Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT

Genetic mismatches in protein coding genes between allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipient and donor can elicit an alloimmunity response via peptides presented by the recipient HLA receptors as minor histocompatibility antigens (mHAs). While the impact of individual mHAs on allo-HSCT outcome such as graft-vs.-host and graft-vs.-leukemia effects has been demonstrated, it is likely that established mHAs constitute only a small fraction of all immunogenic non-synonymous variants. In the present study, we have analyzed the genetic mismatching in 157 exome-sequenced sibling allo-HSCT pairs to evaluate the significance of polymorphic HLA class I associated peptides on clinical outcome. We applied computational mismatch estimation approaches based on experimentally verified HLA ligands available in public repositories, published mHAs, and predicted HLA-peptide affinites, and analyzed their associations with chronic graft-vs.-host disease (cGvHD) grades. We found that higher estimated recipient mismatching consistently increased the risk of severe cGvHD, suggesting that HLA-presented mismatching influences the likelihood of long-term complications in the patient. Furthermore, computational approaches focusing on estimation of HLA-presentation instead of all non-synonymous mismatches indiscriminately may be beneficial for analysis sensitivity and could help identify novel mHAs.
Mapping Ethnic Stereotypes and Their Antecedents in Russia: The Stereotype Content Model

The stereotype content model (SCM), originating in the United States and generalized across nearly 50 countries, has yet to address ethnic relations in one of the world’s most influential nations. Russia and the United States are somewhat alike (large, powerful, immigrant-receiving), but differ in other ways relevant to intergroup images (culture, religions, ideology, and history). Russian ethnic stereotypes are understudied, but significant for theoretical breadth and practical politics. This research tested the SCM on ethnic stereotypes in a Russian sample (N = 1115). Study 1 (N = 438) produced an SCM map of the sixty most numerous domestic ethnic groups (both ethnic minorities and immigrants). Four clusters occupied the SCM warmth-by-competence space. Study 2 (N = 677) compared approaches to ethnic stereotypes in terms of status and competition, cultural distance, perceived region, and four intergroup threats. Using the same Study 1 groups, the Russian SCM map showed correlated warmth and competence, with few ambivalent stereotypes. As the SCM predicts, status predicted competence, and competition negatively predicted warmth. Beyond the SCM, status and property threat both were robust antecedents for both competence and warmth for all groups. Besides competition, cultural distance also negatively predicted warmth for all groups. The role of the other antecedents, as expected, varied from group to group. To examine relative impact, a network analysis demonstrated that status, competition, and property threat centrally influence many other variables in the networks. The SCM, along with antecedents from other models, describes Russian ethnic-group images. This research contributes: (1) a comparison of established approaches to ethnic stereotypes (from acculturation and intergroup relations) showing the stability of the main SCM predictions; (2) network structures of the multivariate dependencies of the considered variables; (3) systematically cataloged images of ethnic groups in Russia for further comparisons, illuminating the Russian historical, societal, and interethnic context.
Impact of educational test features on item difficulties by the linear logistic test model

The aim of the paper is to investigate the effect of item and person properties on item difficulties using the Linear Logistic Test Model (LLTM) and its extensions. The data under investigation are the Italy mathematics data from the Program for International Student Assessment (PISA) 2006. The information regarding the geographical macro-area (North-Italy versus South-Italy) has been used in the application as person property. Furthermore, the comparison on item properties effects between North-Italy versus South-Italy is performed fitting the LLTM for each geographical macro-area.
A new Smith predictor for controlling a process with an integrator and long dead-time

Abstmct-A new Smith predictor for control of a process with an integrator and long dead-time is proposed in this note. The controller deeouples the setpoint response from the load response. This simplifies both design and tuning. Simulation results obtained by controlling a typical process show that the new controller has superior performance compared to previous algorithms.
Content-based Image Retrieval Based On Visual Attention And The Conditional Probability

a novel content-based image retrieval framework was presented in this paper. This framework is used to encode primary visual feature and saliency information as natural image features by simulating visual attention mechanism and using the conditional probability. In this framework, the color volume is used as a novel feature to detect saliency areas. Besides, a novel generalized visual feature representation method, namely the conditional probability histogram, is proposed to describe natural image features. It can integrate primary visual features and saliency information into one whole unit. Experimental results indicate that the proposed algorithm outperform our prior works, namely multi-texton histogram and color difference histogram.
Rich Linguistic Structure from Large-Scale Web Data.

The past two decades have shown an unexpected effectiveness of Web-scale data in natural language processing. Even the simplest models, when paired with unprecedented amounts of unstructured and unlabeled Web data, have been shown to outperform sophisticated ones. It has been argued that the effectiveness of Web-scale data has undermined the necessity of sophisticated modeling or laborious data set curation. In this thesis, we argue for and illustrate an alternative view, that Web-scale data not only serves to improve the performance of simple models, but also can allow the use of qualitatively more sophisticated models that would not be deployable otherwise, leading to even further performance gains. We investigate this hypothesis through the use of both parametric and Bayesian nonparametric modeling techniques. First, by comparing rich parametric models against simpler models, we show that richer modeling of Web data brings about qualitative and quantitative performance gains. Experimental results in the application domain of sentence compression show that richer models lead to systems with improved robustness and generalization power. In the domain of lexical correction we augment a coarse generative model with a discriminative reranking component that incorporates richer contextual information
Implementing a parallel sparse matrix-vector multiplication using dataflow

Sparse matrix-vector multiplication (SpMV) is an important operation in sparse linear algebra problems. According to Bell [1], “they represent the dominant cost in many iterative methods for solving large-scale linear systems”. In this paper we propose a dataflow parallel version of the SpMV kernel using Compressed Sparse Row (CSR) storage format. This implementation is executed in a Dataflow Runtime Environment called Trebuchet [3][4][5]. The dataflow model[2] exposes parallelism by essence. Task execution is triggered as soon as the input data is available. A dataflow program can be described as a dataflow graph where nodes represent instructions (or tasks) and edges represent their input/output dependencies. Two instructions can run concurrently if there is no directed path between them and their pieces of data are available. This differs from Von Neumann model where instructions are guided by control flow and their execution is inherently sequential. Our experimental environment consists of a machine with 4 Quad-Core Intel Core i7-3820 processors running at 3.6GHz and 64 GB RAM. We performed the SpMV kernel in three matrices from University of Florida Sparse Matrix Collection1, listed in Table 1 . Figure 1 presents the results for Dataflow(running on Trebuchet), Intel Math Kernel Library(MKL)2 (which uses OpenMP3 in parallel version) implementations. Results show that with a naive dataflow implementation it is already possible to achieve higher speedups than the ones obtained with Intel MKL. For smalled matrices the dataflow runtime environment overheads become more evident, but for larger ones, Trebuchet provides better results. In order to improve performance, we intend to implement other SpMV kernels using different storage formats and other approaches to get better use of cache locality[6]. Moreover, since dataflow allows more flexibility in describing application dependencies, we may find more interesting parallelization patterns that are easier to implement and provide smaller overheads in dataflow.
Investigation of Enteric Viruses Associated With Runting and Stunting in Day-Old Chicks and Older Broilers in Southwest Nigeria

Enteric viruses are known to have significant economic impact on poultry, especially broiler chicken flocks, because of production losses attributable to poor feed conversion and weight gain. To sustain the Nigerian poultry industry that contributes significantly to the livestock sector of the economy, there is a need to investigate commercial broiler flocks in the country for the presence of enteric viruses causing runting and stunting, growth retardation, and hatchery diseases. Gut contents were collected from 158 day-old and six 14-week old runted/stunted broiler chickens in commercial farms (ten) and hatcheries (six) located in Southwest Nigeria. The samples were examined for the presence of chicken astrovirus (CAstV), avian nephritis virus (ANV), avian rotavirus (AvRV), chicken parvovirus (ChPV), and turkey astroviruses (TAstV-1 and−2) by polymerase chain reaction (PCR) and reverse transcriptase-PCR (RT-PCR) whereas avian reovirus (ARV) and fowl adenovirus (FAdV) by virus isolation (VI), RT-PCR, and PCR. While CAstV was detected in all the birds (100%), sporadic detection of ANV (5%), and ChPV (5%) was observed in day-old and/or older birds. Four isolates were obtained by VI with one isolate being ARV positive and other three FAdV positive by RT-PCR and PCR, respectively. These findings strongly suggest CAstV as a major cause of runting and stunting as well as hatchery condemnations in commercial broilers in Southwest Nigeria, although co-infections with ANV, FAdV, ARV, and ChPV cannot be ruled out. In addition, the possible vertical and horizontal transmissions of these viruses are discussed.
Luciferase Time-based, High-throughput Screening Assay for the Discovery of HIV-1 Inhibitors

With the enhancement of high-throughput screening (HTS) for target-based antiretroviral discovery, fluorescence has been considered the best bioassay. Bioluminescence by genetic reporters has maintained a major place among cell-based virological assay formats. Luminescent bioassays have a wide variety of applications due to their high sensitivity and linearity, even for a range of complex biological samples. In this target-based method, we used an HTS bioluminescence assay and highlighted the detection capabilities of this time-of-addition experiment. Hence, the development of a cell-based assay that uses a phenotypic drug discovery approach based on bioluminescence by stable reporter cells is described. Utilizing this screening method, a bioluminescent, target-based, time-of-addition experiment was performed by adding antiretrovirals with known mechanisms of action to analyze their drug targets by measuring the length of time until the antiretrovirals lost their efficacy in an HIV-1 replication assay. Depending on the viral replication target, the antiretrovirals lost activity at different times: fusion inhibitors acted for 0-2 h; retrotranscriptase inhibitors acted efficiently for the first 4 h; integrase inhibitors acted for 18 h; and protease inhibitors were inactivated after 15 h. The target-based, bioluminescence assay identifies the mode of action of antiretroviral drugs and provides valuable information about drug targets that inhibit HIV replication. This assay delimits the time (hours) for which the addition of an antiviral can be delayed before losing its antiviral activity relative to the replication cycle of HIV. The target of an antiviral compound can be identified both by comparing the relative time until it loses efficacy to that of the reference drugs and by the time elapsed when the antiretroviral loses activity compared to a known control.
Probabilistic temperature forecast by using ground station measurements and ECMWF ensemble prediction system

The ECMWF Ensemble Prediction System 2‐metre temperature forecasts are affected by systematic errors due mainly to resolution inadequacies. Moreover, other errors sources are present: differences in height above sea level between the station and the corresponding grid point, boundary layer parameterisation, and description of the land surface. These errors are more marked in regions of complex orography. A recursive statistical procedure to adapt ECMWF EPS‐2metre temperature fields to 58 meteorological stations on the Mediterranean island of Sardinia is presented. The correction has been made in three steps: (1) bias correction of systematic errors; (2) calibration to adapt the EPS temperature distribution to the station temperature distribution; and (3) doubling the ensemble size with the aim of taking into account the analysis errors. Two years of probabilistic forecasts of freezing are tested by Brier Score, reliability diagram, rank histogram and Brier Skill Score with respect to the climatological forecast. The score analysis shows much better performance in comparison with the climatological forecast and direct model output, for all forecast timse, even after the first step (bias correction). Further gains in skill are obtained by calibration and by doubling the ensemble size. Copyright © 2004 Royal Meteorological Society.
Analysis of the echolocation calls and morphometry of a population of Myotis chiloensis (Waterhouse, 1838) from the southern Chilean temperate forest.

Echolocation is characteristic of bats of the suborder Microchiroptera. Though recent studies of echolocation calls in Latin America have generated significant advances in knowledge about distribution, habitat use and ecology of bats, the recording and analysis of bat calls is barely known in Chile. As a first step in studies on the ecology of the endemic Chilean myotis bat ( Myotis chiloensis ), we carried out morphometric measures and analyzed echolocation calls in a rural site near Pucon (39°15’S 17°W) in the Araucania Region of southern Chile. During January 2009, we obtained 22 records from captured and 75 records from flying individuals. The analysis of calls in searching phase showed that the terminal frequency for this species is 43.4 ± 1.2 kHz, with a mean duration of 2.1 ± 1.0 ms and an interval between pulses of 77.5 ± 16.9 ms. The calls are FM – QCF, as is characteristic for the family Vespertilionidae. The contribution of new morphometric data from captured and released individuals indicates differences from previous studies. The records and acoustic analysis establishes a baseline for more detailed future ecological investigation of this and other bat species in Chile. El sistema de ecolocacion es caracteristico de los murcielagos del suborden Microquiroptera. A pesar de que el estudio de este sistema ha generado significativos avances en el conocimiento de la distribucion, uso de habitat y ecologia de murcielagos en Latinoamerica, el registro y analisis de las llamadas de las especies de Chile aun es incipiente. Con el objetivo de ampliar el conocimiento actual de Myotis chiloensis , se realizaron mediciones morfometricas y analisis de sus llamadas de ecolocacion en un sector rural periferico a la ciudad de Pucon (39°15’S 17°W), Region de la Araucania, sur de Chile. En enero de 2009, fueron obtenidas 22 grabaciones de llamadas de individuos capturados y 75 llamadas de individuos en vuelo. El analisis de las llamadas en fase de busqueda indica que la frecuencia promedio caracteristica para esta especie es 43.4 ± 1.2 kHz, con una duracion promedio de 2.1 ± 1.0 ms y un intervalo entre pulsos de 77.5 ± 16.9 ms. Los componentes que se observan en las llamadas de busqueda para esta especie, son de Frecuencia Modulada (FM) y Frecuencia casi Constante (QCF), las que son caracteristicas de la familia Vespertilionidae. El aporte de nuevos datos morfometricos de los individuos capturados y liberados en el area indican diferencias respecto a estudios anteriores. Los registros y analisis acusticos de este murcielago endemico del sur de Sud America, generan nuevas oportunidades para el estudio de su ecologia y la de otras especies en Chile.
VISUAL COMPONENT-BASED SYSTEM MODELING WITH AUTOMATED SIMULATION DATA COLLECTION AND OBSERVATION

ACCEPTED BY THE GRADUATE COLLEGE iii ABSTRACT Many complex systems can only be studied using dynamical models that can be simulated. Models must have precise structural and behavioral abstractions in order to be correctly simulated. A key challenge in developing and executing simulation models is to have a modeling and simulation environment where users can systematically transition from model creation to simulation experimentation and evaluation. In response, this thesis develops a novel approach for component-based system modeling and simulation. An integrated modeling and simulation tool called Component-based System Modeling and Simulation (CoSMoS) is developed. Its modeling engine supports logical, visual, and persistent model specification with support for automated simulation code generation. Its simulation engine supports visual experimentation configuration and run-time data collection and observation. The CoSMoS tool enables simulation-based system design process with support for model verification and simulation validation. The integrated model specification, simulation code generation, and controlled experimentation capabilities of the CoSMoS tool are demonstrated with a model of an Anti-Virus Network software system. iv To my parents v ACKNOWLEDGMENTS
SSR-Patchwork: An Optimized Protocol to Obtain a Rapid and Inexpensive SSR Library Using First-Generation Sequencing Technology

Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.
A SearchCol Algorithm for the unrelated parallel machine scheduling problem with job splitting

In this dissertation, the unrelated parallel machine scheduling problem with job splitting and sequence independent setup times is addressed, implementing a method to solve it in a recently proposed framework, SearchCol, short for ‘Metaheuristic search by Column Generation’. The study of scheduling problems is of high relevance due to its real-world application in multiple fields, as documented in its vast literature, and also due to its high complexity derived from the diverse environments, variables, restrictions and the combinations of these in different systems. The problem consists in finding a scheduling plan for a set of independent jobs on a set of unrelated parallel machines, considering jobs and machines release dates, sequence independent setup times and the job splitting property, with due date related objectives. The introduction of setup times and job splitting properties in unrelated environments has not been extensively studied, even though its use can play an important role in scheduling. A mixed integer programming model is developed featuring the aforementioned properties, which is then decomposed by machine using the Dantzig-Wolfe decomposition. To solve the decomposed model a hybrid approach entitled SearchCol is applied, which results from the interaction between column generation and metaheuristics. Problem specific heuristics to use in the column generation component of the SearchCol are also developed and diverse alternatives within the global algorithm are tested. A problem specific algorithm for one of the main SearchCol components is also suggested. To evaluate the effectiveness of the model and the proposed algorithms, computational tests are performed and their solutions analysed for a set of test instances.
User Link Prediction based on Logistic Regression Model with Local Similarity Indices in Microblog Network

Jie Lian, Haiqiang Chen, Yun Liu, Fei Xiong, Yuan Wen 1, First Author Key Laboratory of Communication & Information Systems, Beijing Municipal Commission of Education, Beijing JiaoTong University 100044, P.R. China, hugo_lian@163.com *3,Corresponding Author Key Laboratory of Communication & Information Systems, Beijing Municipal Commission of Education, Beijing JiaoTong University 100044, P.R. liuyun@bjtu.edu. cn China Information Technology Security Evaluation Center (CNITSEC), chhq@itsec.gov. cn Key Laboratory of Communication & Information Systems, Beijing Municipal Commission of Education, Beijing JiaoTong University 100044, P.R. China, 08111029@bjtu.edu. cn and 09111026@bjtu.edu. cn
A Prospective Study of Mobile Cloud Computing

In today’s fast moving world, mobile devices such as smartphones, tablets, and other PDAs are a central component in achieving effective and convenient communication. In today fast developing world of IT and commerce, the growth of mobile computing (MC) has become a force to be reckoned with. However, it is not without its own set of challenges; these devices are dependent on battery life span, storage, bandwidth, and security and mobility. These challenges have slowed down the growth of the service quality of these devices. The intrinsic challenges of mobile computing are being overcome by imputing and saving data in cloud computing. It is done by using various service providers aside from the mobile device service providers for hosting the mobile applications’ delivery. Mobile cloud computing is a branch of cloud computing and it provides ease of use and mobility to its users. Mobile cloud computing is described as services of cloud computing that are available in mobile environment. This study offers thorough knowledge of the capabilities and challenges faced in mobile cloud computing.