Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages

ABSTRACT It is almost a cliche that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae, Siphoviridae, and Podoviridae. Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae. Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.
Use of Sericin as an Ingredient of Salad Dressing

Sericin is a structural polypetide of silk, consisting of a unique composition of amino acids. The use of sericin as an ingredient for salad dressing was evaluated in an o/w emulsion system with rape oil and vinegar. The low-viscosity sericin from white cocoon showed poor emulsifying activity, whereas non-separable dressing with a low peroxide value (POV) could be produced by the addition of high-viscosity sericin. The use of colored sericin, prepared from yellow-green cocoon shell, maintained a relatively low POV in spite of low viscosity and emulsifying activity levels. Total content of flavonol aglycons in yellow-green sericin was quantified after acid hydrolysis, showing that relatively high amounts of quercetin and kaempferol were detected in the colored sericin.
Nanometer metal line fabrication using a ZEP520∕50K PMMA bilayer resist by e-beam lithography

In this work, we propose a bilayer resist system with 50K poly methylmethacrylate as the bottom layer and ZEP520 as the top layer for lift-off process. By making use of the different dissolution rates in the rinser for the top and bottom layers, it is possible to create an overhang resist pattern suitable for lift-off. In this specific study, a set of process parameters have been optimized to fabricate Cr metal lines with a width of about 70nm. The process has been used to fabricate nanometer scale magnetic sensors for data storage applications.
Modeling the Role of Striatum in Stochastic Multi Context Tasks

Decision making tasks in changing environments with probabilistic reward schemes present various challenges to the agents performing the task. These agents must use the experience gained in the past trials to characterize the environment which guides their actions. We present two models to predict an agent’s behavior in these tasks - a theoretical model which defines a Bayes optimal solution to the problem under realistic task conditions. The second is a computational model of the basal ganglia which presents a neural mechanism to solve the same. Both the models are shown to reproduce results in behavioral experiments and are compared to each other. This comparison allows us to characterize the theoretical model as a bound on the neural model and the neural model as a biologically plausible implementation of the theoretical model. Furthermore, we predict the performance of the agents in various stochastic regimes which could be tested in future studies.
Global output‐feedback stabilization for a class of stochastic nonlinear systems via sampled‐data control

Summary In this paper, the global sampled-data output-feedback stabilization problem is considered for a class of stochastic nonlinear systems. First, based on output-feedback domination technique and emulation approach, a systematic design procedure for sampled-data output-feedback controller is proposed for a class of stochastic lower-triangular nonlinear systems. It is proved that the proposed sampled-data output-feedback controller will stabilize the given stochastic nonlinear system in the sense of mean square exponential stability. Because of the domination nature of the proposed control approach, it is shown that the proposed control approach can also be used to handle the global sampled-data output-feedback stabilization problems for a more general class of stochastic non-triangular nonlinear systems. Finally, simulation examples are given to demonstrate the effectiveness of the proposed method. Copyright © 2017 John Wiley & Sons, Ltd.
Melting Temperature of Simulated High-Burnup Mixed Oxide Fuels for Fast Reactors

The melting (solidus) temperatures were measured for fuel simulating burnups of 50, 90, 130, 170, 210 and 250 GWd/t (SIMFUEL) which were added non-radioactive soluble fission products (FPs) to unirradiated fast reactor MOX fuel. The melting temperatures for fuels of 250 GWd/t which were blended non-radioactive soluble FPs and irradiated fuels of 110.6 and 119.0 GWd/t were also compared to the SIMFUEL of 250 GWd/t. The melting temperature decrease of the SIMFUEL tended to saturate with increasing burnup and the melting temperatures appeared virtually constant above 170 GWd/t. An equation for melting temperature was obtained from the proposed equation in the previous report by revising the coefficient of the fifth term: where is the expected melting temperature (K), X 1 the plutonium fraction (Pu/(Pu+U)), X 2 the americium fraction (Am/(Pu+U+Am)), and X 3 the burnup (GWd/t). After the temperature measurement, the radial distribution of eight FP oxide additives in SIMFUEL of 250 GWd/t was measured by X-ray m.
European Journal of Education Studies-ISSN 2501-1111

The purpose of this study was to investigate influence of social factors on vocational career choices of students in Catholic-sponsored technical institutions located in the Catholic Diocese of Nakuru, Kenya. The study was guided by the research question: What is the influence of social factors on vocational career choices in the aforementioned institutions? The study was grounded on Krumboltz theory of social learning. The empirical literature covered various societal factors. A Convergent parallel mixed method design was used whereby 292 respondents participated in the study. Purposive, stratified and simple random sampling techniques were applied in sampling of institutions, administrators, teachers and students respectively. For data collection, interview guides were used for teachers and principals while questionnaires were employed to facilitate data collection from students. The Statistical Package for Social Sciences programme was used to aid analysis of quantitative data from the students while qualitative data from teachers and principals were organized into themes. Analysis of both qualitative and quantitative data were done independently then mixed at the end during interpretation. The study revealed that 91.6% of students are influenced by immediate people they interact with. It was also found that 55.6% never had prior working experience. The study revealed that as family and friends influence students in technical and vocational training institutions there is still a large number (49.3%) who make choices according to their own personal interest. Majority of Oloo Antone Onyango, Adhiambo Jacinta, M. , Anyona Jared Ntabo INFLUENCE OF SOCIAL FACTORS ON VOCATIONAL CAREER CHOICES IN TECHNICAL INSTITUTIONS IN KENYA A SURVEY OF CATHOLIC PRIVATE INSTITUTIONS IN NAKURU DIOCESE European Journal of Education Studies Volume 3 │ Issue 11│ 2017 174 the students (61.8%) perceived the courses they were pursuing as being very difficult but also marketable. Electrical installation was found to have the highest number of enrollment for national examinations followed by mechanics. The study recommended to Kenya Institute of Curriculum Development to introduce subjects at high school level that could expose students to vocational careers. It was further recommended that technical institutions should come up with guiding policies on how to help and streamline student’s choices on vocational careers.
A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer’s disease

Characterizing the intermediate phenotypes, such as gene expression, that mediate genetic effects on complex diseases is a fundamental problem in human genetics. Existing methods utilize genotypic data and summary statistics to identify putative disease genes, but cannot distinguish pleiotropy from causal mediation and are limited by overly strong assumptions about the data. To overcome these limitations, we develop Causal Multivariate Mediation within Extended Linkage disequilibrium (CaMMEL), a novel Bayesian inference framework to jointly model multiple mediated and unmediated effects relying only on summary statistics. We show in simulation that CaMMEL accurately distinguishes between mediating and pleiotropic genes unlike existing methods. We applied CaMMEL to Alzheimer’s disease (AD) and found 206 causal genes in sub-threshold loci (p < 10−4). We prioritized 21 genes which mediate at least 5% of local genetic variance, disrupting innate immune pathways in AD.
Transcriptomic characterization of 20 organs and tissues from mouse at single cell resolution creates a Tabula Muris

We have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising nearly 100,000 cells from 20 organs and tissues. These data reveal many new aspects of cell biology, including gene expression in poorly characterized cell populations and the characterization of new populations of cells in many tissues. Furthermore, they allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as immune cells from distinct anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3’-end counting1,2, enabled the survey of thousands of cells at relatively low coverage, while the other, FACS-based full length transcript analysis3, enabled characterization of cell types with high sensitivity and coverage. The cumulative resource provides the foundation for a comprehensive resource of transcriptomic cell biology.
Combined time-resolved SAXS and X-ray Spectroscopy methods

Recently developed equipment suitable for quasi simultaneous data collection of SAXS/WAXS and X-ray spectroscopy is discussed. The main applications for this technique are foreseen to be time-resolved studies in inorganic materials relevant for catalysis research and ceramics. The equipment is described and experimental limitations are discussed. Experiments on nanoparticle synthesis and the formation of inorganic materials for catalysis are used as examples of the usefulness of the developed equipment.
LDDWRR: Least Delay Dynamic Weighted Round-Robin Load Balancing in Software Defined Networking

In traditional network devices, tight coupling of data plane with the control plane so large amount of traffic on the web is not correctly handled by the Traditional network devices. The emerging strategy that decoupled the data plane from control plane is called Software Defined Networking (SDN). Control plane of these devices act like a brain or master. It is also called Software Defined networking controller or Openflow controller. Data plane is called slave that behave according to the instructions given by the master or control plane. To convert a data plane into powerful network devices we have to create Firewall, Load balancer, Intrusion Detection system applications and then run that applications at management plane that is on top of control plane. In such a manner we can convert data plane into powerful network devices according to the application. The application that we have created on the top of control plane is load balancer application that convert the dumb data plane into load balancer. Load balancer architecture consists of number of servers and clients which distributed the client traffic among number of servers based on particular strategy. There are number of strategies are available such as Round Robin, random policy. Each load balancing policy has some advantages and disadvantages. We created “least delay dynamic weighted round robin (LDDWRR)” strategy in this paper and run on the top of SDN controller. Then we evaluate the result of our load balancing strategy by comparing with the round robin strategy. Mininet is used for the experiment and controller that is used as control plane is called POX controller.
Infrared Depletion Spectroscopy and Structure of the 2-Aminopyridine Dimer†

The electronic and vibrational spectra of the 2-aminopyridine (2AP) dimer have been measured using resonant two-photon ionization (R2PI) and IR ion depletion (IR/R2PI) spectroscopy. Only two vibrational bands in the N−H stretch region have been observed at 3319 and 3529 cm-1, which are red-shifted by 120 and 17 cm-1, respectively, relative to the symmetric and antisymmetric N−H vibrations of the monomer. This provides evidence of the cyclic structure of this dimer with two antiparallel N−H· · ·N hydrogen bonds. In addition, ab initio calculations at the B3LYP/6-311++G(d,p) level have been carried out. The cyclic structure is also the calculated minimum energy conformation. Each NH2 group forms a σ-hydrogen bond with the ring nitrogen of the partner. Compared to the dimers of 2-pyridone ((2PY)2) and 2-hydroxypyridine ((2HP)2) and to the mixed dimer ((2PY)·(2HP)), the hydrogen bonds in (2AP)2 are weaker. This is confirmed by the differences in the vibrational spectra and by the computational results. The bi.
Hydrotalcites as Catalysts and Catalysts Precursors for the Synthesis of Biodiesel

This chapter aims at providing an overview of the potential of layered double hydroxides (LDHs) or hydrotalcite-like compounds (HTs) for contributing to the catalysis of the synthesis of biodiesel through the transesterification of triglycerides. First, the main methods of preparation of HTs and the most relevantfeatures of these materials are presented, with emphasis on their basic properties. Afterwards, the literature on the use of HTs as catalysts, catalysts precursors, and supports of transesterification catalysts is reviewed. HTs are promising materials for the synthesis of biodiesel from refined and waste vegetable oils, showing reasonable resistance to water and free fatty acids but an improvement of the chemical stability under the desired reaction conditions is still necessary.
Students’ Preferred Learning Styles & Academic Performance

It is imperative to remember that each individual is a unique learner. Scholars have identified that some learners lean toward specific techniques/strategies for learning. These techniques referred to learning styles or learning preferences. This study elaborates the preferred learning styles of business management students and its impact on academic performance in different universities of Pakistan. To conduct this empirical study Felder’s Index of Learning Styles is used to identify four learning styles: Active/Reflective, Sensing/Intuiting, Visual/Verbal and Sequential/Global. The data is collected from the five universities of the public and private sector of different cities. The results are drawn from a sample of 343 business students. Spearman Rho Correlation is used to test the correlation and Kruskal-Wallis test is applied to evaluate whether there is any significant relationship between different learning styles on the basis of academic performance. The findings of the study show that predominant profile of respondents consists of following preferred learning styles: active, reflective, sensory and intuitive. It also suggests that the academic performance of business students does not affect by any specific learning style. Limitations, future dimensions, and recommendation on the basis of results have been discussed at the end.
Comparison of the transmembrane helices of bovine rhodopsin in the crystal structure and the C α template based on cryo-electron microscopy maps and sequence analysis of the G protein-coupled receptors

G protein-coupled receptors (GPCR) are activated by a diverse array of extracellular signals, ranging from light to polypeptide molecules. The receptors propagate these signals intracellularly using G protein secondary messenger pathways. A common feature in the architecture of these receptors is their seven transmembrane domains. The first crystal structure of a GPCR, bovine rhodopsin, has recently been solved at 2.8 Å. We compared the seven membrane-spanning helices (TMH) from the crystal structure of bovine rhodopsin with those from the low-resolution model of bovine rhodopsin based on the cryo-electron microscopy structure of frog rhodopsin developed by Dr Joyce Baldwin. The model developed by Baldwin used a consensus sequence approach to predict the rotational position of each helix with respect to the other six helices. Superposition of the entire helix bundle of the Baldwin model with the crystal structure gave a RMS difference (RMSD) of 3.2 Å for the 198 C f atoms which suggests a high level of similarity in the arrangement of the helices. Except for TMH IV (RMSD of 4.0 Å), the position of corresponding helices within the helix bundle overlapped well. The superposition of individual helices showed that the RMSD values over 3 Å in the global superposition were largely due to one or more of the following: (i) differences in the unraveling and kinks for these helices, (ii) translation of TMH perpendicular to the membrane and (iii) rotation of helices up to 31°, except for TMH IV in which an additional contribution to the RMSD came from the aforementioned observation. As other crystal structures of GPCRs become available, a comparison with the Baldwin consensus model may reveal larger differences than those observed here.
Strong purifying selection on codon usage bias

Codon usage bias (CUB), where certain codons are used more frequently than expected by chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant paradigm is that the proportion of preferred codons is set by weak selection. Though experimental changes in codon usage have shown large phenotypic effects, genome-wide population genetics estimates have generally been consistent with the weak selection model. Here we use site frequency spectrum and polymorphismlevel data from deep Drosophila melanogaster population genomic sequencing to measure selection on synonymous sites. We find evidence that purifying selection on preferred codons varies in strength from weak to strong (Nes < −10). Our results suggest a new model where the level of CUB in a gene is determined by distribution of selection coefficients across sites. These results also indicate that the functional effect of CUB, and of synonymous sites in general, have been underestimated.
A Brief Review on Plagiarism Detection Methods

Plagiarism, a scientific misbehavior, has turned into a serious problem for researchers and publishers due to increasing and easy access to web-based scientific resources. Plagiarism includes using the scientific content of other documents without referencing the sources and is performed as copy the content directly or copy and change it. Most of the research in different fields are performed well in dealing with direct plagiarism, however, indirect plagiarism is often challenging for them. It is beneficial to study the preceding researches and find their strengths and weaknesses in order to find new ideas for future works. The present paper studies some of the plagiarism methods and a number of researches conducted in the area so far.
How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?

RNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, Differential Gene Expression (DGE) tools typically assume the form of the underlying distribution of gene expression. A recent highly replicated study revealed that RNA-seq gene expression measurements in yeast are best represented as being drawn from an underlying negative binomial distribution. In this paper, the statistical properties of gene expression in the higher eukaryote Arabidopsis thaliana are shown to be essentially identical to those from yeast despite the large increase in the size and complexity of the transcriptome: Gene expression measurements from this model plant species are consistent with being drawn from an underlying negative binomial or log-normal distribution and the false positive rate performance of nine widely used DGE tools is not strongly affected by the additional size and complexity of the A. thaliana transcriptome. For RNA-seq data, we therefore recommend the use of DGE tools that are based on the negative binomial distribution.
A Meta-Analysis Approach to Understanding Maya Fish Use on the Yucatán Peninsula

Abstract. This meta-analysis uses seven previously published fish assemblages from sites in the northern Maya lowlands to evaluate if environmental or human social factors, such as elite status, provided impetus for the increased emphasis on coastal trade during the Terminal to Postclassic periods. Following the political decline of sites in the central and southern Maya lowlands during the Terminal Classic period, the northern Maya lowlands rose in prominence. As political systems changed, so too did economic systems. Using species area curves, richness, nestedness, non-metric multidimensional scaling, evenness, and differences in habitat, this paper addresses to what degree fish trade in the northern Maya lowlands was driven by habitat differences, site distance from the coast, time period, or social status. The results indicate social factors, rather than environmental, explain more of the variation in the fish taxonomic composition at each site. The different taxonomic communities are explained less by specific environmental factors, recovery methods, or identification procedures than by site distance from the coast and social context of the site (i.e., elite versus non-elite). These data demonstrate that meta-analyses can explain how access-based differences—such as site distance from the coast or due to the social context of a particular assemblage—are expressed among large faunal datasets within complex societies.