Miracle-dz/UniFAR-FTUs huggingface dataset:
THE FIRST MITOCHONDRIAL DNA PHYLOGENY OF CUBAN BUTHIDAE (SCORPIONES: BUTHOIDEA)

A partial phylogeny of Cuban scorpions of the family Buthidae (four genera, 12 species) is herein presented, based on molecular data (16S rRNA mitochondrial DNA). The following results are discussed: (1) monophyly of the clades (Rhopalu- rus + Centruroides) and (Alayotityus + Tityus) was supported, while Microtityus (Parvabsonus) always formed a separate clade; (2) monophyly of Centruroides was never supported; (3) previous analyses of systematics and morphology-based phylogenies were confirmed. Key word: Scorpiones, Buthidae, phylogeny, mitocondrial DNA, Cuba. Primeros datos sobre la filogenia de los Buthidae cubanos (Scorpiones: Buthoidea), basados en ADN mi- tocondrial. Resumen: Se presenta una aproximacion filogenetica parcial a los escorpiones cubanos de la familia Buthidae (cuatro gene- ros, 12 especies), basada en datos moleculares (ADN mitocondrial 16S ARNr). Se obtuvieron los siguientes resultados princi- pales: (1) la monofilia de los clados (Rhopalurus + Centruroides) y (Alayotityus + Tityus) siempre fue confirmada, mientras Mi- crotityus (Parvabsonus) siempre formo un clado independiente; (2) la monofilia de Centruroides no fue confirmada en ningun analisis; (3) se confirmaron los analisis previos de sistematica y filogenia basados en morfologia. Palabras clave: Scorpiones, Buthidae, filogenia, ADN mitocondrial, Cuba.
1,1-Bis(3′-Indolyl)-1-(p-Substitutedphenyl)methanes Induce Apoptosis and Inhibit Renal Cell Carcinoma Growth

Purpose: 1,1-Bis(3′-indolyl)-1-(p-substitutedphenyl)methanes [methylene-substituted diindolylmethanes (C-DIM)] containing p-trifluoromethyl, p-t-butyl, and p-phenyl substituents activate peroxisome proliferator-activated receptor γ (PPARγ) and inhibit growth of several different cancer cell lines through receptor-dependent and receptor-independent pathways. The purpose of this study is to investigate the anticancer activity of these compounds in renal cell carcinoma. Experimental Design: The anticancer activity of the p-t-butyl–substituted C-DIM compound (DIM-C-pPhtBu) was investigated in ACHN and 786-0 renal cell carcinoma cell lines and in an orthotopic model for renal carcinogenesis using ACHN cells injected directly into the kidney. Results: PPARγ is overexpressed in ACHN cells and barely detectable in 786-0 cells, and treatment with DIM-C-pPhtBu induces proteasome-dependent degradation of cyclin D1 and variable effects on p21 and p27 expression in both cell lines. DIM-C-pPhtBu also induced several common proapoptotic responses in ACHN and 786-0 cells, including increased expression of nonsteroidal anti-inflammatory drug-activated gene-1 and endoplasmic reticulum stress, which activates death receptor 5 and the extrinsic pathway of apoptosis. Activation of these responses was PPARγ independent. In addition, DIM-C-pPhtBu (40 mg/kg/d) also inhibited tumor growth in an orthotopic mouse model for renal carcinogenesis, and this was accompanied by induction of apoptosis in renal tumors treated with DIM-C-pPhtBu but not in tumors treated with the corn oil vehicle (control). Conclusions: DIM-C-pPhtBu and related compounds are cytotoxic to renal cancer cells and activate multiple proapoptotic and growth-inhibitory pathways. The results coupled with in vivo anticancer activity show the potential of DIM-C-pPhtBu and related C-DIMs for clinical treatment of renal adenocarcinoma.
Assessment of Risky Injection Practices Associated with Hepatitis B, Hepatitis C, and Human Immunodeficiency Virus and Using the Blood-Borne Virus Transmission Risk Assessment Questionnaire

Risky injection practices among injection drug users (IDUs) contribute to the spread of blood-borne infections such as human immunodeficiency virus, hepatitis B, and hepatitis C. The Blood-borne Virus Transmission Risk Assessment Questionnaire (BBV-TRAQ). was developed in Australia to determine risk behaviors for specific infections. Blood testing for human immunodeficiency virus, hepatitis B, and hepatitis C was performed on all participants, and data on blood tests were linked to questionnaires. The BBV-TRAQ was administered to 242 current and former injection drug users in Long Beach, California, and the Long Beach data were compared with the original Australian data. In the comparison of the mean scores on the three subscales and total scores on the BBV-TRAQ between the samples, means for all three subscales and the total BBV-TRAQ score were significantly different, with Long Beach scores consistently lower than the Australian sample. The injecting and sexual risk subscales were significantly different across levels of AIDS risk perception for all three types of injectors; however, the other skin penetration practices subscale had no significant association with AIDS risk perception for any of the injection drug user groups. Despite recent efforts to educate injectors about the risks associated with practices captured by the other skin penetration practices subscale, such as tattooing and sharing razors, this subscale does not have an association with AIDS risk perception. injection drug users in Australia may have better access to health care, giving their self-report of infection greater validity than the California sample.
Lessons from the Field Strategic Data Planning: Lessons from the Field

Many large organizations today are finding that even if they can access data from multiple functions, the lack of logical data integration (common data definitions and codes) across information systems makes it difficult or impossible to answer cross-functional or crossdivisional questions. This reduces their ability to take advantage of potential opportunities or respond to business problems. Strategic Data Planning is one methodology which can address such problems, within the general umbrella of information engineering. Resting on the assumption that a relatively stable group of data entities lies at the center of an organization's information processing needs, SDP is a formalized, top-down, data-centered planning approach that builds a model of the enterprise, its functions, and its underlying data as a basis for identifying and implementing an integrated set of information systems. In spite of strong conceptual arguments for the value of the SDP approach and its use in many organizations, empirical researchers have failed to find clear-cut evidence of its general success. This raises the question of whether the approach is universally appropriate. If success is somewhat problematic, are there lessons that can be drawn from actual organizational experience? The purpose of this paper is to report the results of a series of case studies of SDP efforts, to offer insights on the conditions under which SDP is most effective, and to propose directions for future research.
Dataflow Processing and Optimization on Grid and Cloud Infrastructures

Complex on-demand data retrieval and processing is a characteristic of several applications and combines the notions of querying & search, information filtering & retrieval, data transformation & analysis, and other data manipulations. Such rich tasks are typically represented by data processing graphs, having arbitrary data operators as nodes and their producer-consumer interactions as edges. Optimizing and executing such graphs on top of distributed architectures is critical for the success of the corresponding applications and presents several algorithmic and systemic challenges. This paper describes a system under development that offers such functionality on top of Ad-hoc Clusters, Grids, or Clouds. Operators may be user defined, so their algebraic and other properties as well as those of the data they produce are specified in associated profiles. Optimization is based on these profiles, must satisfy a variety of objectives and constraints, and takes into account the particular characteristics of the underlying architecture, mapping high-level dataflow semantics to flexible runtime structures. The paper highlights the key components of the system and outlines the major directions of its development.
Enriching Facial Blendshape Rigs with Physical Simulation

Oftentimes facial animation is created separately from overall body motion. Since convincing facial animation is challenging enough in itself, artists tend to create and edit the face motion in isolation. Or if the face animation is derived from motion capture, this is typically performed in a mo‐cap booth while sitting relatively still. In either case, recombining the isolated face animation with body and head motion is non‐trivial and often results in an uncanny result if the body dynamics are not properly reflected on the face (e.g. the bouncing of facial tissue when running).
Automatic classification of semantic patterns from the Pattern Dictionary of English Verbs

The paper presents a supervised approach to semantic parsing, based on a new semantic resource, the Pattern Dictionary of English Verbs (PDEV). PDEV lists the most frequent patterns of English verbs identified in corpus. Each argument in a pattern is semantically categorized with semantic types from the PDEV ontology. Each pattern is linked to a set of sentences from the British National Corpus. The article describes PDEV in details and presents the task of pattern classification. The system described is based on a distributional approach, and achieves 66% in Micro-average F1 across a sample of 25 of the most frequent verbs.
Problems when interpreting research results using only p-value and sample size

PROBLEMS WHEN INTERPRETING RESEARCH RESULTS USING O NLY P-VALUE AND SAMPLE SIZE Rink Hoekstra , Henk A.L. Kiers, Addie Johnson and Marleen Groenier University of Groningen, The Netherlands r.hoekstra@rug.nl The following three probabilities seem crucial when interpreting data, especially in the behavioral sciences:1) the probability that an effect is present in the population, 2) the probability that a replication is significant; and 3) the probability that the effect for a single individual in the population is in the expected direction. In our study, we asked 51 subjects (university students and lecturers in psychology) to estimate these probabilities after reading a short description of a hypothetical experiment with as outcomes only p-value and sample size given. Large variations in estimated probabilities were found. However estimates of the probabilities tended to increase as a positive function of sample size for a fixed p-value. Simulation studies show that, assuming a uniform prior distribution for the parameter, this turns out to be incorrect for all three probabilities. INTRODUCTION One of the main goals of statistics is to draw inferences from the data provided by a sample to the population one is interested in. One of the most frequently used methods for this purpose is null hypothesis significance testing (NHST). Although this approach has been heavily criticized for decades, for many researchers it prevails as the most common way to analyse data (e.g., Cohen, 1994; Masson and Loftus, 2003; Tryon, 2001). NHST is designed to assess the strength of the evidence against a null hypothesis ( H
A New Construction of Block Codes From Algebraic Curves

Since discovery of Goppa geometric codes, people have been asking the question: are there different constructions of block codes from algebraic curves that give the same parameters as Goppa geometric codes. Despite of great effort by researchers, no such constructions have been found so far. Although in literature, there are many constructions of block code from algebraic curves, most of them are quite different from the one by Goppa in nature and thus they have different parameters. Some of these constructions have the same parameters as Goppa geometric codes, however it was proved that these are essentially the same codes defined by Goppa. In this paper, we solve this question for the case where the characteristic of the ground field is 2, namely, we present a different construction of block codes from algebraic curves that give the same parameters as Goppa geometric codes for the characteristic 2 case.
Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia

Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.
MCSMC: A new parallel Multi-level Cache Simulator For multi-core processors

Simulation is a widely accepted tool for evaluating any proposed cache system under different application and configuration scenarios because of the high degree of configurability of cache memory which requires extensive design space exploration and identification of performance bottlenecks in system understudy. In this paper we have presented a new multi-level cache Simulator, 'MCSMC' (Multi-level Cache Simulator for Multi-Cores), developed for multi-core processors at NED University. It is a parallel trace-driven multi-level cache simulator based on module and layers approach. The developed simulator has been tested for upto 2048 cores and 10 cache levels with different cache performance parameters. It is coded in Visual C++ using OpenMP and Win32 process / thread libraries.
Comparison of effects of anaesthesia with desflurane and enflurane on liver function.

INTRODUCTION Although most general anaesthesia procedures are performed without any complications, volatile agents may have adverse effects on various living systems. This study aimed to compare the effects of desflurane and enflurane on liver function. METHODS 40 patients, who were in the ASA I-III risk groups and were planned to undergo head and neck surgery of at least three hours' duration, were randomly divided into two groups: the desflurane (Group D) and enflurane groups (Group E). Venous blood samples (5 ml) of the patients were obtained before anaesthesia induction, in the postoperative first hour and on the first and seventh days. The samples were centrifuged and then stored at -80 degrees Celsius until the determination of glutathione S-transferase (GST) levels. For maintenance of anaesthesia in Group D, desflurane (6 percent) was used, while in Group E, enflurane (1.2 percent) was used. RESULTS GST levels were significantly higher in Group E in the postoperative first hour (p-value is 0.002), and on the first day (p-value is 0.025) and seventh day (p-value is 0.035), although there were no differences preoperatively (p-value is more than 0.05). When postoperative levels were compared with preoperative levels, the postoperative GST levels of Group E were significantly higher (first hour [p-value is 0.008], first day [p-value is 0.010], seventh day [p-value is 0.038]). CONCLUSION Subclinical hepatic injury after anaesthesia continues to be an issue of interest, particularly with the development of new, more sensitive methods of measuring GST levels. The increase in GST concentration after anaesthesia is thought to be a result of reduced hepatic blood flow. This study has shown that desflurane has fewer effects than enflurane on liver function tests in lengthy operations of up to 330 minutes.
Text mining school inspection reports in England with R

This short paper reports on the first results of a text mining analysis of publicly-available OFSTED secondary school inspection reports for 1766 schools from 2000 to February 2014. The analysis focuses on what OFSTED has written in reports over this period, and how this relates to the judgment OFSTED has given to a specific school. It serves as a proof-of-concept of how text mining could convey some meaning from a vast amount of documents. The focus of this analysis is on the judgments that OFSTED makes in every report. The analysis was conducted by first ‘scraping’ the reports from the OFSTED website and then utilising sentiment analysis and topic modelling techniques in R to extract features of these documents. There appears to be link between the reports’ judgment and the sentiments in the report, as well as differences in the topics observed. However, interpreting these findings from data mining alone was not straightforward.
Atomic emission method for total boron in blood during neutron-capture therapy.

BACKGROUND Boron neutron-capture therapy (BNCT) is a drug-targeted binary radiotherapy for cancer. The (10)B capture of thermal neutrons induces secondary radiation within cells during irradiation. The most widely used boron carrier is 4-dihydroxyborylphenylalanine (BPA). The duration and timing of the irradiation is adjusted by monitoring (10)B concentrations in whole blood. METHODS We developed a new method for boron determination that uses inductively coupled plasma atomic emission spectrometry (ICP-AES) and protein removal with trichloroacetic acid before analysis. This method was compared with the established but tedious inductively coupled plasma mass spectrometry (ICP-MS), which uses wet ashing as sample pretreatment. Erythrocyte boron concentrations were determined indirectly on the basis of plasma and whole blood boron concentrations and the hematocrit. The hematocrit was determined indirectly by measuring calcium concentrations in plasma and whole blood. RESULTS Within- and between-day CVs were <5%. The recoveries for boron in whole blood were 95.6-96.2%. A strong correlation was found between results of the ICP-AES and ICP-MS (r = 0.994). Marked differences in plasma and erythrocyte boron concentrations were observed during and after infusion of BPA fructose complex. CONCLUSIONS The present method is feasible, accurate, and one of the fastest for boron determination during BNCT. Our results indicate that it is preferable to determine boron in plasma and in whole blood. Indirect erythrocyte-boron determination thus becomes possible and avoids the impact of preanalytical confounding factors, such as the influence of the hematocrit of the patient. Such an approach enables a more reliable estimation of the irradiation dose.
Model based DC power source emulator for electrical and hybrid electrical vehicles drive train tests

In this paper, a real time model based DC power source emulator is presented. The emulator has a modular architecture including a high performance real time simulation core and a kilowatts level electrical power output module. It was designed for Hardware-in-the-Loop (HiL) tests of DC power train in electrical or hybrid electrical vehicles. The emulator architecture is introduced and two applications are presented: a proton exchange membrane (PEM) fuel cell stack emulation (low dynamics) and a supercapacitor bank emulation (high dynamics). The obtained results demonstrate that the designed DC power sources emulator is capable to emulate common DC power sources used in electrical or hybrid electrical vehicle.
Chaos Game Representation for Discriminating Thermophilic from Mesophilic Protein Sequences

Can sequence analysis tell us about the function of protein? A basic question in protein science is which kind of proteins extent thermostability. Chaos game representation (CGR) can investigate the patterns hiding in protein sequence, visually revealing previously unknown structure. In this paper, we convert every protein sequence into a 20-dimensional vector by CGR algorithm, and based on these vectors we discriminate thermophiles from mesophiles using support vector machine (SVM). The overall accuracy achieves 100% in resubstitution test, and 87.12% in Jackknife test. Moreover, Matthews correlation coefficients (MCC) is 0.745.
Decentralised minimum-time average consensus in digraphs

Distributed algorithms for average consensus in directed graphs are typically asymptotic in the literature. In this work, we propose a protocol to distributively reach average consensus in a finite number of steps on interconnection topologies that form strongly connected directed graphs (digraphs). The average consensus value can be computed, based exclusively on local observations at each component, by running a protocol that requires each component to observe and store its own value over a finite and minimal number of steps, and to have knowledge of the number of its out-going links (i.e., the number of components to which it sends information). The proposed algorithm is demonstrated via illustrative examples.
The Maintenance of Synaptic Homeostasis at the Drosophila Neuromuscular Junction Is Reversible and Sensitive to High Temperature

Abstract Homeostasis is a vital mode of biological self-regulation. The hallmarks of homeostasis for any biological system are a baseline set point of physiological activity, detection of unacceptable deviations from the set point, and effective corrective measures to counteract deviations. Homeostatic synaptic plasticity (HSP) is a form of neuroplasticity in which neurons and circuits resist environmental perturbations and stabilize levels of activity. One assumption is that if a perturbation triggers homeostatic corrective changes in neuronal properties, those corrective measures should be reversed upon removal of the perturbation. We test the reversibility and limits of HSP at the well-studied Drosophila melanogaster neuromuscular junction (NMJ). At the Drosophila NMJ, impairment of glutamate receptors causes a decrease in quantal size, which is offset by a corrective, homeostatic increase in the number of vesicles released per evoked presynaptic stimulus, or quantal content. This process has been termed presynaptic homeostatic potentiation (PHP). Taking advantage of the GAL4/GAL80TS/UAS expression system, we triggered PHP by expressing a dominant-negative glutamate receptor subunit at the NMJ. We then reversed PHP by halting expression of the dominant-negative receptor. Our data show that PHP is fully reversible over a time course of 48–72 h after the dominant-negative glutamate receptor stops being genetically expressed. As an extension of these experiments, we find that when glutamate receptors are impaired, neither PHP nor NMJ growth is reliably sustained at high culturing temperatures (30–32°C). These data suggest that a limitation of homeostatic signaling at high temperatures could stem from the synapse facing a combination of challenges simultaneously.