Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Genomics has become a ground-breaking field in all areas of the life sciences. The advanced genomics and the development of high-throughput techniques have lately provided insight into whole-genome characterization of a wide range of organisms. In the post-genomic era, new technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome wide functional regulation of gene expression and metabolic pathways reconstruction. However, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management. Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification of new genes in a wide range of species with fully sequenced genomes. In addition, generation of systematically and syntactically unambiguous nomenclature systems for genomic data across species is a crucial task. Such systems are necessary for adequate handling genetic information in the context of comparative functional genomics. In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks. We also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.
Sesquiterpenes as Immunosuppressants

Background. The search for new immunosuppressive drugs is a high priority. Sesquiterpenes constitute a family of compounds with a great variety of biological activities due to their reactive moieties. Methods. Human tumor cell lines and murine primary cells and human peripheral blood mononuclear cells or primary CD4+ cells from healthy individuals were stimulated in the presence of sesquiterpenes. Cell division was analyzed by 5-(and-6)-carboxyfluorescein diacetate succinimidyl ester, cell cycle progression by Hoecht, and cell death by Anexin-V and propidium iodine staining. Cytokine secretion was analyzed by means of a bioplex assay. Results. Two sesquiterpene derivatives of the 18 previously shown to inhibit vegetal cell growth are shown to block cell division and cell cycle progression in human and murine cell lines and primary cells. Cytokine secretion is also impaired on stimulation in the presence of sesquiterpenes. Conclusions. Here, we show that sesquiterpenes heliannuols constitute a novel family of molecules with potential use as immunosuppressants. Moreover, we show that an assay based on the allelopathic effect of plant leads can be used as a cost-effective screening previous to studies in mammalian cells.
Advanced Material Selection for Semiconductor Switching Devices in Electric Vehicles Using PROMETHEE Method

Electric Vehicle (EV) has emerged as a solution for the growing concerns on pollution and depleting oil resources all over the world. The performance and efficiency of an EV mainly depends on the power electronic switching devices used in it which, in turn depends on the properties of materials used in its fabrication. Traditional semiconductor material like Silicon has been widely used for the fabrication of these switches. However, improvised material technology and incessant demand for better performance has triggered the use of wide band-gap (WBG) semiconductors in switching devices. This paper aims to compare a few WBG semiconductors with traditional semiconductors based on their material properties. A decision making method called PROMETHEE has been used for comparison and the possibly best material for fabrication of switching devices has been chosen based on their rankings achieved. Adoption of the suggested material can improve the performance and efficiency of EV's theoretically.
HIV/Sexually Transmitted Infection Prevalence and Sexual Behavior of Men Who Have Sex With Men in 3 Districts of Botswana: Results From the 2012 Biobehavioral Survey

Background Men who have sex with men (MSM) suffer significant stigma and discrimination; hence, they are reluctant to access health services. The Botswana Second National Strategic Framework for 2010–2016 stipulates the need to increase HIV prevention services for key populations as one of its prevention implementation strategies. We report here the prevalence of HIV and other sexually transmitted infections and risk factors for HIV infection among MSM in Botswana. Methods We conducted a cross-sectional survey using respondent driven sampling in 3 districts of Botswana: Gaborone, Francistown, and Kasane. Results Of the 454 participants recruited, most were Batswana (97.6%) with a mean age of 23.2 years (range, 18–53 years), with 74.9% aged between 20 and 29 years. The overall unadjusted HIV prevalence was 13.1% (95% confidence interval, 10.0–16.3), with 12.3%, 11.7%, and 25.9% in Gaborone, Francistown, and Kasane, respectively. Chlamydia trachomatis prevalence was higher than Neisseria gonorrhoeae in both urine and anal swabs, at 7.1% and 5.9%, respectively, versus 1.4% and 1.7%. Overall, 46.7% of respondents reported having sex with female partners. Men who have sex with men who thought they had a high chance of acquiring HIV had a significantly lower likelihood of using condom consistently than those who reported they had a lower chance of acquiring HIV (odds ratio = 0.4; 95% confidence interval, 0.2–0.7; P = 0.003). Conclusion HIV prevalence of MSM was lower than what has been reported in other sub-Saharan African countries with generalized epidemics; however, their degree of participation in heterosexual sex signifies sexual networks beyond the MSM subpopulation.
A Novel Discovery of IK1 Channel Agonist: Zacopride Selectively Enhances IK1 Current and Suppresses Triggered Arrhythmias in the Rat

Abstract Modulation of the inward rectifier K+ current (IK1) has profound effect on cardiac excitability and underlies new antiarrhythmic strategies. However, IK1-specific pharmacological tools, especially the selective IK1 agonists, are still lacking in the market. Zacopride, a gastrointestinal prokinetic drug, was found to be a selective IK1 channel agonist. By using the whole-cell patch clamp technique, it was found that zacopride (0.1–10 &mgr;mole/L) dose dependently enhanced the IK1 current in isolated rat cardiomyocytes, had no effects on other ion channels, transporters, or pumps. At the same dosage range, zacopride hyperpolarized the resting potential and shortened the action potential duration. When applied at the optimal dose of 1.0 &mgr;mole/L, zacopride could prevent or eliminate aconitine induced after depolarization and triggered activity in isolated cardiomyocytes. In a rat model of aconitine-induced arrhythmias both ex vivo and in vivo, zacopride (1.0 &mgr;mole/L or 25 &mgr;g/kg, respectively) treatment apparently protected the heart from ventricular tachyarrhythmias, which compares favorably with 7.5 mg/kg of lidocaine, a classical aconitine antidote. In conclusion, zacopride was found to be a selective IK1 agonist, and agonizing IK1 could prevent or eliminate aconitine-induced arrhythmias in the rat.
Current Strategy for Staging and Treatment: The BCLC Update and Future Prospects

Staging and treatment indication are relevant topics in the management of patients with hepatocellular carcinoma (HCC) and for optimal results, they have to take into account liver function, tumor stage, and physical status. For any staging system to be meaningful it has to link staging with treatment indication; this should be based on robust scientific data. Currently, the sole proposal that serves both aims is the Barcelona Clinic Liver Cancer (BCLC) approach. It takes into account the relevant parameters of all important dimensions and divides patients into very early/early, intermediate, advanced, and end-stage. Early-stage HCC patients should be considered for potentially curative options such as resection, ablation, and transplantation. Patients at intermediate stage benefit from chemoembolization, whereas patients at an advanced stage, or who cannot benefit from options of higher priority, have sorafenib as the standard treatment. Finally, patients at end-stage should merely receive palliative care.
Classifying Frog Calls Using Gaussian Mixture Model and Locality Sensitive Hashing

Biodiversity conservation is a major concern of modern society. Pressures such as littering, pollution, and climate change deteriorate the natural habitats and reduce biodiversity. To help repair this issue, we need some way to track these habitat damages. We need a bio-indicator. Frogs make excellent bio-indicators due to their permeable skin. This skin allows them to absorb water and Oxygen. However, when they live in polluted areas they also absorb toxins. As pollution rise, some frog populations suﬀer decline. Citizen scientists have been monitoring these frog populations by recording their calls for years. However, this process requires expensive equipment, training, and a sizable time commitment. This paper focuses on the automatic classiﬁcation of frog calls using computer programs. Features were extracted from the audio data and classiﬁed using two classiﬁcation methods: Locality Sensitive Hashing and Gaussian Mixture Modeling. Tests performed on a dataset of frog calls of 15 diﬀerent species produced promising classiﬁcation results for the Gaussian mixture model approach.
ELECTRON MICROSCOPY OF LIVER LESIONS IN PRIMARY BILIARY CIRRHOSIS

An 80 μm bile duct with typical features of chronic non‐suppurative destructive cholangitis was examined by electron microscopy. Many inflammatory cells, including lymphocytes, macrophages and plasma cells infiltrated among epithelial cells of the bile duct. Epithelial cells were compressed and deformed by infiltrating lymphocytes. These lymphocytes were in contact with epithelial cells at small points or large areas. The intercellular distance was about 10 or 20 nm at the contact areas. The mode of contact and intercellular distance coincided with the results of in vitro experiments on lymphocyte cytotoyicity against target cells. Some epithelial cells in contact with lymphocytes showed degenerative changes. Necrotic changes were observed in bile duct epithelial cells undergoing emperipolesis. The invading lymphocyte in the epithelial cell had osmiophilic substances on the surface. These sites of emperipolesis seem to be the areas of lymphocyte cytotoxicity against epithelial cells.
Effects of growth rate on cell extract performance in cell‐free protein synthesis

Cell‐free protein synthesis is a useful research tool and now stands poised to compete with in vivo expression for commercial production of proteins. However, both the extract preparation and protein synthesis procedures must be scaled up. A key challenge is producing the required amount of biomass that also results in highly active cell‐free extracts. In this work, we show that the growth rate of the culture dramatically affects extract performance. Extracts prepared from cultures with a specific growth rate of 0.7/h or higher produced approximately 0.9 mg/mL of chloramphenicol acetyl transferase (CAT) in a batch reaction. In contrast, when the source culture growth rate was 0.3/h, the resulting extract produced only 0.5 mg/mL CAT. Examination of the ribosome content in the extracts revealed that the growth rate of the source cells strongly influenced the final ribosome concentration. Polysome analysis of cell‐free protein synthesis reactions indicated that about 22% of the total 70S ribosomes are in polysomes for all extracts regardless of growth rate. Furthermore, the overall specific production from the 70S ribosomes is about 22 CAT proteins per ribosome over the course of the reaction in all cases. It appears that rapid culture growth rates are essential for producing a productive extract. However, growth rate does not seem to influence specific ribosome activity. Rather, the increase in extract productivity is a result of a higher ribosome concentration. These results are important for cell‐free technology and also suggest an assay for intrinsic in vivo protein synthesis activity. © 2006 Wiley Periodicals, Inc.
A Framework Based on CLP Extended with CHRs for Reasoning with Qualitative Orientation and Positional Information

Several qualitative models have been developed in the last years with the aim of simulating the spatial reasoning process used by humans. However, up to now no model has been developed to represent and reason with several aspects of space (such as orientation, distance and cardinal directions, for instance) in a uniform way, i.e. by referring to the same spatial objects. An approach for the integration of several aspects of space into the same model, based on constraint logic programming extended with constraint handling rules, is proposed in this article. As an example of this approach, the integration of orientation and positional information in the same model is explained.
ANOVA METHOD APPLIED TO PEMFC AGEING FORECASTING USING AN E CHO S TATE N ETWORK

According to the International Energy Agency, an in crease of the requests of energy of 40% could arise in the next decades, mainly due to the emerge nce of developing countries. The problem with the n owaday energy system is the use of fossil energy, which is limited and attempt to disappear in the near futur e. Thus an energy transition has to begin in order to replace th fossil fuels and anticipate their disappearance . Consequently, in recent years, the promotion and de velopment of renewable energy have been realized. O ne of this renewable energy, the energy vector hydrogen, appears to be a promising solution, mainly due to i nteresting performance of Fuel Cells (FC) systems and hydrogen abundance on Earth (it is still important to under lin that the hydrogen does not exist in natural form). Howev er, this research area is still subject to scientif ic and technological bottlenecks. One of these major bottl enecks preventing the industrialization of FC syste m is it limited useful lifetime. It is therefore important to develop reliable tools for the diagnosis and pro gnosis of FC system in order to optimize its efficiency. The aim of this article is to present the results of a sen sibility analysis applied to a prognosis tools called Echo State Netw ork.
Human Fas‐ligand expression on porcine endothelial cells does not protect against xenogeneic natural killer cytotoxicity *

Abstract: Several human leukocyte subsets including natural killer (NK) cells, cytotoxic T lymphocytes (CTL), and polymorphonuclear neutrophils (PMN) participate in cellular immune responses directed against vascularized pig‐to‐human xenografts. As these leukocytes express the death receptor Fas either constitutively (PMN) or upon activation (NK, CTL), we explored in vitro whether the transgenic expression of Fas ligand (FasL) on porcine endothelial cells (EC) is a valuable strategy to protect porcine xenografts. The porcine EC line 2A2 was stably transfected with human FasL (2A2‐FasL) and interactions of 2A2‐FasL with human leukocytes were analyzed using functional assays for apoptosis, cytotoxicity, chemotaxis, adhesion under shear stress, and transmigration. FasL expressed on porcine EC induced apoptosis in human NK and T cells, but did not protect porcine EC against killing mediated by human NK cells. 2A2‐FasL released soluble FasL, which induced strong chemotaxis in human PMN. Adhesion under shear stress of PMN on 2A2‐FasL cells was increased whereas transendothelial migration was decreased. In contrast, FasL had no effect on the adhesion of NK cells but increased their transmigration through porcine EC. Although FasL expression on porcine EC is able to induce apoptosis in human effector cells, it did not provide protection against xenogeneic cytotoxicity. The observed impact of FasL on adhesion and transendothelial migration provides evidence for novel biological functions of FasL.
A rat model of non‐lethal bacterial infection

The purpose of the study was to develop a small animal model of intraperitoneal infection without mortality and with a catabolic response to the infection, viz. to mimic the clinical situation in man. Intraperitoneal infection was induced in female Wistar rats by deposition of a gelatin capsule containing a mixture of Escherichia coli and Bacteroides fragilis and adjuvant substances. Seven groups of animals were infected with different bacterial inocula (0.2–4.3times106 CPU) to establish reproducible and dose‐dependent changes in mortality, body weight in relation to food intake, blood cultures, peripheral blood leukocyte counts, and abscess formation on autopsy. No mortality was observed in animals with an inoculum below 2.2times106 CFU in spite of positive blood cultures. Initial weight loss was followed by weight gain in all animals except the group infected with the low inoculum (0.2times106 CFU). This group had no mortality, was in a catabolic state for three days, indicated by weight loss in spite of nearly normal food intake, and the infectious state was supported by intraperitoneal dissemination of small abscesses. The low‐grade character of the infection was reflected by changes in peripheral blood lymphocyte and neutrophil ***granulocyte concentrations. In conclusion, this study presents a small animal model with a reproducible dose response to the bacterial challenge, allowing prolonged studies of metabolic changes following infection.
Bi-Sparsity Pursuit : A Paradigm for RobustSubspace Recovery Report

Bi-Sparsity Pursuit: A Paradigm for RobustSubspace Recovery Report Title The success of sparse models in computer vision and machine learning is due to the fact that, high dimensional data is distributed in a union of low dimensional subspaces in many real-world applications. The underlying structure may, however, be adversely affected by sparse errors. In this paper, we propose a bi-sparse model as a framework to analyze this problem, and provide a novel algorithm to recover the union of subspaces in presence of sparse corruptions. We further show the effectiveness of our method in a number of applications using real-world vision data.
Improved robust control for multi-link flexible manipulator with mismatched uncertainties

We consider a class of flexible joint manipulator system which is nonlinear and contains uncertainty. The inertial matrix can be used to construct Lyapunov function, even though some of the joints are prismatic. We construct subsystems via backstepping method and suggest a state transformation under which implanted control is used. From this state transformation, a robust controller, which is only based on the possible bound of uncertainty and the uniform positive definiteness of the inertial matrix, is designed to guarantee the practical stability of the system. A numerical example illustrates our conclusions.
Clinical outcome with bevacizumab in patients with recurrent high-grade glioma treated outside clinical trials

Abstract Background. Patients with recurrent high-grade glioma (HGG) have a poor prognosis and there is no defined standard of care. High levels of vascular endothelial growth factor (VEGF) expressed in HGG make the anti-VEGF monoclonal antibody bevacizumab (BEV) of particular interest. Patients and methods. In an ongoing registry data were collected from patients who have received BEV for the treatment of recurrent HGG. The primary objective was the identification of any clinical benefit as assessed by change in Karnofsky Performance Score (KPS), decreased steroid use and duration of treatment. Results. Two hundred and twenty-five patients with HGG were included (176 glioblastoma; 49 anaplastic glioma; median age 52 years). KPS improved in 10% of patients and remained stable in 68%. Steroids were stopped in 37.6% of patients. Median duration of treatment was 5.5 months; 19.1% of patients were treated for more than 12 months. Median overall survival from beginning of BEV treatment was 8.5 months. At the time of analysis, 169 patients (75.1%) had died and 56 patients (24.9%) were alive. Only 21 patients (9.3%) discontinued treatment due to toxicity. Conclusions. Our data reveal valuable palliation with preservation of KPS and an option for steroid withdrawal in patients treated with BEV, supporting the role of this therapy in late-stage disease.
Prediction of Psychosocial Adjustment Using Psychological Wellbeing and Coping Strategies in Patients Suffering from Lymphoma Cancer and Leukemia

The present research tries to predict psychosocial adjustment based on psychological wellbeing and coping strategies in patients suffering from Lymphoma cancer and Leukemiain Tehran, Karaj and Rasht Cities. This research was conducted in 2013 and 2014. Using accessible sampling method, 200 patients who suffered from Lymphoma cancer and Leukemia (93 cancer patients and 107 Leukemia patients) were selected. In order to evaluate research variables, psychosocial adjustment questionnaire in chronic patients, Reef's psychological wellbeing questionnaire and Andler&Parker's questionnaire of coping strategies in stressful conditions were used. Multivariate regression analysis revealed that task-oriented coping strategies predict 14% of variations in psychosocial adjustment, emotion-oriented coping strategies predict 26% and avoidant coping strategies predict 23% and psychological wellbeing predicts 24% of variations in psychosocial adjustment variable. According to the results of the research, it can be said that task-oriented coping strategies and psychological wellbeing act like a dampener against stressful factors and chronic diseases. Moreover, psychological wellbeing acts as a positive factor in cancer patients and improves their psychosocial adjustment. DOI: 10.5901/mjss.2014. v5n20p3123
Vehicle Routing for Urban Snow Plowing Operations

Winter road maintenance planning involves a variety of decisions related to the routing of vehicles for spreading chemicals and abrasives, plowing roadways and sidewalks, loading snow into trucks, and transporting snow to disposal sites. In this paper, we present a model and two heuristic solution approaches based on mathematical optimization for the routing of vehicles for snow plowing operations in urban areas. Given a district and a single depot where a number of plows are based, the problem is to determine a set of routes, each performed by a single vehicle that starts and ends at the district's depot, such that all road segments are serviced while satisfying a set of operational constraints and minimizing a time objective. The formulation models general precedence relation constraints with no assumption on class connectivity, different service and deadhead speed possibilities, separate pass requirements for multilane road segments, class upgrading possibilities, and vehicle road segment dependencies. Several extensions, such as turn restrictions, load balancing constraints, and tandem service requirements, which are required in a real-life application, are also discussed. Two objectives are considered: A hierarchical objective and a makespan objective. The resulting model is based on a multicommodity network flow structure to impose the connectivity of the route performed by each vehicle. The two solution strategies were tested on data from the City of Dieppe, New Brunswick, Canada.