Miracle-dz/UniFAR-FTUs huggingface dataset:
ALS-Associated FUS Mutations Result in Compromised FUS Alternative Splicing and Autoregulation

The gene encoding a DNA/RNA binding protein FUS/TLS is frequently mutated in amyotrophic lateral sclerosis (ALS). Mutations commonly affect its carboxy-terminal nuclear localization signal, resulting in varying deficiencies of FUS nuclear localization and abnormal cytoplasmic accumulation. Increasing evidence suggests deficiencies in FUS nuclear function may contribute to neuron degeneration. Here we report a novel FUS autoregulatory mechanism and its deficiency in ALS-associated mutants. Using FUS CLIP-seq, we identified significant FUS binding to a highly conserved region of exon 7 and the flanking introns of its own pre-mRNAs. We demonstrated that FUS is a repressor of exon 7 splicing and that the exon 7-skipped splice variant is subject to nonsense-mediated decay (NMD). Overexpression of FUS led to the repression of exon 7 splicing and a reduction of endogenous FUS protein. Conversely, the repression of exon 7 was reduced by knockdown of FUS protein, and moreover, it was rescued by expression of EGFP-FUS. This dynamic regulation of alternative splicing describes a novel mechanism of FUS autoregulation. Given that ALS-associated FUS mutants are deficient in nuclear localization, we examined whether cells expressing these mutants would be deficient in repressing exon 7 splicing. We showed that FUS harbouring R521G, R522G or ΔExon15 mutation (minor, moderate or severe cytoplasmic localization, respectively) directly correlated with respectively increasing deficiencies in both exon 7 repression and autoregulation of its own protein levels. These data suggest that compromised FUS autoregulation can directly exacerbate the pathogenic accumulation of cytoplasmic FUS protein in ALS. We showed that exon 7 skipping can be induced by antisense oligonucleotides targeting its flanking splice sites, indicating the potential to alleviate abnormal cytoplasmic FUS accumulation in ALS. Taken together, FUS autoregulation by alternative splicing provides insight into a molecular mechanism by which FUS-regulated pre-mRNA processing can impact a significant number of targets important to neurodegeneration.
Do religious differences matter? An analysis in India

Purpose – This paper aims to analyze the relationship between religious differences (i.e. religious diversity and tolerance diversity), on the one hand, and dysfunctional intergroup conflicts, on the other.Design/methodology/approach – A quantitative research design is used, through which the paper examines 47 public schools in India.Findings – Religious diversity, that is, the distribution of heterogeneous religious affiliations in an organization, is unrelated to dysfunctional intergroup conflicts. By contrast, tolerance diversity, that is, the heterogeneity of organizational members' beliefs regarding the question of how strictly religious commandments should be followed, is positively related to dysfunctional conflicts.Research limitations/implications – The results of this study are limited to public organizations in the Indian context.Practical implications – Since religious diversity is not connected to intergroup conflicts, fostering religious diversity in organizations could render the societal n.
Intellectual Property Protection of Sequential Circuits Using Digital Watermarking

The aspect of intellectual property protection (IPP) has created a deep concern in recent years which has forced the IP owners to incorporate some sort of signature or watermark in their designs. In this regard, Oliveira have suggested a technique of modifying the state transition graph (STG) of sequential circuits incorporating digital watermark in such a way that it is impossible for anyone to even imagine that the watermark exists in the design. Moreover, it assists the IP owner to prove in a court of law his ownership in case of suspected piracy of the design. We have used this technique on a 5-bit sequence detector with a 3-bit signature that helps to detect the piracy. The comparison of simulation results of both watermarked and non-watermarked circuit, using ModelSim simulator, indicate no change in the maximum operating frequency of the circuit. This is the outcome of our work and has not been reported in the literature earlier. Also, the test results of piracy detection circuit confirm that only one output of this detection circuit can monitor the internal state of the sequential machine, thereby detecting the piracy. The details of these are presented in this paper
Islam at Universities in England : Meeting the Needs and Investing in the Future

Here we are reproducing Executive Summary of the report submitted to Mr Bill Rammell, MP, Minister of State for Lifelong Learning, Further and Higher Education, UK, on 10th April 2007 by Dr Ataullah Siddiqui, Director, Markfield Institute of Higher Education, Leicester, UK. *
Dynamic Source Routing Protocol for Ad Hoc Networks Using the Concept Intelligent Agent Fuzzy Logic

This paper presents a Dynamic Source Routing Protocol using Self Healing and Optimizing Routing Technique based on fuzzy logic concepts. The paths generated by conventional dynamical source routing protocol deviate far from the optimal paths because of the lack of knowledge about the global topology and the mobility of nodes. Routing optimality affects the network performance, especially when the load is high. Longer route consumes more bandwidth, power and is more prone to disconnections. Self Healing and Optimizing Routing Technique (SHORT) is a technique that monitors the route and tries to shorten it, if a short-cut is available. The proposed fuzzy logic method is evaluated and compared with conventional method using GloMoSim.
Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A

Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.
More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes

Nosocomial acquisition of Clostridium difficile is well documented, yet recent studies have highlighted the importance of community acquired infections and identified community associated reservoirs for this pathogen. Multiple studies have implicated companion pets and farm animals as possible sources of community acquired C. difficile infections in humans. To explore the potential role of pet dogs in human C. difficile infections we systematically collected canine fecal samples (n = 197) in Flagstaff, AZ. Additionally, nineteen fecal samples were collected at a local veterinary clinic from diarrheic dogs. We used these combined samples to investigate important questions regarding C. difficile colonization in pet canines: 1) What is the prevalence and diversity of C. difficile in this companion pet population, and 2) Do C. difficile isolates collected from canines genetically overlap with isolates that cause disease in humans? We used a two-step sequence typing approach, including multilocus sequence typing to determine the overall genetic diversity of C. difficile present in Flagstaff canines, and whole-genome sequencing to assess the fine-scale diversity patterns within identical multilocus sequence types from isolates obtained within and among multiple canine hosts. We detected C. difficile in 17% of the canine fecal samples with 10% containing toxigenic strains that are known to cause human disease. Sequencing analyses revealed similar genotypes in dogs and humans. These findings suggest that companion pets are a potential source of community acquired C. difficile infections in humans.
Quality of life, self-stigma, and hope in schizophrenia spectrum disorders: a cross-sectional study

Goals The aim of this study was to explore the quality of life, self-stigma, personality traits, and hope in patients with schizophrenia spectrum disorders. Patients and methods A total of 52 outpatients participated in this cross-sectional study. The attending psychiatrist assessed each patient with Mini International Neuropsychiatric Interview (MINI). The patients then completed Quality of Life Satisfaction and Enjoyment Questionnaire (Q-LES-Q), Internalized Stigma of Mental Illness (ISMI) Scale, Temperament and Character Inventory – Revised (TCI-R), Adult Dispositional Hope Scale (ADHS), Drug Attitude Inventory 10 (DAI-10), and Liebowitz Social Anxiety Scale (LSAS)-Self-report. The psychiatrist evaluated Clinical Global Impression Severity – the objective version (objCGI-S), and the patients completed the Clinical Global Impression Severity – the subjective version (subjCGI-S). Each participant also completed Beck Depression Inventory-II (BDI-II), and Beck Anxiety Inventory (BAI). Results The quality of life was significantly higher in employed patients and individuals with higher hope, self-directedness (SD), and persistence (PS). The quality of life was lower among patients with higher number of psychiatric hospitalizations, those with higher severity of the disorder, and individuals who were taking higher doses of antipsychotics. Patients with more pronounced symptoms of depression, anxiety, and social anxiety had a lower quality of life. Finally, the quality of life was lower among individuals with higher harm avoidance (HA) and self-stigmatization (ISMI). Backward stepwise regression was applied to identify the most significant factors connected to self-stigma. The regression analysis showed that occupation, level of depression (BDI-II), attitude to using medication (DAI-10), social anxiety (LSAS), and antipsychotic index were the most relevant factors associated with lower quality of life. Conclusion Detection of the quality of life in the context of personality traits, hope, self-stigma, and demographic and clinical factors may be an important part of the assessment of the patient with schizophrenia.
PRIMARY ATTRACTION OF ZPS LATZDENS (LECONTE) AND HYLASTES GZtACZLZS LECONTE (COLEOPTERA: SCOLYTIDAE) TO HIGH-GIRDLED LODGEPOLE PINE, PZNUS CONTORTA VAR. LATZFOZJA ENGELMANN

Em. 118: 85-88 (1986) In the absence of secondary attraction, 2 species of Scolytidae, Zps l&dens (L.eConte) and Hylastes gracilis LeConte, showed significant preference while in flight for highgirdled over non-girdled lodgepole pines, Pinus contorta var. Zutifoliu Engelmann. In contrast, beetles in 2 genera of Elateridae, Ampedus and Ctenicera, showed significant preference for non-girdled over high-girdled lodgepole pines. Beetles in 12 other families, as well as other scolytids and elaterids, did not show any significant preference or aversion to high-girdled trees. This is the first clear demonstration of primary attraction for a North American Ips species and the second for an Hylastes species.
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or ‘miRNA sponges’ that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge.
Face Recognition using independent component analysis of GaborJet (GaborJet-ICA)

In this paper a new face recognition technique based on Independent Component Analysis of GaborJet (GaborJet-ICA) is proposed. Existing face recognition systems using Gabor wavelets convolve a whole face image with a set of 40 Gabor wavelets. We have derived Gabor feature vector from facial landmarks (fiducial points) known as GaborJets. We then transformed this GaborJet feature vector into the basis space of PCA and ICA. A series of experiments based on ORL database were then performed to evaluate the performance. During our experiments we varied number of subspace dimensions from 2 to 40 and numbers of independent components derived were in the range 1 to 200. As literature on PCA and ICA subject is contradictory, we compared the performance for GaborJet-PCA and GaborJet-ICA. The results show maximum accuracy of 82.25% and 84.5% for GaborJet-PCA and GaborJet-ICA respectively. This proves that the difference in performance between ICA and PCA is of 2.25%, which is insignificant.
Run length control using parallel spectral method

Distributed and parallel simulation has been a popular research topic in recent years. The research has primarily concentrated on correctness and speedup of distributed simulation. The statistical output analysis that is an essential part of simulating stochastic systems has attained only small attention. Parallel simulation is often mentioned as an attractive alternative for steady-state simulations. However, empirical results are not widely reported. In this study we present results of the parallel spectral method. The results are based on 12 simulation models executed in simulated parallel environment and on measured executing times and message passing delays.
Women build games, seriously

Recruitment of students to Computer Science has been a major focus of effort for educators since the dot-com bust in 2001. Two largely disparate themes in these efforts are women and games. There have been numerous efforts to broaden participation in computer science by attracting women to the field. At the same time, games are increasingly used to attract new students. Our interest lies at the intersection of these methods. We began using game design/development projects in our software engineering course, CS121, in 2002. The game focus was extremely successful with many of our students. But a nagging minority of students objected to building games, and women tend to be overrepresented in that group. So while are awed by the power of games to engage and motivate many of our students, we need to ask: Do games in our curriculum reinforce gender stereotypes of Computer Science? Do they foster development of the so-called "Geek mythology? "[7] In short, must we choose: women or games? We argue the answer is no. While traditional game projects may disenfranchise women, our experience shows that serious game projects both attract and engage them. This paper describes our results.
Price Hikes in US Agricultural Commodity Futures Markets: An Empirical Efficiency Test

This paper evaluates how efficient US futures prices have predicted future spot prices since 2006. It uses cointegration and causality methods to assess the efficiency of US commodity futures markets. The cointegration between the spot and futures price is a necessary condition for our definition of market efficiency. It ensures that there exists a long-run equilibrium relationship between the two prices (Ali and Gupta 2011). Causality assists in examining the existence of lead or lag relationships between futures and spot prices in order to make inferences on the directions (unidirectional or bidirectional) of information flow.
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings

Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory algorithms have been proposed. The rapid growing of data that are processed routinely, such as in bioinformatics, requires a large amount of main memory, and this fact has motivated the development of algorithms, to compute the BWT, that work almost entirely in external memory. On the other hand, the related problem of computing the Longest Common Prefix (LCP) array is often instrumental in several algorithms on collection of strings, such as those that compute the suffix-prefix overlap among strings, which is an essential step for many genome assembly algorithms. The best current lightweight approach to compute BWT and LCP array on a set of $m$ strings, each one $k$ characters long, has I/O complexity that is $O(mk^2 \log |\Sigma|)$ (where $|\Sigma|$ is the size of the alphabet), thus it is not optimal. In this paper we propose a novel approach to build BWT and LCP array (simultaneously) with $O(kmL(\log k +\log \sigma))$ I/O complexity, where $L$ is the length of longest substring that appears at least twice in the input strings.
Robust language pair-independent sub-tree alignment

Data-driven approaches to machine translation (MT) achieve state-of-the-art results. Many syntax-aware approaches, such as Example-Based MT and Data-Oriented Translation, make use of tree pairs aligned at sub-sentential level. Obtaining sub-sentential alignments manually is time-consuming and error-prone, and requires expert knowledge of both source and target languages. We propose a novel, language pair-independent algorithm which automatically induces alignments between phrase-structure trees. We evaluate the alignments themselves against a manually aligned gold standard, and perform an extrinsic evaluation by using the aligned data to train and test a DOT system. Our results show that translation accuracy is comparable to that of the same translation system trained on manually aligned data, and coverage improves.
Non-Intrusive Planning the Roadside Infrastructure for Vehicular Networks

In this article, we describe a strategy for planning the roadside infrastructure for vehicular networks based on the global behavior of drivers. Instead of relying on the trajectories of all vehicles, our proposal relies on the migration ratios of vehicles between urban regions in order to infer the better locations for deploying the roadside units. By relying on the global behavior of drivers, our strategy does not incur in privacy concerns. Given a set of α available roadside units, our goal is to select those α-better locations for placing the roadside units in order to maximize the number of distinct vehicles experiencing at least one V2I contact opportunity. Our results demonstrate that full knowledge of the vehicle trajectories are not mandatory for achieving a close-to-optimal deployment performance when we intend to maximize the number of distinct vehicles experiencing (at least one) V2I contact opportunities.
Facial landmark localization in depth images using Supervised Descent Method

This paper proposes using the state of the art 2D facial landmark localization method, Supervised Descent Method (SDM), for facial landmark localization in 3D depth images. The proposed method was evaluated on frontal faces with no occlusion from the Bosphorus 3D Face Database. In the experiments, in which 2D features were used to train SDM, the proposed approach achieved state-of-the-art performance for several landmarks over the currently available 3D facial landmark localization methods.
Evaluation of Direct Plane Fitting for Depth and Parameter Estimation

Recently, a model-based depth estimation technique has been proposed, which estimates surface model parameters by means of Hooke-Jeeves optimization. Assuming a parametric surface model, the parameters best explaining the perspective changes of the surface between different views are estimated. This constitutes a fitting of models directly into stereo images, which is in contrast to the usual approach of fitting models into pre-processed disparity data. In this paper, we conduct a comparison of the image fitting based on Hooke-Jeeves, an image fitting based on gradient descent and a disparity fitting based on RANSAC. We show that the image fitting based on Hooke-Jeeves as well as the image fitting based on gradient descent are sensitive to occlusion. However, we also propose a simple pre-processing that eliminates this problem. Our experiments revealed that all three approaches have a similar depth accuracy. However, tests under challenging conditions show that the fitting based on Hooke-Jeeves is more robust than RANSAC and gradient descent.
Definition of the Role of Tyrosine Residues of the Common β Subunit Regulating Multiple Signaling Pathways of Granulocyte-Macrophage Colony-Stimulating Factor Receptor

ABSTRACT Granulocyte-macrophage colony-stimulating factor (GM-CSF) induces various functions, including the proliferation and differentiation of a broad range of hematopoietic cells. We previously reported that at least two distinct pathways are involved in human GM-CSF receptor signaling; both require the box 1 region of the common β subunit (βc). This region is essential for the activation of JAK2, which is necessary for all the biological functions of GM-CSF. The activation of JAK2 by GM-CSF leads to rapid tyrosine phosphorylation of cellular proteins, including the βc. However, the significance of βc phosphorylation with regard to the regulation of signaling molecules and the expression of GM-CSF functions is less well understood. Here we investigated the role of the cytoplasmic tyrosine residues of the βc by using a series of βc mutants expressed in murine BA/F3 cells. A mutant βc with all eight cytoplasmic tyrosines converted to phenylalanine (Fall) activated JAK2 but not SHP-2, MAPK cascades, STAT5, or the c-fos promoter in BA/F3 cells, and it did not effectively induce proliferation. Adding back each tyrosine to Fall revealed that Tyr577, Tyr612, and Tyr695 are involved in the activation of SHP-2, MAPK cascades, and c-fos transcription, while every tyrosine, particularly Tyr612, Tyr695, Tyr750, and Tyr806, facilitated STAT5 activation. Impaired growth was also restored, at least partly, by any of the tyrosines. These results provide evidence that βc tyrosines possess distinct yet overlapping functions in activating multiple signaling pathways induced by GM-CSF.