Miracle-dz/UniFAR-FTUs huggingface dataset:
A learning-to-rank based fault localization approach using likely invariants

Debugging is a costly process that consumes much of developer time and energy. To help reduce debugging effort, many studies have proposed various fault localization approaches. These approaches take as input a set of test cases (some failing, some passing) and produce a ranked list of program elements that are likely to be the root cause of the failures (i.e., failing test cases). In this work, we propose Savant, a new fault localization approach that employs a learning-to-rank strategy, using likely invariant diffs and suspiciousness scores as features, to rank methods based on their likelihood to be a root cause of a failure. Savant has four steps: method clustering & test case selection, invariant mining, feature extraction, and method ranking. At the end of these four steps, Savant produces a short ranked list of potentially buggy methods. We have evaluated Savant on 357 real-life bugs from 5 programs from the Defects4J benchmark. Out of these bugs, averaging over 100 repeated trials with different seeds to randomly break ties, we find that on average Savant can identify correct buggy methods for 63.03, 101.72, and 122 bugs at top 1, 3, and 5 positions in the ranked lists that Savant produces. We have compared Savant against several state-of-the-art fault localization baselines that work on program spectra. We show that Savant can successfully locate 57.73%, 56.69%, and 43.13% more bugs at top 1, top 3, and top 5 positions than the best performing baseline, respectively.
p21CDKN1A Regulates the Binding of Poly(ADP-Ribose) Polymerase-1 to DNA Repair Intermediates

The cell cycle inhibitor p21CDKN1A was previously found to interact directly with DNA nick-sensor poly(ADP-ribose) polymerase-1 (PARP-1) and to promote base excision repair (BER). However, the molecular mechanism responsible for this BER-related association of p21 with PARP-1 remains to be clarified. In this study we investigate the capability of p21 to influence PARP-1 binding to DNA repair intermediates in a reconstituted BER system in vitro. Using model photoreactive BER substrates containing single-strand breaks, we found that full-length recombinant GST-tagged p21 but not a C-terminal domain truncated form of p21 was able to stimulate the PARP-1 binding to BER intermediates with no significant influence on the catalytic activity of PARP-1. In addition, we investigate whether the activation of PARP-1 through poly(ADP-ribose) (PAR) synthesis, is required for its interaction with p21. We have found that in human fibroblasts and in HeLa cells treated with the DNA alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), the interaction of p21 with PARP-1 was greatly dependent on PAR synthesis. In fact, an anti-PAR antibody was able to co-immunoprecipitate p21 and PARP-1 from extracts of MNNG-treated cells, while blocking PAR synthesis with the PARP-1 inhibitor Olaparib, drastically reduced the amount of p21 co-immunoprecipitated by a PARP-1 antibody. Our results provide the first evidence that p21 can stimulate the binding of PARP-1 to DNA repair intermediates, and that this cooperation requires PAR synthesis.
Quality Features of Metal Matrix Composite Castings

In this paper it is stated, that a set of quality features of metal matrix composite castings diﬀers from the same set for castings of classic materials, although some features are common for both of these material groups. These features (pertaining to a set of quality characteristics of composite castings) have been named as speciﬁc, they have not been determined yet and a description of material quality should be performed (according to the qualitology) on a principle of description of quality characteristics of this product. Therefore, this set of features has been determined. It was proposed to add the following characteristics to the set of speciﬁc features of composite castings quality: matrix material, reinforcement material, binding between components and porosity of the composite casting. In this set a sub-set of quality characteristics of composite castings was also determined.
Break on through to the Other Side—Biophysics and Cell Biology Shed Light on Cell‐Penetrating Peptides

Cell‐penetrating peptides (CPPs) have become widely used vectors for the cellular import of molecules in basic and applied biomedical research. Despite the broad acceptance of these molecules as molecular carriers, the details of the mode of cellular internalization and membrane permeation remain elusive. Within the last two years endocytosis has been demonstrated to be a route of uptake shared by several CPPs. These findings had a significant impact on CPP research. State‐of‐the‐art cell biology is now required to advance the understanding of the intracellular fate of the CPP and cargo molecules. Owing to their presumed ability to cross lipid bilayers, CPPs also represent highly interesting objects of biophysical research. Numerous studies have investigated structure–activity relationships of CPPs with respect to their ability to bind to a lipid bilayer or to cross this barrier. Endocytosis route only relocates the membrane permeation from the cell surface to endocytic compartments. Therefore, biophysical experiments are key to a mechanistic molecular understanding of the cellular uptake of CPPs. However, biophysical investigations have to consider the molecular environment encountered by a peptide inside and outside a cell. In this contribution we will review biophysical and cell‐biology data obtained for several prominent CPPs. Furthermore, we will summarize recent findings on the cell‐penetrating characteristics of antimicrobial peptides and the antimicrobial properties of CPPs. Peptides of both groups have overlapping characteristics. Therefore, both fields may greatly benefit from each other. The review will conclude with a perspective of how biophysics and cell biology may synergize even more efficiently in the future.
Costs and Benefits of Routine Histopathological Examination of Hammertoe Specimens

Background: The purpose of this study was to evaluate the cost and benefit of routinely submitting hammertoe specimens for histopathological examination. We hypothesized that such examination rarely shows a new diagnosis and seldom alters postoperative care. Materials and Methods: Three hundred and fourteen proximal interphalangeal (PIP) joint and 37 extensor tendon specimens from 187 consecutive hammertoe correction surgeries were submitted by 2 surgeons for histopathological examination between January 2009 and December 2011. Each patient’s chart was reviewed to determine whether the histopathological examination revealed a diagnosis other than degenerative joint or degenerative tendon and whether subsequent patient management was altered. The total reimbursements for professional charges were calculated using the average reimbursement from common insurance providers for two Current Procedural Terminology (CPT) codes: 88304 (soft tissue examination) and 88311 (decalcification). Results: Almost all of the specimens were diagnosed as degenerative: 97.5% (307/314) of the PIP specimens and all (37/37) of the tendon specimens. Seven PIP specimens (2.2%, 7/314) from 5 patients (2.7%, 5/187) and no tendon specimens had other diagnoses. These diagnoses were rheumatoid arthritis (5/314, 1.6%), osteomyelitis (1/314, 0.3%), and pigmented villonodular synovitis (PVNS) (1/314, 0.3%). Only the PVNS was a new diagnosis. A total of $56,750 was spent to determine 1 new diagnosis. Conclusion: The routine submission of hammertoe specimens for pathological evaluation was not cost-efficient. Our analysis showed that new diagnoses were rarely found and patient management was not affected. Level of Evidence: Level IV, retrospective case series.
Helicobacter pylori eradication and l-dopa absorption in patients with PD and motor fluctuations

Objective: To investigate if Helicobacter pylori (HP) eradication could make an effective and long-lasting improvement in the pharmacokinetic and clinical response to l-dopa in patients with Parkinson disease (PD) and motor fluctuations. Methods: In a group of 34 HP-infected, motor-fluctuating patients with PD, the short-term (1-week) and long-term (3-month) beneficial effect of HP eradication (n = 17) was investigated in a double-blind fashion in comparison with a generic antioxidant treatment (n = 17), by means of pharmacokinetic, clinical, and gastrointestinal assessments. Results were compared with placebo treatment. Results: Differently from the antioxidant-treated patients, the HP-eradicated patients showed a significant increase of l-dopa absorption, which was coupled with a significant improvement of clinical disability and with a prolonged “on-time” duration, whereas gastritis/duodenitis scores significantly decreased in line with a better l-dopa pharmacokinetics. Conclusions: These data demonstrate a reversible Helicobacter pylori (HP)–induced interference with l-dopa clinical response related to the impaired drug absorption, probably due to active gastroduodenitis. Therefore, the authors suggest that HP eradication may improve the clinical status of infected patients with Parkinson disease and motor fluctuations by modifying l-dopa pharmacokinetics.
Elevated expression of protein regulator of cytokinesis 1, involved in the growth of breast cancer cells

To elucidate molecular mechanisms of mammary carcinogenesis and discover novel therapeutic targets for breast cancer, we previously carried out a genome‐wide expression profile analysis of 81 breast cancer cases by means of a combination of cDNA microarray and laser microbeam microdissection. Among the upregulated genes, we focused on the functional significance of protein regulator of cytokinesis 1 (PRC1) in the development of breast cancer. Western blot analysis using breast cancer cell lines revealed a significant increase in endogenous PRC1 levels in G2/M phase. Treatment of breast cancer cells with small interfering RNA against PRC1 effectively suppressed its expression and inhibited the growth of breast cancer cell lines T47D and HBC5. Furthermore, we found an interaction between PRC1 and kinesin family member 2C/mitotic centromere‐associated kinesin (KIF2C/MCAK) by coimmunoprecipitation and immunoblotting using COS‐7 cells, in which these molecules were introduced exogenously. These findings suggest the involvement of a PRC1–KIF2C/MCAK complex in breast tumorigenesis, and this complex should be a promising target for the development of novel treatments for breast cancer. (Cancer Sci 2007; 98: 174–181)
Are mangroves nursery habitat for transient fishes and decapods?

The term nursery implies a special place for juvenile nekton (fishes and decapod crustaceans) where density, survival, and growth of juveniles and movement to adult habitat are enhanced over those in adjoining juvenile habitat types. We reviewed recent literature concerning these four topics and conducted meta-analyses for density and survival data. Most studies of mangroves as nurseries have addressed only occurrence or density of fishes or decapods, have not used quantitative sampling methods, and have not compared alternate habitats. Comparison of nekton densities among alternate habitats suggests that, at times, lower densities may be typical of mangroves when compared to segrass, coral reef, marsh, and non-vegetated habitats. There is little direct consumption of mangrove detritus by nekton. C, N, and S isotope studies reveal little retention of mangrove production by higher consumers. Densities of prey for transient fishes and decapods may be greater within mangroves than elsewhere, but there has been no verification that food availability affects growth or survival. Experimental evidence indicates that mangrove roots and debris provide refuge for small nekton from predators, thus enhancing overall survival. There is no evidence that more individuals move to adult habitats from mangroves than from alternate inshore habitats. There is an obvious need to devise appropriate experiments to test the nursery functions of mangroves. Such data may then be one more reason to add support for mangrove conservation and preservation.
Rationally designed mutations convert de novo amyloid-like fibrils into monomeric β-sheet proteins

Amyloid fibrils are associated with a variety of neurodegenerative maladies including Alzheimer's disease and the prion diseases. The structures of amyloid fibrils are composed of β-strands oriented orthogonal to the fibril axis (“cross β” structure). We previously reported the design and characterization of a combinatorial library of de novo β-sheet proteins that self-assemble into fibrillar structures resembling amyloid. The libraries were designed by using a “binary code” strategy, in which the locations of polar and nonpolar residues are specified explicitly, but the identities of these residues are not specified and are varied combinatorially. The initial libraries were designed to encode proteins containing amphiphilic β-strands separated by reverse turns. Each β-strand was designed to be seven residues long, with polar (○) and nonpolar (●) amino acids arranged with an alternating periodicity (○●○●○●○). The initial design specified the identical polar/nonpolar pattern for all of the β-strands; no strand was explicitly designated to form the edges of the resulting β-sheets. With all β-strands preferring to occupy interior (as opposed to edge) locations, intermolecular oligomerization was favored, and the proteins assembled into amyloid-like fibrils. To assess whether explicit design of edge-favoring strands might tip the balance in favor of monomeric β-sheet proteins, we have now redesigned the first and/or last β-strands of several sequences from the original library. In the redesigned β-strands, the binary pattern is changed from ○●○●○●○ to ○●○K○●○ (K denotes lysine). The presence of a lysine on the nonpolar face of a β-strand should disfavor fibrillar structures because such structures would bury an uncompensated charge. The nonpolar → lysine mutations, therefore, would be expected to favor monomeric structures in which the ○●○K○●○ sequences form edge strands with the charged lysine side chain accessible to solvent. To test this hypothesis, we constructed several second generation sequences in which the central nonpolar residue of either the N-terminal β-strand or the C-terminal β-strand (or both) is changed to lysine. Characterization of the redesigned proteins shows that they form monomeric β-sheet proteins.
Hf-based high-k dielectrics for p-Ge MOS gate stacks

The physical and electrical properties of the gate stack high-k/Al2O3/GeO2/p-Ge were studied in detail, where the high-k is either HfO2 or alloyed HfO2 (HfZrOy, HfGdOx, or HfAlOx). Electrical measurements combined with x-ray photoelectron spectroscopy chemical bonding analysis and band alignment determination were conducted in order to assess the suitability of hafnium-based high-k for this kind of gate stacks, with emphasis on low density of interface states and border traps. HfAlOx was found to be the most promising high-k from those studied. The authors have also found that the current- voltage trends for the various systems studied can be explained by the band alignment of the samples obtained by our x-ray photoelectron spectroscopy analysis.
The new National Cholesterol Education Program guidelines: clinical challenges for more widespread therapy of lipids to treat and prevent coronary heart disease.

T HE RECENTLY published National Cholesterol Education Program (NCEP) III guidelines present many new clinical challenges to health care providers and their patients. These guidelines recommend stricter target lipid levels as well as a broader approach to risk assessment in an effort to reduce premature death and disability from coronary heart disease (CHD) and stroke. Many more patients, especially in primary prevention, are candidates to improve their lipid profiles under the new guidelines. It has been estimated that, as a direct result of the new NCEP III guidelines, the number of US adults eligible for lipid modification has increased from 52 million to 65 million for therapeutic lifestyle changes, including diet, and almost 3-fold, from about 13 million to 36 million, for drug therapy (Figure). This report identifies and characterizes the untreated patients who would benefit from lipid modification and summarizes the efficacy, safety, and cost profiles of the various statins, the class of drugs with the largest and most conclusive body of evidence to support their more widespread use.
Antidepressant use in multiple sclerosis: epidemiologic study of a large community sample

Depressive symptoms and disorders among individuals with multiple sclerosis (MS) are more common when compared to other chronic illnesses and the general population, but relatively little is known about the use of antidepressant medication in this population. In this cross-sectional study of 542 community-dwelling adults with MS, we examined the prevalence of antidepressant use and employed multivariate logistic regression modeling to identify factors significantly associated with antidepressant use. Thirty-five percent of the sample reported currently using at least one antidepressant medication. Gender, marital status, insurance status, fatigue, and use of disease modifying therapies were all significantly associated with antidepressant use. Just over half of the sample endorsed a clinically significant level of depressive symptoms, and the majority of this group was not currently taking an antidepressant. Conversely, 41% of those with depressive symptoms reported taking at least one antidepressant medication. More research is needed to better understand why people with MS and depressive symptoms use or do not use antidepressant medications and to further explore the possibility of an under-treatment of depressive disorder in this population. Rigorous studies testing the feasibility, acceptability, and efficacy of currently available therapies for depression in the MS population should also be conducted. Multiple Sclerosis 2007; 13: 1046—1053. http://msj.sagepub. com
Attachment style dimensions are associated with brain activity in response to gaze interaction

Aim of the present study was to investigate the time course of brain processes involved in the visual perception of different gaze interactions in woman–child dyads and the association between attachment dimensions and brain activation during the presentation of gaze interactions. The hypothesis was that the woman avoidance will produce a greater activation of primary somatosensory and limbic areas. The attachment styles dimensions avoidant-related will be associated with fronto-limbic brain intensity during the convergence of gaze. Electroencephalogram (EEG) data were recorded using a 256-channel HydroCel Geodesic Sensor Net in 44 female subjects (age: 24 ± 2 years). Event-related potential (ERP) components and standardized low-resolution electromagnetic tomography (sLORETA) were analyzed. Participants were administered the attachment style questionnaire before EEG task. A lower P350 latency was found in the fronto-central montage in response to woman avoidance. sLORETA analysis showed a greater intensity of limbic and primary somatosensory areas in response to woman avoidance compared to the others gaze interactions. In response to convergence gaze, the confidence attachment dimension was negatively correlated with the intensities of the right temporal and limbic areas, and the relationships as secondary attachment dimension were positively correlated with the intensities of the bilateral frontal areas and of the left parietal area.
PAC Subset Selection in Stochastic Multi-armed Bandits

We consider the problem of selecting, from among the arms of a stochastic n-armed bandit, a subset of size m of those arms with the highest expected rewards, based on efficiently sampling the arms. This "subset selection" problem finds application in a variety of areas. In the authors' previous work (Kalyanakrishnan & Stone, 2010), this problem is framed under a PAC setting (denoted "Explore-m"), and corresponding sampling algorithms are analyzed. Whereas the formal analysis therein is restricted to the worst case sample complexity of algorithms, in this paper, we design and analyze an algorithm ("LUCB") with improved expected sample complexity. Interestingly LUCB bears a close resemblance to the well-known UCB algorithm for regret minimization. The expected sample complexity bound we show for LUCB is novel even for single-arm selection (Explore-1). We also give a lower bound on the worst case sample complexity of PAC algorithms for Explore-m.
Cost and Profit Efficiency of the Malaysian Commercial Banks: A Comparison between Domestic and Foreign Banks

This study examines the relative efficiency levels of domestic and foreign commercial banks in Malaysia between 2000 and 2006, using accounting-based ratio, stochastic cost and profit frontier approach. Using accounting-based ratio, the results suggest that interest margin and operating cost are slightly higher for domestic banks than for foreign banks. Further, the results also suggest that profit ratios are slightly higher for foreign banks relative to domestic banks. Using the stochastic frontier approach, the results indicate that domestic banks are found to be more cost-efficient but less profit - efficient relative to foreign banks. Keywords: Efficiency, accounting-based ratios, stochastic cost and profit frontier approach, Malaysia
Association of change in daily step count over five years with insulin sensitivity and adiposity: population based cohort study

Objectives To investigate the association between change in daily step count and both adiposity and insulin sensitivity and the extent to which the association between change in daily step count and insulin sensitivity may be mediated by adiposity. Design Population based cohort study. Setting Tasmania, Australia. Participants 592 adults (men (n=267), mean age 51.4 (SD 12.2) years; women (n=325), mean age 50.3 (12.3) years) who participated in the Tasmanian component of the national AusDiab Study in 2000 and 2005. Main outcome measures Body mass index, waist to hip ratio, and HOMA insulin sensitivity at follow-up in 2005. Results Over the five year period, the daily step count decreased for 65% (n=382) of participants. Having a higher daily step count in 2005 than in 2000 was independently associated with lower body mass index (0.08 (95% confidence interval 0.04 to 0.12) lower per 1000 steps), lower waist to hip ratio (0.15 (0.07 to 0.23) lower), and greater insulin sensitivity (1.38 (0.14 to 2.63) HOMA units higher) in 2005. The mean increase in HOMA units fell to 0.34 (−0.79 to 1.47) after adjustment for body mass index in 2005. Conclusions Among community dwelling, middle aged adults, a higher daily step count at five year follow-up than at baseline was associated with better insulin sensitivity. This effect seems to be largely mediated through lower adiposity.