Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic reconstruction of HCV genotype 1b dissemination in a small city centre: The Camporeale model

Several seroepidemiological population‐based surveys carried out in Italy have shown a high prevalence of hepatitis C virus (HCV) infection. Camporeale (CP), a small Sicilian town with a 10.4% prevalence of HCV mostly genotype 1b, probably represents a specific context, since intravenous drug addiction, and sexual promiscuity are almost absent. In order to reconstruct the pattern of introduction and diffusion of HCV in this ecological niche, the NS5 genomic region of 72 HCV genotype 1 isolates (39 from CP and 33 collected throughout Sicily) was amplified and sequenced. Sequences were aligned and analyzed by BioEdit, PAUP and BEAST, and their molecular evolution compared. Thirty‐eight HCV genotype 1b isolates from CP were associated in a monophyletic “transmission cluster. ” By applying Monte Carlo Markov simulation, it was calculated that HCV was introduced between the end of the 1940s and the beginning of the 1950s. The phylogenetic distance between the CP cluster and other Sicilian isolates confirmed its uniqueness and the local diffusion from a common ancestor. The data obtained from classic phylogenetic analysis, combined with the application of the Bayesian analysis to the study of the coalescence of phylogenetic trees, have shown that, in CP, few HCV native strains have been transmitted in a limited length of time probably through iatrogenic routes, and then have not spread further. J. Med. Virol. 80:1723–1731, 2008. © 2008 Wiley‐Liss, Inc.
Entry of US Medical School Graduates Into Family Medicine Residencies: 2014-2015.

BACKGROUND AND OBJECTIVES This is the 34th national study conducted by the American Academy of Family Physicians (AAFP) that reports retrospectively the percentage of graduates from US MD-granting and DO-granting medical schools who entered Accreditation Council for Graduate Medical Education (ACGME)-accredited family medicine residency programs as first-year residents in 2014. Approximately 8.5% of the 18,241 students graduating from US MD-granting medical schools between July 2013 and June 2014 entered a family medicine residency. Of the 1,458 graduates of the US MD-granting medical schools who entered a family medicine residency in 2014, 80% graduated from 69 of the 131 schools. Eleven schools lacking departments or divisions of family medicine produced only a total of 26 students entering family medicine. In aggregate, medical schools west of the Mississippi River represent less than a third of all US MD-granting schools but have an aggregate rate of students selecting family medicine that is two-thirds higher than schools to the east of the Mississippi. A rank order list of US MD-granting medical schools was created based on the last 3 years' average percentage of graduates who became family medicine residents, using the 2014 and prior AAFP census data. US MD schools continue to fail to produce a primary care workforce, a key measure of social responsibility as measured by their production of graduates entering into family medicine. DO-granting and international medical school graduates filled the majority of ACGME-accredited family medicine first-year resident positions in 2014.
Public Library Users: Perspectives of Socially Vulnerable Populations

Abstract Modern public libraries strive for inclusivity. Part of this effort involves enhancing staff capacity for engaging with socially vulnerable populations. This paper presents the outcomes of a study on library use by homeless adults, one of the most vulnerable of populations. The study employed a mix of methods. Part one was quantitative: a survey of library patrons. A second, qualitative phase involved focus groups – two of which were comprised of homeless patrons. Several areas of concern and need emerged, including physical space, safety, library services, and interactions with the library staff.
Aberrant Expression of Fas Ligand in Mice Deficient for the MHC Class II Transactivator1

The MHC class II transactivator (CIITA) is a critical regulator of MHC class II genes and other genes involved in the Ag presentation pathway. CIITA-deficient mice lack MHC class II expression on almost all APCs. In this study, we show that these mice also have aberrant Fas ligand expression on both CD4 T cells and B cells. We found that Fas ligand expression was greatly increased on CIITA-deficient CD4 T cells during the Th1 differentiation process. However, both CIITA-deficient and control Th1 effector cells up-regulated Fas ligand to similar levels if cells were reactivated. The introduction of CIITA into primary CD4 T cells via retroviral infection resulted in a reduction in the level of Fas ligand and delay in apoptosis after activation. Interestingly, activated B cells from the CIITA-deficient mice also showed increased levels of Fas ligand that could be to some degree inhibited by the introduction of IL-4.
Coordinating Inventory Control and Pricing Strategies with Random Demand and Fixed Ordering Cost: th

An activated oxygen gas sensor element having an increased voltage output under rich gas conditions, short switching response and reduced internal resistance is produced by chemically treating the inner conductive catalyst electrode of the sensor element with an inorganic acid or acid salt and current activating the outer conductive catalyst electrode by applying a direct current to the sensor element, with the outer electrode as an anode, while the outer electrode is at an elevated temperature and in the presence of a nonoxidizing atmosphere.
A Study of Users’ Reactions to a Mixed Online Discussion Model: A Lag Sequential Analysis Approach

There is an increasing growth of Social Network Services (SNSs). A variety of SNSs are applied in online interpersonal platforms. Among them, asynchronous and synchronous discussions are widely examined. However, there is a lack of research into the effects of integrated discussion services that combines asynchronous and synchronous discussions. Thus, the study investigates users’ performances and behavior patterns in a mixed discussion model that integrates asynchronous and synchronous discussions with a lag sequential analysis. The results showed that most groups chose to adopt the mixed discussion model (i.e., using both synchronous and asynchronous discussions), and only one group totally adopted the asynchronous discussion model. The study further analyzed the learners’ learning effectiveness and behavioral patterns, and the results indicated that the groups using the mixed model had a positive performance to a certain extent in terms of learning effectiveness and knowledge construction. In addition, users with the mixed discussion model demonstrated diverse behaviors, which were more complex than that of those with a single-way discussion model. Furthermore, regarding the groups using “balanced synchronous and asynchronous discussions” and the groups “mainly using synchronous discussion supplemented by less asynchronous discussion” in the mixed model (simultaneously using synchronous and asynchronous discussions), those users who mainly used synchronous discussion supplemented by asynchronous discussion had more diverse behaviors of knowledge construction.
Customising parallelism and caching for machine learning

Inductive logic programming is an attractive and expressive paradigm for machine learning. A drawback of inductive logic programs is their demanding computational requirements. We present of FPGA-based multi-processor architecture aimed at fast execution of such programs. The architecture exploits both coarse-grained parallelism at the query level, and fine-grained parallelism in the unification algorithm. Instructions are not required, and the components are customised for a hypothesis space referring only to ground unit clauses in the background knowledge. It also benefits from a distributed memory hierarchy, with a method for including background knowledge to eliminate instructions. The effectiveness of this architecture is demonstrated using a large organic chemistry data set. The proposed architecture is faster and smaller than our previous design based on multiple instruction processors. A single customised processor at 38 MHz can run 9 times faster than a Pentium 4 processor at 1.8GHz; a Xilinx XCV2000E device can accommodate 24 processors running in parallel.
Consumer Acceptance of Accountable-eHealth Systems

In this paper, we present the results of a survey conducted to measure the attitudes of eHealth consumers towards Accountable-eHealth systems, which are designed for information privacy management. We developed a research model that identify the factors contributing to system acceptance from quantitative data of 187 completed survey responses from university students studying non-health-related courses at university (Queensland, Australia). The research model is validated using structural equation modeling and can be used to identify how specific characteristics of Accountable-eHealth systems would affect their overall acceptance by future eHealth consumers.
β‐Amyloid fibril formation is promoted by step edges of highly oriented pyrolytic graphite

The aggregation of the amyloid‐β‐protein (Aβ) is an important step in the pathogenesis of Alzheimer's disease. As Aβ fibrils are not found in all brain regions, endogenous factors may influence Aβ fibril formation. In this study, atomic force microscopy was used to investigate the role of surface phenomena in directing amyloid aggregation. Aβ1‐40 was applied to a surface of highly oriented pyrolytic graphite at a concentration of 0.5 μM. Steps formed by edge‐plane surface defects on the graphite were found to act as a template to promote the assembly of Aβ into fibrils. Initially, after being deposited on the graphite surface, Aβ had a uniform beaded morphology. However, after incubating (aging) the Aβ on the surface for several hours, the Aβ assembled along step edges to form linear aggregates. After more prolonged incubation, the linear Aβ aggregates fused to form mature fibrils with a distinctive helical morphology. The results demonstrate that surface interactions can promote the aggregation of Aβ into amyloid fibrils and they suggest that similar interactions could promote amyloid aggregation in vivo. © 2006 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 519–526, 2006
Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins

Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: a well-studied, stable core enclosing the dsRNA genome and a highly unstable, poorly studied coat responsible for host cell attachment and entry. Here, based on cryo-electron microscopy (cryoEM), we report a 7-Å resolution structure of the infectious BTV virion, including the coat proteins. We show that unlike other dsRNA viruses, the VP2 attachment trimer has a triskelion shape composed of three tip domains branching from a central hub domain. We identify three putative sialic acid-binding pockets in the hub and present supporting biochemical data indicating sugar moiety binding is important for BTV infection. Despite being a nonenveloped virus, the putative VP5 membrane penetration trimer, located slightly inward of the VP2 attachment trimer, has a central coiled-coil α-helical bundle, similar to the fusion proteins of many enveloped viruses (e.g., HIV, herpesviruses, vesicular stomatitis virus, and influenza virus). Moreover, mapping of the amino acid sequence of VP5 to the secondary structural elements identified by cryoEM locates 15 amphipathic α-helical regions on the external surface of each VP5 trimer. The cryoEM density map also reveals few, weak interactions between the VP5 trimer and both the outer-coat VP2 trimer and the underlying core VP7 trimer, suggesting that the surface of VP5 could unfurl like an umbrella during penetration and shedding of the coat to release the transcriptionally active core particle.
ANTECEDENTS OF PERCEIVED COACH SUPPORT 2 Applying Generalizability Theory to Examine the Antecedents of Perceived Coach Support ! ! ! !

Although social support is integral to the coaching process, there is only a limited understanding of the antecedents of perceived coach support. We applied generalizability theory to examine perceived coach support and its antecedents at perceiver, provider, and relational levels of analysis. Two studies were conducted in which athletes rated the degree to which they identified with a selection of coaches, and the personality, competency, and supportiveness of those coaches. Univariate analyses demonstrated that the relational component accounted for a significant amount of variance in perceived coach support in both studies. Multivariate analyses demonstrated that when athletes perceive specific coaches to be highly agreeable, competent, and individuals with whom they share a common identity, they also perceive these same coaches to be particularly supportive in comparison to other coaches.
Modeling and Optimization of Adaptive Foraging in Swarm Robotic Systems

Understanding the effect of individual parameters on the collective performance of swarm robotic systems in order to design and optimize individual robot behaviors is a significant challenge. In this paper we present a macroscopic probabilistic model of adaptive collective foraging in a swarm of robots, where each robot in the swarm is capable of adjusting its time threshold parameters following the rules described by Liu et al. 2007. The swarm adapts the ratio of foragers to resters (division of labor) in order to maximize the net swarm energy for a given food density. A probabilistic finite state machine (PFSM) and a number of difference equations are developed to describe collective foraging at a macroscopic level. To model adaptation we introduce the new concepts of the sub-PFSM and private/public time thresholds. The model has been validated extensively with simulation trials, and results show that the model achieves very good accuracy in predicting the group performance of the swarm. Finally, a real-coded genetic algorithm is used to explore the parameter spaces and optimize the parameters of the adaptation algorithm. Although this paper presents a macroscopic probabilistic model for adaptive foraging, we argue that the approach could be applied to any adaptive swarm system in which the heterogeneity of the system is coupled with its time parameters.
Monocephalus thoracopagus conjoined twins in a goat

Monocephalus thoracopagus is a kind of attached symmetrical twin in which two nearly complete individuals joined front-to-front in the thoracic region with a single head, fused chests, one or two hearts and two lower bodies. A died female kid goat with one head, four ears, four paired limbs and two more or less complete body was referred to the Veterinary Faculty of the Shahid Bahonar University of Kerman. Detailed dissection was done on it and the progress of the duplication process of the internal organs was studied precisely. In the presented case, the way of the articulation of the ribs to the sterna and the progress of the duplication process in the alimentary canal can support the Spencer's spherical theory, saying that “a group of conjoined twins resulting from the union of two embryonic discs (or incomplete fission in one disc) over a common yolk sac”.
Energy-Efficient Resource Allocation in D2D Underlaid Cellular Uplinks

In this letter, we study the joint channel allocation and power control problem to maximize the energy efficiency (EE) of device-to-device (D2D) links in a D2D underlaid cellular network. Due to the location dispersion of D2D pairs and short-distance D2D transmission, it should be preferred that multiple D2D pairs can simultaneously share the resource with cellular users (CUs). To address the nonconvexity of the EE maximization problem, we divide the original problem into two subproblems and propose an iterative algorithm with low complexity to solve it. Simulation results show that the proposed algorithm converges rapidly and the EE of D2D links can be significantly improved compared with existing methods especially for an increasing number of CUs.
Conservative treatments for obesity 1 ’ 2

There is a growing consensus as to the characteristics of conservative treatments for obesity. We will begin by describing these characteristics without attempting a precise definition. Conservative treatments can be characterized in a negative sense as treatments other than surgery or adjunctive instruments such as gastric balloons, very-low-calorie diets, or pharmacotherapy. They can be characterized in a positive sense by the rate of weight loss that they produce: 1% of total body weight per week. Kilograms of weight lost per week is a more conventional measure rate of weight loss but one with two disadvantages. First, it fails to take into account the different weight-loss requirements of patients of differing initial body weights. Heavier persons can, and probably should, lose more weight than lighterpersons. Second, the use of weight loss per week as a measure makes it difficult to compare the weight losses of persons with widely varying initial weights. Using instead the measure of percentage of body weight lost has the advantage of permitting such comparisons, which are of value in the assessment of programs that treat different patient populations. The use of a percentage of total body weight lost as a measure of the rate of weight loss is simple and readily understandable. Thus, the weight loss of a modestly overweight women of 70 kg would be 0.7 kg/wk while that of a severely obese person of 140 kg would be 1.4 kg/wk. Conservative treatments for obesity can be characterized also in terms of the caloric deficitsthat they prescribe. Instead of prescribing a fixed number of calories or a particular caloricdeficit,however, conservative treatments are perhaps best characterized in terms of the percentage of the energy required to maintain the body weight of the individual. This value is ‘-50% of maintenance energy requirements and rarely, if ever, < 40% of these requirements. Defining caloric intake in terms of baseline values permits the individualization of treatment by adjusting caloric deficit to the needs of particular persons. Thus, someone whose energy requirement to maintain body weight is 2000 kcal/d will be reduced to a caloric intake of 1000 kcal with a deficit of 1000 kca! A person with a maintenance energy requirement of 4000 kca! will be reduced to a caloric intake of 2000 kca! /d, leaving a deficit of 2000 kcal.
Construction of algorithms to automatically determine individual indicators when assessing the shape quality of cross-wound packages

The paper addresses issues related to the selection of individual indicators to estimate the shape quality of cross-wound packages, as well as the construction of algorithms to determine them automatically. We have developed a method for evaluating the quality of shape of cross-wound packages based on the integrated indicator. To substantiate individual indicators, an expert poll was performed to rank defects in the shape of packages according to the degree of their influence on the suitability of packages for processing at subsequent technological transitions. To quantify each of the specified defect in the shape of a bobbin, we defined individual indicators that make it possible to quantify their impact. We have developed decisive rules and algorithms to calculate them based on the earlier obtained array of data on the coordinates of points at the bobbin’s surface. We have determined a score-based estimate of the influence of each indicator, which characterizes defects in winding, on the suitability of packages for processing at subsequent technological transitions. A comprehensive assessment of the package shape could be obtained using a method of weighted index. The mean weighted index is constructed as a dependence whose arguments are the individual quality parameters and their weighted parameters. Given this, we derived a dependence to calculate the integrated quality indicator of the bobbin’s shape. The higher the value for this indicator, the higher the quality of the controlled package. We have assessed the applicability of the constructed integrated quality indicator to analyzing the shape of packages. To this end, we analyzed a batch of packages, which confirmed the reproducibility of the process of analysis of the package shape using the proposed integrated indicator; as well as correspondence between estimates, derived using the proposed procedure, and visual assessments. A method for the integrated quantification of package shape makes it possible to conduct optimization experiments and to assign, based on them, such adjustable parameters for winding mechanisms that would ensure that packages of the required quality are received. The process of designing new winding equipment could be based on the necessary means to regulate a winding process
Human metabolic interactions of environmental chemicals

Investigations utilizing recombinant human xenobiotic‐metabolizing enzymes as well as human hepatocytes have revealed a number of interactions not only between different environmental chemicals (ECs) but also between ECs and endogenous metabolites. Organophosphorus insecticides (OPs) are potent inhibitors of the human metabolism of carbaryl, carbofuran, DEET and fipronil, as well as the jet fuel components, nonane and naphthalene. OPs are potent irreversible inhibitors of testosterone metabolism by cytochrome P450 (CYP) 3A4 and of estradiol metabolism by CYP3A4 and CYP1A2. All of these CYP inhibitions are believed to be due to the release of reactive sulfur during CYP‐catalyzed oxidative desulfuration. It has also been shown that the esterase(s) responsible for the initial step in permethrin metabolism in human liver is inhibited by both chlorpyrifos oxon and carbaryl. A number of pesticides, including chlorpyrifos, fipronil and permethrin, and the repellent, DEET, have been shown to be inducers of CYP isoforms in human hepatocytes, with fipronil being the most potent. Several agrochemicals, including fipronil and the pyrethroids, permethrin and deltamethrin, show toxicity toward human hepatocytes with fipronil being the most potent in this regard. Endosulfan‐α, which has shown promise as a model substrate for phenotyping CYP3A4 and CYP2B6 in human liver microsomes, is also an inducer of CYP2B6, acting through the PXR receptor. © 2007 Wiley Periodicals, Inc. J Biochem Mol Toxicol 21:182–186, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20175
Model‐based MPI‐IO tuning with Periscope tuning framework

For many parallel applications, I/O performance is a major bottleneck. MPI‐IO, defined by the MPI forum, can help parallel applications overcome the performance and portability limitations of existing parallel I/O interfaces. Although autotuning has been used to improve the performance of computing kernels, MPI‐IO autotuning has rarely been studied. To automate MPI‐IO performance tuning, we designed and implemented an automatic tuner. The tuner relies on the Periscope tuning framework for transparently passing hints to the MPI‐IO library and for automatically collecting performance data. Unlike computational code, each MPI‐IO function takes a relatively long time to complete. Thus, exhaustively searching through the entire parameter space is impractical. So we developed a performance model that can direct us to shorten the tuning time. Copyright © 2015 John Wiley & Sons, Ltd.