Miracle-dz/UniFAR-FTUs huggingface dataset:
Is the Stack Distance Between Test Case and Method Correlated With Test Effectiveness?

Mutation testing is a means to assess the effectiveness of a test suite and its outcome is considered more meaningful than code coverage metrics. However, despite several optimizations, mutation testing requires a significant computational effort and has not been widely adopted in industry. Therefore, we study in this paper whether test effectiveness can be approximated using a more light-weight approach. We hypothesize that a test case is more likely to detect faults in methods that are close to the test case on the call stack than in methods that the test case accesses indirectly through many other methods. Based on this hypothesis, we propose the minimal stack distance between test case and method as a new test measure, which expresses how close any test case comes to a given method, and study its correlation with test effectiveness. We conducted an empirical study with 21 open-source projects, which comprise in total 1.8 million LOC, and show that a correlation exists between stack distance and test effectiveness. The correlation reaches a strength up to 0.58. We further show that a classifier using the minimal stack distance along with additional easily computable measures can predict the mutation testing result of a method with 92.9% precision and 93.4% recall. Hence, such a classifier can be taken into consideration as a light-weight alternative to mutation testing or as a preceding, less costly step to that.
Estimating photosynthetic capacity from leaf reflectance and Chl fluorescence by coupling radiative transfer to a model for photosynthesis

Summary In photosynthesis models following the Farquhar formulation, the maximum carboxylation rate V cmax is the key parameter. Remote‐sensing indicators, such as reflectance ρ and Chl fluorescence (ChlF), have been proven as valuable estimators of photosynthetic capacity and can be used as a constraint to V cmax estimation. We present a methodology to retrieve V cmax from leaf ρ and ChlF by coupling a radiative transfer model, fluspect, to a model for photosynthesis. We test its performance against a unique dataset, with combined leaf spectral, gas exchange and pulse‐amplitude‐modulated measurements. Our results show that the method can estimate the magnitude of V cmax estimated from the far‐red peak of ChlF and green ρ or transmittance τ, with values of root‐mean‐square error below 10 μmol CO 2 m−2 s−1. At the leaf level, the method could be used for detection of plant stress and tested against more extensive datasets. With a similar scheme devised for the higher spatial scales, such models could provide a comprehensive method to estimate the actual photosynthetic capacity of vegetation.
The Development of Anxiety Sensitivity Interventions from Manual to Computerized

: Excessive anxiety is something that could affect an individual’s behavior if it is not treated well. Excessive anxiety could develop into more serious anxiety disorders that affect attitudes and behavior in the social environment. The purpose of this literature study is to examine the effectiveness of various interventions in reducing anxiety sensitivity by conducting a review of articles related to interventions to reduce anxiety sensitivity. The article review was conducted on 18 international journals between 2008 and 2018 in accordance with the selection criteria. The analysis in this journal review covers the effectiveness of interventions, strengths, and weaknesses of the research methods used. The various interventions used show that reducing anxiety sensitivity using cognitive behavioral therapy (CBT) interventions is still a good option to reduce anxiety sensitivity, followed by other interventions, namely cognitive bias modification (CBM). Based on research subjects, interventions with individual subjects are more widely used than interventions with group subjects. The discussions about the results of the review can be used as recommendations for further research.
Circulating microRNA‐133, microRNA‐17 and microRNA‐25 in serum and its potential diagnostic value in gastric cancer

Gastric cancer is one of the most common malignancies in the world and is considered as the most lethal gastrointestinal cancer. microRNAs (miRNAs) can be very important in detecting a disease at an early stage. The aim of this study was to investigate the microRNA‐17 (miR‐17), miR‐25, and miR‐133b in the serum of gastric cancer subjects. Serum samples were obtained from 120 gastric cancers and 102 healthy subjects. We evaluated expression levels of miR‐17, miR‐25 and miR‐133b by quantitative real‐time polymerase chain reaction. Our results showed that in the patients with gastric cancer, the expression level of miR‐17 and miR‐25 were significantly increased compared with the control group (P < 0.5), while the expression level of miR‐133b was significantly decreased in patient groups compared with control cases (P < 0.5). It seems that expression of miRNAs in Iranian patients with gastric cancer is similar to other patients in other populations. These findings suggested that miR‐17, miR‐25 and miR‐133b could be introduced as potential diagnostic candidates for the detection in gastric cancer patients in the early stage.
Occurrence of Vine Decline Diseases of Muskmelon in Guatemala.

Central American countries have become major production areas of melons (Cucumis melo L.) destined for export to Europe and the United States during the winter months. Double cropping in the same fields year after year has created serious vine decline diseases in melons grown in the Capco area of Guatemala. Vines typically appear healthy until the fruit are approaching maturity, when the crown leaves begin to turn yellow and collapse and the decline gradually radiates outward. There was evidence of slightly water-soaked lesions in the crown of some plants; however, the symptoms were not similar to charcoal rot or gummy stem blight. The roots exhibited some decay, lesions, and discoloration, but were not macerated and rotten. A minimum of 10 affected plants were collected from each of nine fields in the Capco area of Guatemala. Isolations were made from the crown area, primary root, and secondary roots of selected plants by excising 3- to 5-mm pieces and surface sterilizing them for 30 to 60 s with 0.5% sodium hypochlorite. The isolations were made on 2% water agar plus 0.1 g of streptomycin sulfate per liter. Plates were examined for fungal growth daily for 5 days with hyphal tips from all colonies transferred to potato dextrose agar and Synthetischer nährstoffärmer agar (2) and allowed to sporulate. Isolations revealed the presence of several fungi capable of causing vine decline or suspected of being involved in the vine decline complex. Rhizoctonia solani Kühn and Fusarium semitectum Berk. & Ravenel were isolated from more than 50% of plants in some fields. F. semitectum, R. solani, and a Stagonospora-like fungus were isolated from 38, 18, and 17% of the total plants, respectively. R. solani was isolated from the crown more often than from the roots, but its role is not understood. With one exception, F. semitectum was always isolated from the crown area, which may suggest a more significant role in the vine decline complex than suspected previously. The Stagonospora-like fungus, isolated from 30% of the plants from one field, has been reported as a pathogen of cantaloupe that may contribute to the vine decline complex (1). Monosporascus cannonballus Pollack & Uecker and Fusarium oxysporum Schlechtend. :Fr. emend. W. C. Snyder & H. N. Hans. were isolated from 60% of the plants from one field. It was the only field in which M. cannonballus was isolated. Plectosporium tabacinum (van Beyma) M. E. Palm, W. Gams et Nirenberg, a cucurbit pathogen, was isolated infrequently. This is the first report of M. cannonballus, P. tabacinum, and the Stagonospora-like fungus in Guatemala. References: (1) M. E. Miller et al. Phytopathology 86:S3, 1996. (2) H. I. Nirenberg. Mitt. Biol. Bundesanst. Land Forstwirtsch. Berlin-Dahlem. 169:1, 1976.
Neuropsychological deficits in participants at clinical high risk for psychosis recruited from the community: relationships to functioning and clinical symptoms

Abstract Background The current study examined the pattern of neurocognitive impairments in a community-recruited sample of clinical high-risk (CHR) participants and established relationships with psychosocial functioning. Methods CHR-participants (n = 108), participants who did not fulfil CHR-criteria (CHR-negatives) (n = 42) as well as a group of healthy controls (HCs) (n = 55) were recruited. CHR-status was assessed using the Comprehensive Assessment of At-Risk Mental States (CAARMS) and the Schizophrenia Proneness Instrument, Adult Version (SPI-A). The Brief Assessment of Cognition in Schizophrenia Battery (BACS) as well as tests for emotion recognition, working memory and attention were administered. In addition, role and social functioning as well as premorbid adjustment were assessed. Results CHR-participants were significantly impaired on the Symbol-Coding and Token-Motor task and showed a reduction in total BACS-scores. Moreover, CHR-participants were characterised by prolonged response times (RTs) in emotion recognition as well as by reductions in both social and role functioning, GAF and premorbid adjustments compared with HCs. Neurocognitive impairments in emotion recognition accuracy, emotion recognition RT, processing speed and motor speed were associated with several aspects of functioning explaining between 4% and 12% of the variance. Conclusion The current data obtained from a community sample of CHR-participants highlight the importance of dysfunctions in motor and processing speed and emotion recognition RT. Moreover, these deficits were found to be related to global, social and role functioning, suggesting that neurocognitive impairments are an important aspect of sub-threshold psychotic experiences and a possible target for therapeutic interventions.
www.econstor.eu Debt Maturity without Commitment

I analyze how lack of commitment affects the maturity structure of sovereign debt. Governments balance benefits of default induced redistribution and costs due to income losses in the wake of a default. Their choice of shortversus longterm debt affects default and rollover decisions by subsequent policy makers. The equilibrium maturity structure is shaped by revenue losses on inframarginal units of debt that reflect the price impact of these decisions. The model predicts an interior maturity structure with positive gross positions and a shortening of the maturity structure when debt issuance is high, output low, or a cross default more likely. These predictions are consistent with empirical evidence.
Analysis and Modeling of Timbre Perception Features in Musical Sounds

A novel technique is proposed for the analysis and modeling of timbre perception features, including a new terminology system for evaluating timbre in musical instruments. This database consists of 16 expert and novice evaluation terms, including five pairs with opposite polarity. In addition, a material library containing 72 samples (including 37 Chinese orchestral instruments, 11 Chinese minority instruments, and 24 Western orchestral instruments) and a 54-sample objective acoustic parameter set were developed as part of the study. The method of successive categories was applied to each term for subjective assessment. A mathematical model of timbre perception features (i.e., bright or dark, raspy or mellow, sharp or vigorous, coarse or pure, and hoarse or consonant) was then developed for the first time using linear regression, support vector regression, a neural network, and random forest algorithms. Experimental results showed the proposed model accurately predicted these attributes. Finally, an improved technique for 3D timbre space construction is proposed. Auditory perception attributes for this 3D timbre space were determined by analyzing the correlation between each spatial dimension and the 16 timbre evaluation terms.
Combined Nutraceuticals: A Novel Approach to Colitis-Associated Colorectal Cancer?

Abstract Ulcerative colitis is an unremitting and lifelong inflammatory bowel disease that is increasing in prevalence worldwide. Patients display various clinical symptoms such as abdominal pain, diarrhea and fatigue. The etiology of ulcerative colitis remains unknown and the current pharmaceutical treatments are variably effective and not curative, highlighting the need for improved therapeutic approaches. Furthermore, patients with ulcerative colitis are at an increased risk of developing colorectal cancer. Some naturally sourced agents, named nutraceuticals, have been identified to possess anti-inflammatory and antioxidant properties. Of particular interest is Emu Oil, grape seed extract and Japanese Kampo medicine. Previously, Emu Oil has protected and repaired intestinal damage in models of gastrointestinal diseases including colitis and colitis-associated colorectal cancer. Additionally, grape seed extract possesses anticancer properties in vitro. Moreover, Kampo medicine, composed of herbal ingredients, is widely used in Japan for the treatment of various medical conditions and has demonstrated efficacy in targeting cancer cells in vitro. Nutraceuticals in combination have not yet been widely investigated in a setting of colitis-associated colorectal cancer. Investigation into the efficacy of Emu Oil combined with other nutraceuticals, including grape seed extract and Kampo medicine, is warranted as they may provide a novel approach to conventional colitis and colorectal cancer management.
Vitamin D Levels of Outpatients Admitted to a University Hospital in the Marmara Region of Turkey Over 3 Years

Summary Background Vitamin D regulates calcium and phosphorus metabolism, and it is essential for bone formation. Several factors can affect vitamin D levels in plasma. In present study we compare vitamin D levels of outpatients, who admit to Maltepe University Hospital between 2011 and 2013 and had vitamin D measurements regarding gender, age, and season. Methods Hospital records were evaluated to identify the outpatients with vitamin D levels and their gender, age, and vitamin D levels and the seasons of measurements were recorded. Results Data of 4860 subjects (74% female) were analyzed and 69.2% were between 18–64 years old. Vitamin D levels were as follows: 43.1% ≤ 10 ng/mL, 31.9% between 10 ng/mL and 20 ng/mL, 16.1% between 20 ng/mL and 30 ng/mL, and only 8.9% ≥ 30 ng/mL. The number of females with vitamin D levels < 10 ng/mL was significantly higher than that of males, while the number of males with vitamin D levels between 10 ng/mL and 20 ng/mL was significantly higher than that of females (P = 0.001) for each of the individuals, 6.2% and 11.1% had sufficient levels in winter and summer, respectively. Overall, it was observed that 6.6% of individuals between 18–44 years old, 8.2% of individuals between 45–64 years old and 10.3% of individuals over 65 years old had vitamin D levels > 30 ng/mL. Conclusions The prevalence of vitamin D deficiency in outpatients of Maltepe University Hospital in Marmara region was 75% (< 20 ng/mL).
The effects of trans-resveratrol on insulin resistance, inflammation, and microbiota in men with the metabolic syndrome: A pilot randomized, placebo-controlled clinical trial

Background and Aim: The metabolic syndrome (MetS) is a pathological condition comprised of abdominal obesity, insulin resistance, hypertension, and hyperlipidemia. It has become a major threat globally, resulting in rapidly increasing rates of diabetes, coronary heart disease, and stroke. The polyphenol resveratrol (RES) is believed to improve glucose homeostasis and insulin resistance by activating sirtuin, which acetylates and coactivates downstream targets and affects glucose and lipid homeostasis in the liver, insulin secretion in the pancreas, and glucose uptake in skeletal muscle. We studied the effects of RES on insulin resistance, glucose homeostasis, and concomitant effects on adipose tissue metabolism and fecal microbiota in insulin-resistant subjects with the MetS. Methods: A total of 28 obese men with the MetS were studied during a 35-day stay in the Rockefeller University Hospital metabolic unit. Subjects were randomized to receive RES 1 g orally twice daily or placebo while kept weight stable and consuming a western-style diet. At baseline, and after 30 days of RES or placebo administration, subjects underwent testing that included a euglycemic, hyperinsulinemic clamp, 2-h oral glucose tolerance test (GTT), resting energy expenditure, daily blood pressure monitoring, abdominal adipose tissue biopsy, and fecal and blood collections. Results: RES induced no changes in insulin resistance but reduced the 120-min time point and the area under the curve for glucose concentration in the 2-h GTT. In post-hoc analysis, Caucasian subjects showed a significant improvement in insulin sensitivity and glucose homeostasis after GTT, whereas non-Caucasians showed no similar effects. Levels of fasting plasma RES and its primary metabolite dihydroresveratrol were variable and did not explain the racial differences in glucose homeostasis. RES administration to Caucasian subjects leads to an increase in several taxa including Akkermansia muciniphila. Conclusions: RES 2 g administered orally to obese men with MetS and insulin resistance marginally altered glucose homeostasis. However, in a small group of Caucasians, insulin resistance and glucose homeostasis improved. No concomitant changes in adipose tissue metabolism occurred, but fecal microbiota showed RES-induced changes. Relevance for Patients: The MetS increases the risk of diabetes, heart disease, and stroke. A major component of the syndrome is insulin resistance, resulting in systemic inflammation and hyperinsulinemia. The primary treatment consists of lifestyle changes, improved diet, and increased physical activity. This is often unsuccessful. In this study, RES was well tolerated. In Caucasian men, it significantly improved insulin sensitivity and glucose homeostasis. Similar results were found in studies that consisted exclusively of Caucasian men. However, RES presents a novel addition to the current treatment of the MetS and its sequelae.
Efficacy, safety, and tolerability of perampanel in Asian and non‐Asian patients with epilepsy

People of different ethnic or racial backgrounds may experience variations in pharmacokinetic and pharmacodynamic responses to drug therapies. Our post hoc analysis evaluated the efficacy, safety, and tolerability of perampanel in Asian and non‐Asian populations with refractory focal seizures with or without focal to bilateral tonic‐clonic (FBTC) seizures. This analysis pooled data from 4 randomized, placebo‐controlled, phase‐3 studies involving patients aged ≥12 years who have focal seizures with or without FBTC seizures. Patients were receiving 2, 4, 8, or 12 mg perampanel (or placebo) by the end of a 6‐week titration period and for a further 13 weeks during the maintenance phase. Efficacy endpoints included median percent change in seizure frequency per 28 days, and 50% and seizure‐freedom responder rates relative to baseline. The median percent change in seizure frequency per 28 days from baseline was significantly greater than placebo for perampanel 8 and 12 mg (−31.1% and −38.1% change, respectively; each P < 0.0001) in the Asian population, and for perampanel 4, 8, and 12 mg (−21.1% [P = 0.0001], −26.3% [P < 0.0001], and −27.7% [P = 0.0001] change, respectively) in the non‐Asian population. The 50% responder rate relative to baseline was significantly greater than placebo for perampanel 8 and 12 mg (40.1% and 43.8%, respectively; each P < 0.0001) in the Asian population, and for perampanel 4, 8, and 12 mg (29.4% [P = 0.0002], 32.8% [P < 0.0001] and 34.5% [P = 0.0001]), respectively, in the non‐Asian population. Seizure‐freedom rate among all patients was 4.9%‐11.7% for perampanel 2, 4, 8, and 12 mg. The most frequently reported treatment‐emergent adverse events (TEAEs) across both populations were dizziness, somnolence, irritability, headache, and fatigue. The most common psychiatric TEAEs were aggression and irritability. Perampanel demonstrated a favorable and similar risk‐benefit profile in both Asian and non‐Asian populations with refractory focal seizures.
Combination of Treatments With or Without Surgery in Localized Provoked Vulvodynia: Outcomes After Three Years of Follow-Up

Most vulvodynia patients receive combinations of several treatment modalities for their chronic painful condition. If conservative treatments fail, vestibulectomy is considered to be the ultimate treatment option for localized provoked vulvodynia (LPV). The aim of this descriptive study was to analyze relief of pain, quality of life (QoL), and complications associated with combining surgery with conservative treatments among LPV patients, both in short term and after 3 years of follow-up. The study population consisted of a retrospective patient cohort of surgically (n = 16) and only conservatively (n = 50) treated LPV patients. QoL data were assessed by a validated questionnaire (RAND-36). Data were collected by reviewing patient records and by aid of postal questionnaires. Efficacy of treatments in relief of pain was measured by numerical rating scale (NRS). Two months after surgery, the NRS scores assessed by a physician were lower in the surgery group than in patients treated only conservatively (p = 0.008). However, after a median of 36 months of follow-up, self-reported NRS scores and QoL showed no difference between the two patient cohorts. Complication rate after vestibulectomy was 18.8%. The findings suggest that combining surgery with conservative treatments may result in a more effective short-term reduction of pain. However, the effect seemed to be only temporary, as no long-term benefit was achieved.
Immune infiltration in renal cell carcinoma

Immune infiltration of tumors is closely associated with clinical outcome in renal cell carcinoma (RCC). Tumor‐infiltrating immune cells (TIICs) regulate cancer progression and are appealing therapeutic targets. The purpose of this study was to determine the composition of TIICs in RCC and further reveal the independent prognostic values of TIICs. CIBERSORT, an established algorithm, was applied to estimate the proportions of 22 immune cell types based on gene expression profiles of 891 tumors. Cox regression was used to evaluate the association of TIICs and immune checkpoint modulators with overall survival (OS). We found that CD8+ T cells were associated with prolonged OS (hazard ratio [HR] = 0.09, 95% confidence interval [CI].01‐.53; P = 0.03) in chromophobe carcinoma (KICH). A higher proportion of regulatory T cells was associated with a worse outcome (HR = 1.59, 95% CI 1.23‐.06; P < 0.01) in renal clear cell carcinoma (KIRC). In renal papillary cell carcinoma (KIRP), M1 macrophages were associated with a favorable outcome (HR = .43, 95% CI .25‐.72; P < 0.01), while M2 macrophages indicated a worse outcome (HR = 2.55, 95% CI 1.45‐4.47; P < 0.01). Moreover, the immunomodulator molecules CTLA4 and LAG3 were associated with a poor prognosis in KIRC, and IDO1 and PD‐L2 were associated with a poor prognosis in KIRP. This study indicates TIICs are important determinants of prognosis in RCC meanwhile reveals potential targets and biomarkers for immunotherapy development.