Miracle-dz/UniFAR-FTUs huggingface dataset:
Induced Focal Adhesion Kinase (FAK) Expression in FAK-Null Cells Enhances Cell Spreading and Migration Requiring Both Auto- and Activation Loop Phosphorylation Sites and Inhibits Adhesion-Dependent Tyrosine Phosphorylation of Pyk2

ABSTRACT Focal adhesion kinase (FAK) is a nonreceptor protein tyrosine kinase involved in integrin-mediated control of cell behavior. Following cell adhesion to components of the extracellular matrix, FAK becomes phosphorylated at multiple sites, including tyrosines 397, 576, and 577. Tyr-397 is an autophosphorylation site that promotes interaction with c-Src or Fyn. Tyr-576 and Tyr-577 lie in the putative activation loop of the kinase domain, and FAK catalytic activity may be elevated through phosphorylation of these residues by associated Src family kinase. Recent studies have implicated FAK as a positive regulator of cell spreading and migration. To further study the mechanism of adhesion-induced FAK activation and the possible role and signaling requirements for FAK in cell spreading and migration, we utilized the tetracycline repression system to achieve inducible expression of either wild-type FAK or phosphorylation site mutants in fibroblasts derived from FAK-null mouse embryos. Using these Tet-FAK cells, we demonstrated that both the FAK autophosphorylation and activation loop sites are critical for maximum adhesion-induced FAK activation and FAK-enhanced cell spreading and migration responses. Negative effects on cell spreading and migration, as well as decreased phosphorylation of the substrate p130Cas, were observed upon induced expression of the FAK autophosphorylation site mutant. These negative effects appear to result from an inhibition of integrin-mediated signaling by the FAK-related kinase Pyk2/CAKβ/RAFTK/CadTK.
Understanding the effect of ethnic density on mental health: multi-level investigation of survey data from England

Objectives To determine if living in areas where higher proportions of people of the same ethnicity reside is protective for common mental disorders, and associated with a reduced exposure to discrimination and improved social support. Finally, to determine if any protective ethnic density effects are mediated by reduced exposure to racism and improved social support. Design Multi-level logistic regression analysis of national survey data, with area-level, own-group ethnic density modelled as the main exposure. Participants and setting 4281 participants of Irish, black Caribbean, Indian, Pakistani, Bangladeshi, and white British ethnicity, aged 16–74 years, randomly sampled from 892 “middle layer super output areas” in England. Main outcome measures Common mental disorders (assessed via structured interviews); discrimination (assessed via structured questionnaire); and social support and social networks (assessed via structured questionnaire). Results Although the most ethnically dense areas were also the poorest, for each 10 percentage point increase in own-group ethnic density, there was evidence of a decreased risk of common mental disorders, for the full ethnic minority sample (odds ratio 0.94 (95% confidence interval 0.89 to 0.99); P=0.02, trend), for the Irish group (odds ratio 0.21 (0.06 to 0.74); P=0.01, trend), and for the Bangladeshi group (odds ratio 0.75 (0.62 to 0.91); P=0.005, trend), after adjusting for a priori confounders. For some groups, living in areas of higher own-group density was associated with a reduction in the reporting of discrimination and with improved social support and improved social networks. However, none of these factors mediated ethnic density effects. Conclusions A protective effect of living in areas of higher own-group ethnic density was present for common mental disorders for some minority groups. People living in areas of higher own-group density may report improved social support and less discrimination, but these associations did not fully account for density effects.
Bdf1, a yeast chromosomal protein required for sporulation

The BDF1 gene of Saccharomyces cerevisiae is required for sporulation. Under starvation conditions, most cells from the bdf1 null mutant fail to undergo one or both meiotic divisions, and there is an absolute defect in spore formation. The Bdf1 protein localizes to the nucleus throughout all stages of the mitotic and meiotic cell cycles. Analysis of spread meiotic nuclei reveals that the Bdf1 protein is localized fairly uniformly along chromosomes, except that it is excluded specifically from the nucleolus. A bdf1 null mutant displays a reduced rate of vegetative growth and sensitivity to a DNA-damaging agent. The BDF1 gene encodes a 77-kDa protein that contains two bromodomains, sequence motifs of unknown function. Separation-of-function alleles suggest that only one of the two bromodomains is required for sporulation, whereas both are required for Bdf1 function in vegetative cells. We propose that the Bdf1 protein is a component of chromatin and that the mitotic and meiotic defects of the bdf1 null mutant result from alterations in chromatin structure.
Provisioning, parental investment and reproductive success in Jackdaws Corvus monedula

In a nest box colony of Jackdaws, we measured male and female parental investment to determine: (a) its importance for the production of fledged young; and (b) its cost as a constraint on annual reproductive potential. By observing parent roles, provisioning rates, chick growth rates and annual reproductive output we found that most of the variation in annual reproductive output was caused by nestling mortality rather than clutch size or hatching success. Provisioning by the male was continuously demanding of energy and time, from incubation to fledging, and was significantly correlated with nestling growth rate and fledgling survival. Nestling mortality was highest when the demands of provisioning on the male were greatest. Variance in nestling mortality increased between pairs in less productive years and exaggerated differences in parent quality. This evidence suggests that the ability of parents to exploit a variable food supply and provision their young sufficiently, is a key component of annual reproductive output in this species. We argue that provisioning costs might also constrain male Jackdaws to social monogamy by occupying time needed for the successful nurturing of two broods. Jackdaws maximise fledgling output through concerted investment by both parents into single annual broods. This system is comparable to that of other long-lived avian groups such as seabirds.
Risk factors for stomach cancer in Brazil (I): a case-control study among non-Japanese Brazilians in São Paulo.

BACKGROUND Stomach cancer is an important health problem in Brazil, with an estimated 20 000 new cases per year and it was the most frequent cancer site in men and the third most frequent site in women in São Paulo in 1993. Nevertheless, there are no reports of analytical epidemiological study on stomach cancer in Brazil. METHODS A hospital-based case-control study was conducted among Brazilian residents with a non-Japanese background in the city; 236 consecutive cases of histologically confirmed stomach cancer were matched to the same number of controls admitted for non-neoplastic diseases by age (+/-5 years) and gender. The socio-demographic characteristics, personal and family medical history, lifetime history of tobacco use and dietary habits were determined by interview using a structured questionnaire. RESULTS Non-white race, lower educational background and lower family income were more frequent in stomach cancer patients. After adjustment for race and educational background, cigarette smoking, frequent use of oil and frequent consumption of egg were significantly associated with increased risk of stomach cancer, while frequent consumption of fruit and vegetables decreased the risk. These associations did not change substantially after mutual adjustment of the other variables. CONCLUSIONS The present study confirmed that low socio-economic status, cigarette smoking and low consumption of fruit and vegetables were risk factors of stomach cancer in São Paulo, Brazil.
Transgenesis and imaging in birds, and available transgenic reporter lines

Avian embryos are important model organism to study higher vertebrate development. Easy accessibility to developing avian embryos enables a variety of experimental applications to understand specific functions of molecules, tissue–tissue interactions, and cell lineages. The whole‐mount ex ovo culture technique for avian embryos permits time‐lapse imaging analysis for a better understanding of cell behaviors underlying tissue morphogenesis in physiological conditions. To study mechanisms of blood vessel formation and remodeling in developing embryos by using a time‐lapse imaging approach, a transgenic quail model, Tg(tie1:H2B‐eYFP), was generated. From a cell behavior perspective, Tg(tie1:H2B‐eYFP) quail embryos are a suitable model to shed light on how the structure and pattern of blood vessels are established in higher vertebrates. In this manuscript, we give an overview on the biological and technological background of the transgenic quail model and describe procedures for the ex ovo culture of quail embryos and time‐lapse imaging analysis.
Mechanical diagnosis and therapy enhances attitude toward self-management in people with musculoskeletal disorders: A preliminary evidence with a before–after design

Objectives: Mechanical diagnosis and therapy is one of the most common approaches for the management of low back pain. In mechanical diagnosis and therapy, a great emphasis is placed on patient education so that patients can manage their problems by themselves. However, there has been no evidence that mechanical diagnosis and therapy actually enhances patient’s self-management skills. This study aimed to preliminarily investigate whether self-reported skills of self-management for musculoskeletal problems are enhanced through the course of mechanical diagnosis and therapy. Method: Outpatients with musculoskeletal disorders in a local orthopedic clinic were included. The primary outcome measures were the “Self-monitoring and Insight” and “Skill and Technique Acquisition” scores of the Health Education Impact Questionnaire, where higher scores indicate greater self-management skills. Mechanical diagnosis and therapy was undertaken up to a maximum of twice per week for 1 month. The Self-monitoring and Insight and Skill and Technique Acquisition scores before and 1 month after the mechanical diagnosis and therapy interventions were compared. Proportions of patients who exceed the threshold for “reliable change” in the Health Education Impact Questionnaire scores (% >positive “reliable change”) and proportions of patients with the net positive “reliable change” (% net positive “reliable change”) were investigated. Results: Forty-five patients participated and 97.8% completed the 1-month follow-up. The Self-monitoring and Insight and Skill and Technique Acquisition scores significantly increased at the follow-up (Self-monitoring and Insight, p = 0.002; Skill and Technique Acquisition, p < 0.001. The % >positive “reliable change” (Self-monitoring and Insight = 22.2%, Skill and Technique Acquisition = 48.9%) and % net positive “reliable change” (Self-monitoring and Insight = 13.3%, Skill and Technique Acquisition = 46.7%) in this study were comparative to or greater than self-management programs in previous studies (%> positive “reliable change’: Self-monitoring and Insight = 20.5%, Skill and Technique Acquisition = 30.7%; % net positive “reliable change”: Self-monitoring and Insight = 14.1%, Skill and Technique Acquisition = 23.0%). Conclusion: This study provides a preliminary evidence that mechanical diagnosis and therapy enhances patient’s self-management skills, particularly in the self-monitoring skills for symptoms/functions and the self-management skill for symptoms/problems.
Teaching software quality via source code inspection tool

Software Quality Assurance is a sub-process that ensures that developed software meets and complies with defined or standardized quality specifications. Focusing on source code, there are characteristics that can be used to evaluate the quality. Introductory courses must encourage freshmen students to improve internal quality of their source code, but only as sophomore they have contact with Software Engineering concepts, including Quality Assurance. In this paper we present a tool to source code quality evaluation aimed at supporting students to improve their source code and, consequently, their programming skills. The proposed tool uses quality reports (available to professional environment integrate with software repositories) to analyze students' source code and provide a feedback about the student coding. The proposed tool run locally, with few computational resources. In addition, we proposed the methodology to use the proposed tool: it consists of challenging students to perform a set of maintenance tasks in a controlled environment. We prepared a source code by introducing common defects, what decreases the quality of source code, and ask to students to perform maintenance tasks in order to both eliminate the introduced defects and introduce new features. After each modification, the students must evaluate their code using the proposed tool to obtain a feedback about quality of source code. To evaluate the approach and the tool, we created a survey and applied to students and the teacher. As a result, we show the benefits of using the proposed tool to both teachers and students perspectives. The results are positive to enhance the teaching-learning Software Quality Assurance to Software Engineering students.
Differential search algorithm for different economic dispatch problem

This paper presents a Differential Search (DS) algorithm to solve the complex economic load dispatch (ELD) problems. DS algorithm utilizes the Brownian-like random-walk movement used by an organism to migrate. Prime focus of ELD is minimization of fuel costs of thermal generators, involving different constraints such as power balance, ramp rate limits and prohibited operating zone etc. The performance of DS algorithm for solving ELD problems is evaluated and examined by simulating two different small and medium test systems and one large test case system. Simulation results for different test systems show that the computational times and fuel costs obtained by DS are much lesser than many other algorithms reported in the previous literatures.
ExoCarta: A compendium of exosomal proteins and RNA

Exosomes, membrane microvesicles (40–100 nm) secreted by most cell types, can be isolated in several ways while characterizing them is heavily based on electron microscopy and, most importantly, the identification of exosome marker proteins. Researchers rely on the identification of certain exosomal marker proteins including Alix, CD9 and CD63 to confirm the presence of exosomes in their preparations. An evolutionary‐conserved set of protein molecules have been identified in most exosomes studied to date. However, with the complexity of tissue/cell type‐specific proteins being incorporated in the exosomes, some of these so‐called exosomal markers are not always present in all the exosomes. The presence of tissue/cell type‐specific proteins in exosomes allows researchers to isolate them using immunoaffinity capture methods. A compendium for exosomal proteomes will aid researchers in identifying proteins that were more commonly found in various exosomes (exosome markers) and those that are specific to certain tissue/cell type‐derived exosomes. Here, we describe ExoCarta, a compendium for proteins and RNA molecules identified in exosomes. ExoCarta is first of its kind and the resource is freely available to the scientific community through the web (http://exocarta.ludwig.edu.au). We believe that this community resource will be of great biological importance for any future exosome analyses.
Effects of chronic activation of peroxisome proliferator-activated receptor-alpha or high-fat feeding in a rat infarct model of heart failure.

Intracardiac accumulation of lipid and related intermediates (e.g., ceramide) is associated with cardiac dysfunction and may contribute to the progression of heart failure (HF). Overexpression of nuclear receptor peroxisome proliferator-activated receptor-alpha (PPARalpha) increases intramyocellular ceramide and left ventricular (LV) dysfunction. We tested the hypothesis that activation of fatty acid metabolism with fat feeding or a PPARalpha agonist increases myocardial triglyceride and/or ceramide and exacerbates LV dysfunction in HF. Rats with infarct-induced HF (n = 38) or sham-operated rats (n = 10) were either untreated (INF, n = 10), fed a high-fat diet (45% kcal fat, INF + Fat, n = 15), or fed the PPARalpha agonist fenofibrate (150 mg.kg(-1). day(-1), INF + Feno, n = 13) for 12 wk. LV ejection fraction was significantly reduced with HF (49 +/- 6%) compared with sham operated (86 +/- 2%) with no significant differences in ejection fraction (or other functional or hemodynamic measures) among the three infarcted groups. Treatment with the PPARalpha agonist resulted in LV hypertrophy (24% increase in LV/body mass ratio) and induced mRNAs encoding for PPARalpha-regulated genes, as well as protein expression and activity of medium chain acyl-CoA dehydrogenase (compared with INF and INF + Fat groups). Myocardial ceramide content was elevated in the INF group compared with sham-operated rats, with no further change in the INF + Fat or INF + Feno groups. Myocardial triglyceride was unaffected by infarction but increased in the INF + Fat group. In conclusion, LV dysfunction and dilation are not worsened despite upregulation of the fatty acid metabolic pathway and LV hypertrophy or accumulation of myocardial triglyceride in the rat infarct model of HF.
Experimental investigation of water cooled server microprocessors and memory devices in an energy efficient chiller-less data center

Understanding and improving the thermal management and energy efficiency of data center cooling systems is of growing importance from a cost and sustainability perspective. Toward this goal, warm liquid cooled servers were developed to enable highly energy efficient chiller-less data centers that utilize only “free” ambient environment cooling. This approach greatly reduces cooling energy use, and could reduce data center refrigerant and make up water usage. In one exemplary experiment, a rack having such liquid cooled servers was tested on a hot summer day (~32°C) with CPU exercisers and memory exercisers running on every server to provide steady heat dissipation from the processors and from the DIMMs, respectively. Compared to a typical air cooled rack, significantly lower DIMM temperatures and CPU thermal values were observed.
Multiobjective Hybrid Optimization and Training of Recurrent Neural Networks

The application of neural networks to solve a problem involves tasks with a high computational cost until a suitable network is found, and these tasks mainly involve the selection of the network topology and the training step. We usually select the network structure by means of a trial-and-error procedure, and we then train the network. In the case of recurrent neural networks (RNNs), the lack of suitable training algorithms sometimes hampers these procedures due to vanishing gradient problems. This paper addresses the simultaneous training and topology optimization of RNNs using multiobjective hybrid procedures. The proposal is based on the SPEA2 and NSGA2 algorithms for making hybrid methods using the Baldwinian hybridization strategy. We also study the effects of the selection of the objectives, crossover, and mutation in the diversity during evolution. The proposals are tested in the experimental section to train and optimize the networks in the competition on artificial time-series (CATS) benchmark.
Assistive sports video annotation: modelling and detecting complex events in sports video

Video analysis in professional sports is a relatively new assistive tool for coaching. Currently, manual annotation and analysis of video footage is the modus operandi. This is a laborious and time consuming process, which does not afford a cost effective or scalable solution as the demand and uses of video analysis grows. This paper describes a method for automatic annotation and segmentation of video footage of rugby games (one of the sports that pioneered the use of computer vision techniques for game analysis and coaching) into specific events (e.g. a scrum), with the aim to reduce time and cost associated with manual annotation of multiple videos. This is achieved in a data-driven fashion, whereby the models that are used for automatic annotation are trained from video footage. Training data consists of annotated events in a game and corresponding video. We propose a supervised machine learning solution. We use human annotations from a large corpus of international matches to extract video of such events. Dense SIFT (Scale Invariant Feature Transform) features are then extracted for each frame from which a bag-of-words vocabulary is determined. A classifier is then built from labelled data and the features extracted for each corresponding video frame. We present promising results on broadcast video for a international rugby matches annotated by expert video analysts.
Parametric study of irreversible electroporation with different needle electrodes: Electrical and thermal analysis

Abstract Purpose: Irreversible electroporation (IRE) is a new tumour ablation method used in cancer treatment procedures. In a successful IRE treatment it is crucial to impose minimum thermal damage to the tumour and its surrounding healthy tissue, while subjecting the entire tumour to a strong electric field. Method: Here we present a 3D model of a subcutaneous tumour in a four-layer skin using a geometry-based finite element approach. Four common needle electrode configurations were studied in this paper. The study evaluated six essential factors which are important in the electrical and thermal distributions in tumour and normal tissue. Results: The results revealed that a hexagonal 3 × 3 geometry provides the maximum electrical coverage of the tumour, compared to other electrode configurations. However, in some cases the hexagonal 2 × 2 geometry can ablate the entire tumour with less damage to normal tissue. We found that the deeper insertion of 2- and 4-electrode geometries can lead to more damage to healthy tissue. The results also indicate that the insertion of the electrodes into tumour tissue can increase thermal damage dramatically due to existing large electrical conductivity. Conclusion: These findings suggest that needle electrodes should not be placed within the tumour tissue if the goal is to prevent thermal damage. This method can be used as a trade-off between electric field coverage in tumour tissue and thermal damage to both tumour and normal tissue.