Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation

Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue. We found that proteins with in situ O-GlcNAc/Phos cross talk were significantly enriched in some specific gene ontology terms and no obvious evolutionary pressure was observed. Moreover, 3 functional motifs associated with O-GlcNAc/Phos sites were extracted. We further used sequence features and GO features to predict O-GlcNAc/Phos cross talk sites based on phosphorylated sites and O-GlcNAcylated sites separately by the use of SVM model. The AUC of classifier based on phosphorylated sites is 0.896 and the other classifier based on GlcNAcylated sites is 0.843. Both classifiers achieved a relatively better performance compared with other existing methods.
WitchDoctor: IDE support for real-time auto-completion of refactorings

Integrated Development Environments (IDEs) have come to perform a wide variety of tasks on behalf of the programmer, refactoring being a classic example. These operations have undeniable benefits, yet their large (and growing) number poses a cognitive scalability problem. Our main contribution is WitchDoctor - a system that can detect, on the fly, when a programmer is hand-coding a refactoring. The system can then complete the refactoring in the background and propose it to the user long before the user can complete it. This implies a number of technical challenges. The algorithm must be 1) highly efficient, 2) handle unparseable programs, 3) tolerate the variety of ways programmers may perform a given refactoring, 4) use the IDE's proven and familiar refactoring engine to perform the refactoring, even though the the refactoring has already begun, and 5) support the wide range of refactorings present in modern IDEs. Our techniques for overcoming these challenges are the technical contributions of this paper. We evaluate WitchDoctor's design and implementation by simulating over 5,000 refactoring operations across three open-source projects. The simulated user is faster and more efficient than an average human user, yet WitchDoctor can detect more than 90% of refactoring operations as they are being performed - and can complete over a third of refactorings before the simulated user does. All the while, WitchDoctor remains robust in the face of non-parseable programs and unpredictable refactoring scenarios. We also show that WitchDoctor is efficient enough to perform computation on a keystroke-by-keystroke basis, adding an average overhead of only 15 milliseconds per keystroke.
Image Based 3D Face Reconstruction: a Survey

The use of 3D data in face image processing applications has received considerable attention during the last few years. A major issue for the implementation of 3D face processing systems is the accurate and real time acquisition of 3D faces using low cost equipment. In this paper we provide a survey of 3D reconstruction methods used for generating the 3D appearance of a face using either a single or multiple 2D images captured with ordinary equipment such as digital cameras and camcorders. In this context we discuss various issues pertaining to the general problem of 3D face reconstruction such as the existence of suitable 3D face databases, correspondence of 3D faces, feature detection, deformable 3D models and typical assumptions used during the reconstruction process. Different approaches to the problem of 3D reconstruction are presented and for each category the most important advantages and disadvantages are outlined. In particular we describe example-based methods, stereo methods, video-based methods and silhouette-based methods. The issue of performance evaluation of 3D face reconstruction algorithms, the state of the art and future trends are also discussed.
The Barriers to Producing High Quality Library and Information Science Research in Developing Countries: The Case of Pakistan

It is generally recognized that in many developing countries, for a variety of reasons, research output in most disciplines lags behind that in the developed nations. Among the reasons is a range of factors that may hinder good-quality research outputs. This paper focuses on the matter of research quality in library and information science (LIS) in Pakistan as a case study. To test the types of barriers that the researcher believes hinder the production of quality research in Pakistan, a web-based survey was conducted using a questionnaire consisting of structured and open-ended questions. The questionnaire was based on a set of barriers to quality research production, which were identified from the literature. The respondents were asked to indicate their views on the impact of these barriers on the production of quality research. The data was analysed using SPSS. The findings reveal that the lack of critical thinking, a poor research culture, lack of encouragement of research, and inadequate imparting of research skills in LIS education are the most significant barriers. The study suggests that determining the order in which to tackle these barriers will facilitate the production of high-quality research in countries like Pakistan.
The adaptation of a cognitive- behavioural treatment programme for special needs sexual offenders

Summary The need for specialized treatment programmes to address the specific requirements of different populations has been well recognized. One important area of treatment development has been for offenders who are unsuitable for existing mainstream treatment programmes. This paper describes the process of adapting an existing sexual offender treatment programme for use with sexual offenders who have special needs in an Australian correctional setting. The population comprised individuals with a variety of special needs including borderline or mild intellectual functioning, severe literacy problems, significant communication difficulties, and other important deficits and special needs. It should be noted that some of these special needs individuals would not meet the diagnostic criteria for intellectual disability and this programme is aimed at the broader group inclusive of a number of special needs. Therapeutic adaptations have been guided by current research and practice, and specific examples are described and discussed. The authors believe that these adaptations may also have some utility for mainstream sexual offender treatment programmes. Research into the efficacy of these treatment adaptations with this population is currently underway.
Modeling Weather Conditions Consequences on Road Trafficking Behaviors

We provide a model to understand how adverse weather conditions modify traffic flow dynamic. We first prove that the microscopic Free Flow Speed of the vehicles is changed and then provide a rule to model this change. For this, we consider a thresholded linear model, corresponding to an application of a MARS model to road trafficking. This model adapts itself locally to the whole road network and provides accurate unbiased forecasted speed using live or short term forecasted weather data information.
On the Shape of Verbal Networks in Organizations

Almost without exception, organizations contain a pyramid-shaped formal hierarchy of some sort. It is also known that organizations harbour frequent informal relations that do not necessarily follow patterns set by the formal hierarchy. While the shape and features of formal hierarchies are known and understood by most members of organizations, very little is known — by either academics or practitioners — about the shape and attributes of these informal relations. This paper explores regularities in the shape of verbal ties — a relationship that escapes most formal regulation — across the hierarchies of diverse organizations. Results indicate that the verbal networks of the upper echelons of organizations rarely follow a classic hierarchical pattern. Rather, several different morphologies surface. The most common of these regularities — the centre-periphery pattern — has been frequently observed in large human systems, including tribal and modern societies, national and international economies, industries, and political systems, but has not been studied inside organizations.
Stepfamilies in Cultural Context

Abstract The article presents a cross-cultural comparison of stepfamilies. Israeli and American stepfamilies were compared. The samples were similar in socio-demographic characteristics. Using translations of the same instruments, Israeli and American samples were compared for past orientation, acceptance/rejection of difference from non-stepfamilies, focal sub-system, satisfaction and functioning. Similarities and differences between American and Israeli stepfamilies are presented and their association to characteristics of the two societies are discussed. Methodological aspects of conducting cross-cultural research are addressed and directions for future research are suggested.
Discourse, meaning, and political participation

Abstract We present an analysis of part of a data-set from a three-year study called ‘Work, Development and Diversity’ conducted by a network of Argentinean public and private research institutions. We sought to analyze the different ways in which strategic planning for local development, with a participatory approach, had been implemented in four geographic regions of Argentina. In this article we analyze how (1) participants in a given field of practice build strategic discursive actions and orient their interactions guided by their perception of who is included, and in what aspects of the process at stake; (2) participants build discourses that shape what counts as reality. Our analysis shows what happens when participants come together, since they dispute what counts as true, valid or even real, and these disputes can be analyzed through discourse; what may appear to be a linguistic detail is loaded with meaning due to the historical context in which the specific cultural terms are produced (e.g. participant, neighbor, and activist). We also show that in calls for participatory action, any specific community of participants may impose what they determine to be true over the others. When this is achieved, one may say that they have managed to impose a certain simplifying operation over the other participants, thus making it possible for their logic to prevail, and to reduce a certain amount of complexity at play.
Vision-based automatic incident detection system using image sequences for intersections

Traffic incident detection is one of the interesting fields of intelligent transportation system (ITS) which recently rapidly increasing interest in their used. In this paper, we proposed an incident detection system based on incident features and reporting traffic incident in a special intersection using machine vision algorithms. The first step in this algorithm after image sequences acquisition from the video image of CCD camera is vehicle detection. Then the incident features such as direction of the moving vehicles, traffic flow and the rate of changing speed will extract in order to achieve the detection results. Machine vision based algorithm has been used in order to develop the system for incident detection goal. This process gives the best result by total 97.8% of correct rate, 1.02 of false alarm rate and 30(S) is the meantime to detect. The result shows that this algorithm has a good detection rate.
Multiple nicotinic acetylcholine receptor genes are expressed in goldfish retina and tectum

cDNAs encoding a novel nAChR structural subunit (GFn alpha-3) and a ligand-binding subunit (GF alpha-3) have been isolated from a goldfish retina cDNA library. The protein encoded by GFn alpha-3 shares 88% amino acid similarity with that encoded by GFn alpha-2, a structural subunit gene previously identified to be expressed in this system (Cauley et al., 1989). The ligand-binding subunit (GF alpha-3) is likely the goldfish homolog of the rat alpha-3 gene (Boulter et al., 1986). Northern blots and S1 protection experiments show that GFn alpha- 3 and GF alpha-3 genes are expressed in retina and brain. GFn alpha-3 identifies multiple RNAs differing in their 3′ untranslated regions. In situ hybridization analysis demonstrates GFn alpha-3, GFn alpha-2, and GF alpha-3 expression by cells of the retinal ganglion cell layer. Unlike GFn alpha-2 and GF alpha-3, GFn alpha-3 is expressed at highest levels by cells of the retina's inner nuclear layer. In the optic tectum, both GF alpha-3 and GFn alpha-3 genes are expressed by cells of the periventricular zone, as well as more superficial layers. These results suggest the presence of multiple nAChR systems in retina and tectum. In addition, they indicate that tectal nAChRs may arise from remote (ganglion cell) as well as local (tectal cell) synthesis.
Identification of small molecule inhibitors against UBE2C by using docking studies

An increased expression of UBE2C (Ubiquitin-conjugating enzyme E2C) has been associated with high tumor grade and cancer progression. It is an essential indicator of the mitotic destruction events. Our microarray study on cervical cancers showed UBE2C to be over expressed in cervical cancer. Subsequent studies from our laboratory, showed that inhibition of UBE2C can enhance radiation and chemosensitivity. Therefore it can be an appropriate target for drug development to identify potential and specific inhibitor of cancer. To identify small molecule inhibitors, a computational approach was used to model UBE2C and further docking studies were carried out. Different ligand subsets such as ChemBank, PDB, KEGG, Drug-likeness NCI, Not annotated NCI of ligand library ligands were downloaded and docked with UBE2C. Schrodinger tools were used for identifying active sites and docking studies of ligands with UBE2C. Based on glide score, the potential ligands were screened and its interaction with UBE2C was identified. We also analyzed the drug like properties such as absorption, distribution, metabolism, excretion and toxicity (ADME/T) of docked compounds. Our results suggest that 2,4-diimino-1-methyl-1,3,5-triazepan-6-one, sulfuric acid compound with 5,6-diamino-2,4-pyrimidinediol (1:1) and 7-alpha-d-ribofuranosyl-2-aminopurine-5'-phosphate may act as best inhibitors and further in vitro studies, may lead to development of novel and best inhibitor of UBE2C.
Extraction, Protest and Indigeneity in Bolivia: The TIPNIS Effect

In September 2011 Bolivian police raided an encampment of several hundred indigenous people gathered to protest the government’s plan to build a road through their lands. The violence of this event broadened awareness of the TIPNIS protest in Bolivia and abroad, and sparked both a national political crisis and debate about the validity of the government’s credentials as a progressive government that supports indigenous rights. While sustaining that existing analysis has used the TIPNIS controversy to raise important questions about the government, this article questions whether current characterizations of the political dynamics and the interests of the actors involved have been overly simplified. The article demonstrates that the TIPNIS controversy reveals anew the complex and often contradictory dynamics of indigeneity in Bolivia, and argues – in contrast to most recent analysis and media coverage – that indigenous peoples in Bolivia have an intimate relationship with resource extraction. Attention to this intimate relationship and its history is important in order to grasp the claims and aspirations of these communities in the present day.
Modelling the Complexity of the Coaching Process

INTRODUCTION An examination of the considerable landscape of coaching research [1] reveals a range of theoretical and empirical perspectives and insights into coaching. Despite this, an in-depth understanding of the coaching process appears to remain lacking and we seem as far removed from a consensus about the nature of coaching as ever. Consequently, coach development and coaching practice in North America and the UK operates without reference to any guideline or models for good practice that practitioners undoubtedly crave [2, 3, 4]. It would appear that “a model of coaching is required that has at its heart sound theoretical and research foundations, which are applicable to all sports, coaches and age groups” [5, p.105]. If this is the case, and given the scale of current coaching research activity [1]; why have coaching scholars been unable to develop such a model thus far? Perhaps coaching is an enterprise where a definitive set of concepts and principles will always be elusive and as such a singular all encompassing model may not be possible. Alternatively, if it were possible, would such an approach be in the best interests of developing coaching’s conceptual base? The aim of this paper is to build upon earlier work [2] and explore some of the issues surrounding the generation of and outcomes from a coaching process model. This includes a model for coaching (idealistic representation) and a model of coaching (based on empirical research) [2, 4].
Lattice-based Identity-Based Broadcast Encryption

Motivated by the lattice basis delegation technique due to [8], we propose an adaptively secure identity-based broadcast encryption(IBBE) scheme based on the hard worst-case lattice problems. Our construction can be generalized to a hierarchical IBBE (HIBBE) easily. Using the method in [1], we also modify our basic construction to obtain an IBBE in the standard model. To the best of the authors’ knowledge, our construction and its variants constitute the first adaptively secure IBBE schemes from lattices, which are believed secure in the post-quantum environment.
Radial Basis Function Network Training Using a Nonsymmetric Partition of the Input Space and Particle Swarm Optimization

This paper presents a novel algorithm for training radial basis function (RBF) networks, in order to produce models with increased accuracy and parsimony. The proposed methodology is based on a nonsymmetric variant of the fuzzy means (FM) algorithm, which has the ability to determine the number and locations of the hidden-node RBF centers, whereas the synaptic weights are calculated using linear regression. Taking advantage of the short computational times required by the FM algorithm, we wrap a particle swarm optimization (PSO) based engine around it, designed to optimize the fuzzy partition. The result is an integrated framework for fully determining all the parameters of an RBF network. The proposed approach is evaluated through its application on 12 real-world and synthetic benchmark datasets and is also compared with other neural network training techniques. The results show that the RBF network models produced by the PSO-based nonsymmetric FM algorithm outperform the models produced by the other techniques, exhibiting higher prediction accuracies in shorter computational times, accompanied by simpler network structures.
Mother‐Child Mutually Positive Affect, the Quality of Child Compliance to Requests and Prohibitions, and Maternal Control as Correlates of Early Internalization

Motivationally distinct forms of child compliance, mutually positive affect, and maternal control, observed in 3 control contexts in 103 dyads of mothers and their 26–41-month-old children, were examined as correlates of internalization, assessed using observations of children while alone with prohibited temptations and maternal ratings. One form of compliance (committed compliance), when the child appeared committed wholeheartedly to the maternal agenda and eager to endorse and accept it, was emphasized. Mother-child mutually positive affect was both a predictor and a concomitant of committed compliance. Children who shared positive affect with their mothers showed a high level of committed compliance and were also more internalized. Differences and similarities between children's compliance to requests and prohibitions (“Do” vs. “Don't” demand contexts) were also explored. Maternal “Dos” appeared more challenging to toddlers than the “Don'ts. ” Some individual coherence of behavior was also found across both demand contexts. The implications of committed compliance for emerging internalized regulators of conduct are discussed.
CONTEXTUAL EFFECTS ON CONSONANT VOICING PROFILES : A CROSS-LINGUISTIC STUDY

ABSTRACT In this paper we present selected results from a study of the voicing profiles of consonants in five languages, viz. Mandarin Chinese, German, Hindi, Mexican Spanish, and Italian. We will focus here on the voicing properties of stop closures in these languages. The voicing profile is defined as the frame-by-frame voicing status of a speech sound in continuous speech. We propose statistical models that predict the probability of voicing from phone identity, neighbouring phones, and positional and prosodic factors.
Extending postgreSQL to handle OLXP workloads

The importance of database systems to efficiently support OLTP and OLAP mixed workloads, the so-called OLXP workloads, has been recognized recently. Some research projects and also some commercial database systems with focus on the processing of OLXP workloads have appeared in the last few years. In this paper, we present our work to extend the PostgreSQL OSS database system to efficiently handle OLXP workloads. Besides PostgreSQL's traditional OLTP-oriented row data store, we provide a new OLAP-oriented column data store in the form of a new index. Unlike previous works that support both row and column data stores, we propose a column index with no restrictions concerning data size and/or updatability. Therefore, transactional data inserted to PostgreSQL row data store become immediately available for efficient analytical processing using the proposed column store index.
Validity of heavy traffic steady-state approximations in generalized Jackson networks

We consider a single class open queueing network, also known as a generalized Jackson network (GJN). A classical result in heavy-traffic theory asserts that the sequence of normalized queue length processes of the GJN converge weakly to a reflected Brownian motion (RBM) in the orthant, as the traffic intensity approaches unity. However, barring simple instances, it is still not known whether the stationary distribution of RBM provides a valid approximation for the steady-state of the original network. In this paper we resolve this open problem by proving that the re-scaled stationary distribution of the GJN converges to the stationary distribution of the RBM, thus validating a so-called “interchange-of-limits” for this class of networks. Our method of proof involves a combination of Lyapunov function techniques, strong approximations and tail probability bounds that yield tightness of the sequence of stationary distributions of the GJN.