Miracle-dz/UniFAR-FTUs huggingface dataset:
Feature-gathering dependency-based software clustering using Dedication and Modularity

Software clustering is one of the important techniques to comprehend software systems. However, presented techniques to date require human interactions to refine clustering results. In this paper, we proposed a novel dependency-based software clustering algorithm, SArF. SArF has two characteristics. First, SArF eliminates the need of the omnipresent-module-removing step which requires human interactions. Second, the objective of SArF is to gather relevant software features or functionalities into a cluster. To achieve them, we defined the Dedication score to infer the importance of dependencies and utilized Modularity Maximization to cluster weighted directed graphs. Two case studies and extensive comparative evaluations using open source and industrial systems show that SArF could successfully decompose the systems fitting to the authoritative decompositions from a feature viewpoint without any tailored setups and that SArF was superior to existing dependency-based software clustering studies. Besides, the case studies show that there exist measurable authoritativeness limits and that SArF nearly reached the limits.
Biosynthesis of Cylindrospermopsin and 7-Epicylindrospermopsin in Oscillatoria sp. Strain PCC 6506: Identification of the cyr Gene Cluster and Toxin Analysis

ABSTRACT Cylindrospermopsin is a cytotoxin produced by Cylindrospermopsis raciborskii and other cyanobacteria that has been implicated in human intoxications. We report here the complete sequence of the gene cluster responsible for the biosynthesis of this toxin in Oscillatoria sp. strain PCC 6506. This cluster of genes was found to be homologous with that of C. raciborskii but with a different gene organization. Using an enzyme-linked immunosorbent assay and an optimized liquid chromatography analytical method coupled to tandem mass spectrometry, we detected 7-epicylindrospermopsin, cylindrospermopsin, and 7-deoxycylindrospermopsin in the culture medium of axenic Oscillatoria PCC 6506 at the following relative concentrations: 68.6%, 30.2%, and 1.2%, respectively. We measured the intracellular and extracellular concentrations, per mg of dried cells of Oscillatoria PCC 6506, of 7-epicylindrospermopsin (0.18 μg/mg and 0.29 μg/mg, respectively) and cylindrospermopsin (0.10 μg/mg and 0.11 μg/mg, respectively). We showed that these two toxins accumulated in the culture medium of Oscillatoria PCC 6506 but that the ratio (2.5 ± 0.3) was constant with 7-epicylindrospermopsin being the major metabolite. We also determined the concentrations of these toxins in culture media of other Oscillatoria strains, PCC 6407, PCC 6602, PCC 7926, and PCC 10702, and found that, except for PCC 6602, they all produced 7-epicylindrospermopsin and cylindrospermopsin, with the former being the major toxin, except for PCC 7926, which produced very little 7-epicylindrospermopsin. All the cylindrospermopsin producers studied gave a PCR product using specific primers for the amplification of the cyrJ gene from genomic DNA.
The TRPM6 Kinase Domain Determines the Mg·ATP Sensitivity of TRPM7/M6 Heteromeric Ion Channels*

Background: TRPM6 and TRPM7 combine ion channel and α-kinase functions. Results: ATP inhibits TRPM7 but not TRPM6 or heteromeric TRPM6/M7 channels. Disruption of phosphorylation activity of TRPM6 kinase re-establishes ATP sensitivity to heteromeric channels. Conclusion: TRPM6 uncouples heteromeric channels from cellular energy levels. Significance: The altered characteristics of TRPM6/M7 compared with homomeric TRPM7 may enhance Ca2+ and Mg2+ transport in tissues co-expressing both proteins. The transient receptor potential melastatin member 7 (TRPM7) and member 6 (TRPM6) are divalent cation channel kinases essential for magnesium (Mg2+) homeostasis in vertebrates. It remains unclear how TRPM6 affects divalent cation transport and whether this involves functional homomeric TRPM6 plasma membrane channels or heteromeric channel assemblies with TRPM7. We show that homomeric TRPM6 is highly sensitive to intracellular free Mg2+ and therefore unlikely to be active at physiological levels of [Mg2+]i. Co-expression of TRPM7 and TRPM6 produces heteromeric TRPM7/M6 channels with altered pharmacology and sensitivity to intracellular Mg·ATP compared with homomeric TRPM7. Strikingly, the activity of heteromeric TRPM7/M6 channels is independent of intracellular Mg·ATP concentrations, essentially uncoupling channel activity from cellular energy status. Disruption of TRPM6 kinase phosphorylation activity re-introduces Mg·ATP sensitivity to the heteromeric channel similar to that of TRPM7. Thus, TRPM6 modulates the functionality of TRPM7, and the TRPM6 kinase plays a critical role in tuning the phenotype of the TRPM7·M6 channel complex.
Functional connectivity‐based parcellation of amygdala using self‐organized mapping: A data driven approach

The overall goal of this work is to demonstrate how resting state functional magnetic resonance imaging (fMRI) signals may be used to objectively parcellate functionally heterogeneous subregions of the human amygdala into structures characterized by similar patterns of functional connectivity. We hypothesize that similarity of functional connectivity of subregions with other parts of the brain can be a potential basis to segment and cluster voxels using data driven approaches. In this work, self‐organizing map (SOM) was implemented to cluster the connectivity maps associated with each voxel of the human amygdala, thereby defining distinct subregions. The functional separation was optimized by evaluating the overall differences in functional connectivity between the subregions at group level. Analysis of 25 resting state fMRI data sets suggests that SOM can successfully identify functionally independent nuclei based on differences in their inter subregional functional connectivity, evaluated statistically at various confidence levels. Although amygdala contains several nuclei whose distinct roles are implicated in various functions, our objective approach discerns at least two functionally distinct volumes comparable to previous parcellation results obtained using probabilistic tractography and cytoarchitectonic analysis. Association of these nuclei with various known functions and a quantitative evaluation of their differences in overall functional connectivity with lateral orbital frontal cortex and temporal pole confirms the functional diversity of amygdala. The data driven approach adopted here may be used as a powerful indicator of structure–function relationships in the amygdala and other functionally heterogeneous structures as well. Hum Brain Mapp 35:1247–1260, 2014. © 2013 Wiley Periodicals, Inc.
Infant sensitivity to negative maternal emotional shifts: Effects of infant sex, maternal postnatal depression, and interactive style.

This study examined the effects of infant sex, maternal postnatal depression, and maternal interactive style on infant sensitivity to maternal negative emotional shifts. Face-to-face interactions of 68 mother-infant dyads were analyzed at 8 and 18 weeks. Twenty-five (28%) mothers had postnatal depression. Interactions were analyzed in terms of overall maternal interactive style: "sensitive," "anxious," "intrusive," and "sad. " Episodes of negative shifts in maternal emotional expression were recorded, along with expressions of infant sensitivity to these changes. Daughters of depressed mothers showed higher rates of sensitivity to maternal negative emotion whereas their sons showed lower rates, in comparison to both girl and boy infants of well mothers. While maternal interactive style had no effect on 8-week infant sensitivity to maternal negative emotional shifts, high rates of 18-week infant sensitivity were predicted by both an 8-week and a concurrent, "sad" maternal interactive style. The findings are discussed in relation to theories of emotional and interpersonal development.
The Use of the h-Index in Academic Orthopaedic Surgery

Background: The Hirsch index (h-index), widely considered a valuable measure of assessing academic productivity, has been studied in various medical and surgical specialties and has shown strong associations between higher h-indices and academic promotion, as well as with National Institutes of Health (NIH) awards. Additionally, the m-index and e-index may complement the h-index in this assessment of merit. The purpose of this study was to investigate the relationship between the h, m, and e-indices and academic rank for 2,061 academic orthopaedic surgeons in the United States. Methods: The h-indices of faculty members from 120 academic orthopaedic surgery residency programs were organized and calculated using the Scopus and Google Scholar databases. Additionally, m-index and e-index scores were calculated from Google Scholar. After application of exclusion criteria, 2,061 academic orthopaedic surgeons were included. Results: Academic rank (assistant professor, associate professor, professor, and chair) increases as mean h-index, m-index, and e-index scores increase. Among 976 assistant professors, 504 associate professors, 461 professors, and 120 chairs, mean h, m, and e-indices increased with each academic rank. In the comparison of male and female surgeons, there was no significant difference in h, m, or e-index scores, with the exception of increased h-index scores among male assistant professors. Conclusions: Scholarly impact, as defined by academic productivity and scientific relevance, can be classified by the h-index and supplemented by the m and e-indices. This study has revealed well-defined differences in h, m, and e-indices with regard to academic rank among orthopaedic surgeons. Although the h, m, and e-indices may be of value as adjunct assessment devices for scholarly merit, careful consideration of their limitations must be maintained.
Variation among Soybean Cultivars in Mesophyll Conductance and Leaf Water Use Efficiency

Improving water use efficiency (WUE) may prove a useful way to adapt crop species to drought. Since the recognition of the importance of mesophyll conductance to CO2 movement from inside stomatal pores to the sites of photosynthetic carboxylation, there has been interest in how much intraspecific variation in mesophyll conductance (gm) exists, and how such variation may impact leaf WUE within C3 species. In this study, the gm and leaf WUE of fifteen cultivars of soybeans grown under controlled conditions were measured under standardized environmental conditions. Leaf WUE varied by a factor of 2.6 among the cultivars, and gm varied by a factor of 8.6. However, there was no significant correlation (r = −0.047) between gm and leaf WUE. Leaf WUE was linearly related to the sub-stomatal CO2 concentration. The value of gm affected the ratio of maximum Rubisco carboxylation capacity calculated from the sub-stomatal CO2 concentration to that calculated from the CO2 concentration at the site of carboxylation. That is, variation in gm affected the efficiency of Rubisco carboxylation, but not leaf WUE. Nevertheless, there is considerable scope for genetically improving soybean leaf water use efficiency.
Does spiritual care program affect levels of depression in patients with Leukemia? A randomized clinical trial

Background: Although 25-33% of patients with non-hematological malignancies suffer from depression disorder, some studies have reported the rate among patients with leukemia as high as 50%. Furthermore, based on studies chronic disease such as leukemia increases the patients’ spiritual needs and may accelerate the patient problems. Therefore, spirituality has a significant role in adapting to leukemia and coping with its consequent mental disorders such as depression. Owing to the spirituality aspect importance and contradictory results of previous research, this study was hence performed to determine the effects of a spiritual care program on depression of patients with leukemia. Materials and Methods: This randomized clinical trial was conducted in specialized cancer treatment center affiliated to Isfahan University of Medical Sciences (Isfahan, Iran). A total of 64 adult patients with leukemia were randomly divided into experiment and control groups. The spiritual care program including supportive presence and support for religious rituals was implemented for 3 days. Depression sub-scale of 42-item depression, anxiety and stress scale-42 was completed before and after the intervention for both groups. Data was analyzed using ANCOVA, Mann-Whitney U-test, Chi-square, in SPSS statistical software (version 18, SPSS Inc., Chicago, IL). Results: After the intervention, mean score of depression was significantly lower in the experiment group than in the control group (P < 0.01). Comparison the mean score of depression in two groups, revealed the decrees in mean score of depression 11.09 (8.47) after spiritual care program that it was significant (P < 0.001). Conclusion: Our spiritual care program could successfully decrease depression level in patients with leukemia and nurses have to apply a holistic care approach with emphasis on spiritual care to decrease depression, so paid attention to spiritual aspect of patients accompanying with physical aspects in therapy process is recommended.
AGN heating and ICM cooling in the HIFLUGCS sample of galaxy clusters

Active galactic nuclei (AGN) at the center of galaxy clusters with gas cooling times that are much shorter than the Hubble time have emerged as heating agents powerful enough to prevent further cooling of the intracluster medium (ICM). We carried out an intensive study of the AGN heating−ICM cooling network by comparing various cluster parameters to the integrated radio luminosity of the central AGN, LR, defined as the total synchrotron power between 10 MHz and 15 G Hz. This study is based on the HIFLUGCSsample comprising the 64 X-ray brightest galaxy clusters. We adopted the central cooling time, tcool, as the diagnostic to ascertain cooling properties of the HIFLUGCSsample and classify clusters with tcool 7.7 Gyr as non-cool-core (NCC) clusters. We find 48 out of 64 clusters (7 5%) contain cluster center radio sources (CCRS) cospatial with or within 50 h −1 71 kpc of the X-ray peak emission. Furthermore, we find that the p robability of finding a CCRS increases from 45% to 67% to 100% for NCC, WCC, and SCC clusters, respectively. We use a total of∼ 140 independent radio flux-density measurements, with data at more than two frequencies for more than 54% of the sources extending below 500 MHz, enabling the determination of accurate estimates of LR. We find that LR in SCC clusters depends strongly on the cluster scale such that more massive clusters harbor more powerful radio AGN. The same trend is observed between LR and the classical mass deposition rate, ˙ Mclassical in SCC and partly also in WCC clusters, and can be quantified as LR∝ ˙ M 1.69±0.25 classical . We also perform correlations of the luminosity for the brightest cluster galaxy, LBCG, close to the X-ray peak in all 64 clusters with LR and cluster parameters, such as the virial mass, M500, and the bolometric X-ray luminosity, LX. To this end, we use the 2MASS K-band magnitudes and invoke the near-infrared bulge luminosity-black hole mass relation to convert LBCG to supermassive black hole mass, MBH. We find a weak correlation between MBH and LR for SCC clusters, LR∼ M 4.10±0.42 BH , although with a few outliers. We find an excellent correlati on of LBCG with M500 and LX for the entire sample, the SCC clusters showing a tighter trend in both the cases. We discuss the plausible reasons behind these scaling relations in the context of cooling flows and AGN feedback. Our results strongly suggest an AGN-feedback machinery in SCC clusters, which regulates the cooling in the central regions. Since the dispersion in these correlations, such a s that between LR and ˙ Mclassical or LR and MBH, increases in going from SCC to WCC clusters, we conclude there must be secondary processes that work either in conjunction with the AGN heating or independently to counteract the radiative losses in WCC clusters.
Educating future leaders in patient safety

Education of health care professionals has given little attention to patient safety, resulting in limited understanding of the nature of risk in health care and the importance of strengthening systems. The World Health Organization developed the Patient Safety Curriculum Guide: Multiprofessional Edition to accelerate the incorporation of patient safety teaching into higher educational curricula. The World Health Organization Curriculum Guide uses a health system-focused, team-dependent approach, which impacts all health care professionals and students learning in an integrated way about how to operate within a culture of safety. The guide is pertinent in the context of global educational reforms and growing recognition of the need to introduce patient safety into health care professionals’ curricula. The guide helps to advance patient safety education worldwide in five ways. First, it addresses the variety of opportunities and contexts in which health care educators teach, and provides practical recommendations to learning. Second, it recommends shared learning by students of different professions, thus enhancing student capacity to work together effectively in multidisciplinary teams. Third, it provides guidance on a range of teaching methods and pedagogical activities to ensure that students understand that patient safety is a practical science teaching them to act in evidence-based ways to reduce patient risk. Fourth, it encourages supportive teaching and learning, emphasizing the need to establishing teaching environments in which students feel comfortable to learn and practice patient safety. Finally, it helps educators incorporate patient safety topics across all areas of clinical practice.
Engineering nanocomposite membranes : fabrication, modification and application

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Cefoperazone-sulbactam for treatment of intra-abdominal infections: results from a randomized, parallel group study in India.

BACKGROUND Combinations of a third-generation cephalosporin and metronidazole, with or without an aminoglycoside, often are used for the treatment of intra-abdominal infections in surgical settings. Simpler regimens that preserve an adequate spectrum of coverage, but allow easier administration and have fewer side effects, may be a more desirable option. METHODS This randomized, open-label, active comparator study evaluated the effectiveness (non-inferiority hypothesis) of the beta-lactam/beta-lactamase inhibitor combination cefoperazone-sulbactam (2-8 g/day), compared with ceftazidime (2-6 g/day)-amikacin (15 mg/kg/day)-metronidazole (500 mg three times daily) in 154 and 152 subjects, respectively, having intra-abdominal infections. The study was conducted at 17 centers in India. RESULTS Non-inferiority of cefoperazone-sulbactam (91.9%) compared with ceftazidime-amikacin-metronidazole (81.8%) was demonstrated for continued resolution of clinical signs and symptoms at the 30-day follow-up (primary endpoint) with a treatment difference of 10.1% (95% confidence interval 2.1%, 18.1%; pre-defined non-inferiority limit > -12.5%). Superiority of cefoperazone-sulbactam also was demonstrated for this endpoint, with significantly more subjects achieving continued resolution at the 30-day follow-up than in the comparator group (p = 0.015). On microbiologic outcomes, cefoperazone-sulbactam had higher success rates than ceftazidime-amikacin-metronidazole (92.9% vs. 80.0%). The pathogens (202 isolated) isolated most commonly were Escherichia coli (38.6%) and Klebsiella spp. (12.9%). The incidence of treatment-related adverse events was 6.5% and 16.4% in the cefoperazone-sulbactam and ceftazidime-amikacin-metronidazole groups, respectively, with more discontinuations due to treatment-related adverse events in the comparator arm (3.2% vs. 9.9%). CONCLUSION Empirical cefoperazone-sulbactam monotherapy could be a useful adjunct to surgical intervention for intra-abdominal infections.
Analysis of neural progenitors from embryogenesis to juvenile adult in Xenopus laevis reveals biphasic neurogenesis and continuous lengthening of the cell cycle

ABSTRACT Xenopus laevis is a prominent model system for studying neural development, but our understanding of the long-term temporal dynamics of neurogenesis remains incomplete. Here, we present the first continuous description of neurogenesis in X. laevis, covering the entire period of development from the specification of neural ectoderm during gastrulation to juvenile frog. We have used molecular markers to identify progenitors and neurons, short-term bromodeoxyuridine (BrdU) incorporation to map the generation of newborn neurons and dual pulse S-phase labelling to characterise changes in their cell cycle length. Our study revealed the persistence of Sox3-positive progenitor cells from the earliest stages of neural development through to the juvenile adult. Two periods of intense neuronal generation were observed, confirming the existence of primary and secondary waves of neurogenesis, punctuated by a period of quiescence before metamorphosis and culminating in another period of quiescence in the young adult. Analysis of multiple parameters indicates that neural progenitors alternate between global phases of differentiation and amplification and that, regardless of their behaviour, their cell cycle lengthens monotonically during development, at least at the population level. Summary: Our work represents the first continuous analysis of neural progenitor behaviour in X. laevis from early embryogenesis to juvenile stage and identifies two phases of neurogenesis interrupted by a phase of slow increase of the progenitor pool.
Developing a Model of Adolescent Friendship Formation on the Internet

Previous research has been largely silent about what precisely influences online friendship formation and has ignored motives for online communication as potential explanations. Drawing on a sample of 493 adolescents, this study tested a path model of adolescent friendship formation including as predictors introversion/extraversion, online self-disclosure, motive for social compensation, and frequency of online communication. Our path analysis showed that extraverted adolescents self-disclosed and communicated online more frequently, which, in turn, facilitated the formation of online friendships. Introverted adolescents, by contrast, were more strongly motivated to communicate online to compensate for lacking social skills. This increased their chances of making friends online. Among introverted adolescents, a stronger motive for social compensation also led to more frequent online communication and online self-disclosure, resulting in more online friendships. The model suggests that the antecedents of online friendship formation are more complex than previously assumed and that motives for online communication should be studied more closely.