Miracle-dz/UniFAR-FTUs huggingface dataset:
Animal Cytogenetics and Comparative Mapping

ABC Fax + 41 61 306 12 34 E-mail karger@karger.ch www.karger. com © 2004 S. Karger AG, Basel 0301–0171/04/1061–0098$21.00/0 Accessible online at: www.karger. com/cgr Abstract. Hyaluronidase genes (HYAL) encode hyaluronidase enzymes required for hyaluronan degradation. Both in humans and in mouse, clustered hyaluronidase genes have been identified. Here, the porcine hyaluronidase cluster consisting of genes HYAL1, HYAL2 and HYAL3 was characterized. The porcine cDNA sequences and proteins share homologies to human orthologs of 85 and 81% for HYAL1, 87 and 89% for HYAL2 and 86 and 83% for HYAL3, respectively. The porcine hyaluronidase proteins approximately share a 40% homology with each other. Furthermore, genes FUS1 and FUS2 were found within this cluster, which was assigned to SSC13q21. A total of seven SNPs were detected in the genes (four in HYAL1, two in HYAL2 and one in HYAL3). Three of the four SNPs in HYAL1 led to amino acid exchanges (C622G → Asp24 to Glu; C633T → Pro28 to Leu, and G1298T → Ala250 to Ser). The amino acid replacements induce putative changes in the extended strand at Asp24, in the extended strand and the random coil at Pro28, and finally in the random coil and the alpha helix at Ala250. Frequency estimations for four SNPs located in genes HYAL1 and HYAL3 using animals (n = 295) of nine European and six Chinese pig breeds indicated several significant deviations. For example, there were no significant differences in allele frequencies between pigs representing breeds Hampshire and Jiangquhai at SNP C633T (HYAL1), but between Hampshire respectively Jiangquhai animals and Rongchang pigs. Analysis of the same breeds at SNP C588T (HYAL3) indicates significant differences between Hampshire and Jiangquhai respectively Rongchang, but not between Jiangquhai and Rongchang. The breed Göttingen Minipig displayed significant differences concerning two SNPs with respect to the other European pig breeds tested. For all three hyaluronidase genes, N-glycosylation sites are typical. For HYAL2 the lysosomal character was proven. The catalytic site responsible for HAase activity is conserved in the three enzymes. Expression of hyaluronidases was determined by RT-PCR and quantitative PCR. Broad gene expression was observed in different tissues for the three genes, respectively.
Genome-Wide Association Study of Autistic-Like Traits in a General Population Study of Young Adults

Lay abstract: It has been proposed that autistic-like traits in the general population lie on a continuum, with clinical Autism Spectrum Disorder (ASD), representing the extreme end of this distribution. The current study undertook a genome-wide association (GWA) scan of 965 young Western Australian adults to identify novel risk variants associated with autistic-like traits. No associations reached genome-wide significance; however, a review of nominally associated single nucleotide polymorphisms (SNPs) indicated two positional candidate loci that have been previously implicated in autistic-like trait etiology. Scientific abstract: Research has proposed that autistic-like traits in the general population lie on a continuum, with clinical ASD representing the extreme end of this distribution. Inherent in this proposal is that biological mechanisms associated with clinical ASD may also underpin variation in autistic-like traits within the general population. A GWA study using 2,462,046 SNPs was undertaken for ASD in 965 individuals from the Western Australian Pregnancy Cohort (Raine) Study. No SNP associations reached genome-wide significance (p < 5.0 × 10−8). However, investigations into nominal observed SNP associations (p < 1.0 × 10−5) add support to two positional candidate genes previously implicated in ASD etiology, PRKCB1, and CBLN1. The rs198198 SNP (p = 9.587 × 10−6), is located within an intron of the protein kinase C, beta 1 (PRKCB1) gene on chromosome 16p11. The PRKCB1 gene has been previously reported in linkage and association studies for ASD, and its mRNA expression has been shown to be significantly down regulated in ASD cases compared with controls. The rs16946931 SNP (p = 1.78 × 10−6) is located in a region flanking the Cerebellin 1 (CBLN1) gene on chromosome 16q12.1. The CBLN1 gene is involved with synaptogenesis and is part of a gene family previously implicated in ASD. This GWA study is only the second to examine SNPs associated with autistic-like traits in the general population, and provides evidence to support roles for the PRKCB1 and CBLN1 genes in risk of clinical ASD.
ROAR: Robust Label Ranking for Social Emotion Mining

Understanding and predicting latent emotions of users toward online contents, known as social emotion mining, has become increasingly important to both social platforms and businesses alike. Despite recent developments, however, very little attention has been made to the issues of nuance, subjectivity, and bias of social emotions. In this paper, we fill this gap by formulating social emotion mining as a robust label ranking problem, and propose: (1) a robust measure, named as G-mean-rank (GMR), which sets a formal criterion consistent with practical intuition; and (2) a simple yet effective label ranking model, named as ROAR, that is more robust toward unbalanced datasets (which are common). Through comprehensive empirical validation using 4 real datasets and 16 benchmark semi-synthetic label ranking datasets, and a case study, we demonstrate the superiorities of our proposals over 2 popular label ranking measures and 6 competing label ranking algorithms. The datasets and implementations used in the empirical validation are available for access.
Logger4u: Predicting debugging statements in the source code

Software logging is an essential programming practice that saves important runtime information that can be used later by software developers for troubleshooting, debugging and monitoring the software. Even though software logging has numerous benefits this practice is underutilized because of lack of any formal guiding principles to developers for making strategic and efficient logging decisions. Logging should be optimized because too much logging can cause performance overheads; sparse logging can leave out vital information that might give clues to developers about the real issues. In absence of any formal guidelines developers rely solely on their domain knowledge and experience while making logging decisions. In order to lessen this effort of making decisions we have proposed a machine learning based framework, Logger4u for if-block logging prediction. We extract and use 28 distinctive static features from the source code helpful in making well informed logging decisions. We use Support Vector Machine (two variants, 1 linear and 1 RBF kernel based) models, Multilayer Perceptron with back propagation model and Random forest model in our work. Our approach gives encouraging results for if-block logging task. The accuracy achieved by the Linear SVM, MLP, Random Forest and kernel SVM are 73.05%, 74.62%, 79.84% and 81.22% respectively
Inclusion for People with Developmental Disabilities: Measuring an Elusive Construct

ABSTRACT The philosophy of inclusion for people with intellectual and developmental disabilities (IDD) has evolved over the last 50 years. Over time, inclusion research has shifted from a focus on deinstitutionalization to understanding the extent to which individuals with IDD are meaningfully involved in the community and social relationships. Yet, there has been no agreed on way to measure inclusion. Many different measurement and data collection techniques have been used in the literature. This study proposes a brief measure of inclusion that can be used with family members and on survey instruments.
Understanding and Using Fisher's p . Part 2: A Reference Bayesian Hypothesis Test

In Part 2 of this article, a reference Bayesian hypothesis test is constructed that corresponds exactly to the single-parameter ABIC1 of Part 1. An important role is played here by a hitherto rather neglected (and initially purely empirical) law of numbers (see Benford (1938)) that had first been propounded in 1881 (see Newcomb (1881)). This hypothesis test is then extended to small samples, where another important role is played by the p-statistic; this time in setting an upper bound to the false discovery rate, regardless of the number of degrees of freedom involved.
ADL dependence and perceived health among elderly deaf sign-language users: A comparison with a matched group of elderly hearing people

The main purpose of the study was to investigate dependence in ADL and perceived health among elderly deaf sign-language users and to compare these findings with data from a matched hearing elderly population sample. Data on the deaf population were collected through assessments and structured interviews in sign language. Data on the hearing population were retrieved from the Swedish National Study and Ageing and Care (SNAC), while only a few variables from the questionnaire were used in the present study. Each deaf individual was matched by three hearing persons. Matching was performed according to gender, age, and living situation. The main finding is that elderly deaf sign-language users are more dependent in ADL but simultaneously report better health than their hearing counterparts. The differences in ADL dependence can be explained by factors linked to the communication problems experienced by deaf sign-language users, but also by cultural factors. The better health reported by the deaf sample may be attributed to adaptive mechanisms that deaf sign-language users have been claimed to develop. This research provides new information on a vulnerable group of elderly people, i.e. deaf sign-language users, that has previously been given little scientific attention.
The political economy of telecommunications reforms

Since most of the dramatic changes in telecommunications policies occurred in the past two decades, sufficient data to evaluate the many differences in details across countries are only now emerging. Using a new data set on privatization, competition, regulation, and tariff policies of the telecommunications sector, this paper investigates the political economy of Telecommunications reforms. The authors empirically analyze the explanatory power of various factors - including sectoral performances, constituents characteristics, political structure, as well as macroeconomic variables - in shaping countries' decision of reforms. The authors are able to test some influential hypotheses in the literature of policy reforms such as the crisis hypothesis, the constituents demand hypothesis, the private-interest hypothesis, the ideology hypothesis, and some hypotheses emerging from the new institutional economics.
Intelligent Support for Information Retrieval of Web Documents

The main goal of this research was to investigate the means of intelligent support for retrieval of web documents. We have proposed the architecture of the web tool system --- Trillian, which discovers the interests of users without their interaction and uses them for autonomous searching of related web content. Discovered pages are suggested to the user. The discovery of user interests is based on analysis of documents visited by the users previously. We have created a module for completely transparent tracking of the user's movement on the web, which logs both visited URLs and contents of web pages. The post analysis step is based on a variant of the suffix tree clustering algorithm. We primarily focus on overall Trillian architecture design and the process of discovering topics of interests. We have implemented an experimental prototype of Trillian and evaluated the quality, speed and usefulness of the proposed system. We have shown that clustering is a feasible technique for extraction of interests from web documents. We consider the proposed architecture to be quite promising and suitable for future extensions.
Hypothesis Testing Under Mutual Information Privacy Constraints in the High Privacy Regime

Hypothesis testing is a statistical inference framework for determining the true distribution among a set of possible distributions for a given data set. Privacy restrictions may require the curator of the data or the respondents themselves to share data with the test only after applying a randomizing <italic>privacy mechanism</italic>. This work considers mutual information (MI) as the privacy metric for measuring leakage. In addition, motivated by the Chernoff-Stein lemma, the relative entropy between pairs of distributions of the output (generated by the privacy mechanism) is chosen as the utility metric. For these metrics, the goal is to find the optimal privacy-utility tradeoff (PUT) and the corresponding optimal privacy mechanism for both binary and <inline-formula> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula>-ary hypothesis testing. Focusing on the high privacy regime, Euclidean information-theoretic approximations of the binary and <inline-formula> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula>-ary PUT problems are developed. The solutions for the approximation problems clarify that an MI-based privacy metric preserves the privacy of the source symbols in inverse proportion to their likelihoods.
The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.
Neuromuscular taping in multiple sclerosis. A pilot study.

BACKGROUND AND AIM OF THE WORK Neuromuscular Taping (NT) is a relatively new device that induces micro-movements by stimulating receptors in the skin. The aim of this study was to analyze the effect of the application of Neuromuscular Taping (NT) on motor performance and quality of life in a cohort of multiple sclerosis (MS) patients. METHODS Twenty MS patients with Expanded Disability Status Scale < or = 4 (EDSS); clinically stable disease; absence of relapses during the last 3 months; absence of rehabilitation treatment or symptomatic drugs acting on muscular tone or fatigue for at least 2 months; a stable disease modifying treatment for at least 3 months; were treated with the application of NT. It was applied four times at 4-day intervals on the weakest side of the hamstrings muscles. The treatment efficacy on motor performance was evaluated by the six minute walking test (6MWT), measured at the beginning of treatment (TO), at the end of NT application (T1), and three weeks after the last treatment application (T2). Moreover, Short Form 36 health survey (SF-36) was administered to evaluate the quality of life. RESULTS The mean distance covered during the 6MWT improved significantly between TO and the successive T1 and T2 measurements, passing from 342.6 +/- 148.9 mt at TO to 395.8 +/- 146.0 mt at T2 (p=0.03). The SF-36 showed a statistically significant improvement in most items. CONCLUSIONS The application of NT was able to improve significantly the motor performance and the quality of life in our small case series of MS patients. (www.actabiomedica.it).
The ‘good-enough society’, the ‘good-enough citizen’ and the ‘good-enough student’: Where is children’s participation agenda moving to in Brazil?

This article discusses how the new paradigm of children’s participation rights and competence has maintained unchallenged the subjectivity considered apt to be included as an opinion giver in the polity. ‘Developmentalism’ continues to feed as a theoretical input and a practical regulation of adult–children relationships. The article, based on an empirical investigation with Brazilian children, discusses how participation views of students and school staff, premised on the ‘good-enough student’, commit participation to an unchallenged school hierarchy and non-reciprocal adult-child relationships. This single standpoint from where one envisages the educational process leads to a de-politicization of school life. Consequently, the effective inclusion of children in society, constituting an important political challenge of our time, must be faced so that children’s participation can become more real and less rhetorical.
Mathematical approach to model rapidly elongated free-burning arcs in air in electric power circuits

A two-terminal equivalent model of rapidly elongated freeburning arcs in air is presented that is designed to be used in systematic simulations of both existing and new switching concepts of circuit breakers in electric power circuits. The proposed model is based on the combination of a Mayr-type and a Cassie-type differential equation. These are modified in order to take into account the influence of the elongation of the arc on the power balance of the arc as well as the voltage drop near the electrodes. Comparisons are made of experiments and simulations carried out in a current-commutation circuit using currents of about 1 kA and arc voltages of about 100 V. The simulation results are in good agreement with the measured current and voltage traces.
Dual-Clustering-Based Hyperspectral Band Selection by Contextual Analysis

Hyperspectral image (HSI) involves vast quantities of information that can help with the image analysis. However, this information has sometimes been proved to be redundant, considering specific applications such as HSI classification and anomaly detection. To address this problem, hyperspectral band selection is viewed as an effective dimensionality reduction method that can remove the redundant components of HSI. Various HSI band selection methods have been proposed recently, and the clustering-based method is a traditional one. This agglomerative method has been considered simple and straightforward, while the performance is generally inferior to the state of the art. To tackle the inherent drawbacks of the clustering-based band selection method, a new framework concerning on dual clustering is proposed in this paper. The main contribution can be concluded as follows: 1) a novel descriptor that reveals the context of HSI efficiently; 2) a dual clustering method that includes the contextual information in the clustering process; 3) a new strategy that selects the cluster representatives jointly considering the mutual effects of each cluster. Experimental results on three real-world HSIs verify the noticeable accuracy of the proposed method, with regard to the HSI classification application. The main comparison has been conducted among several recent clustering-based band selection methods and constraint-based band selection methods, demonstrating the superiority of the technique that we present.
TETRAD and SEM.

The authors have given us a lucid, concise, and accurate account of the TETRAD project, an account likely to clear much of the confusion over the philosophy of graph-based causal discovery methods. As one who has been active in the exploration and formulation of this philosophy, I am very pleased to see TETRAD arrive at this stage of development and now presented as a practical modeling tool for the research community. In this commentary, I wish to expand an aspect of TETRAD which the authors, by using the analogy with ordinary statistical estimation, have played down: the importance of TETRAD to the foundations of structural equations modeling (SEM). The assumptions underlying statistical estimation are of fundamentally diierent character from those underlying causal modeling tasks, and TETRAD, by fostering an understanding of these diierences, can help establish not only its own legitimacy but the legitimacy of the entire SEM enterprise. Thus, I will rst add a few arguments in support of the assumptions underlying TETRAD and then attempt to show that, even if these assumptions are not fully embraced, the general lessons learned from graphical causal modeling are destined to have a profound impact on SEM's practice and philosophy. The operation of TETRAD is based on two assumptions: \causal independence" and \faithfulness. " 1 While the assumption of causal independence is rarely challenged, the faithfulness assumption has drawn quite a few objections and is a likely target for further criticism from SEM researchers. I would like therefore to elaborate some additional rationale for faithfulness. Because TETRAD relies primarily on nonexperimental data, causal claims are issued with guarantees weaker than those obtained through controlled randomized experiments. Pearl and Verma (1991) expressed these guarantees in terms of two orthogonal notions: minimality and stability. 2 Minimality guarantees that any alternative structure compatible 1 Causal independence, also known as \Reichenbach's Principle" or \no correlation without causation," is rooted in the principle of no action at a distance Arntzenius, 1990]. The notion of faithfulness (also called \DAG-isomorphism" and \nondegeneracy" Pearl, 1988, p. 391]) was termed \stability" by Pearl and Verma (1991) to emphasize the invariance of certain independencies to functional form. 2 These guarantees were advanced in connection with the discovery algorithm IC (for \Inferred Causation") which was developed in parallel with and on the same principles as the PC algorithm of Spirtes et al. (1993).
Multimodal ways of eliciting students' voice

For some time researchers have been exploring how students might best be supported to express their ideas, opinions and feelings and to demonstrate what they know and can do. In this paper, we discuss some of the implications of sociocultural view of learning for how classroom research is conducted and describe some of the approaches we have used to generate information on student classroom experiences. Over the course of our work we have found that the use of multiple and multimodal data generation methods allows student with different interests and abilities to take an active part in research. We then detail some of the challenges and rewards involved in working with students in these ways as part of a research agenda focused on enhancing teaching and learning.