Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliable Fix Patterns Inferred from Static Checkers for Automated Program Repair

Fix pattern-based patch generation is a promising direction in automated program repair (APR). Notably, it has been demonstrated to produce more acceptable and correct patches than the patches obtained with mutation operators through genetic programming. The performance of pattern-based APR systems, however, depends on the fix ingredients mined from fix changes in development histories. Unfortunately, collecting a reliable set of bug fixes in repositories can be challenging. In this article, we propose investigating the possibility in an APR scenario of leveraging fix patterns inferred from code changes that address violations detected by static analysis tools. To that end, we build a fix pattern-based APR tool, Avatar, which exploits fix patterns of static analysis violations as ingredients for the patch generation of repairing semantic bugs. Evaluated on four benchmarks (i.e., Defects4J, Bugs.jar, BEARS, and QuixBugs), Avatar presents the potential feasibility of fixing semantic bugs with the fix patterns inferred from the patches for fixing static analysis violations and can correctly fix 26 semantic bugs when Avatar is implemented with the normal program repair pipeline. We also find that Avatar achieves performance metrics that are comparable to that of the closely related approaches in the literature. Compared with CoCoNut, Avatar can fix 18 new bugs in Defects4J and 3 new bugs in QuixBugs. When compared with HDRepair, JAID, and SketchFix, Avatar can newly fix 14 Defects4J bugs. In terms of the number of correctly fixed bugs, Avatar is also comparable to the program repair tools with the normal fault localization setting and presents better performance than most program repair tools. These results imply that Avatar is complementary to current program repair approaches. We further uncover that Avatar can present different bug-fixing performances when it is configured with different fault localization tools, and the stack trace information from the failed executions of test cases can be exploited to improve the bug-fixing performance of Avatar by fixing more bugs with fewer generated patch candidates. Overall, our study highlights the relevance of static bug-finding tools as indirect contributors of fix ingredients for addressing code defects identified with functional test cases (i.e., dynamic information).
Two-photon excited surface plasmon enhanced energy transfer between DAPI and gold nanoparticles: Opportunities in intra-cellular imaging and sensing

We have demonstrated energy transfer between 4’-6-Diamidino-2-phenylindole (DAPI), a commonly used DNA label, and gold nanoparticles under two-photon excitation in solution using fluorescence lifetime imaging microscopy (FLIM). With comparable size and concentration, gold nanorods (GNRs) are shown to provide more efficient energy transfer than gold nanospheres (GNSs). We attribute this transfer enhancement effect to the longitudinal surface plasmon mode of GNRs overlapping with the excitation wavelength. Energy transfer under two-photon excitation between GNRs and DAPI has also been observed in cell culture and found to be in accord with the solution phase results.
Credible interventionism: economic ideas of government and macroeconomic policy in the Great Recession

ABSTRACT The macroeconomic policies of advanced economies during the Great Recession were characterised by a curious mixture of unconventional market interventions executed through depoliticised governance structures. We explain this phenomenon by developing a theoretical framework that focuses on the ideational and institutional influence of government-related economic ideas by combining insights of constructivist institutionalism and historical institutionalism. Specifically, we argue that the dominant government-related idea of ‘policy credibility’ – the need to convince markets of government commitment to refrain from ‘politicised’ interventions – was crucial for the adoption of depoliticised macroeconomic interventionism. The ideational dominance of ‘policy credibility’ and its pre-crisis institutionalisation enabled significant policy interventions as long as depoliticised decision-making was maintained and consolidated. We demonstrate this argument through a comparative in-depth analysis of monetary and fiscal policy in two very different cases among advanced economies – the UK and Israel.
Measuring Aesthetic Preferences of Neural Style Transfer: More Precision With the Two-Alternative-Forced-Choice Task

Abstract The present work compares the two-alternative forced choice (2AFC) task to rating scales for measuring aesthetic perception of neural style transfer-generated images and investigates whether and to what extent the 2AFC task extracts clearer and more differentiated patterns of aesthetic preferences. To this aim, 8250 pairwise comparisons of 75 neural style transfer-generated images, varied in five parameter configurations, were measured by the 2AFC task and compared with rating scales. Statistical and qualitative results demonstrated higher precision of the 2AFC task over rating scales in detecting three different aesthetic preference patterns: (a) convergence (number of iterations), (b) an inverted U-shape (learning rate), and (c) a double peak (content-style ratio). Important for practitioners, finding such aesthetically optimal parameter configurations with the 2AFC task enables the reproducibility of aesthetic outcomes by the neural style transfer algorithm, which saves time and computational cost, and yields new insights about parameter-dependent aesthetic preferences.
Disinfection of Human Amniotic Membrane Using a Hydrodynamic System with Ozonated Water

ABSTRACT Human amniotic membrane (hAM) has a great potential in regenerative medicine as it can be disinfected, preserved, and stored. The present study evaluated a hydrodynamic system that uses ozonated water for disinfecting hAM and assessed possible morphological alterations using histological analysis and scanning electron microscopy (SEM). hAM fragments were experimentally contaminated with Staphylococcus aureus (103 CFU/mL) and submitted to disinfection processes for 5, 10 and 15 minutes (1.95, 3.9 and 5.85 mg/cm2 (O3), respectively). The results of the water microbiological analysis showed that no microbial growth was detected in all water samples. The hAM surface monitoring with swab method and the analysis of fragment inoculated directly into the culture media revealed that no microbial growth was detected after 10 and 15 minutes. The SEM and histological analysis of hAM revealed that morphological alterations in the epithelium began after 10 minutes 3.9 mg/cm2 (O3) of the disinfection process, and significant changes in the epithelial cells were observed after 15 minutes (5.85 mg/cm2 (O3)). These findings indicates that the structural integrity of hAM was maintained during the process and suggest that the technique is a promising system to disinfect this biological material.
The robustness of the covariance analysis of a one-way classification

SUMMARY The effect of non-normality and the effect of treatment slope interaction in the analysis of covariance is studied. Unlike the analysis of variance F-test the analysis of covariance F-test is found to be appreciably affected by non-normality even in balanced classifications. The degree of sensitivity to non-normality is determined by the distribution of the concomitant variables. The violation of the assumption of no treatment-slope interaction does not seem to have serious effect on the F-test in large samples, but a much more serious effect appears to be that of a quadratic component of regression on the F-test. Atiqullah (1962) has shown that the extent to which the analysis of variance F-test is influenced by non-normality depends on the structure of the design matrix, A, in the usual linear model for the problem. In balanced set-ups the design matrix, A, possesses the property of quadratic balance which is characterized by the matrix A (A'A) 1-A' having its diagonal terms all equal. This property practically nullifies the effect of non-normality on inferences drawn from the F-test in the standard orthogonal cross-classified set-ups, such as balanced two or more-way arrangements, Latin squares, balanced incomplete block designs, etc. But in the analysis of covariance the linear model contains, besides the design matrix A, a matrix of concomitant observations and therefore the sensitivity of F-test to non-normality will be determined both by the structure of the design matrix A and the nature of the concomitant matrix X. In balanced classifications, it is thus the concomitant variables alone which will determine sensitivity to non-normality. This fact also follows from the discussion of Box & Watson (1962) who have discussed robustness to non-normality of regression tests and have shown that it is the extent of non-normality in the independent variables which determines sensitivity to non-normality. In the first part of the present paper we investigate in more detail the influence which the concomitant variables have in determining sensitivity to non-normalityin the analysis of covariance F-test and obtain expressions for judging the effect of non-normality in practical situations. In the second part of the paper we discuss how far the analysis of covariance, as usually applied on the presumption of no interaction between treatments and slope, will be sensitive to situations entailing interactions or to a model containing quadratic gradient.
Best Arm Identification in Stochastic Bandits: Beyond β-optimality

This paper investigates a hitherto unaddressed aspect of best arm identification (BAI) in stochastic multi-armed bandits in the fixed-confidence setting. Two key metrics for assessing bandit algorithms are computational efficiency and performance optimality (e.g., in sample complexity). In stochastic BAI literature, there have been advances in designing algorithms to achieve optimal performance, but they are generally computationally expensive to implement (e.g., optimization-based methods). There also exist approaches with high computational efficiency, but they have provable gaps to the optimal performance (e.g., the $\beta$-optimal approaches in top-two methods). This paper introduces a framework and an algorithm for BAI that achieves optimal performance with a computationally efficient set of decision rules. The central process that facilitates this is a routine for sequentially estimating the optimal allocations up to sufficient fidelity. Specifically, these estimates are accurate enough for identifying the best arm (hence, achieving optimality) but not overly accurate to an unnecessary extent that creates excessive computational complexity (hence, maintaining efficiency). Furthermore, the existing relevant literature focuses on the family of exponential distributions. This paper considers a more general setting of any arbitrary family of distributions parameterized by their mean values (under mild regularity conditions). The optimality is established analytically, and numerical evaluations are provided to assess the analytical guarantees and compare the performance with those of the existing ones.
X-Ray Spectral Variability and Complex Absorption in the Seyfert 1 Galaxies NGC 4051 and MCG -6-30-15

Results are presented on Ginga observations of the Seyfert 1 galaxies NGC 4051 and MCG -6-30-15, which reveal the presence of large-amplitude (greater than 50 percent) spectral variations in both objects, thus confirming and extending previous Exosat results. These variations are associated with spectral changes; it was found that the spectra are steeper for the brighter sources. The observed positive correlation between the spectral index and the luminosity provides strong constraints to radiative models and rules out models where the spectrum becomes harder when the X-ray luminosity increases. 60 refs.
Analysis of the photospheric epoch spectra of type 1a supernovae SN 1990N and SN 1991T

This paper presents an LTE analysis of the photospheric epoch optical and IUE UV spectra of the recent Type Ia supernovae SN 1990N and SN 1991T. It is found that SN 1990N has matter moving as fast as 40,000 km/s, while SN 1991T has matter moving as fast as 20,000 km/s. The exponential density profile with e-folding velocity of 3160 km/s suggested by deflation and delayed/late-detonation explosion models is adequate for calculating fits to the observed spectra. Findings on the iron peak elements suggest that in both SNe some nuclear burning continues into the outer ejecta or the newly synthesized elements are mixed into the outer ejecta. The observed spectra of SN 1990N are consistent with a composition of the inner envelope like that of model W7. Intermediate-mass elements with abundances higher than solar are probably in the outer ejecta of both SNe, while silicon, sulfur, and calcium are underabundance in SN 1991T relative to SN 1990N by factors of order 3, 3, and 120, respectively.
Several dimensional properties of the spectrum of a uniform algebra

The author has previously introduced a generalized Silov boundary which seems useful in studying analytic structure of several dimensions in the spectrum of a uniform algebra 2ί. Related generalizations of 2ϊ-convexity, 2ί-polyhedra, etc. are developed here. Several different but equivalent approaches to these various generalizations are described. The generalized boundaries discussed here are related to the "qholomorphic functions" of the author, and to 2ϊ-holomorphic convexity.
Effect of childhood maltreatment on cognitive function and its relationship with personality development and social coping style in major depression disorder patients: A latent class model and network analysis

Study objectives The study aimed to (1) analyze the interrelationships among different types of childhood adversity, diverse personality dimensions, and individual coping style integratively among major depressive disorder (MDD) patients and healthy participants using a network approach; (2) explore the latent class of child maltreatment (CM) and its relationship with cognitive function. Methods Data were collected from the Objective Diagnostic Markers and Personalized Intervention in MDD Patients (ODMPIM) study, including 1,629 Chinese participants. Using the Childhood Trauma Questionnaire to assess CM, the Simplified Coping Style Questionnaire to measure individual coping style, Eysenck Personality Questionnaire Revised-Short Form for personality characters, and a series of neurocognitive tests, including seven tests with 18 subtests for cognitive assessments. We used the “Network Module” in Jeffreys’s Amazing Statistics Program (JASP) and R package for network analysis. A latent class analysis was performed with SAS9.4. Results Child maltreatment was more common in MDD patients than in healthy controls, except for emotional abuse. Network analysis showed that emotional abuse, emotional neglect, physical abuse, and physical neglect formed quadrangle connections. Personality dimensions were associated with physical neglect and emotional abuse. All types of CM (excluding sex abuse) showed an association with coping style. Emotional neglect showed the highest centrality measures. Physical neglect had a high level of closeness. To a concerning strength, emotional and physical neglect showed the highest levels. The structure of the networks is variant between groups (M = 0.28, P = 0.04). Latent class analysis (LCA) revealed that three classes provided the best fit statistics. Neglect and abuse classes tended to perform more poorly on the five cognitive domains. Conclusion This study provided insights on multi-type of CM. Neglect played an important role in different routes through the relation between CM with personality traits and social coping style. However, neglect has often been ignored in previous studies and should receive more public attention.
Functional timing or rhythmical timing, or both? A corpus study of English and Mandarin duration

It has been long held that languages of the world are divided into rhythm classes so that they are either stress-timed, syllable-timed or mora-timed. It is also known for a long time that duration serves various informational functions in speech. But it is unclear whether these two kinds of uses of duration are complementary to each other, or they are actually one and the same. There has been much empirical research that raises questions about the rhythm class hypothesis due to lack of evidence of the suggested isochrony in any language. Yet the alleged cross-language rhythm classification is still widely taken for granted and continues to be researched. Here we conducted a corpus study of English, an archetype of a stress-timed language, and Mandarin, an alleged syllable-timed language, to look for evidence of at least a tendency toward isochrony when much of the informational use of duration is controlled for. We examined the relationship between segment and syllable duration and the relationship of syllable and phrase duration in the two languages. The results show that in English syllables are largely incompressible to allow stress-timing because segment duration is inflexible to allow variable syllable duration beyond its functional use. Surprisingly, Mandarin does show a small tendency toward both equal syllable duration and equal phrase duration. Additionally, the duration of pre-boundary syllables in English increases linearly with break index, whereas in Mandarin, the duration increase stops after break index 2, which is accompanied by the insertion of silent pauses. We conclude, therefore, timing and duration in speech are predominantly used for encoding information rather being controlled by a rhythmic principle, and the residual equal-duration tendency in the two languages examined here show exactly the opposite patterns from the predictions of the rhythm class hypothesis.
Biomarkers of alloimmune events in pediatric kidney transplantation

Alloimmune events such as the development of de novo donor-specific antibody (dnDSA), T cell-mediated rejection (TCMR), and antibody-mediated rejection (ABMR) are the primary contributors to kidney transplant failure in children. For decades, a creatinine-based estimated glomerular filtration rate (eGFR) has been the non-invasive gold standard biomarker for detecting clinically significant alloimmune events, but it suffers from low sensitivity and specificity, especially in smaller children and older allografts. Many clinically “stable” children (based on creatinine) will have alloimmune events known as “subclinical acute rejection” (based on biopsy) that merely reflect the inadequacy of creatinine-based estimates for alloimmune injury rather than a distinct phenotype from clinical rejection with allograft dysfunction. The poor biomarker performance of creatinine leads to many unnecessary surveillance and for-cause biopsies that could be avoided by integrating non-invasive biomarkers with superior sensitivity and specificity into current clinical paradigms. In this review article, we will present and appraise the current state-of-the-art in monitoring for alloimmune events in pediatric kidney transplantation. We will first discuss the current clinical standards for assessing the presence of alloimmune injury and predicting long-term outcomes. We will review principles of biomarker medicine and the application of comprehensive metrics to assess the performance of a given biomarker against the current gold standard. We will then highlight novel blood- and urine-based biomarkers (with special emphasis on pediatric biomarker studies) that have shown superior diagnostic and prognostic performance to the current clinical standards including creatinine-based eGFR. Finally, we will review some of the barriers to translating this research and implementing emerging biomarkers into common clinical practice, and present a transformative approach to using multiple biomarker platforms at different times to optimize the detection and management of critical alloimmune events in pediatric kidney transplant recipients.
The association of BTLA gene polymorphisms with non-small lung cancer risk in smokers and never-smokers

Introduction Lung cancer is the predominant cause of death among cancer patients and non-small cell lung cancer (NSCLC) is the most common type. Cigarette smoking is the prevailing risk factor for NSCLC, nevertheless, this cancer is also diagnosed in never-smokers. B and T lymphocyte attenuator (BTLA) belongs to immunological checkpoints which are key regulatory molecules of the immune response. A growing body of evidence highlights the important role of BTLA in cancer. In our previous studies, we showed a significant association between BTLA gene variants and susceptibility to chronic lymphoblastic leukemia and renal cell carcinoma in the Polish population. The present study aimed to analyze the impact of BTLA polymorphic variants on the susceptibility to NSCLC and NSCLC patients’ overall survival (OS). Methods Using TaqMan probes we genotyped seven BTLA single-nucleotide polymorphisms (SNPs): rs2705511, rs1982809, rs9288952, rs9288953, rs1844089, rs11921669 and rs2633582 with the use of ViiA 7 Real-Time PCR System. Results We found that rs1982809 within BTLA is associated with NSCLC risk, where carriers of rs1982809G allele (AG+GG genotypes) were more frequent in patients compared to controls. In subgroup analyses, we also noticed that rs1982809G carriers are significantly overrepresented in never-smokers, but not in smokers compared to controls. Additionally, the global distribution of the haplotypes differed between the never-smokers and smokers, where haplotypes A G G C A, C G A C G, and C G A T G were more frequent in never-smoking patients. Furthermore, the presence rs1982809G (AG+GG genotypes) allele as well as the presence of rs9288953T allele (CT+TT genotypes) increased NSCLC risk in females’ patients. After stratification by histological type, we noticed that rs1982809G and rs2705511C carriers were more frequent among adenocarcinoma patients. Moreover, rs1982809G and rs2705511C correlated with the more advanced stages of NSCLC (stage II and III), but not with stage IV. Furthermore, we showed that rs2705511 and rs1982809 significantly modified OS, while rs9288952 tend to be associated with patients’ survival. Conclusion Our results indicate that BTLA polymorphic variants may be considered low penetrating risk factors for NSCLC especially in never-smokers, and in females, and are associated with OS of NSCLC patients.