Miracle-dz/UniFAR-FTUs huggingface dataset:
Experiments with Hierarchical Concept-Based Search

Many digital libraries use hierarchical indexing schema, such as MeSH to enable concept based search in the retrieval phase. However, improving or outperforming the traditional full text search isn't trivial. We present an extensive set of experiments using a hierarchical concept based search retrieval method, applied in addition to several baselines, within the Vaidruya search and retrieval framework. Concept Based Search applied in addition to a low baseline is outperforming significantly, especially when queried on concepts in the third level and using disjunction within the hierarchical trees.
Gender classification using KPCA and SVM

A new technique to construct feature vector for gender classification is proposed in this paper. Here, new feature reduction technique is used to remove the irrelevant features of images. Feature reduction also helps in reducing the over fitting problem of the dataset. KPCA is a kernel based PCA which maps data from original space to non-linear feature space. Kernel trick helps in reducing the expensive computation of mapping data to higher dimensional space. Optimal parameter of SVM C and Ύ are learned using cross validation dataset. Features obtained using KPCA are used to classify images into male or female using SVM. Images of different databases i.e. AT@T, Faces94 and Georgia Tech have been used to validate the efficiency of the proposed technique. Proposed technique has better generalization performance as compare to other existing techniques.
A spatial analysis approach to evacuation management: shelter assignment and routing

Evacuation planning requires an integrated analysis of heterogeneous spatial datasets including population, road network and facilities. It is a complex and challenging task to delineate evacuation circumstances and make reasonable connections among the datasets which evacuation management of emergency situations will be based on. An evacuation management system requires an easy configuration by evacuation managers who do not necessarily have full knowledge of Geographic Information Systems (GIS) but need to understand the situation promptly and provide decisive instructions that can be fulfilled only when they can manage datasets and develop new workflows in various scenarios. A spatial analysis platform provides toolkits for spatial data acquisition and processing, analysis, and visualisation from/to online open sources. Such toolkits built in typical GIS software are utilised in this paper to show the feasibility of enabling users to manage spatial data and customise their analysis by combining common data analysis tools to meet their requirements in evacuation planning. Case studies are provided to demonstrate the usability of these toolkits in Brisbane flood evacuation management.
Biomarkers for Circadian Rhythm Disruption Independent of Time of Day

Frequent shift work causes disruption of the circadian rhythm and might on the long-term result in increased health risk. Current biomarkers evaluating the presence of circadian rhythm disturbance (CRD), including melatonin, cortisol and body temperature, require 24-hr (“around the clock”) measurements, which is tedious. Therefore, these markers are not eligible to be used in large-scale (human) studies. The aim of the present study was to identify universal biomarkers for CRD independent of time of day using a transcriptomics approach. Female FVB mice were exposed to six shifts in a clockwise (CW) and counterclockwise (CCW) CRD protocol and sacrificed at baseline and after 1 shift, 6 shifts, 5 days recovery and 14 days recovery, respectively. At six time-points during the day, livers were collected for mRNA microarray analysis. Using a classification approach, we identified a set of biomarkers able to classify samples into either CRD or non-disrupted based on the hepatic gene expression. Furthermore, we identified differentially expressed genes 14 days after the last shift compared to baseline for both CRD protocols. Non-circadian genes differentially expressed upon both CW and CCW protocol were considered useful, universal markers for CRD. One candidate marker i.e. CD36 was evaluated in serum samples of the CRD animals versus controls. These biomarkers might be useful to measure CRD and can be used later on for monitoring the effectiveness of intervention strategies aiming to prevent or minimize chronic adverse health effects.
Splice isoform estrogen receptors as integral transmembrane proteins

Use of ecliptic pHluorin-fused ER46 and TIRFM identifies ER46 as a type I transmembrane protein in live human ECs. The transmembrane mutant ER46-Ile386Cys obscures the N-terminal ectodomain and effects a marked reduction in membrane-impermeant estrogen binding, with diminished rapid eNOS activation and NO production.
Population differences in elastin maturation in optic nerve head tissue and astrocytes.

PURPOSE Glaucomatous optic neuropathy is characterized by remodeling of the extracellular matrix with disorganization of elastic fibers in the optic nerve head (ONH). There are significant differences in prevalence of glaucomatous optic neuropathy between African Americans (AAs) and Caucasian Americans (CAs). The goal of this study was to evaluate differences in elastin synthesis and maturation in ONH tissue and cells of AA and CA donors with no eye disease, to provide a basis for underlying racial differences in susceptibility to elevated intraocular pressure. METHODS The amount of mature elastin in ONHs from each group of donors was evaluated by desmosine radioimmunoassay. The distribution of elastic fibers in ONH tissue was investigated by immunofluorescent staining. Elastin and lysyl oxidase mRNA levels and alternative splicing of elastin in ONH astrocytes were investigated by quantitative PCR. Tropoelastin protein expression was assessed by immunoblot analysis. RESULTS ONHs from AA donors had significantly reduced levels of desmosine compared with those of CAs. In contrast, elastin mRNA and tropoelastin synthesis were elevated in ONH astrocytes from AA individuals. The inclusion of exon 23 in elastin mRNA and lysyl oxidase-like 2 mRNA levels was significantly reduced in astrocytes from AA compared with CA donors. CONCLUSIONS A reduced number of cross-linking domains in elastin and decreased lysyl oxidase-like 2 expression leads to decreased amount of mature elastin in ONHs from healthy AA individuals compared with CA donors. These results suggest ELN and LOXL2 as candidate susceptibility genes for population-specific genetic risk of primary open-angle glaucoma (POAG).
Effective Exploration and Visualization of Large Execution Traces

Understanding the behaviour of a software system can be made easier if dynamic analysis techniques are used. Runtime information is typically represented in the form of execution traces. Raw traces, however, can be extremely large - often millions of lines long. In previous work, we presented a tool called SEAT (Software Exploration and Analysis Tool), which is a trace visualization tool that supports several features for rapid exploration of lengthy traces. In this paper, we present the new features supported by SEA T, namely, the ability to plug-in new trace filtering algorithms, a usable control widget called PictureTree for displaying traces, and several new views that display useful information about the trace under study.
Annotation of Tutorial Dialogue Goals for Natural Language Generation

We annotated transcripts of human tutoring dialogue for the purpose of constructing a dialogue-based intelligent tutoring system, CIRCSIM-Tutor. The tutors were professors of physiology who were also expert tutors. The students were 1st year medical students who communicated with the tutors using typed communication from separate rooms. The tutors made use of a rich variety of strategies, some specific to particular content areas and others more general, such as showing that the student holds contradictory beliefs about the domain. In this article, we describe our model of hierarchical goal structure for tutorial dialogues. We catalog each major pedagogical method we found in the dialogues, showing its structure and illustrating the features needed to represent each subgoal in its correct narrative and interpersonal context. We compare our goal structure with other analyses of tutorial dialogues.
Function of PIAS proteins in steroid receptor-dependent signaling

5 ORIGINAL PUBLICATIONS. 6 ABBREVIATIONS . 7 REVIEW OF THE LITERATURE. 8 1. PIAS PROTEIN FAMILY. 8 1.1. Discovery of PIAS proteins. 8 1.2. Structure of PIAS proteins . 9 1.3. Expression of PIAS proteins . 11 1.4. PIAS proteins in cytokine-signaling pathway . 12 1.5. Other interaction partners and functions of PIAS proteins . 13 2. STEROID RECEPTOR-MEDIATED SIGNALING . 14 2.1. General transcription machinery. 15 2.2. Nuclear receptor superfamily . 16 2.3. Mode of steroid receptor action. 17 2.3.1. Coactivators. 19 Complexes with histone acetyltransferase activity.21 Complexes with ATP-dependent chromatin remodeling activity . 21 TRAP/DRIP complexes.22 2.3.2. Corepressors. 22 2.4. Androgen receptor . 23 3. COVALENT MODIFICATIONS IN NUCLEAR RECEPTOR FUNCTION . 24 3.1. Modification of structural proteins of chromatin. 24 3.2. Modification of transcription factors . 25 3.2.1. Ubiquitination and proteasome-mediated degradation . 26 4. SUMO-1 MODIFICATION. 27 4.1. Enzymes involved in SUMO modification pathway . 28 4.1.1. E1, E2 and E3 activities . 29 4.1.2. SUMO C-terminal hydrolases and isopeptidases . 30 4.2. SUMO target proteins and possible functions of sumoylation. 31 4.2.1. Regulation of protein targeting and protein–protein interactions . 32 4.2.2. Sumoylation of transcription factors. 33 4.2.3. Regulation of protein stability . 34 4.3. Future perspectives . 34 AIMS OF THE STUDY . 35 METHODS.36 THE SEQUENCES OF PIAS PROTEINS USED IN THIS STUDY.36 RESULTS AND DISCUSSION . 37 1. PIAS PROTEINS FUNCTION AS STEROID RECEPTOR COREGULATORS (I, II) . 37 2. DOMAINS IMPORTANT FOR COREGULATOR FUNCTION OF PIAS PROTEINS (I, II, III) . 38 3. PIAS PROTEINS ARE MODIFIED BY SUMO-1 (III) . 40 4. PIAS PROTEINS INTERACT WITH SUMO-1-MODIFIED PROTEINS AND COLOCALIZE WITH SUMO-1 IN NUCLEI (III) . 42 5. PIAS PROTEINS MODULATE TRANSCRIPTION FACTORS BY FUNCTIONING AS SUMO-1 E3 LIGASES (III, IV). 44 6. SUMO-1 MODIFICATIONS REGULATE THE FUNCTION OF GRIP1 (III, IV) . 46 7. PIAS PROTEINS COOPERATE WITH GRIP1 IN STEROID RECEPTOR-DEPENDENT TRANSCRIPTION (II, IV). 49 CONCLUSIONS . 52 ACKNOWLEDGEMENTS . 53 REFERENCES . 54
End-User Regression Testing for Privacy

Privacy in social computing systems has become a major concern. End-users of such systems find it increasingly hard to understand complex privacy settings. As software evolves over time, this might introduce bugs that breach users’ privacy. Further, there might be system-wide policy changes that could change users’ settings to be more or less private than before. We present a novel technique that can be used by end-users for detecting changes in privacy, i.e., regression testing for privacy. Using a social approach for detecting privacy bugs, we present two prototype tools. Our evaluation shows the feasibility and utility of our approach for detecting privacy bugs. We highlight two interesting case studies on the bugs that were discovered using our tools. To the best of our knowledge, this is the first technique that leverages regression testing for detecting privacy bugs from an end-user perspective.
Application of Systematic Data Mining for Prediction of Biological Quality Indices

Data mining is not only a simple application of an algorithm on the data set. It is rather a systematic approach that is absolutely necessary, if we want to obtain useful and meaningful patterns from data. This paper shows how the usage of systematic data mining can help to simplify the first determination of the quality of marine habitats in the western Baltic Sea. The Benthic Quality Index (BQI) has been introduced within the European Union Water Framework Directive to assess the quality of marine habitats. The index is based on sensitivity/tolerance classification and quantitative information on the composition of soft-bottom macro fauna. The calculation of the index is based on the exact designation of the found taxa.
Metabolomics: Bridging the Gap between Pharmaceutical Development and Population Health

Metabolomics has emerged as an essential tool for studying metabolic processes, stratification of patients, as well as illuminating the fundamental metabolic alterations in disease onset, progression, or response to therapeutic intervention. Metabolomics materialized within the pharmaceutical industry as a standalone assay in toxicology and disease pathology and eventually evolved towards aiding in drug discovery and pre-clinical studies via supporting pharmacokinetic and pharmacodynamic characterization of a drug or a candidate. Recent progress in the field is illustrated by coining of the new term—Pharmacometabolomics. Integration of data from metabolomics with large-scale omics along with clinical, molecular, environmental and behavioral analysis has demonstrated the enhanced utility of deconstructing the complexity of health, disease, and pharmaceutical intervention(s), which further highlight it as an essential component of systems medicine. This review presents the current state and trend of metabolomics applications in pharmaceutical development, and highlights the importance and potential of clinical metabolomics as an essential part of multi-omics protocols that are directed towards shaping precision medicine and population health.
Gender And Dynamic Agency: Theory And Evidence On The Compensation Of Female Top Executives

Survey and experimental evidence point to the existence of a pervasive set of culturally-related barriers. These include lack of mentoring and role models, exclusion from informal networks, gender based stereotyping, display of style different than the organizational norms, difficulties in engaging in negotiations and inhospitable corporate culture. Based on this evidence, we consider two alternative hypotheses regarding possible determinants of gender differences in the structure of compensation. The first hypothesis is that female executives have lower impact. Specifically, we allow for a lower effect of effort on the probability of high profits for female executives (probability-impact). Alternatively, we consider the case where for given effort, female executives give rise to higher volatility in firm profits (productivity-impact). The second hypothesis is that female executives have lower effectiveness - that is, they have a smaller role in the determination of a firm's profits, for a given impact of their effort. We find that the version of the model in which female executives have lower effectiveness is consistent with the observed gender differences in the structure of executive compensation. The version with lower impact fails to replicate, among the other things, the lower fraction of performance pay earned by female executives.
Bacterial whole genome phylogeny using proteome comparison and optimal reversal distance

Traditional phylogenetic tree reconstruction is based on point mutations of a single gene. This approach is hardly suitable for genomes whose genes are almost identical and hardly captures evolutionary scenarios. To reconstruct a more conclusive phylogenetic tree of bacterial genome, all currently available complete bacterial genomic sequences were downloaded from the National Center for Biotechnology Information (NCBI). Each individual proteome was blasted against the collection and provided a number of homologous genes shared with others. Moreover, the syntenies of each two genomes can be considered as two signed permutations. One permutation can be rearranged into another in finite steps, called reversal distance. These two measures were combined and yield a phylogenetic tree that is highly consistent with the bacterial taxonomy.
GP-pro: the generative programming protocol generator for routing in mobile ad hoc networks

Routing in mobile ad hoc networks (MANETs) where network topology is highly dynamic is not a trivial task. Routing protocols have been profoundly researched but only three of them have reached the RFC status (AODV[7], OLSR[5] and TBPRF[6]). On the other hand, the constantly increasing network requirements in terms of bandwidth, robustness, reliability and quality of service for a broad range of multiplatform scenarios demand for fast development and implementation of routing protocols that satisfy specific user and network requirements. However, current practices for protocol development and implementation are costly error-prone and time-consuming, especially when existing knowledge is not properly reused. Generative Programming is an attractive solution that makes use of reusable components and is also empowered with the knowledge to automatically assemble them. This paper discusses the design and development of the GP- Pro protocol generator (based on generative programming), for automatic generation of ad hoc routing protocols, according to user requirements expressed by means of a specification language. GP-Pro is designed to be extensible, with the explicit goal of generating a large number of different protocols by different component combinations. GP-Pro addresses the generation of proactive, reactive and position-based routing protocols.
Utilising a multi-agent system to support the deployment of contextualised mLearning services

Enhancement of an InfoStation-based multiagent architecture is presented. The focus of the enhancement is the system's capability to facilitate the contextualisation of delivered service content. It adapts to varying operating environments inherent to this type of wireless access architecture, and to service delivery modes dictated by, or matched to, the personal context of the user. The educational opportunities thereby created such as support for dispersed distance learning and enriched learning environment are discussed.
A Fusion Approach for Facial Expression Using Local Binary Pattern and a Pseudo 3D Face Model

The discovery of association between local facial feature and regional feature of image for recognizing facial expression is one of the current challenges in the regard of facial expression recognition. In this paper, we propose an approach fusing different complementary methods that can facilitate recognition of facial expression by exploring the knowledge on the face. The approach incorporates the joint work of Local Binary Pattern to extract the holistic facial area for recognizing facial expression. To deal with regional feature of face, a pseudo 3Dface model is established for segmenting facial regions. Final, a propagation method is introduced to recognize the facial expression. Unlike many previous studies, the presented approach recognizes expressions from regional feature instead of holistic facial features or complete texture information. In order to validate our proposed approach, we have conducted experiments on the Extended Cohn-Kanade (CK+) facial expression database with an recognition rate of 91.7%.
Assessment of Polarimetric SAR Interferometry for Improving Ship Classification based on Simulated Data

This paper uses a complete and realistic SAR simulation processing chain, GRECOSAR, to study the potentialities of Polarimetric SAR Interferometry (POLInSAR) in the development of new classification methods for ships. Its high processing efficiency and scenario flexibility have allowed to develop exhaustive scattering studies. The results have revealed, first, vessels' geometries can be described by specific combinations of Permanent Polarimetric Scatterers (PePS) and, second, each type of vessel could be characterized by a particular spatial and polarimetric distribution of PePS. Such properties have been recently exploited to propose a new Vessel Classification Algorithm (VCA) working with POLInSAR data, which, according to several simulation tests, may provide promising performance in real scenarios. Along the paper, explanation of the main steps summarizing the whole research activity carried out with ships and GRECOSAR are provided as well as examples of the main results and VCA validation tests. Special attention will be devoted to the new improvements achieved, which are related to simulations processing a new and highly realistic sea surface model. The paper will show that, for POLInSAR data with fine resolution, VCA can help to classify ships with notable robustness under diverse and adverse observation conditions.
MMIC-oscillator designs for ultra low phase noise

Various balanced VCO-topologies like cross-connected (negative gm), coupled cross-connected, coupled Colpitt and Clapp oscillators, all with a fully integrated tank are reported. In this study, different MMIC/RFIC technologies such as SiGe HBT, InGaP-GaAs-HBT, PHEMT, MHEMT, and CMOS are represented and parameters such as phase-noise, output power, dc-power consumption, and tuning range are compared. All oscillators are designed for low phase noise. Low phase noise can be achieved by CMOS, PHEMT and MHEMT technologies although SiGe and InGaP-GaAs HBT based oscillators have demonstrated the lowest phase noise. Both fundamental and second harmonic VCOs are represented in the evaluation.
Clinical Scenarios for Discordant Anti-Xa

Anti-Xa test measures the activity of heparin against the activity of activated coagulation factor X; significant variability of anti-Xa levels in common clinical scenarios has been observed. Objective. To review the most common clinical settings in which anti-Xa results can be bias. Evidence Review. Guidelines and current literature search: we used PubMed, Medline, Embase, and MEDION, from 2000 to October 2013. Results. Anti-Xa test is widely used; however the assay underestimates heparin concentration in the presence of significant AT deficiency, pregnancy, end stage renal disease, and postthrombolysis and in patients with hyperbilirubinemia; limited published data evaluating the safety and effectiveness of anti-Xa assays for managing UH therapy is available. Conclusions and Relevance. To our knowledge this is the first paper that summarizes the most common causes in which this assay can be affected, several “day to day” clinical scenarios can modify the outcomes, and we concur that these rarely recognized scenarios can be affected by negative outcomes in the daily practice.
Scalable Deep Document / Sequence Reasoning with Cognitive Toolkit

Deep Neural Networks (DNNs) have revolutionized the way that machines understand language and have allowed us to create models that answer textual questions, translate pairs of languages, and intelligently compare document corpora. At the heart of these successes lie core techniques that fall into the area of sequence understanding. While powerful, dealing with variable-size sequences in DNNs requires deep understanding and experience in creating such networks, which can be daunting to many scientists and engineers. This tutorial will focus on introducing core concepts, end-to-end recipes, and key innovations facilitated by the cross-platform fully open-source Cognitive Toolkit (formerly called CNTK) with superior scalability (up to 1000 GPUs) for very large data corpora. Specifically, we will present tutorials on basic sequence understanding, intermediate sequence-to-sequence translation (both with and without attention), and the advanced Reasoning Network (ReasoNet) which has achieved industry-leading results in reading comprehension.