Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Use of Rapid Type Analysis for Detecting the Dead Method Smell in Java Code

Rapid Type Analysis (RTA) is an algorithm for call graph construction, which is known to be fast and to well approximate virtual method calls. In this paper, we explore its use in the context of refactoring, namely we defined an approach that relies on RTA for the detection of the dead method smell in Java code. We implemented this approach in a prototype of supporting tool we named Dead Code Finder (DCF). We empirically assessed DCF (and the underlying approach) through an experiment on four open-source Java desktop application. We compared DCF with three baseline tools. The results indicate that DCF outperforms these baselines in terms of accuracy of the detected dead methods.
Characterization of Perinatal Risk Factors and Complications Associated With Nonsyndromic Craniosynostosis

Background: Certain intrauterine risk factors are known to increase the risk of premature cranial suture fusion and may cause complications during birth. Some of these risk factors may be modifiable. Therefore, the authors sought to characterize the institutional patterns of prenatal risk factors and perinatal complications in nonsyndromic craniosynostosis patients compared to normal births from the surrounding area to identify areas for possible intervention or prevention. Methods: The medical records of all infants with nonsyndromic craniosynostosis and full birth records born at Duke University Health System from 2006 to 2017 were retrospectively reviewed. Maternal comorbidities, prenatal risk factors, and perinatal complications were collected. The North Carolina State Center for Health Statistics was queried for perinatal statistics from Durham county and the Northeastern Perinatal Care Region to represent a control cohort of normal births from the same time period and region. The primary outcome investigated was the incidence of prenatal risk factors and complications at birth associated with premature fusion of cranial sutures. Results: Eighty births with nonsyndromic craniosynostosis were included in this study. The majority of these patients were males (61.7%) and born via cesarean section (55.0%). Intrauterine growth restriction occurred in 10.0% and head trauma during delivery occurred in 2.5%. Twinning (14.8% vs 3.6%, P < 0.0001), cesarean births (55.5% vs 30.0%, P < 0.0001), and breech presentation (17.3% vs 3.2%, P < 0.0001) were significantly more common in craniosynostosis patients. Prenatally, mothers of craniosynostosis infants had higher incidence of gestational diabetes (13.5% vs 5.0%, P < 0.0001) and oligohydramnios (6.1% vs 1.3%, P < 0.0001) compared to regional controls. Conclusion: This study demonstrates that premature suture fusion is associated with prenatal risk factors such as gestational diabetes and oligohydramnios. Continued research into potentially modifiable prenatal risk factors and more refined prenatal diagnostic tools has the potential to reduce both the incidence of premature suture fusion and the sequelae of birth complications in this population.
Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility

Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.
The speaker-independent lipreading play-off; a survey of lipreading machines

Lipreading is a difficult gesture classification task. One problem in computer lipreading is speaker-independence. Speaker-independence means to achieve the same accuracy on test speakers not included in the training set as speakers within the training set. Current literature is limited on speaker-independent lipreading, the few independent test speaker accuracy scores are usually aggregated within dependent test speaker accuracies for an averaged performance. This leads to unclear independent results. Here we undertake a systematic survey of experiments with the TCD-TIMIT dataset using both conventional approaches and deep learning methods to provide a series of wholly speaker-independent benchmarks and show that the best speaker-independent machine scores 69.58% accuracy with CNN features and an SVM classifier. This is less than state-of-the-art speaker-dependent lipreading machines, but greater than previously reported in independence experiments.
Pubertal recalibration of cortisol reactivity following early life stress: a cross-sectional analysis.

BACKGROUND Children adopted from orphanages or other such institutions tend to display blunted reactivity to stressors - even years after arriving in their generally supportive and highly resourced postadoption homes. Puberty, a proposed sensitive period for environmental influences on stress-mediating systems, may provide an opportunity for postinstitutionalized children to recalibrate stress response systems in accordance with their now more supportive living situations. METHODS This cross-sectional study examined the hypothalamic-pituitary-adrenocortical (HPA)-axis reactivity of 280 children ages 7 through 14 years; 122 children were adopted from institutions in 14 countries between the ages of 6 months and 5 years, after spending an average of 95% of their lives in institutional care, and 158 children of similarly high socioeconomic status in their biological families served as the nonadopted comparison group. All of the children were assessed by nurses for Tanner stage and, on a different day, completed the Trier Social Stress Test for Children. RESULTS Using a linear mixed-effects model and seven measures of salivary cortisol, results indicated that early-pubertal postinstitutionalized children showed blunted HPA axis reactivity compared to nonadopted children, but mid/late-pubertal postinstitutionalized children displayed higher reactivity similar to the nonadopted comparison children. CONCLUSIONS This is the first evidence of possible pubertal recalibration of HPA axis reactivity to a psychosocial stressor in postinstitutionalized children, which provides a promising avenue for future research regarding the protective factors of the postadoption environment and subsequent physiological, behavioral, and psychopathological outcomes.
Association between GPX1 and SOD2 genetic polymorphisms and overall survival in patients with metastatic urothelial bladder cancer: a single-center study in Serbia.

PURPOSE Purpose: Urothelial bladder cancer (UBC) is the most common malignancy of urinary tract in the developed world. In metastatic UBC, systemic chemotherapy still remains the mainstay of initial treatment. Inter-individual differences in treatment outcome partially may be the consequence of genetic variations in enzymes that modulate oxidative stress. Therefore, we aimed to determine the potential prognostic role of single nucleotide polymorphism (SNP) of the two antioxidant enzymes glutathione peroxidase 1 (GPX1) and superoxide dismutase 2 (SOD2) in metastatic UBC patients treated with cisplatin-based chemotherapy. METHODS Methods: This prospective single-center hospital-based case-control study included 33 patients with metastatic UBC treated with cisplatin-based chemotherapy and 227 healthy controls. GPX1 SNP (rs1050450) was assessed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and SOD2 SNP (rs4880) was determined by quantitative PCR (q-PCR). Overall survival (OS) was evaluated using Kaplan–Meier survival analysis during 2-year follow up period, with the log-rank test for prognostic significance. RESULTS Results: No significant difference was observed in the distributions of GPX1 and SOD2 gene variants between patients and controls (p˃0.05). Regarding GPX1 polymorphism, no impact of GPX1 polymorphism on OS could be demonstrated (p˃0.05). Finally, Kaplan-Meier survival analysis showed no association between SOD2 polymorphism and OS (p˃0.05). CONCLUSIONS Conclusions: No association was found between polymorphism of GPX1 and SOD2 and OS in patients with metastatic urothelial bladder cancer treated with cisplatin-based chemotherapy.
Cross-sectional white matter microstructure differences in age and trait mindfulness

The process of aging can be characterized by a decline in cognitive performance, which may be accompanied by deterioration in specific structural properties of the brain. In this study we sought to investigate to what extent mindfulness changes over the aging process, and which alterations in brain structure can be associated to aging and concomitant changes in mindfulness. We collected Mindful Attention Awareness Scale questionnaire data to assess trait mindfulness and acquired diffusion-weighted imaging data fitted to the diffusion tensor model (DTI) in a group of 97 middle-aged to elderly participants. Our results showed that trait mindfulness increased with age. In terms of white matter structure our results suggested that there was a general increase of omnidirectional diffusion, which favored radial over axial diffusivity, leading to a decrease in fractional anisotropy (FA) in older participants. We further showed that trait mindfulness mediated the FA-age effect in a localized area consisting of the internal and external capsule, as well as the corona radiata. The implication of this mediation analysis is that trait mindfulness may deter age-associated neurocognitive decline, perhaps by preventing age-associated microlesions specifically in cortico-subcortical white matter tracts. This study can be considered a pioneer of using DTI studies to investigate the relationship between age and trait mindfulness.
Aortic Lumen Area Is Increased in Ruptured Abdominal Aortic Aneurysms and Correlates to Biomechanical Rupture Risk

Purpose: To investigate how 2-dimensional geometric parameters differ between ruptured and asymptomatic abdominal aortic aneurysms (AAAs) and provide a biomechanical explanation for the findings. Methods: The computed tomography angiography (CTA) scans of 30 patients (mean age 77±10 years; 23 men) with ruptured AAAs and 60 patients (mean age 76±8 years; 46 men) with asymptomatic AAAs were used to measure maximum sac diameter along the center lumen line, the cross-sectional lumen area, the total vessel area, the intraluminal thrombus (ILT) area, and corresponding volumes. The CTA data were segmented to create 3-dimensional patient-specific models for finite element analysis to compute peak wall stress (PWS) and the peak wall rupture index (PWRI). To reduce confounding from the maximum diameter, 2 diameter-matched groups were selected from the initial patient cohorts: 28 ruptured AAAs and another with 15 intact AAAs (diameters 74±12 vs 73±11, p=0.67). A multivariate model including the maximum diameter, the lumen area, and the ILT area of the 60 intact aneurysms was employed to predict biomechanical rupture risk parameters. Results: In the diameter-matched subgroup comparison, ruptured AAAs had a significantly larger cross-sectional lumen area (1954±1254 vs 1120±623 mm2, p=0.023) and lower ILT area ratio (55±24 vs 68±24, p=0.037). The ILT area (2836±1462 vs 2385±1364 mm2, p=0.282) and the total vessel area (3956±1170 vs 4338±1388 mm2, p=0.384) did not differ statistically between ruptured and intact aneurysms. The PWRI was increased in ruptured AAAs (0.80 vs 0.48, p<0.001), but the PWS was similar (249 vs 284 kPa, p=0.194). In multivariate regression analysis, lumen area was significantly positively associated with both PWS (p<0.001) and PWRI (p<0.01). The ILT area was also significantly positively associated with PWS (p<0.001) but only weakly with PWRI (p<0.01). The lumen area conferred a higher risk increase in both PWS and PWRI when compared with the ILT area. Conclusion: The lumen area is increased in ruptured AAAs compared to diameter-matched asymptomatic AAAs. Furthermore, this finding may in part be explained by a relationship with biomechanical rupture risk parameters, in which lumen area, irrespective of maximum diameter, increases PWS and PWRI. These observations thus suggest a possible method to improve prediction of rupture risk in AAAs by measuring the lumen area without the use of computational modeling.
Detection of Dinophysis Species and Associated Okadaic Acid in Farmed Shellfish: a Two-year Study from The Western Mediterranean Area

Abstract Introduction Diarrhoetic shellfish poisoning (DSP), an alimentary intoxication known to lead to intestinal symptoms, and caused by toxins produced by some dinoflagellates (including several Dinophysis), represents a serious threat to public health. The aim of this paper was to provide information about the occurrence and abundance of potentially toxic harmful algal species causing DSP, and the associated concentration of okadaic acid (OA) toxins. The departing assumption was that in the study area there was an increase in the presence both of Dinophysis species and OA and its derivates that could result in a risk to the health of seafood consumers. Material and Methods During 2015–2016, water and shellfish samples were collected in the Mediterranean area (Sardinia, Italy). Dinophysis cells were counted according to Utermöhl’s method from water samples, while mass spectrometry was used to identify lipophilic toxins in molluscs. Results A total of 46 non-compliant samples of Mytilus galloprovincialis were observed. Their non-compliance concerned their OA levels above the legal limit. Among toxic dinoflagellates, D. acuminata and D. sacculus were the species found mostly during DSP events. Conclusion No cases of human intoxication have been reported, but continuous surveillance of toxic phytoplankton is necessary to predict and prevent its harmful effects on human health.
Community perceptions and personal accounts of HIV discordance in rural western Kenya

Among HIV-discordant couples, the literature is sparse regarding issues related to stigma, relationships and coping. Objectives were to explore: 1) perceptions about discordant HIV status; 2) understanding of HIV discordancy; 3) effects of discordancy on couples; and 4) adaptation and coping strategies for discordant HIV status. A survey was administered to 202 members of heterosexual discordant couples in rural western Kenya. In addition, to understand the community perspective, in-depth interviews (IDI) (n = 26) and focus group discussions (FGD) (n = 10) were conducted with community opinion leaders, healthcare workers and members of discordant couples. More than 70% of men (73.4%) and women (80.4%) surveyed agreed that their relationship changed for the worse when they disclosed their HIV status to their partner. Participants of IDIs and FGDs provided several explanations for discordancy including the perception that discordancy is a lie, the negative partner has “thick blood”, HIV infection is a punishment for sexual promiscuity or cultural disobedience, and that HIV is a punishment from God. Members of discordant couples reported experiencing tension and fear, stigma and rejection, and changes in partner support. Adaptation and coping strategies included counselling, sero-sorting and pursuing concordancy with the uninfected partner. HIV discordancy in a relationship can potentially cause long-term negative emotional and physical consequences. There is an acute need to develop and disseminate locally sensitive HIV-discordant couple counselling messages, and to provide couple-centred HIV care and treatment. Communication can help couples rebuild and rebalance their relationship and adjust to a new normal.
Quality of Life in a Randomized Breast Cancer Prevention Trial of Low-Dose Tamoxifen and Fenretinide in Premenopausal Women

Menopausal symptoms are the main reason for withdrawal in tamoxifen prevention trials. Here, we present Menopause Quality of Life (MenQoL) assessment within a randomized 2 × 2 phase II clinical trial of low-dose tamoxifen and the synthetic retinoid fenretinide. A total of 235 premenopausal women at higher risk for breast cancer were randomized to either tamoxifen 5 mg daily, fenretinide 200 mg daily, their combination, or placebo. Climacteric symptoms were investigated using the MenQoL questionnaire which was self-administered at each visit for 2 years of treatment and for 1 year of follow-up. CYP2D6 was genotyped in subjects taking tamoxifen to study the association with menopausal symptoms. The MenQoL effect size analysis showed no statistically significant difference among the four treatment arms for all four domains (vasomotor, physical, psychosocial, and sexual). Vasomotor symptoms only slightly increased under tamoxifen, with a score at year two of 1.45, 1.21, 0.58, and 1.17 in the combined, tamoxifen, fenretinide, and placebo arms, respectively. Compared with the slow metabolizers, a higher percentage of subjects with CYP2D6 extensive metabolizer genotype complained of a ≥3 score in the vasomotor, psychosocial, and sexual domain in the tamoxifen arms (P value = 0.01, 0.007, and 0.007, respectively). QoL in premenopausal or perimenopausal women was not significantly worsened by low-dose tamoxifen or fenretinide. Our findings suggest that a low dose of tamoxifen may increase its acceptability for breast cancer prevention.
Learning to Route Efficiently with End-to-End Feedback: The Value of Networked Structure

We introduce efficient algorithms which achieve nearly optimal regrets for the problem of stochastic online shortest path routing with end-to-end feedback. The setting is a natural application of the combinatorial stochastic bandits problem, a special case of the linear stochastic bandits problem. We show how the difficulties posed by the large scale action set can be overcome by the networked structure of the action set. Our approach presents a novel connection between bandit learning and shortest path algorithms. Our main contribution is an adaptive exploration algorithm with nearly optimal instance-dependent regret for any directed acyclic network. We then modify it so that nearly optimal worst case regret is achieved simultaneously. Driven by the carefully designed Top-Two Comparison (TTC) technique, the algorithms are efficiently implementable. We further conduct extensive numerical experiments to show that our proposed algorithms not only achieve superior regret performances, but also reduce the runtime drastically.
Feather degradation by keratinolytic bacteria and biofertilizing potential for sustainable agricultural production

Feathers account for 5–7% of the total weight of chicken have become one of the major pollutants due to their recalcitrant nature. Feather which is constituted of 90% keratin can be a good source of peptides, amino acids, and minerals for use as organic fertilizer. Traditional feather degradation methods consume large amount of energy and reduces the overall quality of the proteins. However, degradation of keratin by keratinolytic bacteria may represent as an alternative for the development of cheap, cost effective, eco‐friendly, and easily available nitrogen (N) and minerals rich source as potential organic fertilizers. Keratinase enzymes from bacteria are serine‐type proteases showing optimal activity at pH 6 to 9 and 30 to 50 °C. Mechanism of degradation includes, sulfitolysis, proteolysis, followed by deamination. Keratinolytic bacteria showing antagonism against important plant pathogens may act as biocontrol agent. Feather hydrolyzate can also be employed as nitrogenous fertilizers for plant growth. Tryptophan release from the feather degradation can act as precursor for plant phytohormone, indole‐3‐acetic acid (IAA). Solubilization of inorganic phosphate (P) by keratinolytic bacteria may further elevate the growth of plant. Application of hydrolyzate increases the water holding capacity, N, carbon (C) and mineral content of the soil. It elevates protein, amino acids, and chlorophyll content of plant. Feather hydrolyzate enhances seed germination and growth of plant. Soil application further increases the population of beneficial bacteria. The use of keratinolytic bacteria having antagonistic and plant growth promoting activities, and feather hydrolyzate can emerge as sustainable and alternative tools to promote and improve organic farming, agro‐ecosystem, environment, human health, and soil biological activities.
Management and treatment of children with medulloblastoma in Serbia, a middle-income country.

PURPOSE The aim of this study was to present the management and treatment of children with medulloblastoma in Serbia, a middle-income country (MIC). METHODS The data of 87 children diagnosed with medulloblastoma and treated at the Institute for Oncology and Radiology of Serbia from 2000 to 2013 were analyzed. RESULTS The children's median age was 8.3 years (range 2.5-17.3). Eighty-two (94.2%) were 3 years or older. Sixtytwo (71.3%) patients had stage M0 medulloblastoma, 12 (13.8%) had stage M1 and 13 (14.9%) had stage M2 or M3. As of October 2015, 51 (58.6%) patients were alive and 31 (35.6%) had died. Five patients (5.7%) were lost to followup. Twenty-six patients relapsed. The median follow-up time was 58 months (range 4-187). Mean overall survival (OS) was 76.4% at 3 years, 66.2% at 5 years and 59.2% at 10 years. Mean disease-free survival (DFS) was 75.8% at 3 years, 62.8% at 5 years and 56.6% at 10 years. Mean OS of stage M0 patients was 86.4% at 3 years, 74% at 5 years and 63.1% at 10 years. The OS of stage M1, M2 and M3 patients combined was 48.9% at 3 years, 44.0% at 5 years and 37.7% at 10 years. CONCLUSION In Serbia, a MIC, it is possible to achieve good treatment results in children with medulloblastoma using international treatment guidelines and recommendations, available resources and an experienced team of professionals dedicated to pediatric neurooncology.