Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of meaningful associations in genomic data using partial correlation coefficients

MOTIVATION A major challenge of systems biology is to infer biochemical interactions from large-scale observations, such as transcriptomics, proteomics and metabolomics. We propose to use a partial correlation analysis to construct approximate Undirected Dependency Graphs from such large-scale biochemical data. This approach enables a distinction between direct and indirect interactions of biochemical compounds, thereby inferring the underlying network topology. RESULTS The method is first thoroughly evaluated with a large set of simulated data. Results indicate that the approach has good statistical power and a low False Discovery Rate even in the presence of noise in the data. We then applied the method to an existing data set of yeast gene expression. Several small gene networks were inferred and found to contain genes known to be collectively involved in particular biochemical processes. In some of these networks there are also uncharacterized ORFs present, which lead to hypotheses about their functions. AVAILABILITY Programs running in MS-Windows and Linux for applying zeroth, first, second and third order partial correlation analysis can be downloaded at: http://mendes.vbi. vt.edu/tiki-index.php? page=Software. SUPPLEMENTARY INFORMATION Supplementary information can be found at: URL to be decided.
Experiences of self-practice/self-reflection in cognitive behavioural therapy: a meta-synthesis of qualitative studies.

BACKGROUND Self-practice/self-reflection is a valuable training strategy which involves therapists applying therapeutic techniques to themselves, and reflecting on the process. PURPOSE To undertake a meta-synthesis of qualitative studies exploring therapists' experiences of self-practice/self-reflection in cognitive behavioural therapy (CBT). This would integrate, and interpret, the current literature in order to develop a new understanding, and contribute to the development of CBT training programmes. METHODS The meta-synthesis encompassed three distinct phases: undertaking a comprehensive and systematic literature search; critically appraising the papers; and synthesising the data using the meta-ethnographic method. RESULTS The literature search identified 378 papers, ten met the criteria for inclusion. After critical appraisal, all were included in the synthesis. The synthesis identified 14 constructs, which fell into three broad categories: 'experience of self-practice/self-reflection'; 'outcomes of self-practice/self-reflection'; and 'implications for training'. This synthesis found that self-practice allows therapists to put themselves into their clients' shoes, experiencing the benefits that therapy can bring but also the problems that clients can run in to. This experience increases therapists' empathy for their clients, allowing them to draw on their own experiences in therapy. As a result, therapists tend to feel both more confident in themselves and more competent as a therapist. The self-practice/self-reflection process was facilitated by reflective writing and working with others, particularly peers. CONCLUSIONS Self-practice/self-reflection is a valuable training strategy in CBT, which has a range of beneficial outcomes. It can also be used as a means of continuing personal and professional development. PRACTITIONER POINTS Self-practice of CBT techniques, and reflecting on the process, can be a useful training strategy and helpful for ongoing development Therapists could consider developing a 'self-case' study, rather than using the exercises as one-off techniques, recording reflections in writing, and sharing reflections with peers. Self-practice/self-reflection can be particularly helpful for increasing empathy for clients, highlighting the difficulties they may encounter.
Diversion of containerized trade: case analysis of the role of Iranian ports in global maritime supply chain

This article aims to analyze the potential of Iranian ports for carrying some containerized cargo, from the Far East to the European Union, which is usually transported via traditional shipping routes. The idea of diverting cargo via an ‘Iran route’ emerged from an examination of economic, trade and maritime transportation trends and events. This study presents a new idea for a freight route, designed in four segments for the benefit of the carrier. In order to make assumptions about the future in what are undisputedly widespread uncertain conditions, a scenario method has been employed. Following this a plausible future plan for a new terminal has been developed taking into account geographical, technical and economic themes for serving the container transit market until 2011.
Mitochondrial respiratory defects promote the Warburg effect and cancer progression

ABSTRACT In the past decade mitochondria have emerged as an important cellular signaling hub controlling metabolism, epigenetics, and cell fate. Dysfunctional mitochondria initiate a retrograde nuclear response that influences the cellular reprograming observed in various human pathologies, including cancer. New data suggest that loss of cytochrome c oxidase function promotes the Warburg effect and upregulates several genes with roles in tumor development.
Phylogenetic Position and In Situ Identification of Ectosymbiotic Spirochetes on Protists in the Termite Gut

ABSTRACT Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp. , Stephanonympha sp. , and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut protists.
In silico study of the human rhodopsin and meta rhodopsin II/S‐arrestin complexes: Impact of single point mutations related to retina degenerative diseases

We propose two models of the human S‐arrestin/rhodopsin complex in the inactive dark adapted rhodopsin and meta rhodopsin II form, obtained by homology modeling and knowledge based docking. First, a homology model for the human S‐arrestin was built and validated by molecular dynamics, showing an average root mean square deviation difference from the pattern behavior of 0.76 Å. Then, combining the human S‐arrestin model and the modeled structure of the two human rhodopsin forms, we propose two models of interaction for the human S‐arrestin/rhodopsin complex. The models involve two S‐arrestin regions related to the N domain (residues 68–78; 170–182) and a third constituent of the C domain (248–253), with the rhodopsin C terminus (330–348). Of the 22 single point mutations related to retinitis pigmentosa and congenital night blindness located in the cytoplasmatic portion of rhodopsin or in S‐arrestin, our models locate 16 in the interaction region and relate two others to possible dimer formation. Our calculations also predict that the light activated complex is more stable than the dark adapted rhodopsin and, therefore, of higher affinity to S‐arrestin. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Job Satisfaction and Organizational Commitment Relationship: Effect of Personality Variables

The purpose of the study was to explore the relationship between Job Satisfaction and Organizational Commitment and to investigate the moderating effects of Trust and Locus of Control on the relationship between Job Satisfaction and Organizational Commitment. The study was administered on 247 middle level managers belonging to private sector organizations. Four validated instruments were used in the study. Statistical tools like Descriptive Statistics, Factor Analysis, Pearson Product Moment Correlation and Hierarchical Regression Analysis were used to analyze the data. The study found that Job satisfaction was positively related to Organizational Commitment and Trust and Locus of Control moderated Job satisfaction and Organizational Commitment relationship. The findings of this study can assist the administrator and policy makers to understand the managerial effectiveness from the perspective of personal traits. Efforts can be made to explore managers’ perception towards themselves and their roles. The future academic endeavours might make use of the present study as a stepping-stone for further exploratory and confirmatory research towards a more complete understanding of the satisfaction considerations in particular.
Autotuning GEMMs for Fermi

In recent years, the use of graphics chips has been recognized as a viable way of accelerating scientic and engineering applications, even more so since the introduction of the Fermi architecture by NVIDIA, with features essential to numerical computing, such as fast double precision arithmetic and memory protected with error correction codes. Being the crucial component of numerical software packages, such as LAPACK and ScaLAPACK, the general dense matrix multiplication routine is one of the more important workloads to be implemented on these devices. This article presents a methodology for producing matrix multiplication kernels tuned for a specic architecture, through a canonical process of heuristic autotuning, based on generation of multiple code variants and selecting the fastest ones through benchmarking. The key contribution of this work is in the method for generating the search space; specically, pruning it to a manageable size. Performance numbers match or exceed other available implementations.
Cellular Underwater Wireless Optical CDMA Network: Potentials and Challenges

Underwater wireless optical communications are an emerging solution to the expanding demand for broadband links in oceans and seas. In this paper, a cellular underwater wireless optical code division multiple-access network is proposed to provide broadband links for commercial and military applications. The optical orthogonal codes are employed as signature codes of underwater mobile users. Fundamental key aspects of the network, such as its backhaul architecture, its potential applications, and its design challenges, are presented. In particular, a promising underwater localization and positioning scheme based on this cellular network is presented. Furthermore, the proposed network is used as infrastructure of centralized, decentralized and relay-assisted underwater sensor networks for high-speed real-time monitoring. Finally, probable design challenges, such as cell edge coverage, blockage avoidance, power control, and network capacity, are addressed.
A Theory of the Value of Grandchildren

As innovations in medical technology extend average longevity, grandparents become increasingly present during the lives of their grandchildren. We propose a theory that seeks to explain differential investment in grandchildren. The theory relies on a fundamental assumption of uncertainty reduction to explain why grandparents in post-industrial societies might find it rational to invest in at least one of their grandchildren. We advance numerous illustrative hypotheses about end of life uncertainty, as well as proportional and differential investments in grandchildren, and discuss the relevance of existing empirical literature.
The Effect of Customer Aggression on Burnout

The service sector is currently the fastest growing economic sector. However, for employees in this sector, the high level of customer interaction may be the reason for undesired consequences such as customer aggression. This study aimed to demonstrate the effect on the burnout level of bank employees exposed to verbal abuse. The study sample comprised 161 employees of private banks sector. The mean age of the study participants was 32.20±5.79 years and the mean duration of employment was 7.63±5.79 years. In the data analysis, , correlation and regression analysis were used. From the results of the analyses, the finding was obtained that verbal abuse signficantly increased the emotional burnout and depersonalization levels of bank employees. DOI: 10.5901/ajis.2014. v3n4p369
Tumor suppression in basal keratinocytes via dual non-cell-autonomous functions of a Na,K-ATPase beta subunit

The molecular pathways underlying tumor suppression are incompletely understood. Here, we identify cooperative non-cell-autonomous functions of a single gene that together provide a novel mechanism of tumor suppression in basal keratinocytes of zebrafish embryos. A loss-of-function mutation in atp1b1a, encoding the beta subunit of a Na,K-ATPase pump, causes edema and epidermal malignancy. Strikingly, basal cell carcinogenesis only occurs when Atp1b1a function is compromised in both the overlying periderm (resulting in compromised epithelial polarity and adhesiveness) and in kidney and heart (resulting in hypotonic stress). Blockade of the ensuing PI3K-AKT-mTORC1-NFκB-MMP9 pathway activation in basal cells, as well as systemic isotonicity, prevents malignant transformation. Our results identify hypotonic stress as a (previously unrecognized) contributor to tumor development and establish a novel paradigm of tumor suppression. DOI: http://dx.doi. org/10.7554/eLife.14277. 001
CLSH: Cluster-based Locality-Sensitive Hashing

Locality-sensitive hashing (LSH) usually consumes large memory in similarity search, which limits its scalability for large scale applications. In this paper, we propose a novel cluster-based locality-sensitive hashing (CLSH) approach, which extends the conventional LSH framework and aims at indexing and searching large scale high-dimensional datasets. We first utilize a clustering algorithm to partition the raw feature dataset into clusters, and map these clusters to a distributed cluster. Then, LSH method is applied to construct the index for each cluster, and we present two criteria to choose the cluster(s) for further detailed search in order to improve the search quality. This proposed framework comes with following properties. Firstly, CLSH can cope with large scale feature dataset. Secondly, the generated clusters can guide the feature dataset automatical mappings to a distributed cluster. After that, the search time can be reduced a lot by searching on multiple computing nodes. Experiments show that the proposed approach outperforms the existing approaches in terms of efficiency and scalability.
Supporting Autonomy in the Classroom: Ways Teachers Encourage Student Decision Making and Ownership

In addition to classroom activities, teachers provide personal and instructional supports meant to facilitate the developing sense of student autonomy. In this article, we offer a way of thinking about autonomy-supportive practices that suggests that such practices can be distinguished at a featural level and that different practices may in fact have different outcomes in terms of student classroom behavior. Specifically, we propose that autonomy support can be manifested in the classroom in at least 3 distinct ways: organizational autonomy support (e.g., allowing students some decision-making role in terms of classroom management issues), procedural autonomy support (e.g., offering students choices about the use of different media to present ideas), and cognitive autonomy support (e.g., affording opportunities for students to evaluate work from a self-referent standard). We offer vignettes of teachers in their classes to illustrate our proposition that autonomy support may be carried out on several planes and may produce different outcomes. Whereas organizational autonomy support may encourage a sense of well-being and comfort with the way a classroom functions and procedural autonomy support may encourage initial engagement with learning activities, cognitive autonomy support may foster a more enduring psychological investment in deep-level thinking.
Assessment of deep tissue hyperalgesia in the groin – a method comparison of electrical vs. pressure stimulation

Deep pain complaints are more frequent than cutaneous in post‐surgical patients, and a prevalent finding in quantitative sensory testing studies. However, the preferred assessment method – pressure algometry – is indirect and tissue unspecific, hindering advances in treatment and preventive strategies. Thus, there is a need for development of methods with direct stimulation of suspected hyperalgesic tissues to identify the peripheral origin of nociceptive input.
Effects of Phytoestrogens Genistein and Daidzein on Prostacyclin Production by Human Endothelial Cells

The molecular mechanisms of the vascular effects of phytoestrogens are poorly studied. Prostacyclin is a potent vasodilator synthesized by two isoforms of cyclooxygenase (COX) in endothelium. This study examine the effects of two phytoestrogens, the isoflavones genistein and daidzein, on prostacyclin production by cultured human umbilical vein endothelial cells (HUVECs) and the possible role of not only estrogen receptors but also both COX isoforms. The two phytoestrogens significantly increased prostacyclin release in a time- and dose-dependent (0.01-1 μM) manner, being higher than control after 24 h. Selective inhibitors of COX-1, SC-560 [5-(4-chlorophenyl)-1-(4-methoxypjenyl)-3-(trifluoromethyl)-1H-pyrazole], and COX-2, NS-398 (N-[2-(cyclohexyloxy)-4 nitrophenyl]-methanesulfonamide), were used to investigate the relative contribution of each enzyme. Both inhibitors decreased basal production of prostacyclin, but only COX-2 inhibition completely abolished the isoflavone-stimulated prostacyclin production. Phytoestrogens also increased COX-2 mRNA expression and protein content without affecting COX-1 levels. All these effects were mediated through estrogen receptor activation since treatment of cells with the estrogen receptor antagonist ICI 182780 [7α-[9[(4,4,5,5,5-pentafluoropentyl)sulfinyl]nonyl]-estra-1,3,5(10)-triene-3,17β diol] completely abolished the isoflavone-induced increase in prostacyclin production, COX-2 mRNA expression, and COX-2 protein content. The results clearly support the hypothesis that genistein and daidzein increased HUVEC prostacyclin production through estrogen receptor-dependent mechanism, which involved the enhancement of COX-2 protein and activity.
Web-Based Bengali News Corpus for Lexicon Development and POS Tagging

Lexicon development and Part of Speech (POS) tagging are very important for almost all Natural Language Processing (NLP) applications. The rapid development of these resources and tools using machine learning techniques for less computerized languages requires appropriately tagged corpus. We have used a Bengali news corpus, developed from the web archive of a widely read Bengali newspaper. The corpus contains approximately 34 million wordforms. This corpus is used for lexicon development without employing extensive knowledge of the language. We have developed the POS taggers using Hidden Markov Model (HMM) and Support Vector Machine (SVM). The lexicon contains around 128 thousand entries and a manual check yields the accuracy of 79.6%. Initially, the POS taggers have been developed for Bengali and shown the accuracies of 85.56%, and 91.23% for HMM, and SVM, respectively. Based on the Bengali news corpus, we identify various word-level orthographic features to use in the POS taggers. The lexicon and a Named Entity Recognition (NER) system, developed using this corpus, are also used in POS tagging. The POS taggers are then evaluated with Hindi and Telugu data. Evaluation results demonstrates the fact that SVM performs better than HMM for all the three Indian languages.
‘It's Already Gone Too Far’: Women and the Transition into Marriage in Lombok, Indonesia

Kawin lari is a form of socially sanctioned elopement whereby a young woman is ostensibly ‘stolen’ from her natal home by a man who wishes to become her husband. It remains a popular method for entering marriage in Lombok. Typically, the marriage is later formalised under Islam. This paper focuses on marital choice and how women in the village of Teduk who kawin lari, may acquiesce to marriage, rather than assert an active choice over who and when to marry. I argue that kawin lari propels many women into an ambivalent zone which causes a rupture in their social identity as gadis (virgin), although their physical virginity may still be intact. Therefore, kawin lari creates a phase of heightened ambiguity and ambivalence regarding women's status. Many women describe kawin lari as an act that places them in a situation which has sudah terlanjur (already gone too far), although the practice can also facilitate women's agency in marital choice.
Supporting a Nation of Learners: The Role of School Counseling in Educational Reform

The most recent school reform agenda directed the development of national standards across the academic content areas to improve educational practice and pedagogy. U.S. Department of Education's (1994) Goals 2000: The Educate America Act and its subsequent nationwide implementation largely ignored the involvement of school counseling in school reform efforts. Counselors in schools face the challenge of preparing students to meet the expectations of these higher academic standards and to become well-educated and contributing members of an ever changing and complex society. The development of the National Standards for School Counseling Programs (American School Counselor Association, 2003) positioned school counseling to play an increasingly important role in contemporary school improvement and in support of the recent educational legislative agenda the No Child Left Behind Act (U.S. Department of Education, 2001).
FUDGETS: a graphical user interface in a lazy functional language

This paper describes an implementation of a small windowbased graphical user interface toolkit for X Windows written in the lazy functional language LML. By using this toolkit, a H askell or LML programmer can crest e a user interface with menus, buttons and other graphical interface objects, without conforming to more or less imperative programming paradigms imposed if she were to use a traditional (imperative) toolkit. Instead, the power of the abstraction methods provided by Haskell or LML are used. The main abstraction we use is the fr.dget. Fudgets are combined in a hierarchical structure, and they interact by message passing, The current implementation is baaed on a sequential evaluator, but by using non-determinism and oracles, we suggest how the fudgets can evaluate in parallel. We believe that the toolkit can be extended to a full-feathered and practically useful high level graphical toolkit.