Miracle-dz/UniFAR-FTUs huggingface dataset:
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI), and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.
Zinc Finger Gli1 Mutant Δδg Binding (mm-pbsa) a Δδg Binding (mm-gbsa) A

Table S1. In silico alanine scanning for residues of ZF4 and ZF5 most involved in Gli1-ZF binding to DNA. a values are in kcal/mol. Deviation is the Standard Error of the Mean (SEM) * Energy contribution was calculated by considering explicit bridging water molecules. Movie S1. Molecular Dynamics trajectory of Gli1ZF/DNA. The movie shows the conformational behavior of the Gli1ZF/DNA complex in explicit water (TIP3P type, removed for clarity of presentation) simulated by classic Molecular Dynamics with Amber11. Trajectory was visualized with VMD. The movie describes the Gli1ZF/DNA system in its geometrical and energetic convergence status. Gli1 is showed as colored surface (different colors corresponds to different
Delegation forwarding

Mobile opportunistic networks are characterized by unpredictable mobility, heterogeneity of contact rates and lack of global information. Successful delivery of messages at low costs and delays in such networks is thus challenging. Most forwarding algorithms avoid the cost associated with flooding the network by forwarding only to nodes that are likely to be good relays, using a quality metric associated with nodes. However it is non-trivial to decide whether an encountered node is a good relay at the moment of encounter. Thus the problem is in part one of online inference of the quality distribution of nodes from sequential samples, and has connections to optimal stopping theory. Based on these observations we develop a new strategy for forwarding, which we refer to as delegation forwarding. We analyse two variants of delegation forwarding and show that while naive forwarding to high contact rate nodes has cost linear in the population size, the cost of delegation forwarding is proportional to the square root of population size. We then study delegation forwarding with different metrics using real mobility traces and show that delegation forwarding performs as well as previously proposed algorithms at much lower cost. In particular we show that the delegation scheme based on destination contact rate does particularly well.
Exploring the potential of video technologies for collaboration in emergency medical care: Part I. Information sharing

We are investigating the potential of 3D telepresence, or televideo, technology to support collaboration among geographically separated medical personnel in trauma emergency care situations. 3D telepresence technology has the potential to provide richer visual information than current 2D video conferencing techniques. This may be of benefit in diagnosing and treating patients in emergency situations where specialized medical expertise is not locally available. The 3D telepresence technology does not yet exist and there is a need to understand its potential before resources are spent on its development and deployment. This poses a complex challenge. How can we evaluate the potential impact of a technology within complex, dynamic work contexts when the technology does not yet exist? To address this challenge we conducted an
Semantic Web Recommendation application

This paper focuses on a semantically-enhanced Social Web Recommendation application, called Taste It! Try It! It is a mobile restaurants' review and recommendation application based on a Linked Data source and integrated with a social network. The application is consuming Linked Data (while creating the reviews), producing semantic annotations (about the reviewed entities), and then, querying the gathered data in order to offer personalized recommendations.
Edinburgh Research Explorer The case for open source software

Computational techniques and software applications for the quantitative content analysis of texts are now well established, and many qualitative data software applications enable the manipulation of input variables and the visualization of complex relations between them via interactive and informative graphical interfaces. Although advances in text analysis have helped researchers mine text data for semantic content and identify language patterns in text with greater facility, interactional dynamics and patterns of talk have been neglected. This article introduces a new open-source tool, Interactional Discourse Lab. This tool is designed to map dynamics in spoken interaction and to represent them in easily accessible visual form, capturing aspects such as the frequency and patterning of exchanges, and the distribution of turns and discourse features. It is designed to contribute, with other analytical tools such as those used in text analysis, to the development of interactional topographies. The paper sets the tool within a wider case for the development of open-source software in applied linguistics as a platform for methodological innovation.
A Unique Role for Nonmuscle Myosin Heavy Chain IIA in Regulation of Epithelial Apical Junctions

The integrity and function of the epithelial barrier is dependent on the apical junctional complex (AJC) composed of tight and adherens junctions and regulated by the underlying actin filaments. A major F-actin motor, myosin II, was previously implicated in regulation of the AJC, however direct evidence of the involvement of myosin II in AJC dynamics are lacking and the molecular identity of the myosin II motor that regulates formation and disassembly of apical junctions in mammalian epithelia is unknown. We investigated the role of nonmuscle myosin II (NMMII) heavy chain isoforms, A, B, and C in regulation of epithelial AJC dynamics and function. Expression of the three NMMII isoforms was observed in model intestinal epithelial cell lines, where all isoforms accumulated within the perijunctional F-actin belt. siRNA-mediated downregulation of NMMIIA, but not NMMIIB or NMMIIC expression in SK-CO15 colonic epithelial cells resulted in profound changes of cell morphology and cell-cell adhesions. These changes included acquisition of a fibroblast-like cell shape, defective paracellular barrier, and substantial attenuation of the assembly and disassembly of both adherens and tight junctions. Impaired assembly of the AJC observed after NMMIIA knock-down involved dramatic disorganization of perijunctional actin filaments. These findings provide the first direct non-pharmacological evidence of myosin II-dependent regulation of AJC dynamics in mammalian epithelia and highlight a unique role of NMMIIA in junctional biogenesis.
Lost in the Storm: The Sociology of the Black Working Class, 1850 to 1990

Contemporary sociologists implicitly have assumed that the race-class debate has been resolved: Blacks tend to fall in one of two categories—”the black middle class” or the “truly disadvantaged. ” However, lost amid the controversies over the supposed privileges of the former and the problems of the latter is the plight of the “forgotten” category of blacks: the black working class. Accordingly, we present a sociological analysis of the black working class and ask: How has the black working class changed compared to its white counterpart from 1850 to 1990? Employing the Integrated Public Use Microdata Series (IPUMS) for our analysis, we find that for the last five decades blacks are more likely to be working class than middle class or bottom class. In addition, blacks currently are more likely to be working class than are whites. In fact, in recent decades the percentage of blacks who are working class exceeds those for whites and, indeed, are higher than ever recorded for whites.
Advancing psychotherapy and evidence‐based psychological interventions

Psychological models of mental disorders guide research into psychological and environmental factors that elicit and maintain mental disorders as well as interventions to reduce them. This paper addresses four areas. (1) Psychological models of mental disorders have become increasingly transdiagnostic, focusing on core cognitive endophenotypes of psychopathology from an integrative cognitive psychology perspective rather than offering explanations for unitary mental disorders. It is argued that psychological interventions for mental disorders will increasingly target specific cognitive dysfunctions rather than symptom‐based mental disorders as a result. (2) Psychotherapy research still lacks a comprehensive conceptual framework that brings together the wide variety of findings, models and perspectives. Analysing the state‐of‐the‐art in psychotherapy treatment research, “component analyses” aiming at an optimal identification of core ingredients and the mechanisms of change is highlighted as the core need towards improved efficacy and effectiveness of psychotherapy, and improved translation to routine care. (3) In order to provide more effective psychological interventions to children and adolescents, there is a need to develop new and/or improved psychotherapeutic interventions on the basis of developmental psychopathology research taking into account knowledge of mediators and moderators. Developmental neuroscience research might be instrumental to uncover associated aberrant brain processes in children and adolescents with mental health problems and to better examine mechanisms of their correction by means of psychotherapy and psychological interventions. (4) Psychotherapy research needs to broaden in terms of adoption of large‐scale public health strategies and treatments that can be applied to more patients in a simpler and cost‐effective way. Increased research on efficacy and moderators of Internet‐based treatments and e‐mental health tools (e.g. to support “real time” clinical decision‐making to prevent treatment failure or relapse) might be one promising way forward. Copyright © 2013 John Wiley & Sons, Ltd.
Exploring the Impact of Consumer Ethnocentrism on Decision Making Process Across the Product Categories

The purpose of this study is to explore the impact of consumer ethnocentrism on decision making process across the product categories. Results are derived from primary data collected from a consumer sample in Bosnia and Herzegovina. Structural equitation modeling method was used to test the propositions. The empirical results have provided the conclusion that consumer ethnocentrism has a positive impact on consumers’ attitudes, beliefs and intentions. Purchase behavior is influenced by consumer ethnocentrism for two of the three product categories studied.
Low power dissipation MOS ternary logic family

An MOS ternary-logic family comprising a set of inverters, NOR gates, and NAND gates is proposed. These gates are used to design basic ternary arithmetic and memory circuits. The circuits thus obtained are then used to synthesize complex ternary arithmetic circuits and shift registers. The ternary circuits developed are shown to have some significant advantages relative to other known ternary circuits; these include low power dissipation and reduced propagation delay and component count. For a given dynamic range, the complexity of the new ternary circuits is shown to be comparable to that of corresponding binary circuits. Nevertheless, the associated reduction in the wordlength in the case of the ternary circuits tends to alleviate to a large extent the pin limitation problem associated with VLSI implementation. The authors conclude with an implementation of the cyclic convolution, an application in which a significant advantage can be gained through the use of ternary digital hardware.
Connectivity transformation for mesh metamorphosis

In previous mesh morphing techniques, the vertex set and connectivity of an in-between mesh are fixed and only the vertex positions are interpolated between input meshes. With this restriction, to accurately represent both source and target shapes, an in-between mesh should contain a much larger number of vertices than input meshes. This paper proposes a novel approach for mesh morphing, which includes connectivity changes in a metamorphosis. With the approach, an in-between mesh contains only the vertices from the input meshes and so the in-between vertex count does not exceed the sum of source and target vertex counts. The connectivity changes are realized by a sequence of edge swap operation, determined by considering the geometric errors from the input meshes. Experimental results demonstrate that the proposed approach generates almost same in-between shapes as the metamesh-based approach with a much smaller number of vertices.
Post-traumatic stress and disability

Background Post-traumatic stress is thought to account for significant disability. It is also known to be highly comorbid with other psychiatric conditions such as depression and alcohol dependence. Aims To determine the relationship between post-traumatic stress, depression, alcohol dependence and disability. Method Seventy armed services personnel were assessed for DSM–IV diagnoses of post-traumatic stress disorder, major depressive disorder and alcohol dependence, and with continuous measures of symptoms of post-traumatic stress, depression and alcohol dependence following a traumatic event. These variables, as predictors of disability (using the Sheehan Disability Scale), were analysed using multivariate analysis of variance, analysis of covariance and multiple regression backward elimination models. Results No significant interaction was found for the diagnostic variables even after controlling for the continuous symptom measures. In the regression models, symptoms of depression were a significant predictor of total disability (R 2=0.39). Symptoms of alcohol dependence and post-traumatic stress did not significantly predict disability. Conclusions Since post-traumatic stress was not found to be associated with disability, its clinical importance may be questionable.
Recent advances in understanding the molecular mechanisms regulating C. elegans transcription

We review recent studies that have advanced our understanding of the molecular mechanisms regulating transcription in the nematode C. elegans. Topics covered include: (i) general properties of C. elegans promoters; (ii) transcription factors and transcription factor combinations involved in cell fate specification and cell differentiation; (iii) new roles for general transcription factors; (iv) nucleosome positioning in C. elegans “chromatin”; and (v) some characteristics of histone variants and histone modifications and their possible roles in controlling C. elegans transcription. Developmental Dynamics 239:1388–1404, 2010. © 2010 Wiley‐Liss, Inc.
Longitudinal Study of Epileptiform EEG Patterns in Normal Children

Summary: EEG were recorded in 3,726 children, from 6 to 13 years of age who were neurologically normal and had no history of epileptic seizures. The records were taken during wakefulness, at rest, and during hyperventilation. In 131 cases (3.54%) epileptiform patterns were found. They consisted of 3 count/sec spike and slow waves discharges (4 cases), multiple spike and slow wave complexes (37 cases), midtemporal spikes (50 cases), rolandic or parietal spikes (27 cases), occipital spikes (2 cases), and multifocal spikes (11 cases). Half of the subjects with EEG abnormalities had behavior problems and/or slight psychomotor ability disturbances. Follow‐up studies over an 8 to 9 year period were performed. These demonstrated the spontaneous disappearance of the EEG abnormalities, usually within school age or, at the latest, during adolesence. Only seven individuals developed epileptic seizures of the primary generalized type which responded well to anticonvulsant drug treatment. From this study we can deduce that the epileptiform EEG patterns that often are found in children during school age have no clinical relationship to epilepsy in the great majority of cases. The relationship with epilepsy exists probably on a genetic level for the generalized discharges. The spike foci are non‐epileptic in nature in all probability, especially if they emerge from a fairly normal background activity and their duration is very similar to that of the constituents of the background activity, as found in the majority of these subjects. On the contrary, it is probable that these alterations express difficulties in affective or motor adaptation during childhood.
Meta-Analysis on the Roles of Fathers in Parenting: Are They Unique?

ABSTRACT A meta-analysis was undertaken, including 34 studies, to determine whether fathers play a unique role in parenting that is different from mothers’ roles. Statistical analyses were done to determine the extent to which the effects of fathering children were distinct from that of mothering. In addition to examining this phenomena overall, the meta-analysis also specifically examined social measurements, psychological indicators, and academic achievement. The possible unique effects of fatherhood were also examined in relation to the age and gender of the child. The results indicate consistent statistically significant effects that emerged for the unique role that fathers have. This association between fathering and the outcome variables held across social measurements, psychological indicators, and academic achievement. This relationship also held for both boys and girls and across age groups. The effects of the unique role of fathering yielded effect sizes of about . 14 to . 23 of a standard deviation unit.
Mapping Perceptions of Burnout in the Information Technology Profession: A Study Using Social Representations Theory

Job-related burnout in information technology professionals is seen as a serious issue for organizations and individuals. While the substantial body of research on job stress and burnout can provide valuable insights into the prevention of burnout in IT as well as interventions, we argue that drawing upon this work should be done with caution. In particular, generalizability of the learnings beyond the occupations studied (predominantly people-oriented and/or caregiving roles) cannot be assumed. As a first step toward assessing the applicability of existing burnout research to IT, the purpose of the study described in this paper is to understand how IT professionals make sense of and assign meaning to burnout in the profession. The study uses an approach based on social representations theory, which was first formulated by French social psychologist Serge Moscovici. Social representations are defined as the shared images and concepts through which we organize our world. Transcripts from in-depth interviews of 20 IT professionals were contentanalyzed and 22 key topics (concepts) identified. Quantitative methods (including analysis of similarity and analyses to determine the relational structure of the concepts) were used to create a social representations map of these professionals’ understandings of burnout. The map provides preliminary evidence of elements that are central/peripheral to those understandings, pointing to implications for the applicability of existing theory on burnout as well as priorities for future research.
The Ad Hoc On-Demand Distance-Vector Protocol : Quality of Service Extensions

Ad Hoc On-Demand Distance-Vector routing protocol provides fast and efficient route establishment between mobile nodes that need to communicate with each other. Since AODV has been specifically designed for ad hoc wireless networks, it has minimal control overhead and route acquisition latency. In addition to unicast routing, AODV supports multicast and broadcast as well. Moreover, AODV can be extended to support Quality of Service (QoS). The goal of this paper is to take a closer look at these QoS extensions. Since the QoS extensions are relatively new concept, it is not that clear yet how to properly utilize them. They may introduce some problems as well.
OmniArt: Multi-task Deep Learning for Artistic Data Analysis

Vast amounts of artistic data is scattered on-line from both museums and art applications. Collecting, processing and studying it with respect to all accompanying attributes is an expensive process. With a motivation to speed up and improve the quality of categorical analysis in the artistic domain, in this paper we propose an efficient and accurate method for multi-task learning with a shared representation applied in the artistic domain. We continue to show how different multi-task configurations of our method behave on artistic data and outperform handcrafted feature approaches as well as convolutional neural networks. In addition to the method and analysis, we propose a challenge like nature to the new aggregated data set with almost half a million samples and structured meta-data to encourage further research and societal engagement.
Fast realistic human body deformations for animation and VR applications

Virtual Actors now play an important role in computer-generated films, Virtual Environments, Telecooperative work, and multimedia. In order to make these actors realistic, it is essential to represent their body shape during the motion. In this paper we present different methods for representing realistic deformations for virtual humans with various characteristics: sex, age, height, weight. Our methods based on a combination of metaballs and splines could be applied to frame-by-frame computer generated-films and Virtual Environments. Several examples are presented: autonomous actors, animation based on flock of birds, networked Virtual Environments.