Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study

Fifty percent of variability in HIV-1 susceptibility is attributable to host genetics. Thus identifying genetic associations is essential to understanding pathogenesis of HIV-1 and important for targeting drug development. To date, however, CCR5 remains the only gene conclusively associated with HIV acquisition. To identify novel host genetic determinants of HIV-1 acquisition, we conducted a genome-wide association study among a high-risk sample of 3,136 injection drug users (IDUs) from the Urban Health Study (UHS). In addition to being IDUs, HIV- controls were frequency-matched to cases on environmental exposures to enhance detection of genetic effects. We tested independent replication in the Women’s Interagency HIV Study (N=2,533). We also examined publicly available gene expression data to link SNPs associated with HIV acquisition to known mechanisms affecting HIV replication/infectivity. Analysis of the UHS nominated eight genetic regions for replication testing. SNP rs4878712 in FRMPD1 met multiple testing correction for independent replication (P=1.38x10-4), although the UHS-WIHS meta-analysis p-value did not reach genome-wide significance (P=4.47x10-7 vs. P<5.0x10-8) Gene expression analyses provided promising biological support for the protective G allele at rs4878712 lowering risk of HIV: (1) the G allele was associated with reduced expression of FBXO10 (r=-0.49, P=6.9x10-5); (2) FBXO10 is a component of the Skp1-Cul1-F-box protein E3 ubiquitin ligase complex that targets Bcl-2 protein for degradation; (3) lower FBXO10 expression was associated with higher BCL2 expression (r=-0.49, P=8x10-5); (4) higher basal levels of Bcl-2 are known to reduce HIV replication and infectivity in human and animal in vitro studies. These results suggest new potential biological pathways by which host genetics affect susceptibility to HIV upon exposure for follow-up in subsequent studies.
Mechatronics modeling of a branching tendon-driven robot

This paper presents the mechatronic design of a new tendon-driven manipulator. The new design is capable of many dexterous grasping and manipulation tasks. The principle design is to use the new branching tendons to control bones which are found in musculoskeletal systems. In branching tendons, multiple tendons are connected at a point. Reducing the number of actuators in the branching tendons makes a lightweight arm. The kinematic and the dynamic analysis of the under-actuated manipulator are carried out in a mechatronic simulation. A three link manipulator simulated on contact problem with the disturbance force. The tension in branched tendon is investigated to show the ability of back bone manipulators including the pretension.
Improvement of utterance clustering by using employees' sound and area data

In this paper, we propose to use staying area data toward the estimation of serving time for customers. To classify utterances enables us to estimate conversation types between speakers. However, its performance becomes lower in real environments. We propose a method using area data with sound data to solve this problem. We also propose a method to estimate the conversation types using the decision trees. They were tested with the data recorded in a Japanese restaurant. In the experiment to classify utterances, the proposed method performed better than the method using only sound data. In the experiment to estimate the conversation types, we succeeded to recover 70% of the mis-classified conversations using both of sound and area data.
Two-Phase Sampling and Weighting

Non-response or other missingness may be occurred in various forms. In this paper, we consider unit non-response, and hence make attempts for adjustments by appropriate weighting. Our special exercise is concerned a two-phase sampling case so that, first, a large sample survey has been conducted with a rather general questionnaire. In the end of this face-to-face contact the interviewer has asked whether a respondent is willing to participate in the second step survey with a very detailed questionnaire concentrating on one of the themes of this initial survey. This procedure leads to the three missingness mechanisms. First there is nonresponse to the initial survey, next there is missingness due to voluntariness of the respondents to participate in the second survey, and finally, it is expected that some more missingness occurs although these volunteers say to be willing to participate in the second survey. Our problem is now how to weight as correctly as possible the second survey respondents so that the results from this survey are reasonable. This paper first analyses missingness differences in these 3 steps using a Finnish data set, and then suggests a weighting technique that uses both the classic methods, that is, post-stratification and calibration, but our main interest lies in a redesign of the response propensity modelling method.
SMSP jamming identification based on Matched Signal transform

In this paper, a new algorithm of jamming recognition based on Matched Signal transform (MST) is proposed according to the characteristic of the Smeared Spectrum (SMSP) jamming. The analytical representations of SMSP jamming in the time domain is derived and the difference that the jamming has a different frequency modulation (FM) rate from the radar signal is studied, then a special filter is designed to identify the jamming type. The simulation shows that this method is feasible and has a fairly high correct identification ratio.
The philosophy of Lisp

We consider here the importance of an overall systems viewpoint in avoiding computer-related risks. According to Webster's, a system is a regularly interacting or interdependent group of items forming a unified whole. In computer systems, one person's components may be another person's system, and one person's system may in turn be one of another person's components. That is, each layer of abstraction may have it own concept of a system. We speak of a memory system, a multiprocessor system, a distributed system, a multisystem system, a networked system, and so on. A system design can most effectively be considered as a unified whole when it is possible to analyze the interdependent subsystems individually and then to evaluate, reason about, and test the behavior of the entire system based on the interactions among the subsystems. This is particularly true of distributed systems that mask the presence of distributed storage, processing, and control. At each layer of abstraction, it is desirable to design (sub)systems that are context-free, but in reality there may be subtle interactions that must be accommodated—particularly those involving the operating environment.
A New Method for Soccer Video Summarizing Based on Shot Detection , Classification and Finite State Machine

This paper presents a novel method for the automatic extraction of summaries in soccer video based on shot detection, shot classification and FSM. Our method consists of four stages (Figure 1): playfield segmentation, shot detection, shot classification, soccer video word extraction and finding out the appropriate sub-words which present summaries using the Finite State Machine (FSM) and domain knowledge. The segmentation of the playfield is a preprocessing step; we make use of it in the next stages. In shots detection, we use the Discrete Cosine Transform MultiResolution (DCT-MR) to extract the different types of shot transition. A statistical method is used to classify shots in three major classes (long shot, medium shot and close-up shot). Then, we extract the word presenting the soccer video using shot detection and classification. Finally, we look for sub-words that can be function as summaries (or highlights) using the Finite State Machine (FSM). Experimental results demonstrate the effectiveness and efficiency of the proposed method.
Digital Histology: An Interactive CD Atlas with Review Text

treatment of the circuitry that allows for complex calculations like ocular pursuits is fascinating. Somehow the brain's circuitry decomposes information into constituents (for example, vision into color, movement, contrast, and texture), then reassembles salient information, and miraculously produces a coherent experience. From this explanation, one question arose: although sound travels slower than light, the fusion of sensory information from the ear and eye feels seamless. Berthoz explains that sight and sound jibe because the brain introduces a delay in visual stimuli processing. An interesting example to illustrate how a coherent experience gets disrupted is in somatoparaphrenia. Specifically, caloric vestibular stimulation by injecting warm water into the ear of a patient causes denial of his own limbs. For example, one patient denied that her left arm was her own. She said: "This is my mother's arm. " It is this combination of choice examples that illustrate important concepts underlying our current understanding of movement that makes this book a thoughtprovoking read. Short of describing each topic in overbearing detail, the summary is that the brain not only formulates hypotheses and tests them using the sensory receptors, but evolution made the brain a machine for predicting. In sum to learn more about movement, read this book.
Herd: A Scalable, Traffic Analysis Resistant Anonymity Network for VoIP Systems

Effectively anonymizing Voice-over-IP (VoIP) calls requires a scalable anonymity network that is resilient to traffic analysis and has sufficiently low delay for high-quality voice calls. The popular Tor anonymity network, for instance, is not designed for the former and cannot typically achieve the latter. In this paper, we present the design, implementation, and experimental evaluation of Herd, an anonymity network where a set of dedicated, fully interconnected cloud-based proxies yield suitably low-delay circuits, while untrusted superpeers add scalability. Herd provides caller/callee anonymity among the clients within a trust zone (e.g., jurisdiction) and under a strong adversarial model. Simulations based on a trace of 370 million mobile phone calls among 10.8 million users indicate that Herd achieves anonymity among millions of clients with low bandwidth requirements, and that superpeers decrease the bandwidth and CPU requirements of the trusted infrastructure by an order of magnitude. Finally, experiments using a prototype deployment on Amazon EC2 show that Herd has a delay low enough for high-quality calls in most cases.
Implementation of 6-Port 3D transformer in injection-locked frequency divider

This paper proposes a 6-port 3-dimensional (3-D) transformer used to improve the performance of injection-locked frequency divider (ILFD). The aim of the 3-D transformer is to reduce chip size and to reduce power consumption. The CMOS LC-tank ILFD is implemented using the direct injection nMOS between the differential outputs of an nMOS-core cross-coupled VCO. At the supply voltage of 0.6 V, the free-running frequency of ILFD is tunable from 4.81 GHz to 5.3 GHz. At the incident power of 0 dBm and VDD = 0.6 V, the total locking range is about 3 GHz, from the incident frequency 8.9 to 11.9 GHz for the ILFD in the divide-by-2 mode. The core power consumption is 1.02 mW. The die area is 0.394 × 0.623 mm2.
Optical spectroscopy and photometry of the neutron star RX J1856.5{3754 ?

We present spectroscopy and imaging with the Very Large Telescope (VLT) of the neutron star RX J1856.5-3754. Little is known about the nature of this source other than that it is a nearby hot neutron star. Our VLT spectrum does not show any strong emission or absorption features. With considerable care to photometric calibration, we obtain photometric measurements over the optical and ultra-violet (UV) using our VLT observations and a detailed analysis of archival Hubble Space Telescope data. We find that the entire optical to UV spectral energy distribution is well described by a slightly reddened Rayleigh-Jeans tail (f_λ = (2.96 ± 0.06) x 10^(-19) (λ/5000˚A)^(−4) 10^((−0.4)(0.12±0.05)(A_λ/A_V −1.138)) erg s^(−1) cm^(−2) ˚A^(−1), where A_λ/A_V, where is the reddening curve; implied V = 25.58 ± 0.02). The reddening is consistent with the interstellar absorption inferred from X-ray spectroscopy. The simplest explanation for this Rayleigh-Jeans emission is that the optical-UV radiation arises from thermal emission from the surface of the neutron star. The high degree to which the data conform to the Rayleigh-Jeans tail significantly limits contributions from other sources of emission. In particular, our observations are inconsistent with the presence of an accretion disk and also strongly constrain the amount of magnetospheric emission from this enigmatic neutron star.
Ontology-based Approach for Interoperability of Digital Collections

This paper presents solutions and lessons learned in the FinnONTO project carried out in Finland in 2003–2007. The paper focuses on three aspects of interoperability of digital collections. First, transforming thesauri to ontologies. Second, publishing ontologies for the use of indexers and content providers. Third, ontology based methods for improving the end user access to digital collections. The first aspect is analysed through case studies done with Finnish thesauri. The second is discussed by presenting the ONKI ontology server. The last aspect is demonstrated in the scope of the semantic portal CultureSampo for publishing cultural heritrage on the Semantic Web.
Research Resource Management for * Thai Language Processing Service

This paper presents the research on the Development of Resources on Network for Natural Language Processing Research. The goal of this project has been the study, design and implementation of Research Resource Management for Thai Language Processing Service. The service consists of Knowledge Sources of Thai language, computational linguistic throughout software tools for mutual benefits. The service is also aimed to provide language processing via internet, such as automatically indexing, automatically clustering and intelligent search engine for Thai text. Since information systems are changing to be very large set of data, complex data types including multimedia types and heterogeneous system, research resource management for Thai language processing service is necessary. To meet the next generation of Thai language Processing applications and information system, research resource management is implemented based on PHASME application– oriented service functions and AHYDS (Advanced Hypermedia Delivery System). At the current state, the Linguistic Knowledge & Tools, and Thai language processing have been developed. The output of some applications will be kept in the Extended Binary Graph data structure of the PHASME engine.
Periodic Distribution of a Putative Nucleosome Positioning Motif in Human, Nonhuman Primates, and Archaea: Mutual Information Analysis

Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.
EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment

The Ebola virus disease (EVD) is a rare and deadly disease affecting humans and other primates caused by infection with a virus of the family Filoviridae, genus Ebolavirus [1]. The March 2014 Ebola epidemic is the largest in history, affecting multiple countries in West Africa, with more than 11,301 deaths reported by the World Health Organization by March 2016. Methods based on polymerase chain reaction (PCR) are commonly used for virus detection with the advantage of requiring low amounts of viral samples, minimal manipulation, and minimal equipment. In particular, quantitative PCR (qPCR) has been used for the sensitive and fast identification of patients with EVD [2–7]. However, the high genetic diversity of RNA viruses poses a challenge for the design of efficient nucleic acid-based assays, as suggested by the high substitution rate observed in Ebola virus from the 2014 outbreak [5,8]. Recent studies suggest that false-negative diagnosis or inefficient therapeutics can occur due to sequence variation at binding sites of PCR primers, probes, small interfering RNAs (siRNAs), or monoclonal antibodies targeting the Ebola virus [5,9]. For this reason, the selection of reliable oligonucleotides and target genomic regions for use in nucleic acid-based assays is crucial for the correct diagnosis and treatment of EVD.
The centrality of RNA for engineering gene expression

Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next‐generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell.
Weak Formulation of Gradient Augmented Level set method to Stephan type problems

Problems associated with dendritic crystallization requires careful implementation of numerical methods. In the past few years various methods have been developed [F.Gibou et al., 2003; F.Gibou and R.Fedkiw, 2005] to track topologically complex, solid-liquid interface in crystal growth simulation. In this work we employ gradient augmented level set method [Nave et al., 2010] to track interface. For maintaining signed distance function we implemented partial differential equation approach from [Anumolu and Trujillo, 2012] and also PhysBAM inbuilt fast marching method, but the results presented here use fast marching method. We discretize the heat equation on a Cartesian grid using implicit backward Euler method and for the nodes neighboring interface, the discretization is performed as proposed in [F.Gibou et al., 2003]. The jump in the first derivatives of the temperature is used to compute interface velocity and Gibbs-Thompson equation is used to compute temperature at the interface. In the following sections, we first describe interface advection methods, followed by heat equation, which is followed by Stephan problem and finally
Color correction without color patterns for stereoscopic camera systems

Color consistency between image pairs from stereo camera systems is crucial for 3D display systems as well as depth estimation by stereo matching. Even though we use the same type of cameras with the same hardware settings, color response can be significantly different due to the variation of lighting conditions and radiometric characteristics. In this paper, we propose a color correction method for stereoscopic camera systems. Previously, color patterns were used to search out color matches between two or multiple images. In spite of accurate estimation of the previous work, using color patterns has the limitation for various applications. Without color patterns, we automatically find correspondences of a stereo pair using feature detection and RANSAC-based stereo matching. Then, by calculating color transform matrix, we reduce color discrepancy between the stereo pair. The accuracy of color correction is dependent on feature detectors, matching procedures and color transform methods. Experimental results show that appropriate types of them should be chosen according to target applications in the view of the processing time and accuracy.
Shrinkage learning to improve SVM with hints

The Support Vector Machine (SVM) is one of the most effective and used algorithms, when targeting classification. Despite its large success, SVM is mainly afflicted by two issues: (i) some hyperparameters must be tuned in advance and are, in practice, identified through computationally intensive procedures; (ii) possible a-priori knowledge about the problem (e.g. doctor expertise in medical applications) cannot be straightforwardly exploited. In this paper, we introduce a new approach, able to cope with the two previous problems: several experiments, performed on real-world benchmarking datasets, show that our method outperforms, on average, other techniques proposed in the literature.
Theories on Common Adolescent Pain Syndromes Theories on Common Adolescent Pain Syndromes Chronic Pain-effects on Families @bullet School Absenteeism @bullet Comorbidity and Pain @bullet Psychological Interventions @bullet Coping Strategies Theories on Adolescent Pain

Pain is a prevalent condition among adolescents. In fact, 30–40% of children and adolescents report experiencing pain at least once a week (Palermo 2000), and 5–25% of adolescents report some form of recurrent or chronic pain (Perquin et al. 2000; Goodman and McGrath 1991). Of those reporting recurrent pain, 30–40% of children report pain episodes at least once a week (Kristjansdottir 1997). In terms of specific pain conditions, data indicate that the most common chronic pain conditions among adolescents are headaches, abdominal pain, back pain, and musculoskeletal pain (Goodman and McGrath 1991; Morsy 2006). Data also suggest that pain can be a long-term condition for children. In community samples, El-Metwally and colleagues (2004) found that 54% of children reporting musculoskeletal pain continued to experience pain at a 1-year follow-up. Not surprisingly, pain is also a long-term condition in clinic-referred samples. Martin and colleagues (2007) found that the majority (62%) of children who presented for treatment at a multidisciplinary clinic continued to report pain from 1 to 6 years later. It is interesting to note that reports of chronic and recurrent pain tend to differ between sexes and across development. Prevalence data consistently suggest that reports of pain are more common in girls than boys (McGrath et al. 2000; Viry et al. 1999), a pattern that is fairly consistent across pain conditions and nationalities (Haugland et al. 2001).