Miracle-dz/UniFAR-FTUs huggingface dataset:
The Apoptotic Protease-Activating Factor 1-Mediated Pathway of Apoptosis Is Dispensable for Negative Selection of Thymocytes1

Negative selection is a process to delete potentially autoreactive clones in developing thymocytes. Programmed cell death or apoptosis is thought to play an important role in this selection process. In this study, we investigated the role of apoptotic protease-activating factor 1 (Apaf1), a mammalian homologue of CED-4, in programmed cell death during the negative selection in thymus. There was no developmental abnormality in thymocytes from newborn Apaf1−/− mice in terms of CD4 and CD8 expression pattern and thymocyte number. Clonal deletion by endogenous male H-Y Ag of Apaf1-deficient thymocytes with transgenic expression of H-Y Ag-specific TCRs (H-Y Tg/Apaf1−/− thymocytes) was normally observed in lethally irradiated wild-type mice reconstituted with fetal liver-derived hemopoietic stem cells. Clonal deletion induced in vitro by a bacterial superantigen was also normal in fetal thymic organ culture. Thus, Apaf1-mediated pathway of apoptosis is dispensable for the negative selection of thymocytes. However, H-Y Tg/Apaf1−/− thymocytes showed partial resistance to H-Y peptide-induced deletion in vitro as compared with H-Y Tg/Apaf1+/− thymocytes, implicating the Apaf1-mediated apoptotic pathway in the negative selection in a certain situation. In addition, the peptide-induced deletion was still observed in H-Y Tg/Apaf1−/− thymocytes in the presence of a broad spectrum caspase inhibitor, z-VAD-fmk, suggesting the presence of caspase-independent cell death pathway playing roles during the negative selection. We assume that mechanisms for the negative selection are composed of several cell death pathways to avoid failure of elimination of autoreactive clones.
Non-Negative Matrix Factorization with Auxiliary Information on Overlapping Groups

Matrix factorization is useful to extract the essential low-rank structure from a given matrix and has been paid increasing attention. A typical example is non-negative matrix factorization (NMF), which is one type of unsupervised learning, having been successfully applied to a variety of data including documents, images and gene expression, where their values are usually non-negative. We propose a new model of NMF which is trained by using auxiliary information of overlapping groups. This setting is very reasonable in many applications, a typical example being gene function estimation where functional gene groups are heavily overlapped with each other. To estimate true groups from given overlapping groups efficiently, our model incorporates latent matrices with the regularization term using a mixed norm. This regularization term allows group-wise sparsity on the optimized low-rank structure. The latent matrices and other parameters are efficiently estimated by a block coordinate gradient descent method. We empirically evaluated the performance of our proposed model and algorithm from a variety of viewpoints, comparing with four methods including MMF for auxiliary graph information, by using both synthetic and real world document and gene expression data sets.
College student travel: A revised model of push motives

The purpose of the current study was to determine push motives of students attending US colleges and universities and to confirm if an existing push motivation model would find support and statistical acceptance in the college and university market. A total of 484 students were surveyed to collect data. Important push motivation factors for the college student market included ‘Knowledge’, ‘Sports’, and ‘Adventure’. Although a confirma-tory factor analysis revealed that the model was quite plausible based on the evaluation of five overall model fit indices, there were notable exceptions as well. Marketing implications based on these findings are discussed.
An Improved Threshold Free Algorithm for Maternal and Fetal Heart Rate Detection

This research work proposes an improved algorithm to extract maternal and fetal heart rate from an ECG measured of the mother‟s abdomen. Recently various research efforts have been devoted to this field. The most recent ones include filtering and threshold methods, wavelet methods, neural networks and others. Each of these methods has different effectiveness and weaknesses. In spite of the fact that their performance is quite apt, the main weakness is that these methods are threshold dependent. Recent developments resulted in threshold free detection of heart rate that involves fixed length RR moving interval, calculated on the basis of normal maximum and minimum heart rate. In the proposed algorithm, we update the length of RR moving interval every time a peak is detected, based on the average maternal heart rate. The effectiveness of this algorithm lies in the fact that it uses optimized RR interval length, which is more capable of detecting a peak towards the end of the ECG which was left undetected using fixed length RR interval algorithm. This algorithm is implemented using MATLAB. The results showed that our proposed approach performs better compared to the fixed length RR interval approach.
Gonad differentiation and puberty onset in the zebrafish: Evidence for the dependence of puberty onset on body growth but not age in females

Puberty is the period in the vertebrate life cycle that marks the transition from sexual immaturity to maturity, enabling an animal to acquire adult reproductive functions. Puberty, an important point in vertebrate reproductive life, has been under extensive study in the past decades. It has been known for a long time that the initiation of puberty in mammals is closely associated with body growth and metabolism; however, there has been no equivalent report in small model teleosts such as the zebrafish. Using morphological and histological analysis, this study was undertaken to examine the timing of gonad differentiation and female maturation (puberty) in the zebrafish, with particular emphasis on the potential impact of body growth on the onset of puberty. Our data showed that gonad differentiation in the zebrafish completed around 35 days post‐fertilization (dpf) in females and 45 dpf in males. Puberty in females is initiated at around 45 dpf. Our experiments provided clear evidence that the initiation of puberty in female zebrafish was strongly correlated with body size but not age, supporting the importance of the growth axis in the onset of puberty. This study provides essential information on basic characteristics of growth and reproduction in zebrafish. Mol. Reprod. Dev. 80: 384–392, 2013. © 2013 Wiley Periodicals, Inc.
Flexible Gates: Dynamic Topologies and Functions for FG Nucleoporins in Nucleocytoplasmic Transport

ABSTRACT The nuclear envelope is a physical barrier between the nucleus and cytoplasm and, as such, separates the mechanisms of transcription from translation. This compartmentalization of eukaryotic cells allows spatial regulation of gene expression; however, it also necessitates a mechanism for transport between the nucleus and cytoplasm. Macromolecular trafficking of protein and RNA occurs exclusively through nuclear pore complexes (NPCs), specialized channels spanning the nuclear envelope. A novel family of NPC proteins, the FG-nucleoporins (FG-Nups), coordinates and potentially regulates NPC translocation. The extensive repeats of phenylalanine-glycine (FG) in each FG-Nup directly bind to shuttling transport receptors moving through the NPC. In addition, FG-Nups are essential components of the nuclear permeability barrier. In this review, we discuss the structural features, cellular functions, and evolutionary conservation of the FG-Nups.
SE-SYSTEMS, TIMING MECHANISMS, AND TIME-VARYING CODES

We show that synchronized extension systems [17] can be successfully used to simulate timing mechanisms incorporated into grammars and automata [3, v 7-9, v 12]. Further, we introduce the concept of a time-varying code as a natural generalization of L-codes, and the relationship with classical codes, gsm codes and SE-codes is established. Finally, an algorithm for testing the time-varying code property in case of periodicity is given.
Learning task-dependent speech variability in discriminative acoustic model adaptation

We present a new discriminative method of acoustic model adaptation that deals with a task-dependent speaking style. We have focused on differences of expressions or speaking styles between tasks and set the objective of this method as improving the recognition accuracy of indistinctly pronounced phrases dependent on a speaking style. The adaptation appends subword models for frequently observable variants of subwords in the task. To find the task-dependent variants, low-confidence words are statistically selected from words with higher frequency in the task's adaptation data by using their word lattices. Subword models dependent on the words are discriminatively trained by using linear transforms with a minimum phoneme error (MPE) criterion. For the MPE training, subword accuracy discriminating between the variants and the originals is also investigated. In speech recognition experiments, the proposed adaptation with the subword variants relatively reduced the word error rate by 4.4% in a Japanese conversational broadcast task.
A cross cultural study of concepts of intimacy and perspective taking abilities in American and Chinese young adults.

A CROSS CULTURAL STUDY OF CONCEPTS OF INTIMACY AND PERSPECTIVE TAKING ABILITIES IN AMERICAN AND CHINESE YOUNG ADULTS SEPTEMBER 1993 JUN-CHIH GISELA LIN, B.A. TAMKING UNIVERSITY, TAIWAN, ROC. M.Ed., UNIVERSITY OF MASSACHUSETTS AMHERST Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor John C. Carey Intimacy is an important aspect of human life. Little is known, however, about cultural differences of concepts of intimacy from a developmental perspective. Individuals' capacities for concepts of intimacy are manifested by their Social Cognitive Development stages. The main purpose of this dissertation is to examine cultural differences of concepts of intimacy and Social Cognitive Developmental stages in American and Chinese young adults. The first chapter reviews relevant literature; cross-cultural methodological considerations and suggestions for future intimacy research are also addressed. The second chapter describes an empirical study to test the cultural differences of concepts of intimacy and perspective taking abilities in American and Chinese female university students; it also examines whether the results of the relationship between concepts of relationships and perspective taking abilities support Selman's (1980) assumptions.
‘We're still human beings, we're not aliens’: promoting the citizenship rights and cultural diversity of Traveller children in schools: Scottish and English perspectives

This article examines the experiences of Traveller children in schools. It uses data from two studies (one in Scotland and the other in England) to examine Traveller children's views about attending school (particularly in relation to their values and ambitions), their experiences of racism and prejudice and their views on how teachers perceive them. In our research, we draw from case study data to argue that despite public policy discourse around citizenship, the reality is one in which Traveller children continue to be viewed as outsiders. Due to this positioning, they do not enjoy the same rights as other children and they are not regarded as full citizens in the school environment. We argue that in order for schools to consider issues of diversity and inclusion, they must address ways in which Traveller children can be included as full citizens in schools, particularly in relation to their marginalised position in society. Language: en
LIG statistical machine translation systems for IWSLT 2010

This paper describes the systems developed by the LIG laboratory for the 2010 IWSLT evaluation. We participated to the AE BTEC task and to the new TALK task. For AE BTEC task we developed two different systems: a statistical phrase-based system and a hierarchical phrasebased system using the Moses toolkit. The combination of these systems, which improves the results on different development sets, makes our final submission. This year, we concentrated on the new TALK task. The development of a reference translation system, as well as an ASR output translation system, is presented. For this latter task, re-punctuating the ASR output, before translation, seems to be very useful, while segmenting the ASR flow, which is also discussed in this paper, has shown to be less useful. Unsuccessful attempts to exploit ASR lattices instead of ASR 1best are also presented at the end of this article.
Thr202Ala in thyA Is a Marker for the Latin American Mediterranean Lineage of the Mycobacterium tuberculosis Complex Rather than Para-Aminosalicylic Acid Resistance

ABSTRACT Single nucleotide polymorphisms (SNPs) involved in the development of resistance represent powerful markers for the rapid detection of first- and second-line resistance in clinical Mycobacterium tuberculosis complex (MTBC) isolates. However, the association between particular mutations and phenotypic resistance is not always clear-cut, and phylogenetic SNPs have been misclassified as resistance markers in the past. In the present study, we investigated the utility of a specific polymorphism in thyA (Thr202Ala) as a marker for resistance to para-aminosalicyclic acid (PAS). Sixty-three PAS-susceptible MTBC strains comprising all major phylogenetic lineages, reference strain H37Rv, and 135 multidrug-resistant (MDR) strains from Germany (comprising 8 PAS-resistant isolates) were investigated for the presence of Thr202Ala. In both strain collections, the Thr202Ala SNP was found exclusively in strains of the Latin American Mediterranean (LAM) lineage irrespective of PAS resistance. Furthermore, PAS MICs (0.5 mg/liter) for selected LAM strains (all containing the SNP) and non-LAM strains (not containing the SNP), as well as the results of growth curve analyses performed in liquid 7H9 medium in the presence of increasing PAS concentrations (0 to 2.0 mg/liter), were identical. In conclusion, our data demonstrate that the Thr202Ala polymorphism in thyA is not a valid marker for PAS resistance but, instead, represents a phylogenetic marker for the LAM lineage of the M. tuberculosis complex. These findings challenge some of the previous understanding of PAS resistance and, as a consequence, warrant further in-depth investigations of the genetic variation in PAS-resistant clinical isolates and spontaneous mutants.
The pathobiology and pathology of aseptic implant failure

Pathological assessment of periprosthetic tissues is important, not only for diagnosis, but also for understanding the pathobiology of implant failure. The host response to wear particle deposition in periprosthetic tissues is characterised by cell and tissue injury, and a reparative and inflammatory response in which there is an innate and adaptive immune response to the material components of implant wear. Physical and chemical characteristics of implant wear influence the nature of the response in periprosthetic tissues and account for the development of particular complications that lead to implant failure, such as osteolysis which leads to aseptic loosening, and soft-tissue necrosis/inflammation, which can result in pseudotumour formation. The innate response involves phagocytosis of implant-derived wear particles by macrophages; this is determined by pattern recognition receptors and results in expression of cytokines, chemokines and growth factors promoting inflammation and osteoclastogenesis; phagocytosed particles can also be cytotoxic and cause cell and tissue necrosis. The adaptive immune response to wear debris is characterised by the presence of lymphoid cells and most likely occurs as a result of a cell-mediated hypersensitivity reaction to cell and tissue components altered by interaction with the material components of particulate wear, particularly metal ions released from cobalt-chrome wear particles. Cite this article: Professor N. A. Athanasou. The pathobiology and pathology of aseptic implant failure. Bone Joint Res 2016;5:162–168. DOI: 10.1302/2046-3758.55. BJR-2016-0086.
Resilience, stress hormones, and health outcomes in women with HIV

vii TABLE OF CONTENTS ix LIST OF TABLES xi LIST OF FIGURES xii LIST OF ABBREVIATIONS xiii CHAPTER ONE: General Introduction 1 CHAPTER TWO: Study #1 Resilience, Childhood Sexual Abuse, Depressive symptoms, and Health-Related Quality of Life in Women with and at Risk for HIV 28 Introduction 27 Methods 29 Results 32 Discussion 39 Tables and Figures 45 CHAPTER THREE: Study #2 Abuse and Resilience in Women with HIV in Relation to HAART Medication Adherence and HIV Viral 49
Word Embeddings with Limited Memory

This paper studies the effect of limited precision data representation and computation on word embeddings. We present a systematic evaluation of word embeddings with limited memory and discuss method-s that directly train the limited precision representation with limited memory. Our results show that it is possible to use and train an 8 -bit ﬁxed-point value for word embedding without loss of performance in word/phrase similarity and dependency parsing tasks.
The psychological conditions that predict work engagement among tertiary education employees

This study investigated the extent to which the psychological conditions and job characteristics predicted work engagement amongst higher education employees (n = 149, females = 60%) from a South African University. The participants completed a variety of instruments on psychological conditions of work, job characteristics and work engagement viz; the Work Engagement Scale (WES), Psychological Meaningfulness Scale (PMS), Job Enrichment Scale (JES), Work-Role Fit Scale (W-RFS), Co-Worker Relations Scale (C-WRS), Psychological Availability Scale (PAS), Self-Consciousness Scale (SCS), Job Resources Scale (JRS), Outside Activities Scale (OAS), Psychological Safety Scale (PSS), Supervisory Relations Scale (SRS) and the Co-Worker Norms Scale (CWNS). Data analysis applied multiple regression to predict work engagement from psychological meaningfulness, psychological availability and job characteristics and also to determine the mediation effect of psychological condition of availability on the relationship between work engagement and job characteristics (resources). Findings suggest psychological meaningfulness to predict work engagement and to mediate the relationship between job characteristics and work engagement. Psychological resources for work engagement should emphasise a sense of meaningfulness as a resource for work participation.
eMoto: affectively involving both body and mind

It is known that emotions are experienced by both body and mind. Oftentimes, emotions are evoked by sub-symbolic stimuli, such as colors, shapes, gestures, or music. We have built eMoto, a mobile service for sending affective messages to others, with the explicit aim of addressing such sensing. Through combining affective gestures for input with affective expressions that make use of colors, shapes and animations for the background of messages, the interaction pulls the user into an embodied 'affective loop'. We present a user study of eMoto where 12 out of 18 subjects got both physically and emotionally involved in the interaction. The study also shows that the designed 'openness' and ambiguity of the expressions, was appreciated and understood by our subjects.
Small-scale effects on transverse vibrational behavior of single-walled carbon nanotubes with arbitrary boundary conditions

In the present paper, the differential transformation method is employed to develop a semi-analytical solution for free transverse vibration of single-walled carbon nanotube (SWCNT) with arbitrary boundary conditions. The small scale effect is taken into consideration via Eringen’s nonlocal elasticity theory while the transverse shear deformation effects and rotary inertia are taken into account in presented Timoshenko beam theory. Through variational formulation and the Hamilton's principle the governing differential equations and the boundary conditions are derived and then solved by a semi-analytical method called differential transformation method (DTM) for various frequency modes of beams and different edge conditions. Comparisons made between the present results and results reported by well-known references for special cases treated before, have confirmed accuracy and efficiency of the presented approach. The effects of several parameters such as transverse shear deformation effects, slenderness ratios, boundary conditions and small scale on vibration characteristics of SWCNT are examined. The present study illustrates that the vibration characteristics of an SWCNT are strongly dependent on the small scale parameters.
Animating Wrinkles by Example on Non-Skinned Cloth

The simulation of cloth with rich folds and wrinkles is a computationally expensive process. In this paper, we introduce an example-based algorithm for fast animation of plausible cloth wrinkles. Our algorithm does not depend on a character's pose, therefore it is valid for loose dresses, curtains, etc., not just cloth defined by skinning techniques. Central to our approach is a correspondence between low and high-resolution cloth deformations, both at the training and synthesis stages. Based on this correspondence, we define an algorithm for synthesizing cloth wrinkles as a function of the deformation of a low-resolution cloth and a set of example poses. We demonstrate the animation of plausible high-resolution wrinkles at high frame rates, suitable for interactive applications such as video games.
CLONING OF CHITINASE-LIKE PROTEIN1 CDNA FROM DICYEMID MESOZOANS (PHYLUM: DICYEMIDA)

Dicyemid mesozoans are endoparasites found in the renal sacs of benthic cephalopods. Adult dicyemids insert the distinct anterior region, termed a “calotte,” into renal tubules of the host. We cloned cDNA encoding chitinase-like protein from the dicyemid Dicyema japonicum (Dicyema-clp1), and also cloned the gene fragment corresponding to the cDNA. Dicyema-clp1 has the hydrophobic amino acid–rich region, but not the chitin-binding domains at the C terminus. Analyses using the SignalP prediction program suggest this hydrophobic amino acid–rich region is the anchor sequence to plasma membranes. The putative catalytic site in glyco18 domain exhibited 1 substitution from aspartic acid to asparagine. The gene fragment had short 9 introns (22–26 bp), and the coding sequence consisted of 10 exons (30–233 bp). Specific and strong expression of Dicyema-clp1 was detected in the calotte of vermiform stages by whole mount in situ hybridization. N-acetyl-d-glucosamine was detected on the outer surface of both peripheral cells of dicyemids and epidermal cells of host renal appendages. Dicyema-clp appears to be associated with N-acetyl-d-glucosamine in the interface between dicyemid peripheral cells and epidermal cells of the host renal appendage, and possibly aids in adhering the calotte to host epidermal cells.