Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Functional Gene Relationships Using the Semantic Gene Organizer (SGO)

Understanding functional gene relationships is a major challenge in bioninformatics and computational biology. Currently, many approaches extract gene relationships via term co-occurrence models from the biomedical literature. Unfortunately, however, many genes that are experimentally identified to be related have not been previously studied together. As a result, many automated models fail to help researchers understand the nature of the relationships. In this work, the particular schema used to mine genomic data is called Latent Semantic Indexing (LSI). LSI performs a singular-value decomposition (SVD) to produce a low-rank approximation of the data set. Effectively, it allows queries to be interpreted in a more concept-based space and can allow for gene relationships to be discovered that would ordinarily be overlooked by other models.
Maternal Genistein Alters Coat Color and Protects Avy Mouse Offspring from Obesity by Modifying the Fetal Epigenome

Genistein, the major phytoestrogen in soy, is linked to diminished female reproductive performance and to cancer chemoprevention and decreased adipose deposition. Dietary genistein may also play a role in the decreased incidence of cancer in Asians compared with Westerners, as well as increased cancer incidence in Asians immigrating to the United States. Here, we report that maternal dietary genistein supplementation of mice during gestation, at levels comparable with humans consuming high-soy diets, shifted the coat color of heterozygous viable yellow agouti (Avy/a) offspring toward pseudoagouti. This marked phenotypic change was significantly associated with increased methylation of six cytosine–guanine sites in a retrotransposon upstream of the transcription start site of the Agouti gene. The extent of this DNA methylation was similar in endodermal, mesodermal, and ectodermal tissues, indicating that genistein acts during early embryonic development. Moreover, this genistein-induced hypermethylation persisted into adulthood, decreasing ectopic Agouti expression and protecting offspring from obesity. Thus, we provide the first evidence that in utero dietary genistein affects gene expression and alters susceptibility to obesity in adulthood by permanently altering the epigenome.
HP1-Mediated Formation of Alternative Lengthening of Telomeres-Associated PML Bodies Requires HIRA but Not ASF1a

Approximately 10% of cancers use recombination-mediated Alternative Lengthening of Telomeres (ALT) instead of telomerase to prevent telomere shortening. A characteristic of cells that utilize ALT is the presence of ALT-associated PML nuclear bodies (APBs) containing (TTAGGG)n DNA, telomere binding proteins, DNA recombination proteins, and heterochromatin protein 1 (HP1). The function of APBs is unknown and it is possible that they are functionally heterogeneous. Most ALT cells lack functional p53, and restoration of the p53/p21 pathway in these cells results in growth arrest/senescence and a substantial increase in the number of large APBs that is dependent on two HP1 isoforms, HP1α and HP1γ. Here we investigated the mechanism of HP1-mediated APB formation, and found that histone chaperones, HIRA and ASF1a, are present in APBs following activation of the p53/p21 pathway in ALT cells. HIRA and ASF1a were also found to colocalize inside PML bodies in normal fibroblasts approaching senescence, providing evidence for the existence of a senescence-associated ASF1a/HIRA complex inside PML bodies, consistent with a role for these proteins in induction of senescence in both normal and ALT cells. Moreover, knockdown of HIRA but not ASF1a significantly reduced p53-mediated induction of large APBs, with a concomitant reduction of large HP1 foci. We conclude that HIRA, in addition to its physical and functional association with ASF1a, plays a unique, ASF1a-independent role, which is required for the localization of HP1 to PML bodies and thus for APB formation.
Towards Automatic Evaluation of Wordnet Synsets

Increasing and varied applications of wordnets call for the creation of methods to evaluate their quality. However, no such comprehensive methods to rate and compare wordnets exist. We begin our search for wordnet evaluation strategies by attempting to validate synsets. As synonymy forms the basis of synsets, we present an algorithm based on dictionary definitions to verify that the words present in a synset are indeed synonymous. Of specific interest are synsets in which some members “do not belong”. Our work, thus, is an attempt to flag human lexicographers’ errors by accumulating evidences from myriad lexical sources.
GEMMA: Multi-objective Optimization of Energy Consumption of GUIs in Android Apps

This tool demonstration describes GEMMA, a tool aimed at optimizing the colors used by Android apps, with the goal of reducing the energy consumption on (AM)OLED displays while keeping the user interface visually attractive for end-users. GEMMA has been developed as a distributed architecture to ensure scalability. It is composed of a Web-based client and processing nodes that are capable of analyzing multiple requests (apps) concurrently. The underlying approach makes use of power models, color theory, and multi-objective genetic algorithms. The empirical evaluation of GEMMA indicated its ability to reduce energy consumption while producing color combinations pleasant enough for the users. Also, a qualitative analysis conducted with app developers highlighted the potential applicability of the tool in an industrial context.VIDEO: https://www.youtube. com/watch? v=k-5ReMVwK0c.
Crowdsourcing: Low complexity, Minimax Optimal Algorithms

We consider the problem of accurately estimating the reliability of workers based on noisy labels they provide, which is a fundamental question in crowdsourcing. We propose a novel lower bound on the minimax estimation error which applies to any estimation procedure. We further propose Triangular Estimation (TE), an algorithm for estimating the reliability of workers. TE has low complexity, may be implemented in a streaming setting when labels are provided by workers in real time, and does not rely on an iterative procedure. We further prove that TE is minimax optimal and matches our lower bound. We conclude by assessing the performance of TE and other state-of-the-art algorithms on both synthetic and real-world data sets.
The Development of Ontology for Metabolic Pathways Using METHONTOLOGY

Understanding the biological function of an organism and how they interact to yield a living cell is the major challenge of the post genome-sequencing era. To understand the cellular function, most scientists and biologists study parts of metabolic pathway which contains various kinds of pathways and large volume of knowledge including genes, gene products, chemical compounds, enzyme reactions that interlinked each other. Moreover, the identification and validation of drug targets in drug discovery depends critically on knowledge of the metabolic pathways in which potential target molecules operate within cells. For this reason, the study of biochemical pathways is the focus of numerous drug discovery researches and is central to the stage of many biopharmaceutical and genomic companies. In order to provide better access to relevant knowledge, the knowledge of domain should be conceptualized and formalized by providing a domain-specific vocabulary using ontology-based approach. The methodology for ontology development, METHONTOLOGY is used as the methodology in developing and constructing the ontology for metabolic pathway. This paper presents how to build a domain ontology following METHONTOLOGY and using the ontology conceptualization tools, Protege.
Joint-MAP Tomographic Reconstruction with Patch Similarity Based Mixture Prior Model

Tomographic reconstruction from noisy projections do not yield adequate results. Mathematically, this tomographic reconstruction represents an ill-posed problem due to information missing caused by the presence of noise. Maximum a posteriori (MAP) or Bayesian reconstruction methods offer possibilities to improve the image quality as compared with analytical methods in particular by introducing a prior to guide the reconstruction and regularize the noise. With an aim to achieve robust utilization of continuity/connectivity information and overcome the heuristic weight update for other nonlocal prior methods, this paper proposes a novel patch similarity based mixture (PSM) prior model for tomographic reconstruction. This prior is defined by a weighted Gaussian distance between neighborhood intensities. The weight quantifies the similarity between local neighborhoods and is computed using a maximization entropy constraint. This prior is then introduced within a joint image/weight MAP computed tomography reco.
Framework for integrating outcome-based assessment in online assessment: Research in progress

The use of online examination in place of paper-based assessment has attracted a plethora of attention from educators and researchers alike. The reason for this stems from the advantages of online examinations, such as effectiveness, objectiveness, and flexibility. However, creating valid and reliable examinations remains a challenge. Often used as a framework for educational assessments, bloom's taxonomy greatly influences the formulation of course outcomes and examination questions. An ideal examination should consist of set of well-aligned questions that extensively meet all the course outcomes and correspond to the different levels of Bloom's taxonomy. Moodle is a popular widespread open source Learning Management System (LMS) that can be used to create examination questions. However, it is lacking in its reporting mechanisms that enables the classification of various questions based on the course outcomes and Bloom's Taxonomy. The objective of this paper is to propose and describe a framework to integrate outcome-based assessment into LMS. This alignment is significant in order to ensure high quality examination assessment as well as to help teachers develop a balanced examination that encompasses all the course outcomes and different levels of Bloom's taxonomy.
THEORETICAL BACKGROUND AND EXPERIMENTAL EVALUATION OF THE TECHNIQUE FOR ULTRASTRUCTURAL IMMUNOLOCALISATION OF THE H-SUBUNIT AND L-SUBUNIT OF FERRITIN

1) Introduction Ferritin, the major intracellular protein responsible for the storage of iron in all cell types consists of 24 subunits of various combinations of two types, the H-subunit and the Lsubunit (Chapter 1). The combination of these two subunits in the ferritin protein shell plays an important role in ferritin’s iron handling capabilities. In the bone marrow, iron is differently metabolised by the cells of the erythron including erythroblasts, reticulocytes and red blood cells on the one hand, and the macrophage on the other. Furthermore, iron is shuttled between the cells of the erythron and the macrophage to support erythropoiesis. In order to investigate the role of the H-subunit and the Lsubunit of ferritin in the handling of iron by cells of the bone marrow it is necessary to investigate the expression of the two subunits of ferritin at the single cell level.
Subtle Facial Animation Transfer from 2D Videos to 3D Faces with Laplacian Deformation

Realistic facial animation transfer from one individual to others has been a persistent challenge. In this paper, we present an effective method that transfers facial animation from 2D videos onto 3D faces in a visually pleasing manner. Our method is based on a Laplacian deformation framework. We represent the facial animation with the displacements of a set of feature points. By the assumption that the feature points move only in the X-Y directions, we can map the displacements of the feature points from a 2D video to a 3D face. These displacements are used to drive the Laplacian deformation and calculate the deformed positions of the non-feature points on the 3D face. The approach produces accurate, realistic and smooth transfer. Furthermore, the method is efficient and practical, and the interface is intuitive. The proposed technique outperforms previous methods based on machine learning and anatomy in terms of speed and applicability. Our method is useful for a wide range of applications, such as, avatars, character animation for 3D films, computer games, and online chatting. The versatility of our approach is demonstrated by some special effects, such as expression exaggeration and expression imitation.
Tracking the Human Hand

We introduce a method for extracting information about human hands present in colour images largely based on work done by Daniel Heckenberg and Brian Lovell. It relies heavily on isolating the hand in the image using a statistical model of skin colour. Following this, it employs solely imagebased techniques to determine the locations of the fingers, and performs a simplistic gesture recognition to illustrate its usefulness. A thorough analysis of empirical results is presented. Melanie Coggan and Adrian Ghizaru – Tracking the Human Hand
A Semi-Supervised Framework for Feature Mapping and Multiclass Classification

We propose a semi-supervised framework incorporating feature mapping with multiclass classification. By learning multiple classification tasks simultaneously, this framework can learn the latent feature space effectively for both labeled and unlabeled data. The knowledge in the transformed space can be transferred not only between the labeled and unlabeled data, but also across multiple classes, so as to improve the classification performance given a small amount of labeled data. We show that this problem is equivalent to a sequential convex optimization problem by applying constraint concave-convex procedure (CCCP). Efficient algorithm with theoretical guarantee is proposed and computational issue is investigated. Extensive experiments have been conducted to demonstrate the effectiveness of our proposed framework.
Significant ecological impact on the progression of fluoroquinolone resistance in Escherichia coli with increased community use of moxifloxacin, levofloxacin and amoxicillin/clavulanic acid.

OBJECTIVES To determine trends in ciprofloxacin resistance and co-resistance to other antibiotic classes in blood isolates of Escherichia coli, and to investigate if there is an ecological relationship to the community use of fluoroquinolones and other antibiotics. METHODS Forty-two Spanish hospitals of the European Antimicrobial Resistance Surveillance Network collected ciprofloxacin and other antibiotic susceptibility data for non-duplicate consecutive E. coli isolates from patients with bacteraemia between 2001 and 2009. The nationwide ambulatory use of antibiotics between 1997 and 2008 was determined by WHO methods, and the co-evolution of both parameters was further analysed. RESULTS Of the 28 307 E. coli blood isolates, 27.9% were ciprofloxacin non-susceptible (CIPNS), increasing from 17.6% in 2001 to 32.7% in 2009. A continuous increase was observed between CIPNS and other resistances, including cephalosporin resistance due to the production of extended-spectrum β-lactamases (ESBLs) and non-susceptibility to both amoxicillin/clavulanic acid and tobramycin. Although the total use of antibiotics did not increase, community use of levofloxacin, moxifloxacin and amoxicillin/clavulanic acid increased by 307.2%, 62.6% and 70.1%, respectively. Yearly rates of CIPNS E. coli strongly correlated with the use of levofloxacin, moxifloxacin and amoxicillin/clavulanic acid (r(2 )> 0.80; P < 0.005 in all cases). CONCLUSIONS The rapid increase in CIPNS E. coli causing bacteraemia was closely related to the increase in resistance to amoxicillin/clavulanic acid, production of ESBLs and resistance to aminoglycosides. Community use of fluoroquinolones (mainly moxifloxacin and levofloxacin) and of amoxicillin/clavulanic acid represents a significant driver in the progression of fluoroquinolone resistance in bacteraemic E. coli.
Identifying a financial conditions index for South Africa

The global financial crisis that began in 2007-08 demonstrated how severe the impact of financial markets’ stress on real economic activity can be. In the wake of the financial crisis policy-makers and decision-makers across the world identified the critical need for a better understanding of financial conditions, and more importantly, their impact on the real economy. To this end, we have constructed a financial conditions index (FCI) for the South African economy, to enable the gauging of financial conditions and to better understand the macro-financial linkages in the country. The FCI is constructed using monthly data over the period 1966 to 2011, and is based on a set of sixteen financial variables, which include variables that define the state of international financial markets, asset prices, interest rate spreads, stock market yields and volatility, bond market volatility and monetary aggregates. We explore different methodologies for constructing the FCI, and find that rolling-window principal components analysis (PCA) yields the best result. We furthermore investigate whether it is beneficial to purge the FCI of the real effects of inflation, economic growth and interest rates, and use the identified FCI in in-sample causality testing with three macroeconomic variables.
Research on the blind separation algorithm and its improved algorithm based on maximizing the SINR

The problem of noise amplification in the multichannel blind separation of communication signals is researched. A new algorithm and its improved algorithm to seek the separation matrix is proposed based on the idea of maximizing the signal-to-interference-plus-noise power ratio (SINR). When the condition number of the separation matrix is large, the separation matrix sought by this algorithm and its improved algorithm can beautifully solve the problem of separation performance degradation caused by noise amplification. Simulation results show that this algorithm and its improved algorithm can reduce the bit error rate effectively and improve the performance of blind separation, exhibiting practical application value.
Motor imagery recognition and its cerebral mapping

This paper proposes to relate a Linear Discriminant Analysis Classification based system with Quality Similarity Clustering process and a Brain Mapping Technique in order to clarify the brain activity differences that could sustain the better classification rates between each of the Motor Imagery (MI - flex right arm, flex left arm, close right hand, close left hand). To achieve this goal the Eletroencephalogram (EEG) entropy was used as principal feature and a Principal Component Analyses (PCA) was also used. EEG signal, from each of the 8-channel transversal set up, was acquired from electrodes Fz, Cz, Pz and Oz to electrodes F3, F4, C3, C4, P3, P4, O1, and O2. Results showed that for each MI there is an specific topographic distribution of the cortex activation. A common point was the minor activation of the motor area. The principal areas were the frontal and the parietal ones. The clustering analysis showed, considering 20% of similarity, that the points which possibly contribute to motor imagery recognition came from those areas. Furthermore, the best results in the classification process were reached to distinguish between left arm and left hand with 89.74% and between arms and hands with 80.77%. Both of these scenes were possible using only the information provided by the frontal electrodes, and this agree with brain mapping. The activation of frontal and parietal lobes reflects the network involved in sensory-motor integration (posterior parietal), decision-making (prefrontal) and preparation of motor response (premotor). Our finding that the frontal electrodes were the most representative may be related to the fact that the premotor cortex is responsible for motor planning and thus, should be the most active area in distinguishing between different motor movements.
Multimodal gaze stabilization of a humanoid robot based on reafferences

Gaze stabilization is fundamental for humanoid robots. By stabilizing vision, it enhances perception of the environment and keeps regions of interest inside the field of view. In this contribution, a multimodal gaze stabilization combining proprioceptive, inertial and visual cues is introduced. It integrates a classical inverse kinematic control with vestibulo-ocular and optokinetic reflexes. Inspired by neuroscience, our contribution implements a forward internal model that modulates the reflexes based on the reafference principle. This principle filters self-generated movements out of the reflexive feedback loop. The versatility and effectiveness of this method are experimentally validated on the ARMAR-III humanoid robot. We first demonstrate that all the stabilization mechanisms (inverse kinematics and reflexes) are complementary. Then, we show that our multimodal method, combining these three modalities with the reafference principle, provides a versatile gaze stabilizer able to handle a large panel of perturbations.
Analysis of the embrasure dimensions between maxillary central incisors in relation to the topography of the interdental papilla

Purpose To analyze the dimensions of the embrasure space between the maxillary central incisors as potential factors influencing interdental papilla fill and height. Methods The embrasure dimensions between the maxillary central incisors of 100 subjects (40 females/60 males) were assessed with clinical, study model, and radiographic examinations. Variables of the complete and deficient papilla fill groups were compared. Multiple regression analyses were performed to investigate potential influence of the distance between the contact point and bone crest (CP_BC), horizontal interdental distance (HID), and facio-lingual thickness (FLT) at the papilla base on complete/deficient papilla fill and papilla height (PH). Results CP_BC was the only variable that showed a significant difference between the complete and deficient papilla groups (P<0.05). When the CP_BC was less than 5 mm, the embrasure spaces between the maxillary central incisors were completely filled with interdental papilla. Multiple regression analyses revealed that a significant predictor for complete/deficient papilla fill was CP_BC, and significant predictors for PH were CP_BC and HID (P<0.05). Conclusions The chances of complete papilla fill increased as CP_BC decreased, while PH increased as CP_BC and HID increased. However, the FLT of the papilla base did not appear to affect papilla fill or PH. From an esthetic perspective, CP_BC as well as HID should be considered as factors influencing the topography of interdental papilla.
AIS Electronic

Despite the researchers’ and practitioners’ enthusiasm for the global diffusion of information technology governance (ITG) concept and frameworks, there is a general lack of cultural awareness in ITG research. This paper examines both whether Chinese culture influences the performance ITG capabilities in organizations and how this influence is manifested. An analytical framework rooted in contingency theory is used in this paper to examine the fit (i.e., complementarity or conflicting) between ITG capabilities and Chinese cultural values. On the basis of the dynamic nature of cultural values, this paper proposes four conditions that are expected to compensate existing conflicts. These conditions are: a firm’s dependency on Confucian entrepreneurship; social reputation; and shared goals; as well as its exposure to international business environment. The authors also bridge general cultural dimensions and indigenous Chinese culture values, which enables a cross-cultural comparison to be made. By exploring the potential influences of national culture on ITG, this paper contributes to the contextualization of ITG and benefits the cross-country transfer of ITG concepts and practices.