear to have experienced rapid expansion from a potentially small population with reduced genetic diversity. These contrasting patterns create difficulties when attempting to manage and mitigate a species that continues to spread among ports and marinas around the world.
An Exploration into the Perception of Music Interventions in Hospitals amongst Healthcare Professionals

In order to raise awareness of how music can be used beneficially in hospitals, it is necessary to further understand the perception of music interventions amongst those working in this setting. A mixed methods approach was employed. Thirty-one healthcare professionals completed an online survey or interview asking how much live music existed in hospitals, their knowledge of music interventions, and expected effects. Attitudes towards introducing live music, where this would be appropriate, and willingness to learn more were also investigated. Four participants also took part in a follow up study. Live music was found to be uncommon, with no standardised internal system to enable it. Participants had little knowledge of research surrounding the use of music in medical settings. However, only 36% of this sample of healthcare professionals were willing to learn more. Observing a music session had a significant effect on the perception of the efficacy of music. Having observed a live session, healthcare professionals thought it would have a long term benefit to patients. There was interest in increasing the amount of live music on the ward and integrating a music therapist into the healthcare team. Therefore, this study highlights the importance of increasing awareness of music interventions amongst healthcare professionals, through observing music sessions and presenting evidence of the benefits of these during training programmes and Continued Professional Development (CPD) in order to create a more positive perception of music within hospitals.
Conditional gene ablation of Stat3 reveals differential signaling requirements for survival of motoneurons during development and after nerve injury in the adult

Members of the ciliary neurotrophic factor (CNTF)/leukemia inhibitory factor (LIF)/cardiotrophin gene family are potent survival factors for embryonic and lesioned motoneurons. These factors act via receptor complexes involving gp130 and LIFR-β and ligand binding leads to activation of various signaling pathways, including phosphorylation of Stat3. The role of Stat3 in neuronal survival was investigated in mice by Cre-mediated gene ablation in motoneurons. Cre is expressed under the neurofilament light chain (NF-L) promoter, starting around E12 when these neurons become dependent on neurotrophic support. Loss of motoneurons during the embryonic period of naturally occurring cell death is not enhanced in NF-L–Cre; Stat3flox/KO mice although motoneurons isolated from these mice need higher concentrations of CNTF for maximal survival in culture. In contrast, motoneuron survival is significantly reduced after facial nerve lesion in the adult. These neurons, however, can be rescued by the addition of neurotrophic factors, including CNTF. Stat3 is essential for upregulation of Reg-2 and Bcl-xl expression in lesioned motoneurons. Our data show that Stat3 activation plays an essential role for motoneuron survival after nerve lesion in postnatal life but not during embryonic development, indicating that signaling requirements for motoneuron survival change during maturation.
Determinants of young vacationers’ recycling and conservation behavior when traveling

We investigated key cognitive determinants that predict young vacationers’ recycling and water/energy/local resources conservation intention when traveling. We also examined the role of gender in this intention formation, used structural equation modeling, and tested for metric invariance. Results showed that environmental values, concern, and awareness significantly contribute to the generation of young vacationers’ intention to engage in recycling and to conserve water, energy, and local resources at a destination. In addition, environmental values had the strongest relationship with recycling and conservation intention, and gender significantly moderated the impact of environmental awareness on their intention. Overall, the findings inform researchers and practitioners about young vacationers’ environmentally sustainable tourism behavior.