Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses

The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability.
Integrating Science and the Humanities : Toward a Second Wave 1

The relationship between the sciences and the humanities has long been a fraught one—a tension famously captured by C.P. Snow in the phrase “The Two Cultures” (Snow 1959/1993). The belief that humanists study “texts”—in the broad sense that this term has acquired in recent decades—while scientists study “things” is still commonplace in modern universities. The two groups typically perform their work in different parts of the campus, are served by separate funding agencies, and are governed in their work by radically different methodologies and theoretical assumptions. Attempts to bridge the two cultures have often taken the form of hostile takeovers: humanists trying to forcibly bring the work of scientists under the umbrella of arbitrary, interpretable “inscriptions” or scientists arguing for the explanatory irrelevance of human phenomena not amenable to quantification. Recent decades have, however, seen the rise of voices arguing for an alternative approach—“consilience” (Wilson 1998) or “vertical integration” (Tooby and Cosmides 1992, Slingerland 2008)—which argues that humanistic and scientific work should be brought together into a shared explanatory framework. This seems at first glance like a fairly uncontroversial idea, and indeed the adjective “interdisciplinary” is often bandied about as a term of approval in both the sciences and the humanities. However, the call for consilience, which requires extending interdisciplinarity across the sciences/humanities divide, has for the most part been met with by indifference or outright hostility by the majority of humanists. For instance, the work of the person responsible for popularizing the term “consilience” in recent years, E.O. Wilson, has since the 1970s inspired a backlash among humanists of such intensity
Enterprise Resource Systems Software Implementation

Enterprise resource planning systems are complex yet single, integrated software programs that runs off a single database so that the various departments can easily share information and communicate with each other. The integrated approach can have a tremendous payback if companies implement the software correctly. This chapter illustrates the implementation steps as followed by major corporations in the United States, and provide an insight into the practical implementation issues. A business case for such systems is introduced in this chapter as well. The chapter provides seven ERP issues and elaborates these issues in the context of implementation. The implementation details during conceptualization, design, implementation, go-live, and operation stages are provided with a note to practitioners on ERP implementation. IntroductIon Enterprise resource planning (ERP) software attempts to integrate all departments and functions across a company onto a single computer system that can serve all those different departments’ particular needs (Koch 2002). Each of those departments typically has its own computer system optimized for the particular way that the department does its work. But ERP combines them all together into a single, integrated software program that runs off a single database so that the various departments can more easily share information and communicate with each other. That integrated approach can have a tremendous payback if companies install the software correctly. Typically, when a customer places an order, that order begins a mostly paper-based journey from in-basket to in-basket around the company, often being keyed and re-keyed into different departments’ computer systems along the way. These activities cause delays and errors. Meanwhile, no
Schistosomiasis Coinfection in Children Influences Acquired Immune Response against Plasmodium falciparum Malaria Antigens

Background Malaria and schistosomiasis coinfection frequently occurs in tropical countries. This study evaluates the influence of Schistosoma haematobium infection on specific antibody responses and cytokine production to recombinant merozoite surface protein-1-19 (MSP1-19) and schizont extract of Plasmodium falciparum in malaria-infected children. Methodology Specific IgG1 to MSP1-19, as well as IgG1 and IgG3 to schizont extract were significantly increased in coinfected children compared to P. falciparum mono-infected children. Stimulation with MSP1-19 lead to a specific production of both interleukin-10 (IL-10) and interferon-γ (IFN-γ), whereas the stimulation with schizont extract produced an IL-10 response only in the coinfected group. Conclusions Our study suggests that schistosomiasis coinfection favours anti-malarial protective antibody responses, which could be associated with the regulation of IL-10 and IFN-γ production and seems to be antigen-dependent. This study demonstrates the importance of infectious status of the population in the evaluation of acquired immunity against malaria and highlights the consequences of a multiple infection environment during clinical trials of anti-malaria vaccine candidates.
Alcohol and Tobacco Content in UK Video Games and Their Association with Alcohol and Tobacco Use Among Young People

Abstract To determine the extent to which video games include alcohol and tobacco content and assess the association between playing them and alcohol and smoking behaviors in adolescent players in Great Britain. Assessment of substance in the 32 UK bestselling video games of 2012/2013; online survey of adolescent playing of 17 games with substance content; and content analysis of the five most popular games. A total of 1,094 adolescents aged 11–17 years were included as participants. Reported presence of substance content in the 32 games; estimated numbers of adolescents who had played games; self-reported substance use; semiquantitative measures of substance content by interval coding of video game cut scenes. Nonofficial sources reported substance content in 17 (44 percent) games but none was reported by the official Pan European Game Information (PEGI) system. Adolescents who had played at least one game were significantly more likely ever to have tried smoking (adjusted odds ratio [OR] 2.70, 95 percent confidence interval [CI] 1.75–4.17) or consumed alcohol (adjusted OR 2.35, 95 percent CI 1.70–3.23). In the five most popular game episodes of alcohol actual use, implied use and paraphernalia occurred in 31 (14 percent), 81 (37 percent), and 41 (19 percent) intervals, respectively. Tobacco actual use, implied use, and paraphernalia occurred in 32 (15 percent), 27 (12 percent), and 53 (24 percent) intervals, respectively. Alcohol and tobacco content is common in the most popular video games but not reported by the official PEGI system. Content analysis identified substantial substance content in a sample of those games. Adolescents who play these video games are more likely to have experimented with tobacco and alcohol.
Relation between the fluid energy equation and the response of a hotwire anemometer in time-dependent flows

The behavior of hot-wire and related anemometers working in a constant-temperature mode is analyzed from the point of view of the dynamics of the energy equation in the fluid. In general there is no unique functional relationship between the magnitude of the local flow velocity and the heat rate for the sensor, though approximations may be valid under certain conditions. Some suggestions of sufficiency conditions for extending static calibration to dynamic flows are given, and the question of their validity in practical cases is raised.
A multi-level level generator

Generating content at multiple levels of abstraction simultaneously is an open challenge in procedural content generation. Representing and automatically replicating the style of a human designer is another. This paper addresses both of these challenges through extending a previously devised methodology for pattern-based level generation. This method builds on an analysis of Super Mario Bros levels into three abstraction levels: micro-, meso- and macro-patterns. Micro-patterns are then used as building blocks in a search-based PCG approach that searches for macro-patterns, which are defined as combinations of meso-patterns. Results show that we can successfully generate levels that replicate the macro-patterns of selected input levels, and we argue that this constitutes an approach to automatically analysing and replicating style in level design.
Adapting hidden Markov models for ASL recognition by using three-dimensional computer vision methods

We present an approach to continuous American sign language (ASL) recognition, which uses as input 3D data of arm motions. We use computer vision methods for 3D object shape and motion parameter extraction and an ascension technologies 'Flock of Birds' interchangeably to obtain accurate 3D movement parameters of ASL sentences, selected from a 53-sign vocabulary and a widely varied sentence structure. These parameters are used as features for hidden Markov models (HMMs). To address coarticulation effects and improve our recognition results, we experimented with two different approaches. The first consists of training context-dependent HMMs and is inspired by speech recognition systems. The second consists of modeling transient movements between signs and is inspired by the characteristics of ASL phonology. Our experiments verified that the second approach yields better recognition results.
Toxin-Based Therapeutic Approaches

Protein toxins confer a defense against predation/grazing or a superior pathogenic competence upon the producing organism. Such toxins have been perfected through evolution in poisonous animals/plants and pathogenic bacteria. Over the past five decades, a lot of effort has been invested in studying their mechanism of action, the way they contribute to pathogenicity and in the development of antidotes that neutralize their action. In parallel, many research groups turned to explore the pharmaceutical potential of such toxins when they are used to efficiently impair essential cellular processes and/or damage the integrity of their target cells. The following review summarizes major advances in the field of toxin based therapeutics and offers a comprehensive description of the mode of action of each applied toxin.
Processing and Optimizing Main Memory Spatial-Keyword Queries

Important cloud services rely on spatial-keyword queries, containing a spatial predicate and arbitrary boolean keyword queries. In particular, we study the processing of such queries in main memory to support short response times. In contrast, current state-of-the-art spatial-keyword indexes and relational engines are designed for different assumptions. Rather than building a new spatial-keyword index, we employ a cost-based optimizer to process these queries using a spatial index and a keyword index. We address several technical challenges to achieve this goal. We introduce three operators as the building blocks to construct plans for main memory query processing. We then develop a cost model for the operators and query plans. We introduce five optimization techniques that efficiently reduce the search space and produce a query plan with low cost. The optimization techniques are computationally efficient, and they identify a query plan with a formal approximation guarantee under the common independence assumption. Furthermore, we extend the framework to exploit interesting orders. We implement the query optimizer to empirically validate our proposed approach using real-life datasets. The evaluation shows that the optimizations provide significant reduction in the average and tail latency of query processing: 7- to 11-fold reduction over using a single index in terms of 99th percentile response time. In addition, this approach outperforms existing spatial-keyword indexes, and DBMS query optimizers for both average and high-percentile response times.
Vector bundles and theta functions on curves of genus 2 and 3

Let SUcir) be the moduli space of vector bundles of rank r and trivial determinant on a curve C. A general E in SUcir) defines a divisor 0£ in the linear system |r0|, where 0 is the canonical theta divisor in Pic^"1 (C). This defines a rational map 6: SUcir) --■*■ |r0|, which turns out to be the map associated to the determinant bundle on SUcir) (the positive generator of Pic iSUcir)). In genus 2 we prove that this map is generically finite and dominant. The same method, together with some classical work of Morin, shows that in rank 3 and genus 3 the theta map is a finite morphism - in other words, every vector bundle in SUcO) admits a theta divisor. Introduction. Let C be a smooth projective complex curve, of genus g > 2. The moduli space SUcir) of semi-stable vector bundles of rank r on C, with trivial determinant, is a normal projective variety, which can be considered as a nonabelian analogue of the Jacobian variety JC. It is actually related to JC by the following construction, which goes back (at least) to (N-R). Let J8~x be the translate of JC parameterizing line bundles of degree g - 1 on C, and 0 C J8~l the canonical theta divisor. For E e SUcir), consider the locus
Page-Level Data Extraction Approach for Web Pages Using Data Mining Techniques

Web data extraction has been an important part for many Web data analysis applications. In this paper, we formulate the data extraction problem as the decoding process of page generation based on structured data and tree templates[1]. We propose a unsupervised, page-level data extraction approach to deduce the schema and templates for each individual Deep Website, contains either singleton or multiple data records in one Webpage. FiVaTech applies tree matching, tree alignment, and mining techniques to achieve the challenging task. In experiments, FiVaTech has much higher precision than EXALG and is comparable with other record-level extraction systems like ViPER and MSE. The experiments show an encouraging result for the test pages used in many state-of-the-art Web data extraction works [3].
Minimising Dynamic Power Consumption in On-Chip Networks

The provision of a general-purpose on-chip communication network is becoming increasingly important in the design of complex SoCs and chip-multiprocessors. In this paper we explore how the power consumed by such on-chip networks may be reduced through the application of clock and signal gating optimisations. We describe how the effectiveness of such optimisations may be maximised and demonstrate that very large reductions in power requirements are possible. A detailed analysis of where power is consumed in an optimised on-chip network is then provided. Results are obtained from fully place and routed standard-cell designs implemented in a 90nm technology. Our 64-bit on-chip network has a maximum operating frequency of 800MHz, in the best-case the combined latency for traversing a network router and link is a single clock cycle
Penetration of moxifloxacin into the human pancreas following a single intravenous or oral dose.

OBJECTIVES Failure to prevent secondary infectious complications in acute necrotizing pancreatitis (ANP) is attributable in part to the limited penetration of antimicrobial drugs. As newer quinolones are particularly attractive owing to their antimicrobial activity, for the first time we studied the penetration of moxifloxacin into pancreatic tissue in patients. PATIENTS AND METHODS In this prospective, non-comparative clinical trial, 60 patients undergoing elective pancreas resection received a single oral or intravenous (iv) dose of 400 mg moxifloxacin for perioperative antimicrobial prophylaxis. The concentration of moxifloxacin was measured in samples taken from blood and from pancreatic tissue at the beginning and at the end of resection. RESULTS Mean moxifloxacin concentrations in pancreatic tissue following iv or oral administration were 3.1+/-0.9 and 2.7+/-1.4 mg/kg at 3-3.7 h post-dose (first sampling) and 3.6+/-1.5 and 3.1+/-1.8 mg/kg at 4.3-5.3 h post-dose (second sampling), respectively. Corresponding mean plasma concentrations of moxifloxacin were 1.8+/-0.5 and 1.2+/-0.6 mg/L (first sampling) and 1.5+/-0.4 and 1.0+/-0.5 mg/L (second sampling), respectively. From first to second sampling, the mean tissue-to-plasma ratios varied from 1.8+/-0.6 to 2.6+/-1.2 (iv) and from 2.4+/-0.8 to 3.1+/-1.2 (oral). Pancreatic tissue concentrations of moxifloxacin exceeded the MIC90 for the relevant pathogens covered by moxifloxacin for at least 5 h after dosing. CONCLUSIONS Moxifloxacin has been demonstrated to penetrate efficiently into human pancreatic tissue following iv or oral administration. From a pharmacological perspective, moxifloxacin appears to be promising for prophylaxis and treatment of local pancreas infections. Whether it is beneficial in the prevention and therapy of infectious complications in patients with ANP should be investigated in a controlled clinical trial.
Mobile Agents for World Wide Web Distributed Database Access

The popularity of the Web as a universal access mechanism for network information has created the need for developing Web-based DBMS client/server applications. However, the current commercial applet-based approaches for accessing database systems offer limited flexibility, scalability, and robustness. We propose a new framework for Web-based distributed access to database systems based on Java-based mobile agents. The framework supports lightweight, portable, and autonomous clients as well as operation on slow or expensive networks. The implementation of the framework using the aglet workbench shows that its performance is comparable to, and in some case outperforms, the current approach. In fact, in wireless and dial-up environments and for average size transactions, a client/agent/server adaptation of the framework provides a performance improvement of approximately a factor of ten. For the fixed network, the gains are about 40 percent and 30 percent, respectively. We expect our framework to perform even better when deployed using different implementation platforms as indicated by our preliminary results from an implementation based on Voyager.
Interaction Evaluation for Human-Computer Co-creativity: A Case Study

Interaction design has been suggested as a framework for evaluating computational creativity by Bown (2014). Yet few practical accounts on using an Interaction Design based evaluation strategy in Computational Creativity Contexts have been reported in the literature. This study paper describes the evaluation process and results of a human-computer co-creative poetry writing tool intended for children in a school context. We specifically focus on one formative evaluation case utilizing Interaction Design evaluation methods, offering a suggestion on how to conduct Interaction Design based evaluation in a computational creativity context, as well as, report the results of the evaluation itself. The evaluation process is considered from the perspective of a computational creativity researcher and we focus on challenges and benefits of the interaction design evaluation approach within a computational creativity project context.
Positive Selection of Natural Poly-Reactive B Cells in the Periphery Occurs Independent of Heavy Chain Allelic Inclusion

Natural autoreactive B cells are important mediators of autoimmune diseases. Receptor editing is known to play an important role in both central and peripheral B cell tolerance. However, the role of allelic inclusion in the development of natural autoreactive B cells is not clear. Previously, we generated μ chain (TgVH3B4I) and μ/κ chains (TgVH/L3B4) transgenic mice using transgene derived from the 3B4 hybridoma, which produce poly-reactive natural autoantibodies. In this study, we demonstrate that a considerable population of B cells edited their B cells receptors (BCRs) via light chain or heavy chain allelic inclusion during their development in TgVH3B4I mice. Additionally, allelic inclusion occurred more frequently in the periphery and promoted the differentiation of B cells into marginal zone or B-1a cells in TgVH3B4I mice. B cells from TgVH/L3B4 mice expressing the intact transgenic 3B4 BCR without receptor editing secreted poly-reactive 3B4 antibody. Interestingly, however, B cell that underwent allelic inclusion in TgVH3B4I mice also produced poly-reactive autoantibodies in vivo and in vitro. Our findings suggest that receptor editing plays a minor role in the positive selection of B cells expressing natural poly-reactive BCRs, which can be positively selected through heavy chain allelic inclusion to retain their poly-reactivity in the periphery.
Almost universal codes for fading wiretap channels

We consider a fading wiretap channel model where the transmitter has only statistical channel state information, and the legitimate receiver and eavesdropper have perfect channel state information. We propose a sequence of non-random lattice codes which achieve strong secrecy and semantic security over ergodic fading channels. The construction is almost universal in the sense that it achieves the same constant gap to secrecy capacity over Gaussian and ergodic fading models.
Psychosocial risk factors for tobacco use among adolescents with asthma.

OBJECTIVE To determine the prevalence of smoking among adolescents with asthma and smoking's psychosocial risk factors (environmental smoking exposure, autonomy, depression). METHOD Participants were 2,039 adolescents with asthma and 2,039 matched controls from the Add Health study. RESULTS The prevalence of ever smoking among adolescents with asthma was 56%. Among ever smokers with asthma, the prevalence of current smoking was 48%, and the prevalence of current smokers having made a recent attempt to stop smoking was 57%. Having parents who have smoked, exposure to friends who smoke, and depression were significant psychosocial risk factors for ever smoking. Asthma and exposure to friends who smoke were significantly associated with current smoking, and attempts to stop smoking were significantly associated with asthma and depression. CONCLUSIONS Psychosocial risk factors for smoking among adolescents with and without asthma appear similar. Research on the role of illness in tobacco control is warranted.