Miracle-dz/UniFAR-FTUs huggingface dataset:
Pitx2-microRNA pathway that delimits sinoatrial node development and inhibits predisposition to atrial fibrillation

Significance Atrial Fibrillation (AF) is the most common sustained cardiac arrhythmia in the human population. It is critical to elucidate the molecular mechanisms underlying AF, given that the prevalence of AF is expected to dramatically increase as the human population ages. We identified a microRNA (miR)-regulated genetic pathway that delimits sinoatrial node development and inhibits AF. To our knowledge, our data are the first genetic evidence showing that miR deletion results in AF predisposition. Moreover, to our knowledge, our data are the first demonstration that sinoatrial node regulatory genes are regulated by miRs. Our findings suggest attractive therapeutic targets to treat AF given that miR-based therapeutics are feasible using miR antagonists and mimics. The molecular mechanisms underlying atrial fibrillation, the most common sustained cardiac arrhythmia, remain poorly understood. Genome-wide association studies uncovered a major atrial fibrillation susceptibility locus on human chromosome 4q25 in close proximity to the paired-like homeodomain transcription factor 2 (Pitx2) homeobox gene. Pitx2, a target of the left-sided Nodal signaling pathway that initiates early in development, represses the sinoatrial node program and pacemaker activity on the left side. To address the mechanisms underlying this repressive activity, we hypothesized that Pitx2 regulates microRNAs (miRs) to repress the sinoatrial node genetic program. MiRs are small noncoding RNAs that regulate gene expression posttranscriptionally. Using an integrated genomic approach, we discovered that Pitx2 positively regulates miR-17-92 and miR-106b-25. Intracardiac electrical stimulation revealed that both miR-17-92 and miR-106b-25 deficient mice exhibit pacing-induced atrial fibrillation. Furthermore electrocardiogram telemetry revealed that mice with miR-17-92 cardiac-specific inactivation develop prolonged PR intervals whereas mice with miR-17-92 cardiac-specific inactivation and miR-106b-25 heterozygosity develop sinoatrial node dysfunction. Both arrhythmias are risk factors for atrial fibrillation in humans. Importantly, miR-17-92 and miR-106b-25 directly repress genes, such as Shox2 and Tbx3, that are required for sinoatrial node development. Together, to our knowledge, these findings provide the first genetic evidence for an miR loss-of-function that increases atrial fibrillation susceptibility.
Controlled matching game for user association and resource allocation in multi-rate WLANs?

The deployment of IEEE 802.11 based WLANs in populated areas is such that many mobile terminals are covered by several Access Points (APs). These mobiles have the possibility to associate to the AP with the strongest signal (best-RSSI association scheme). This can lead to poor performances and overloaded APs. Moreover, the well known anomaly in the protocol at the MAC layer may also lead to very unpredictable performances and affect the system throughput due to the presence of heterogeneous data rate nodes and the shared nature of the 802.11 medium. The goal of this paper is to propose an alternative approach for the association. We model the joint resource allocation and mobile user association as a matching game with complementarities, peer effects and selfish players. We focus on the throughput fairness allocation induced by the saturated regime with equal packet sizes. We propose a novel three-stages mechanism for the modeling and control of load balancing, resource allocation and user association. We show that the proposed mechanism can greatly improve the efficiency of 802.11 with heterogeneous nodes and reduce the negative impact of peer effects such as the anomaly in IEEE 802.11.
A Nonlinear $M$-Estimation Approach to Robust Asynchronous Multiuser Detection in Non-Gaussian Noise

A nonlinear M-estimation approach is proposed to solve the multiuser detection problem in asynchronous code-division multiple-access (CDMA) systems where the ambient noise is impulsive and the delays are not known. We treat the unknown delays as nuisance parameters and the transmitted symbols as parameters of interest. We also analyze the asymptotic performance of the proposed estimator and propose suboptimal but computationally efficient procedures for solving the nonlinear optimization function. Simulation results show considerable improvements over the conventional approaches
Human Liver Methionine Cycle: MAT1A and GNMT Gene Resequencing, Functional Genomics, and Hepatic Genotype-Phenotype Correlation

The “methionine cycle” plays a critical role in the regulation of concentrations of (S)-adenosylmethionine (AdoMet), the major biological methyl donor. We set out to study sequence variation in genes encoding the enzyme that synthesizes AdoMet in liver, methionine adenosyltransferase 1A (MAT1A) and the major hepatic AdoMet using enzyme, glycine N-methyltransferase (GNMT), as well as functional implications of that variation. We resequenced MAT1A and GNMT using DNA from 288 subjects of three ethnicities, followed by functional genomic and genotype-phenotype correlation studies performed with 268 hepatic biopsy samples. We identified 44 and 42 polymorphisms in MAT1A and GNMT, respectively. Quantitative Western blot analyses for the human liver samples showed large individual variation in MAT1A and GNMT protein expression. Genotype-phenotype correlation identified two genotyped single-nucleotide polymorphisms (SNPs), reference SNP (rs) 9471976 (corrected p = 3.9 × 10−10) and rs11752813 (corrected p = 1.8 × 10−5), and 42 imputed SNPs surrounding GNMT that were significantly associated with hepatic GNMT protein levels (corrected p values < 0.01). Reporter gene studies showed that variant alleles for both genotyped SNPs resulted in decreased transcriptional activity. Correlation analyses among hepatic protein levels for methionine cycle enzymes showed significant correlations between GNMT and MAT1A (p = 1.5 × 10−3) and between GNMT and betaine homocysteine methyltransferase (p = 1.6 × 10−7). Our discovery of SNPs that are highly associated with hepatic GNMT protein expression as well as the “coordinate regulation” of methionine cycle enzyme protein levels provide novel insight into the regulation of this important human liver biochemical pathway.
An analytical model and an optimal scheduling heuristic for collective resource management

We study the problem of collective resource management. We first introduce the problem through real-world examples. Then we generalize the problem and build an analytical model using queuing theory. Based on this model, we evaluate the expected average waiting time of tasks. We present data from simulations, and compare the expected average waiting time from theoretical calculations to that from our experiments. We propose an optimal task scheduling heuristic. We conclude with a brief discussion of our future research plans.
Automated segmentation of medial temporal lobe subregions on in vivo T1‐weighted MRI in early stages of Alzheimer's disease

Medial temporal lobe (MTL) substructures are the earliest regions affected by neurofibrillary tangle pathology—and thus are promising biomarkers for Alzheimer's disease (AD). However, automatic segmentation of the MTL using only T1‐weighted (T1w) magnetic resonance imaging (MRI) is challenging due to the large anatomical variability of the MTL cortex and the confound of the dura mater, which is commonly segmented as gray matter by state‐of‐the‐art algorithms because they have similar intensity in T1w MRI. To address these challenges, we developed a novel atlas set, consisting of 15 cognitively normal older adults and 14 patients with mild cognitive impairment with a label explicitly assigned to the dura, that can be used by the multiatlas automated pipeline (Automatic Segmentation of Hippocampal Subfields [ASHS‐T1]) for the segmentation of MTL subregions, including anterior/posterior hippocampus, entorhinal cortex (ERC), Brodmann areas (BA) 35 and 36, and parahippocampal cortex on T1w MRI. Cross‐validation experiments indicated good segmentation accuracy of ASHS‐T1 and that the dura can be reliably separated from the cortex (6.5% mislabeled as gray matter). Conversely, FreeSurfer segmented majority of the dura mater (62.4%) as gray matter and the degree of dura mislabeling decreased with increasing disease severity. To evaluate its clinical utility, we applied the pipeline to T1w images of 663 ADNI subjects and significant volume/thickness loss is observed in BA35, ERC, and posterior hippocampus in early prodromal AD and all subregions at later stages. As such, the publicly available new atlas and ASHS‐T1 could have important utility in the early diagnosis and monitoring of AD and enhancing brain‐behavior studies of these regions.
LDB: Localization with Directional Beacons for Sparse 3D Underwater Acoustic Sensor Networks

In this paper, we propose a novel distributed localization scheme LDB, a 3D localization scheme with directional beacons for Underwater Acoustic Sensor Networks (UWA-SNs). LDB localizes sensor nodes using an Autonomous Underwater Vehicle (AUV) as a mobile beacon sender. Mounted with a directional transceiver which creates conical shaped directional acoustic beam, the AUV patrols over the 3D deployment volume with predefined trajectory sending beacons with constant interval towards the sensor nodes. By listening two or more beacons sent from the AUV, the nodes can localize themselves silently. Through theoretical analysis, we provide the upper bound of the estimation error of the scheme. We also evaluate the scheme by simulations and the results show that our scheme can achieve a high localization accuracy, even in sparse networks.
Brane cosmologies without orbifolds

We study the dynamics of branes in configurations where 1) the brane is the edge of a single anti-de Sitter (AdS) space and 2) the brane is the surface of a vacuum bubble expanding into a Schwarzschild or AdS-Schwarzschild bulk. In both cases we find solutions that resemble the standard Robertson-Walker cosmologies although in the latter, the evolution can be controlled by a mass parameter in the bulk metric. We also include a term in the brane action for the scalar curvature. This term adds a contribution to the low energy theory of gravity which does not need to affect the cosmology but which is necessary for the surface of the vacuum bubble to recover four dimensional gravity.
Draft Genome Sequence of the Nonstarter Bacteriocin-Producing Strain Enterococcus mundtii CRL35

ABSTRACT Enterococcus mundtii CRL35 is a bacteriocinogenic strain isolated from an artisanal cheese of northwestern Argentina. Here we report its draft genome sequence, consisting of 82 contigs. In silico genomic analysis of biotechnological properties was performed to determine the potential of this microorganism to be used in a food model system.
Voxel carving for specular surfaces

We present an novel algorithm that reconstructs voxels of a general 3D specular surface from multiple images of a calibrated camera. A calibrated scene (i.e. points whose 3D coordinates are known) is reflected by the unknown specular surface onto the image plane of the camera. For every viewpoint, surface normals are associated to the voxels traversed by each projection ray formed by the reflection of a scene point. A decision process then discards voxels whose associated surface normals are not consistent with one another. The output of the algorithm is a collection of voxels and surface normals in 3D space, whose quality and size depend on user-set thresholds. The method has been tested on synthetic and real images. Visual and quantified experimental results are presented.
Chess State

Chess detection algorithm is an implementation capable of recognizing chess board, locate the squares and detect chess pieces from an image. This algorithm will work for a couple of viewing angles between 30 to 60 degrees. This is constructed using image processing techniques. Firstly the chess board is segmented from the input image, and then Hough’s transform is used to detect crosses. Next, each square, with some vicinity around it, is extracted, parsed and checked to see if it contains chess piece. Then in each of the segments, pieces in the vicinity margin are removed, leaving only the chess piece of the main square. The test piece is oriented vertically and compared with the pre-defined training set. The area score is later calculated by taking difference of scaled training pieces and the test piece. The one resulting in the lowest score is the best matching piece. Keywords—chess detection; chess piece recognition
Automatic Prediction of Perceived Traits Using Visual Cues under Varied Situational Context

Automatic assessment of human personality traits is a non-trivial problem, especially when perception is marked over a fairly short duration of time. In this study, thin slices of behavioral data are analyzed. Perceived physical and behavioral traits are assessed by external observers (raters). Along with the big-five personality trait model, four new traits are introduced and assessed in this work. The relationship between various traits is investigated to obtain a better understanding of observer perception and assessment. Perception change is also considered when participants interact with several virtual characters each with a distinct emotional style. Encapsulating these observations and analysis, an automated system is proposed by firstly computing low level visual features. Using these features a separate model is trained for each trait and performance is evaluated. Further, a weighted model based on rater credibility is proposed to address observer biases. Experimental results indicate that a weighted model show major improvement for automatic prediction of perceived physical and behavioral traits.
Rust fungal effectors mimic host transit peptides to translocate into chloroplasts

Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane-rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified CTP1 (chloroplast-targeted protein 1), a candidate effector from the poplar leaf rust fungus Melampsora larici-populina that carries a predicted transit peptide and accumulates in chloroplasts. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts, and is cleaved after translocation. CTP1 is part of a Melampsora-specific family of polymorphic secreted proteins whose members translocate and are processed in chloroplasts in a N-terminal signal-dependent manner. Our findings reveal that fungi have evolved effector proteins that mimic plant-specific sorting signals to traffic within plant cells.
RESPIRATORY COMPLAINTS AND SPIROMETRIC PARAMETERS IN TILE AND CERAMIC FACTORY WORKERS

Background: Respiratory disorders are among the most common occupational diseases. Tile and ceramic industry is quite popular in Iran and workers in this industry are exposed to harmful dust particles affecting their respiratory system. Materials and Methods: This study was conducted in a tile and ceramic factory. The study group consisted of factory workers of the production units; whereas, the control group included the executive employees of the factory. A questionnaire was designed covering all the required data. There were a total of 411 workers. After considering the exclusion criteria, 243 workers in the study group were compared with 168 controls in terms of their respiratory status. Results: Respiratory complaints were significantly higher in the study group compared to controls (p=0.023). Frequency of abnormal spirometric findings was significantly higher in the study group (p<0.001). A significant correlation was found between the occupational exposure to tile and ceramic dust and abnormal spirometric findings after adjusting for age, duration of employment and smoking habits (p<0.05). Conclusion: Our study results demonstrated that occupational exposure to ceramic and tile dust can harm workers’ respiratory system. Therefore, it is recommended to diminish workers’ exposure to tile dust by proper implementation of respiratory protection programs. Also, filling out the standard respiratory questionnaire and performing the pulmonary function tests are advised for workers in their periodic examination programs. (Tanaffos 2009; 8(4): 19-25)
Sentiment Analysis in Arabic tweets

Social media platforms such as blogs, social networking sites, content communities and virtual worlds are tremendously becoming one of the most powerful sources for news, markets, industries, and much more. They are a wide platform full of thoughts, emotions, reviews and feedback, which can be used in many aspects. Despite these great avails, and with the increasingly enormous number of Arabic users on the internet, little research has tied these two together in a high and accurate professional manner [1]. This paper deals with Arabic Sentiment Analysis. We developed a framework that makes it possible to analyze Twitter comments or “Tweets” as having positive, negative or neutral sentiments. This can be applied in a wide range of applications ranging from politics to marketing. This framework has many novel aspects such as handling Arabic dialects, Arabizi and emoticons. Also, crowdsourcing was utilized to collect a large dataset of tweets.
X linked complicated spastic paraplegia, MASA syndrome, and X linked hydrocephalus owing to congenital stenosis of the aqueduct of Sylvius: variable expression of the same mutation at Xq28.

Some 20 years ago Robert Lehrke, a psychologist from Minnesota working in a state hospital for the mentally retarded, suggested that genes that determine the major intellectual traits are carried on the X chromosome. ' 2 At that time Lehrke was severely criticised on the grounds that his hypothesis was inherently improbable,3 and that the evidence was meagre and could be interpreted in other ways.4 5 Since then more medical evidence has accumulated to support two of the steps in Lehrke's argument. (1) "The well documented excess of males among the mentally retarded (25-500%o)". Two further studies6 7 have shown that this male excess results from mutations on the X chromosome, using as evidence the excess of affected brothers over affected sisters and calculating this as a gene frequency for X linked forms of mental retardation. (2) "A review of families published at that time with mental retardation showing anX linked pattern ofinheritance-which only numbered 5, together with 5 new families that he had identifed". In the former group three were shown later to have the fragile X syndrome and this
International Journal of High Performance Computing Applications a Lightweight Virtual Machine Monitor for Blue Gene/p a Lightweight Virtual Machine Monitor for Blue Gene/p

In this paper, we present a lightweight, micro-kernel-based virtual machine monitor (VMM) for the Blue Gene/P supercomputer. Our VMM comprises a small m-kernel with virtualization capabilities and, atop, a user-level VMM component that manages virtual Blue Gene/P cores, memory, and interconnects; we also support running native applications directly atop the m-kernel. Our design goal is to enable compatibility to standard operating systems such as Linux on BG/P via virtualization, but to also keep the amount of kernel functionality small enough to facilitate shortening the path to applications and lowering operating system noise. Our prototype implementation successfully virtualizes a Blue Gene/P version of Linux with support for Ethernet-based communication mapped onto Blue Gene/P's collective and torus network devices. Our first experiences and experiments show that our VMM still shows a substantial performance hit, and that support for native application environments is a key requirement towards fully exploiting the capabilities of a supercomputer. Altogether, our approach poses an interesting operating system alternative for supercomputers, providing the convenience of a fully featured commodity software stack, while also promising to deliver the scalability and low latency of an HPC operating system.
Cost of stress urinary incontinence: a claims data analysis.

OBJECTIVES The primary objectives of this research were to: (i) identify and present methodologies for estimating three types of 'cost-of-illness' measures using healthcare and disability claims data -- specifically 'cost of treatment', 'incremental cost of patient', and 'incremental cost of illness'; and (ii) perform a case-study analysis of these cost measures for women treated for stress urinary incontinence (SUI). STUDY DESIGN AND METHODS In this paper, we discuss aspects of cost-of-illness methodologies in the context of SUI. We first distinguish between 'cost of treatment' (i.e. the costs of treating a specific condition), 'incremental cost of patient' (i.e. the additional costs associated with patients with a particular condition, irrespective of any comorbid conditions they may also have), and 'incremental cost of illness' (i.e. the additional costs resulting from a particular illness, as distinct from the costs of other conditions that the patient might have, including conditions which might have caused the illness in question). The latter case is in many ways the most complex to model, requiring controls for related causal conditions. We then applied these three methodologies by analysing the costs associated with SUI. Using data from a large employer claims database (n > 100 000), we estimated a series of regression models that reflected cost of treatment, incremental cost of patient, and incremental cost of illness for SUI. RESULTS The three approaches yielded substantially different results. For many purposes the incremental cost-of-illness model provides the most appropriate results, as it controls for comorbid conditions, as well as patient demographics. On a per capita basis using the incremental cost-of-illness model, patients with SUI had direct costs that were 134% more than those for their controls and indirect costs that were 163% more than those for controls. Estimating costs for the average (i.e. mean) person results in dollar-termed estimates of the costs of SUI. In particular, we found that in 1998, the average direct medical cost of SUI was $US5642 and the indirect workplace cost of SUI was $US4208. CONCLUSIONS Since the various methods yield substantially different results, it is important that the end user of cost-of-illness analyses of claims data have a clear purpose in mind when reporting the cost of the condition of concern. The incremental cost-of-illness measure for claims data has substantial advantages in terms of enhancing our understanding of the specific cost impact of SUI.
Phylogenetic Analysis of West Nile Virus, Nuevo Leon State, Mexico

West Nile virus RNA was detected in brain tissue from a horse that died in June 2003 in Nuevo Leon State, Mexico. Nucleotide sequencing and phylogenetic analysis of the premembrane and envelope genes showed that the virus was most closely related to West Nile virus isolates collected in Texas in 2002.