Miracle-dz/UniFAR-FTUs huggingface dataset:
Easing software evolution: change-data and domain-driven approach

Quick and quality changes to a software application to add new feature or change existing feature, depend largely on the code architecture and its atomic responsibilities. As the application evolves, the code undergoes modifications and drifts away from its original design, leading to anomalies in the code structure and non-atomic, non-modular architecture. In this paper, we propose a defect and change-data driven approach to analyze the application, and determine the modules that need re-factoring. Improving the code structure by leveraging the domain knowledge is the key. We validate the approach by applying to an existing financial system. The preliminary analysis for the case-study reveals that the approach creates meaningful structure from the legacy code, which enables the developers to quickly identify the code that implements a given functionality.
The role of iNOS in alcohol‐dependent hepatotoxicity and mitochondrial dysfunction in mice

Nitric oxide (NO) is now known to control both mitochondrial respiration and organelle biogenesis. Under conditions of ethanol‐dependent hepatic dysfunction, steatosis is increased, and this is associated with increased expression of inducible nitric oxide synthase (iNOS). We have previously shown that after chronic exposure to ethanol, the sensitivity of mitochondrial respiration to inhibition by NO is enhanced, and we have proposed that this contributes to ethanol‐dependent hypoxia. This study examines the role of iNOS in controlling the NO‐dependent modification of mitochondrial function. Mitochondria were isolated from the livers of both wild‐type (WT) and iNOS knockout (iNOS−/−) mice that were fed an isocaloric ethanol‐containing diet for a period of 5 weeks. All animals that consumed ethanol showed some evidence of fatty liver; however, this was to a lesser extent in the iNOS−/− mice compared to controls. At this early stage in ethanol‐dependent hepatic dysfunction, infiltration of inflammatory cells and the formation of nitrated proteins was also decreased in response to ethanol feeding in the iNOS−/− animals. Mitochondria isolated from wild‐type ethanol‐fed mice showed a significant decrease in respiratory control ratio and an increased sensitivity to NO‐dependent inhibition of respiration relative to their pair‐fed controls. In contrast, liver mitochondria isolated from iNOS−/− mice fed ethanol showed no change in the sensitivity to NO‐dependent inhibition of respiration. In conclusion, the hepatic response to chronic alcohol‐dependent cytotoxicity involves a change in mitochondrial function dependent on the induction of iNOS. (HEPATOLOGY 2004;40:565–573.)
IEEE 802.11e wireless LAN - resource sharing with contention based medium access

Controlling medium access priorities in wireless networks is difficult when multiple radio stations operate according to the popular IEEE 802.11 contention-based protocol. Although the new standard 802.lie defines enhancements for controlling priorities in this distributed medium access control protocol, it does not provide algorithms for the calculation of the achievable throughput per station, when different stations operate with the different priorities. Such an algorithm is discussed in this paper. The evaluation by means of simulation indicates that the algorithm approximates the achievable throughput in many different scenarios.
Partial Information , Knowledge , and Uniform Strategies

We present two versions of alternating-time temporal logics with uniform strategies, interpreted in a novel way on transition systems for modelling situations in which agents with partial information interact to determine the way the system updates. The logic uATL allows us to model what properties agents can enforce when they act according to strategies based on their knowledge, but we show that agents’ knowledge cannot always be modelled based on the state of the system, so we also introduce the history based logic euATL which is stronger than uATL and allows us to model agents’ knowledge based on the history of a system’s execution. Apart from the usual memoryless strategies, we distinguish state-based memory, where agents recall the history of previous states, from perfect recall, where agents also recall their actions. We show that this makes a difference. Our logics both include three strategic operators for groups, representing the case where all the agents in the group cooperate actively, but do not share their knowledge, the case where some agents in the group may be passive, and the case where all the agents in the group share their knowledge. We include a detailed comparison to the literature on the subject.
Can sugarcoated fingerprints be used to identify lurking viruses?

Comparative proteomics is increasingly used to detect biomarkers and therapeutic targets that differ between healthy and diseased populations; however, differences in posttranslational modifications have received less attention. In this issue, Yang et al. (Proteomics 2016, 16, 1872–1880) present data indicating that a glycoproteomics approach can detect N‐glycosylated membrane protein differences between non‐HIV‐infected and latently infected human CD4+ T‐cell lines, identifying 172 proteins differentially expressed by these cells. Latently infected CD4+ T cells are thought to represent the major barrier to eventual HIV cure, but do not express detectable levels of viral protein and have not been shown to express biomarkers that can distinguish them from the vastly more abundant uninfected CD4+ T‐cell population. The findings of Yang et al. suggest that glycoproteomic analyses may have untapped potential to identify novel biomarkers and therapeutic targets in cell populations not readily distinguishable be standard proteomic analyses.
A program for neuropsychological investigation of deep brain stimulation (PNIDBS) in movement disorder patients: development, feasibility, and preliminary data.

OBJECTIVE This technical report and feasibility study propose a standardized method for collecting neuropsychological data in patients undergoing the deep brain stimulation (DBS) procedure. BACKGROUND Programs for standardizing motor data collected in studies investigating surgical therapies for Parkinson disease are already widely used (e.g., Core Assessment Program for Intracerebral Transplantations). The development and rationale for the proposed Program for Neuropsychological Investigation of Deep Brain Stimulation (PNIDBS) are outlined, and support for the feasibility of these methodologies is provided via preliminary data. METHOD The PNIDBS includes a core battery of neuropsychological tests that assesses a wide range of cognitive functions (attention, language, visuospatial, memory, and executive) as well as depression. Using the PNIDBS, three Parkinson disease and two dystonia patients were evaluated at baseline and after surgery, once with stimulation off and once with stimulation on. RESULTS Patients with severe motor disabilities were able to complete the PNIDBS. These preliminary data suggest that the DBS procedure as a whole had a minimal impact on cognitive functioning in most patients studied. There was also some evidence that the one patient who showed cognitive decline after the DBS procedure had demographic and clinical characteristics that may have put him at risk for this decline. CONCLUSIONS The procedures in the PNIDBS were systematically developed and are feasible to execute. The relatively brief core battery has multiple versions and can be supplemented to meet individual investigator needs. By evaluating the components of the DBS procedure (electrode placement and stimulation), the PNIDBS can address clinical questions regarding the cognitive effects of the DBS procedure as well as investigate basic scientific issues regarding how different cognitive functions are affected when subcortical-prefrontal circuits are manipulated by the DBS procedure.
Combining NLP And Semantics For Mining Software Technologies From Research Publications

The natural language processing (NLP) community has developed a variety of methods for extracting and disambiguating information from research publications. However, they usually focus only on standard research entities such as authors, affiliations, venues, references and keywords. We propose a novel approach, which combines NLP and semantic technologies for generating from the text of research publications an OWL ontology describing software technologies used or introduced by researchers, such as applications, systems, frameworks, programming languages, and formats. The method was tested on a sample of 300 publications in the Semantic Web field, yielding promising results.
Studies on vaccination against bacillary dysentery. 2. Safety tests and reactogenicity studies on a live dysentery vaccine intended for use in field trials.

In view of the encouraging results obtained in active mouse protection experiments, several batches of live oral vaccine prepared from streptomycin-dependent Shigella flexneri were tested in vitro for any indication of reversion to streptomycin-independence and in man for their reactogenicity.The in vitro tests provided no evidence of reversion.In man, major reactions were observed in only 1.4% of volunteers, all those so affected being heterotypic Shigella carriers in whom clinical exacerbation was induced. Both the intensity and the frequency of the minor reactions observed in other volunteers depended on the size of the vaccine dose administered. The dosage was also directly related to the duration of shedding of the vaccinal strain in the faeces and to the clinical exacerbation shown by heterotypic carriers.Both the phagocytic activity and the serum antibody titres were equally low before and after vaccination, but post-vaccination copro-antibody titres were 8-32 times higher with homologous than with heterologous antigens.
Extension of the two-microphone noise reduction method for binaural hearing aids

Noise reduction is one of the most crucial functions, if not the most, in hearing aids, as hearing impaired people have great difficulty in understanding speech in noisy environments. In the past, we proposed a two-microphone noise reduction system with one-channel output. In this paper, we further extend this previously proposed noise reduction method for hearing aids application by applying the same noise reduction mechanism to the two channels, producing the binaural output signals which are expected to preserve the binaural benefits giving birth to listenerpsilas own "binaural gain". The experimental results in various acoustic environments demonstrate its superiority in suppressing interfering signals in comparison of traditional noise reduction algorithms, followed by the discussion on its ability in preserving the ability of sound source localization.
Heavy Genealogy: Mapping the Currents, Contraflows and Conflicts of the Emergent Field of Metal Studies, 1978-2010

What is metal studies? How can we define and characterize it? How has it emerged as a body of academic enquiry? What are its dominant disciplinary strands, theoretical concepts and preferred methodologies? Which studies have claimed most attention, defined the goals of scholarship, typical research strategies and values? How has the claim for the legitimacy or symbolic value of metal scholarship been achieved (if it has): over time and through gradual acceptance or through conflict and contestation? How can this process of formation, or strategy of legitimation, be mapped, examined and interrogated and which methods of historical, institutional and cultural analysis are best suited to this task? Working with the most complete bibliography to date of published research on heavy metal, music and culture (the MSBD), this article employs Foucault’s archaeological “method” to examine the institutional, cultural and political contexts and conflicts that inform the genealogy of this scholarship. Such analysis reveals a formative, largely negative account of heavy metal to be found in the “sociology of rock”; a large volume of psychology work, examining heavy metal music preference as an indicator of youth risk, deviance and delinquency; sociological work on youth and deviancy critical of the values of this research and its links to social policy and politics; culminating in the work of Weinstein and Walser, who advocate a perspective sympathetic to the values of heavy metal fans themselves. Following Bourdieu, I interpret such symbolic strategies as claims for expertise within the academic field that are high or low in symbolic capital to the extent they can attain disciplinary autonomy. I then go on to examine the most recent strands of research, within cultural studies and ethnomusicology, concerned with the global metal music diaspora, and consider to what extent such work is constitutive of a coherent subfield of metal studies that can be distinguished from earlier work and what the implications of this might be.
The PWM phase-shifted plus feed-forward control of the boost converter applied in supercapacitor energy storage system

High-power boost converter is an important part in supercapacitor energy storage system. The decline of supercapacitor's terminal voltage should be considered when design the converter. The advantages and disadvantages of the asymmetry half-bridge bidirectional converter are discussed. A novel PWM phase-shift plus feed-forward control method was proposed, which uses input voltage feed-forward to control duty cycle and output voltage feed-back to control phase shift angle. This control strategy could reduce the peak current of the transformer's leakage inductance, promote the converter's efficiency and ensure the switches' ZVS. The converter's operation is analyzed and the average model and small signal model are built. The control system was designed. The control strategy was verified by simulation.
Characterization of the heat shock response in Brucella abortus and isolation of the genes encoding the GroE heat shock proteins

In an effort to define the heat shock response in the bovine intracellular pathogen Brucella abortus, a rough variant lacking extensive lipopolysaccharide was pulse-labeled with [35S]methionine following exposure to elevated temperatures. The major heat shock proteins observed following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography migrate at 70, 62, 18, and 10 kDa. The maximum response was observed between 42 and 46 degrees C and within 2 to 3 h of the shif in temperature and varied slightly for the different proteins. Accumulation of the 62-kDa heat shock protein (62-kDa Hsp) was observed to continue for up to 5 h following the shift in temperature. In an effort to better define the heat shock response and its potential relationship with protective immunity, genes encoding the major heat shock proteins were isolated from recombinant libraries constructed from B. abortus S19 and S2308 and sequenced. The 62-kDa Hsp shares more than 60% amino acid homology with members of the GroEL family and is immunoprecipitated with polyclonal antibodies to Escherichia coli GroEL and monoclonal antibodies to mycobacterial Hsp 65. Western blot (immunoblot) analysis with pooled sera from vaccinated and infected cattle revealed that the 62-kDa Hsp is a predominantly recognized antigen. The roles of these gene products during environmental stress and in protective immunity against brucellosis are under investigation.
Raising Girlyboys: A Parent's Perspective

An increasing number of children are expressing themselves in gender-expansive or gender-variant ways. A subgroup of those children are girlyboys: boys who accept themselves as boys but cross culturally defined gender lines in their attitudes, behaviors, and desires. Using clinical material, written accounts, and personal observations, this paper investigates the experience of parents raising these boys. Facilitative parenting is differentiated from obstructive parenting within the rubric that gender-fluid outcome is healthy and parents can have influence in this arena. The experience of parents with their girlyboys is also offered as a window through which to view a young boy's protogay development. Analysis is made of the ways in which the psychoanalytic lens has traditionally blurred or distorted our thinking about parents' roles in gender-variant children's development. An alternative view of parenting, informed by the work of post-modern psychoanalytic gender theorists, is proffered, with an end to reinforcing healthy gender-fluid development.
Pharmacokinetics and Pharmacodynamics of Zoledronic Acid in Cancer Patients with Bone Metastases

The pharmacokinetics, pharmacodynamics, and safety of zoledronic acid (Zometa®), a new‐generation bisphosphonate, were evaluated in 36 patients with cancer and bone metastases. Zoledronic acid (by specific radioimmunoassay) and markers of bone turnover were determined in plasma and urine after three consecutive infusions (qx28 days) of 4 mg/5 min (n = 5), 4 mg/15 min (n = 7), 8 mg/15 min (n = 12), or 16 mg/15 min (n = 12). Zoledronic plasma disposition was multiphasic, with half‐lives of 0.2 and 1.4 hours representing an early, rapid decline of concentrations from the end‐of‐infusion Cmax to < 1% of Cmax at 24 hours postdose and half‐lives of 39 and 4526 hours describing subsequent phases of very low concentrations between days 2 and 28 postdose. AUC0‐24h and Cmax were dose proportional and showed little accumulation (AUC0_24h ratio between the third and first dose was 1.28). Prolonging the infusion from 5 to 15 minutes lowered Cmax by 34%, with no effect on AUC0‐24h. Urinary excretion of zoledronic acid was independent of infusion duration, dose, or number of doses, showing average Ae0‐24h of 38% ± 13%, 41% ± 14%, and 37% ± 17%, respectively, after 4, 8, and 16 mg. Only trace amounts of drug were detectable in post 24‐hour urines. Renal clearance (Ae0‐24h)/(AUC0‐24h) was on average 69 ± 28, 81 ± 40, and 54 ± 34 ml/min after 4, 8, and 16 mg, respectively, and showed a moderate correlation (r = 0.5; p < 0.001) with creatinine clearance, which was 84 ± 23, 82 ± 25, and 80 ± 40 ml/min for the dose groups at baseline. Adverse events and changes from baseline in vital signs and clinical laboratory variables showed no relationship in terms of type, frequency, or severity with zoledronic acid dose or pharmacokinetic parameters. Zoledronic acid produced significant declines from baseline in serum and/or creatinine‐corrected urine C‐telopeptide (by 74%), N‐telopeptide (69%), pyridinium cross‐links (19–33%), and calcium (62%), with an increasing trend (by 12%) in bone alkaline phosphatase. There was no relationship of the magnitude and duration of these changes with zoledronic acid dose, Ae0‐24j, AUC0‐24h, or Cmax. The antiresorptive effects were evident within 1 day postdose and were maintained over 28 days across all dose levels, supporting monthly dosing with 4 mg zoledronic acid.
Inhibition of DNA primase by nucleoside triphosphates and their arabinofuranosyl analogs.

DNA primase (EC 2.7.7.6) produces an RNA oligomer of approximately 10 bases, which is required by DNA polymerase alpha (EC 2.7.7.7) for the initiation of DNA synthesis. We partially purified DNA primase from acute lymphocytic leukemia cells from patients using several chromatography columns. Poly(dT) and poly(dC), but not poly(dA) or poly(dG), were good templates for ribonucleoside triphosphate (rNTP)-dependent DNA synthesis (i.e., DNA primase activity), and they were used in the study of the effect of natural and arabinofuranosyl nucleoside triphosphates on DNA primase activity. The Km for GTP in the poly(dC) primase assay was approximately 175 microM. All noncomplementary natural rNTPs and deoxyribonucleoside triphosphates (dNTPs) inhibited poly(dC) primase activity to a similar extent (Ki values of ATP and CTP were 610 and 517 microM, respectively). 1-beta-D-Arabinofuranosylcytosine 5'-triphosphate (araCTP) and 9-beta-D-arabinofuranosyladenine 5'-triphosphate (araATP) were more potent inhibitors of poly(dC) primase activity than were CTP and ATP (Ki values were approximately 125 microM). araCTP, araATP, CTP, and ATP inhibited DNA primase activity in a manner competitive with GTP. The concentration required to inhibit poly(dC) DNA primase activity by 50% was determined for a number of arabinofuranosyl nucleoside triphosphate analogs, and the relative potency of inhibition of DNA primase activity was as follows: rNTP = dNTP = 5-aza-dCTP less than ara-5-azaCTP = araTTP = araATP = araCTP less than 2-fluoro-araATP = 2'-azido-2'-deoxy araCTP less than 2'-fluoro-araTTP = 2'-fluoro-5-iodo-araCTP = 2'-fluoro-5-methyl-araCTP. In the poly(dT) primase assay ATP did not follow classic Michaelis-Menten kinetics (ATP exhibited positive cooperativity with a Hill coefficient of 2.0). However, this assay was very sensitive to araCTP (apparent Ki of 25 microM). In summary, these experiments suggested that DNA primase is controlled by the levels of ribonucleoside triphosphates, and that the perturbation of these pools by any agent could lead to the inhibition of DNA primase and thereby inhibit DNA synthesis. Furthermore, aranucleoside triphosphate analogs directly inhibited DNA primase, and it is possible that this effect may contribute to the cytotoxicity of these compounds.
Beat Keeping in a Sea Lion As Coupled Oscillation: Implications for Comparative Understanding of Human Rhythm

Human capacity for entraining movement to external rhythms—i.e., beat keeping—is ubiquitous, but its evolutionary history and neural underpinnings remain a mystery. Recent findings of entrainment to simple and complex rhythms in non-human animals pave the way for a novel comparative approach to assess the origins and mechanisms of rhythmic behavior. The most reliable non-human beat keeper to date is a California sea lion, Ronan, who was trained to match head movements to isochronous repeating stimuli and showed spontaneous generalization of this ability to novel tempos and to the complex rhythms of music. Does Ronan's performance rely on the same neural mechanisms as human rhythmic behavior? In the current study, we presented Ronan with simple rhythmic stimuli at novel tempos. On some trials, we introduced “perturbations,” altering either tempo or phase in the middle of a presentation. Ronan quickly adjusted her behavior following all perturbations, recovering her consistent phase and tempo relationships to the stimulus within a few beats. Ronan's performance was consistent with predictions of mathematical models describing coupled oscillation: a model relying solely on phase coupling strongly matched her behavior, and the model was further improved with the addition of period coupling. These findings are the clearest evidence yet for parity in human and non-human beat keeping and support the view that the human ability to perceive and move in time to rhythm may be rooted in broadly conserved neural mechanisms.