Miracle-dz/UniFAR-FTUs huggingface dataset:
A Precise Method-Method Interaction-Based Cohesion Metric for Object-Oriented Classes

The building of highly cohesive classes is an important objective in object-oriented design. Class cohesion refers to the relatedness of the class members, and it indicates one important aspect of the class design quality. A meaningful class cohesion metric helps object-oriented software developers detect class design weaknesses and refactor classes accordingly. Several class cohesion metrics have been proposed in the literature. Most of these metrics are applicable based on low-level design information such as attribute references in methods. Some of these metrics capture class cohesion by counting the number of method pairs that share common attributes. A few metrics measure cohesion more precisely by considering the degree of interaction, through attribute references, between each pair of methods. However, the formulas applied by these metrics to measure the degree of interaction cause the metrics to violate important mathematical properties, thus undermining their construct validity and leading to misleading cohesion measurement. In this paper, we propose a formula that precisely measures the degree of interaction between each pair of methods, and we use it as a basis to introduce a low-level design class cohesion metric (LSCC). We verify that the proposed formula does not cause the metric to violate important mathematical properties. In addition, we provide a mechanism to use this metric as a useful indicator for refactoring weakly cohesive classes, thus showing its usefulness in improving class cohesion. Finally, we empirically validate LSCC. Using four open source software systems and eleven cohesion metrics, we investigate the relationship between LSCC, other cohesion metrics, and fault occurrences in classes. Our results show that LSCC is one of three metrics that explains more accurately the presence of faults in classes. LSCC is the only one among the three metrics to comply with important mathematical properties, and statistical analysis shows it captures a measurement dimension of its own. This suggests that LSCC is a better alternative, when taking into account both theoretical and empirical results, as a measure to guide the refactoring of classes. From a more general standpoint, the results suggest that class quality, as measured in terms of fault occurrences, can be more accurately explained by cohesion metrics that account for the degree of interaction between each pair of methods.
Behavior-level observability don't-cares and application to low-power behavioral synthesis

Many techniques for power management employed in advanced RTL synthesis tools rely explicitly or implicitly on observability don't-care (ODC) conditions. In this paper we present a systematic approach to maximizing the effectiveness of these techniques by generating power-friendly RTL descriptions in a behavioral synthesis tool. We first introduce the concept of behavior-level observability and investigate its relation with observability under a given schedule, using an extension of Boolean algebra. We then propose an efficient algorithm to compute behavior-level observability on a data-flow graph. Our algorithm exploits knowledge about select and Boolean instructions, and allows certain forms of other knowledge, once uncovered, to be considered for stronger observability conditions. We also describe a behavioral synthesis flow where behavior-level observability is used to guide the scheduler toward maximizing the likelihood that execution of power-hungry instructions will be avoided under a latency constraint. Experimental results show that our approach is able to reduce total power, and it outperforms a previous method in [15] by 17.7% on average, on a set of real-world designs. To the best of our knowledge, this is the first work to use a comprehensive behavioral-level observability analysis to guide optimizations in behavioral synthesis.
Recognition of b-lactam antibiotics by rat peptide transporters , PEPT 1 and PEPT 2 , in LLC-PK 1 cells

Terada, Tomohiro, Hideyuki Saito, Mayumi Mukai, and Ken-ichi Inui. Recognition of b-lactam antibiotics by rat peptide transporters, PEPT1 and PEPT2, in LLC-PK1 cells. Am. J. Physiol. 273 (Renal Physiol. 42): F706–F711, 1997. —PEPT1 and PEPT2 are H1-coupled peptide transporters expressed preferentially in the intestine and kidney, respectively, which mediate uphill transport of oligopeptides and peptide-like drugs such as b-lactam antibiotics. In the present study, we have compared the recognition of b-lactam antibiotics by LLC-PK1 cells stably transfected with PEPT1 or PEPT2 cDNA. Cyclacillin (aminopenicillin) and ceftibuten (anionic cephalosporin without an a-amino group) showed potent inhibitory effects on the glycylsarcosine uptake in the PEPT1-expressing cells. Other b-lactams, such as cephalexin, cefadroxil, and cephradine (aminocephalosporins), inhibited modestly the PEPT1-mediated glycylsarcosine uptake. Except for ceftibuten, these b-lactams showed much more potent inhibitions on the glycylsarcosine uptake via PEPT2 than via PEPT1. Comparison of the inhibition constant (Ki) values between cefadroxil and cephalexin suggested that the hydroxyl group at the NH2-terminal phenyl ring increased affinity for both PEPT1 and PEPT2. It is concluded that PEPT2 has a much higher affinity for b-lactam antibiotics having an a-amino group than PEPT1 and that substituents at the NH2-terminal side chain of these drugs are involved in the recognition by both peptide transporters.
Feasibility of using high-definition transcranial direct current stimulation (HD-tDCS) to enhance treatment outcomes in persons with aphasia.

BACKGROUND Transcranial direct current stimulation (tDCS) enhances treatment outcomes post-stroke. Feasibility and tolerability of high-definition (HD) tDCS (a technique that increases current focality and intensity) for consecutive weekdays as an adjuvant to behavioral treatment in a clinical population has not been demonstrated. OBJECTIVE To determine HD-tDCS feasibility outcomes: 1) ability to implement study as designed, 2) acceptability of repeated HD-tDCS administration to patients, and 3) preliminary efficacy. METHODS Eight patients with chronic post-stroke aphasia participated in a randomized crossover trial with two arms: conventional sponge-based (CS) tDCS and HD-tDCS. Computerized anomia treatment was administered for five consecutive days during each treatment arm. RESULTS Individualized modeling/targeting procedures and an 8-channel HD-tDCS device were developed. CS-tDCS and HD-tDCS were comparable in terms of implementation, acceptability, and outcomes. Naming accuracy and response time improved for both stimulation conditions. Change in accuracy of trained items was numerically higher (but not statistically significant) for HD-tDCS compared to CS-tDCS for most patients. CONCLUSIONS Regarding feasibility, HD-tDCS treatment studies can be implemented when designed similarly to documented CS-tDCS studies. HD-tDCS is likely to be acceptable to patients and clinicians. Preliminary efficacy data suggest that HD-tDCS effects, using only 4 electrodes, are at least comparable to CS-tDCS.
RTTool: A Tool for Extracting Relative Thresholds for Source Code Metrics

Meaningful thresholds are essential for promoting source code metrics as an effective instrument to control the internal quality of software systems. Despite the increasing number of source code measurement tools, no publicly available tools support extraction of metric thresholds. Moreover, earlier studies suggest that in larger systems significant number of classes exceed recommended metric thresholds. Therefore, in our previous study we have introduced the notion of a relative threshold, i.e., a pair including an upper limit and a percentage of classes whose metric values should not exceed this limit. In this paper we propose RTTOOL, an open source tool for extracting relative thresholds from the measurement data of a benchmark of software systems. RTTOOL is publicly available at http://aserg.labsoft. dcc.ufmg. br/rttool.
Predictive factors for local recurrence in 2006 patients with surgically resected small breast cancer.

BACKGROUND Analyses of predictive factors for local recurrences are important, as an increasing number of patients with early breast cancer opt for a breast-conserving procedure. This study investigates whether factors predictive of local recurrence differ between patients treated with conservative or radical surgery. PATIENTS AND METHODS Two thousands and six patients with invasive breast carcinoma (< or =25 mm) were included. Of these patients, 717 were treated conservatively (lumpectomy and breast irradiation) and 1289 were treated with total mastectomy. All patients had axillary dissection and received lymph node irradiation if axillary nodes were positive. Most patients did not receive adjuvant chemotherapy or additive hormonal treatments. The mean duration of follow-up was 20 years. The main end point was the total local recurrence rate. The risk factors of local recurrence were estimated by multivariate analyses and interaction tests were used for intergroup comparisons. RESULTS Statistically significant predictive factors for mastectomized patients were histological grade, extensive axillary node involvement (10 nodes or more), and inner quadrant tumors, which were of borderline significance. Young age, however, was not a prognostic indicator for local recurrence. The main statistically significant factor for patients treated with a conservative approach was young age (< or =40 years). These younger patients had a five-fold increased risk of developing a breast recurrence compared with patients older than 60 years. CONCLUSIONS Younger patients with early breast cancer treated with breast-conserving surgery should in particular be followed up at regular intervals so that any sign of local failure can be diagnosed early.
Improved Variational Autoencoders for Text Modeling using Dilated Convolutions

Recent work on generative modeling of text has found that variational auto-encoders (VAE) incorporating LSTM decoders perform worse than simpler LSTM language models (Bowman et al., 2015). This negative result is so far poorly understood, but has been attributed to the propensity of LSTM decoders to ignore conditioning information from the encoder. In this paper, we experiment with a new type of decoder for VAE: a dilated CNN. By changing the decoder's dilation architecture, we control the effective context from previously generated words. In experiments, we find that there is a trade off between the contextual capacity of the decoder and the amount of encoding information used. We show that with the right decoder, VAE can outperform LSTM language models. We demonstrate perplexity gains on two datasets, representing the first positive experimental result on the use VAE for generative modeling of text. Further, we conduct an in-depth investigation of the use of VAE (with our new decoding architecture) for semi-supervised and unsupervised labeling tasks, demonstrating gains over several strong baselines.
Graphene Nanoelectronics: Metrology, Synthesis, Properties and Applications

Introduction. - Scanning Tunneling Microscopy and Spectroscopy of Graphene. - Epitaxy of Graphene on Metals. - The Electronic Properties of Adsorbates on Graphene. - PN Junction Devices in Graphene. - Magneto-transport in Graphene Nanostructures. - Modeling and Simulation: from Graphene Chemistry to Electronic circuits. - Ab-initio Calculations of Graphene Oxide. - Quantum to Boltzmann Transport in Graphene. - Field-Modulation in Armchair Graphene Nanoribbons. - Field-Modulation in Bilayer Graphene. - Theory of Mesoscopic Graphene Systems, Rings and Superlattices. - Possible Ordered States in Graphene Systems. - Conduction in Graphene Nanoribbons. - Electronic and Transport Properties of Nanographene and Nanoribbons. - Electronic Structure of Monolayer and Bilayer Graphene Nanoribbons and their Device Application: A Computational Study. - Epitaxy of Graphene on SiC.
Effect of Vitamin D 3 Supplementation on Upper Respiratory Tract Infections in Healthy Adults The VIDARIS Randomized Controlled Trial

THE ROLE OF VITAMIN D IN INfectious diseases and the potential impact of vitamin D supplementation as a preventive measure for infectious diseases are unclear. Vitamin D has a role in both innate and adaptive immune responses. Of particular interest is the induction by vitamin D of cathelicidins, a group of antimicrobial peptides produced by neutrophils, macrophages, and epithelial cells. Epidemiological studies show an association between low vitamin D levels and a variety of respiratory tract infections. For example, vitamin D insufficiency is associated with increased risk of developing tuberculosis. The association of vitamin D insufficiency and susceptibility to viral respiratory tract infections is also un-
Procedure for isolation of bacterial lipopolysaccharides from both smooth and rough Pseudomonas aeruginosa and Salmonella typhimurium strains

Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. It is now well established that within a single organism, size heterogeneity of this molecule can exist. We have developed a LPS isolation procedure which is effective in extracting both smooth and rough LPS in high yields (51 to 81% of the LPS present in whole cells as quantitated by using hydroxy fatty acid, heptose, and 2-keto-3-deoxyoctonate yields) and with a high degree of purity. The contamination by protein (0.1% by weight of LPS), nucleic acids (1%), lipids (2 to 5%), and other bacterial products was low. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the LPS demonstrated the presence of a high degree of size heterogeneity in the isolated smooth LPS as well as the presence of significant amounts of rough-type LPS. The Pseudomonas aeruginosa LPS interacted well with a monoclonal antibody in a variety of immunochemical analyses. The usefulness of the procedure was demonstrated by comparing LPS preparations obtained from wild-type and mutant strains of P. aeruginosa and Salmonella typhimurium. For example, it was shown that the LPS of an antibiotic supersusceptible mutant Z61 of P. aeruginosa, which was previously characterized as identical to wild type with respect to the ratio of smooth to rough LPS molecules isolated by the phenol-water procedure, actually contained only a small proportion of O-antigenic side chains.
The Effects of Common Genetic Variants in Oncogenes on Ovarian Cancer Survival

Purpose: The 5-year survival rate for invasive epithelial ovarian cancer is <35%. It has been suggested that common, germline genetic variation may influence survival after cancer diagnoses, which might enable the prediction of response to treatment and survival in the clinical setting. The aim of this study was to evaluate associations between common germline genetic variants in the oncogenes BRAF, ERBB2, KRAS, NMI, and PIK3CA, and survival after a diagnosis of epithelial ovarian cancer. Experimental Design: We evaluated the association between 34 tagging single nucleotide polymorphisms and survival in 1,480 cases of invasive epithelial ovarian cancer cases from three different studies. Cox regression analysis, stratified by study, was used to estimate per rare allele hazard ratios (HR). Results: The minor allele rs6944385 in BRAF was significantly associated with poor survival [HR, 1.19; 95% confidence intervals (95% CI), 1.02-1.39; P = 0.024]. The association remained after adjusting for prognostic factors (adjusted HR, 1.20; 95 CI, 1.03-1.40; P = 0.018). A haplotype of BRAF was also associated with poor survival (HR, 1.24; 95% CI, 1.02-1.51; P = 0.029) and was more significant after adjustment (HR, 1.44; 95% CI, 1.15-1.81; P = 0.001). We also found evidence of an association between a KRAS haplotype and poor survival in serous subtype (HR, 1.69; 95% CI, 1.21-2.38; P = 0.002), but this was no longer significant after adjustment. Finally, when analyses were restricted to the serous histologic subtype, the rare allele rs10842513 in KRAS, was associated with poor survival (HR, 1.40; 95% CI, 1.10-1.78; P = 0.007). Conclusion: Common genetic variants in the BRAF and KRAS oncogenes may be important in the prediction of survival in patients with invasive epithelial ovarian cancer.
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

Significance Bacterial adaptation through horizontal gene transfer is central to microbial evolution and, in the context of antibiotic resistance, represents a growing clinical threat. Conjugative plasmids are key mediators of genetic exchange both within and between species. Experimental studies have mostly focused on plasmid population dynamics in single-species populations, but between-species transfer could counteract purifying selection and maintain plasmids in hosts that would otherwise lose them. We show that plasmids can be lost from single-species populations, even when their genes are under selection, because beneficial genes are captured by the chromosome. In contrast, experiments and models show that, in a two-species community, between-species transfer maintains community-wide access to plasmids, promoting the spread of the ecologically and clinically important genes they carry. Horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. Conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. In some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to plasmid-borne genes. To investigate the evolutionary importance of alternative hosts to plasmid population dynamics in an ecologically relevant environment, we established simple soil microcosm communities comprising two species of common soil bacteria, Pseudomonas fluorescens and Pseudomonas putida, and a mercury resistance (HgR) plasmid, pQBR57, both with and without positive selection [i.e., addition of Hg(II)]. In single-species populations, plasmid stability varied between species: although pQBR57 survived both with and without positive selection in P. fluorescens, it was lost or replaced by nontransferable HgR captured to the chromosome in P. putida. A simple mathematical model suggests these differences were likely due to pQBR57’s lower intraspecific conjugation rate in P. putida. By contrast, in two-species communities, both models and experiments show that interspecific conjugation from P. fluorescens allowed pQBR57 to persist in P. putida via source–sink transfer dynamics. Moreover, the replacement of pQBR57 by nontransferable chromosomal HgR in P. putida was slowed in coculture. Interspecific transfer allows plasmid survival in host species unable to sustain the plasmid in monoculture, promoting community-wide access to the plasmid-borne accessory gene pool and thus potentiating future evolvability.
Help seeking and barriers to treatment in a community sample of Mexican American and European American women with eating disorders.

OBJECTIVE The study examined treatment seeking for eating disorders in Mexican American and European American women. METHOD One hundred forty-five women with eating disorders (76 Mexican American, 69 European American) were diagnosed using the Structured Clinical Interview for DSM-IV-TR (SCID-IV) and Eating Disorder Examination (EDE). RESULTS Only 28% of the sample reported having sought treatment for their eating problems and only 17% had received treatment. Both groups were equally likely to believe they have significant eating problems and to want help. However, Mexican Americans were less likely to have sought treatment and, having sought help, were less likely to have been diagnosed or treated. European Americans were more likely to have utilized psychotherapists, psychiatrists, and psychotropic medications, whereas Mexican Americans largely had sought help from general practitioners for weight concern. The two groups endorsed similar barriers to treatment seeking. CONCLUSION Results support clinical impressions that eating disorders largely go undetected and untreated. Nonspecialists may be likely to fail to detect eating disorders.
Ieee Transactions on Wireless Communications Performance Analysis of Massive Mimo for Cell-boundary Users

—In this paper, we consider massive multiple-input multiple-output (MIMO) systems for both downlink and uplink scenarios, where three radio units (RUs) connected via one digital unit (DU) support multiple user equipments (UEs) at the cell-boundary through the same radio resource, i.e., the same time-frequency slot. For downlink transmitter options, the study considers zero-forcing (ZF) and maximum ratio transmission (MRT), while for uplink receiver options it considers ZF and maximum ratio combining (MRC). For the sum rate of each of these, we derive simple closed-form formulas. In the simple but practically relevant case where uniform power is allocated to all downlink data streams, we observe that, for the downlink, vector normalization is better for ZF while matrix normalization is better for MRT. For a given antenna and user configuration, we also derive analytically the signal-to-noise-ratio (SNR) level below which MRC should be used instead of ZF. Numerical simulations confirm our analytical results.
Urinary Phthalates and Increased Insulin Resistance in Adolescents

BACKGROUND Di-2-ethylhexylphthalate (DEHP) is an environmental chemical commonly found in processed foods. Phthalate exposures, in particular to DEHP, have been associated with insulin resistance in adults, but have not been studied in adolescents. METHODS: Using cross-sectional data from 766 fasting 12- to 19-year-olds in the 2003–2008 NHANES, we examined associations of phthalate metabolites with continuous and categorical measures of homeostatic model assessment of insulin resistance (HOMA-IR). RESULTS: Controlling for demographic and behavioral factors, diet, continuous age, BMI category, and urinary creatinine, for each log (roughly threefold) increase in DEHP metabolites, a 0.27 increase (95% confidence interval 0.14–0.40; P < .001) in HOMA-IR was identified. Compared with the first tertile of DEHP metabolite in the study population (14.5% insulin resistant), the third tertile had 21.6% prevalence (95% confidence interval 17.2%–26.0%; P = .02). Associations persisted despite controlling for bisphenol A, another endocrine-disrupting chemical commonly found in foods, and HOMA-IR and insulin resistance were not significantly associated with metabolites of lower molecular weight phthalates commonly found in cosmetics and other personal care products. CONCLUSIONS: Urinary DEHP concentrations were associated with increased insulin resistance in this cross-sectional study of adolescents. This study cannot rule out the possibility that insulin-resistant children ingest food with higher phthalate content, or that insulin-resistant children excrete more DEHP.
Statistical Post-Editing for a Statistical MT System

Statistical post-editing (SPE) techniques have been successfully applied to the output of Rule Based MT (RBMT) systems. In this paper we investigate the impact of SPE on a standard Phrase-Based Statistical Machine Translation (PB-SMT) system, using PB-SMT both for the ﬁrst-stage MT and the second stage SPE system. Our results show that, while a naive approach to using SPE in a PB-SMT pipeline produces no or only modest improvements, a novel combination of source context modelling and thresholding can produce statistically signiﬁcant improvements of 2 BLEU points over baseline using technical translation data for French to English.