Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation of transient receptor potential ankyrin 1 by hydrogen peroxide

Hydrogen peroxide (H2O2), which is contained in industrial products, is also generated within cells. H2O2 causes pain but it has not been elucidated how it activates sensory neurons in the pain pathway. Here we show that transient receptor potential ankyrin 1 (TRPA1), expressed by sensory neurons in the pain pathway, is a receptor for H2O2. H2O2 activated mouse TRPA1 to induce Ca2+ influx and elicit non‐selective cation currents. These effects of H2O2 were mimicked by both reactive oxygen species and reactive nitrogen species. Cysteine‐reducing agents suppressed H2O2‐induced TRPA1 activation, whereas cysteine‐oxidizing agents activated TRPA1. H2O2 caused Ca2+ influx in a subset of dorsal root ganglia neurons, which responded to allyl isothiocyanate, a TRPA1 ligand. These results suggest that TRPA1 might be involved in the sensation of pain caused by H2O2.
Building Successful Knowledge Repository Systems: Knowledge Refinement, Quality and Usage

Existing research on knowledge repositories has largely focused on supply-side driven research questions, such as employee motivation to contribute knowledge. This research turns attention to the demand-side issue of knowledge usage. Using the Information Systems (IS) success framework (DeLone and McLean 2003), this research theorizes knowledge quality as an important antecedent to knowledge usage. A conceptual framework delineates dimensions of knowledge quality from two perspectives. Moreover, an Input-Process-Output model of knowledge refinement process is proposed, and a causal model is offered to explain determinants of knowledge refinement effectiveness. Qualitative interviews and a survey study have been designed and are soon to be conducted with authors, validators and users of Eureka, a successful global knowledge repository system of the Xerox company. Implications for knowledge management research and managerial practices are discussed.
Negative acculturation context variables as predictors of acculturation outcomes in a mine in the North–West Province

This article reports on the results of a project investigating the acculturation process within a mainstream context, in order to predict the ill health and perceived work success of mineworkers in a mine in the North-West Province. 1 This proposition was explored by investigating the relationship between the acculturation context and individual intervening factors, mapped into variables, and acculturation outcomes (ill health and work success). A cross-sectional survey design was used to gather the data from a convenience sample of participants from the mine examined (n = 288), utilizing adapted and self-developed measuring instruments to investigate the mainstream cultural domain, an individual separation acculturation strategy, psychological acculturation outcomes, and sociocultural acculturation outcomes. The findings demonstrate that statistical significant relations exist between investigated variables, that ill health and work success can be viewed from an acculturation perspective, and that the acculturation context and individual intervening factors, can be used to predict psychological and sociocultural acculturation outcomes. Limitations of the study and recommendations for future research and the organisation are provided.
Major Qualifying Projects ( All Years ) Major Qualifying Projects June 2012 Modeling Photonic Crystal Band Structures Using Hermite FEM

Maxwell’s vector field equations represent significant challenges for the numerical solution of electric and magnetic fields in complex geometries. With increasing complexity in the design of electromagnetic devices as in automobiles, metamaterials, and optical interconnects, it becomes imperative to develop compact algorithms for electrodynamic calculations that will generate high accuracy with minimal computational time. We solve the field equations for the example of a two-dimensional photonic crystal using the finite element method with Hermite interpolation polynomials. We demonstrate that the Hermite interpolation polynomials, due to their derivative continuity across elements, yield accurate predictions of the fields in a photonic crystal at a much lower computational cost than conventional approaches to this problem.
RNA interference-mediated gene silencing of cyclophilin A enhances the radiosensitivity of PAa human lung adenocarcinoma cells in vitro

Radiotherapy is currently the major therapeutic strategy for patients with lung cancer. However, radioresistance and various side effects continue to present challenging issues for this form of treatment. A recent study demonstrated that cyclophilin A (CyPA) was overexpressed in non-small cell lung cancer and, therefore, presents a novel potential therapeutic target. In addition, gene-radiotherapy is a novel method for cancer treatment. Therefore, the objective of the present study was to investigate the potential effect of CyPA silencing on radiosensitivity in human lung adenocarcinoma in vitro. The stable CyPA-silencing lung adenocarcinoma (PAa) cell line was generated using lentivirus-mediated small hairpin RNAs. The knockdown of CyPA was determined using fluorescent microscopy and western blot analysis. Cells were irradiated using various doses of cobalt-60 (0, 2, 4, 6 and 8 Gy). The radiosensitizing effects were determined by a clonogenic survival assay. Apoptosis and cell cycle distribution were evaluated using flow cytometry. Silencing of CyPA significantly increased the apoptosis of PAa cells. In addition, the radiosensitivity of cells was markedly enhanced following CyPA silencing. Furthermore, silencing of CyPA, in combination with irradiation, induced G2/M phase cell cycle arrest. Taken together, the data suggest that the silencing of CyPA, combined with radiation therapy, may increase the therapeutic efficacy of lung cancer treatment through regulation of the cell cycle and apoptosis-associated signaling pathways.
Minimum-time motions of manipulators with obstacles by successive searches for minimum-overload trajectories

We present a practical method for finding obstacle free minimum-time motions for manipulators subject to the bounds of velocity-dependent actuator forces. The optimal motion planning problem is converted into a finite dimensional nonlinear programming by means of parameter optimizations with quintic B-splines. We introduce the concept of the minimum-overload trajectories in which the motion time is specified to be faster than the motors can handle, and the actuator overloads are minimized during the motion. By successive searches for the minimum-overload trajectories, the minimum-time motions are determined for a spatial 6-link manipulator without simplifying any of the kinematic, dynamic or geometric properties of the manipulator or the obstacles. In the resultant minimum-time motions, almost all of the joint actuators are close to saturation during the motions.
Wide-area parallel programming using the remote method invocation model

Java’s support for parallel and distributed processing makes the language attractive for metacomputing applications, such as parallel applications that run on geographically distributed (wide-area) systems. To obtain actual experience with a Java-centric approach to metacomputing, we have built and used a high-performance wide-area Java system, called Manta. Manta implements the Java Remote Method Invocation (RMI) model using different communication protocols (active messages and TCP/IP) for different networks. The paper shows how widearea parallel applications can be expressed and optimized using Java RMI. Also, it presents performance results of several applications on a wide-area system consisting of four Myrinetbased clusters connected by ATM WANs. We finally discuss alternative programming models, namely object replication, JavaSpaces, and MPI for Java.
A Bayesian Network Approach to Program Generation

Genetic programming (GP) is a powerful optimization algorithm that has been applied to a variety of problems. This algorithm can, however, suffer from problems arising from the fact that a crossover, which is a main genetic operator in GP, randomly selects crossover points, and so building blocks may be destroyed by the action of this operator. In recent years, evolutionary algorithms based on probabilistic techniques have been proposed in order to overcome this problem. In the present study, we propose a new program evolution algorithm employing a Bayesian network for generating new individuals. It employs a special chromosome called the expanded parse tree , which significantly reduces the size of the conditional probability table (CPT). Prior prototype tree-based approaches have been faced with the problem of huge CPTs, which not only require significant memory resources, but also many samples in order to construct the Bayesian network. By applying the present approach to three distinct computational experiments, the effectiveness of this new approach for dealing with deceptive problems is demonstrated.
Three‐dimensional analysis of bone remodeling following ridge augmentation of compromised extraction sockets in periodontitis patients: A randomized controlled study

OBJECTIVES The aim of this study was to analyze linear and volumetric hard tissue changes in severely resorbed alveolar sockets after ridge augmentation procedure and to compare them with spontaneous healing using three-dimensional cone beam computed tomography (CBCT). MATERIAL AND METHODS Thirty patients (mean age 53.2 ± 6.3 years) requiring tooth extraction for advanced periodontitis were randomly allocated to test and control groups. The test sites were grafted using a collagenated bovine-derived bone (DBBM-C) covered with a collagen membrane, while control sites had spontaneous healing. Both groups healed by secondary intention. Linear and volumetric measurements were taken on superimposed CBCT images obtained after tooth extraction and 12 months later. RESULTS Greater horizontal shrinkage, localized mainly in the crestal zone, was observed in the control group (4.92 ± 2.45 mm) compared to the test group (2.60 ± 1.24 mm). While both groups presented a rebuilding of the buccal wall, it was most pronounced in the grafted sockets (2.50 ± 2.12 mm vs. 0.51 ± 1.02 mm). A significant difference was also registered in the percentage of volume loss between grafted and non-grafted sites (9.14% vs. 35.16%, p-value <.0001). CONCLUSION Alveolar sockets with extensive buccal bone deficiencies undergo significant three-dimensional volumetric alterations following natural healing. The immediate application of a slow-resorbing xenograft with a covering collagen membrane seems to be effective in improving alveolar ridge shape and dimensions, thus potentially reducing the need for adjunctive regenerative procedures at the time of implant placement.
Speech enhancement and features compensation algorithms for continuous speech recognition

The degradation of the speech signal due to adverse conditions generates low accuracy rates in speech recognition systems. The authors propose mixing two methods: pre-extraction of features for speech enhancement and post-extraction of features for features compensation. According to their main focus, they are fundamentally oriented to minimize the misfit caused by noise insertion in the speech signal. These methods will be applied before and after the extraction of features, respectively, therefore allowing the best possible estimation of the clear signal from its degraded version.
Compensation of analog rotor position errors due to nonideal sinusoidal encoder output signals

This paper proposes a compensation algorithm of analog rotor position errors due to nonideal sinusoidal encoder signals. The position sensors such as resolvers or incremental encoders are being replaced by sinusoidal encoders that offer much higher resolution. However, the periodic position errors are generated by the gain and offset errors between sine and cosine signals. In this paper, the effects of the gain and offset errors are analyzed by using dq-axis component. The analog position errors can be easily corrected by integral operation of the d-axis component. Therefore, the proposed algorithm does not need additional hardware and much computation time. The validity of the proposed algorithm is verified through experimental results.
Spots of adult male red-spotted newts are redder and brighter than in females: evidence for a role in mate selection?

As aquatic adults, eastern red-spotted newts (Notophthalmus v. viridescens) are generally green with two rows of dorsal spots, which vary in number between individuals and range in colour from orange to red. The function of these spots is unknown, but it is possible that they serve as sexual ornamentations and we examined this hypothesis by testing for sexual dimorphism in spot characteristics. We used an image analysis approach that has been used previously with this and other amphibian species to compare the number, size and colour – redness (hue score) and brightness – of spots in 100 male and 100 female aquatic adult newts captured during the breeding season in Virginia. While we found no apparent sex-related differences in the numbers of spots, and only a minor difference in spot sizes, we discovered that adult male red-spotted newts had significantly redder and more brightly coloured dorsal spots than did females. We also found that spot brightness is positively associated with body size. As male red-spotted newts entice females to mate in part with a highly visual display (the “hula dance”), the sexual dimorphism in spot colour we found could be associated with this display. Our results, taken together with current knowledge on the carotenoid pigments behind the red spot colour, suggest a role for spot coloration in the mating system of N. v. viridescens that should be examined further and considered in other studies of mate choice. In a more general sense, this discovery also leads us to question if this phenomenon is present in other amphibian species previously thought to be “monomorphic”.
Developmental regulation of calcineurin isoforms in the rodent kidney: association with COX-2.

Calcineurin (Cn)-Aalpha-deficient mice develop abnormalities of postnatal kidney development, similar to that of cyclooxygenase (COX)-2-deficient mice. The present study was undertaken to examine expression and regulation of Cn isoforms in the developing kidney during the postnatal period and further characterize the relationship between Cn and COX-2. The protein expressions of all three Cn isoforms, including Cn-Aalpha, -Abeta, and -B, as determined by immunoblotting, increased in parallel in the first postnatal week and declined gradually with age. Renal Cn-Aalpha and -Abeta mRNA expressions were both developmentally regulated in the same fashion as their protein expressions, whereas renal Cn-B1 mRNA was not obviously induced in the first postnatal week. Immunohistochemistry demonstrated colocalization of Cn-Aalpha, Cn-Abeta, and COX-2 in the same cells of thick ascending limb and macula densa. Administration with cyclosporine A (2.5 mg.kg(-1). day(-1)) during the postnatal period remarkably suppressed renal COX-2 expression as assessed by both immunoblotting and immunohistochemistry. Deletion of Cn-Aalpha but not Cn-Abeta in mice significantly reduced renal COX-2 expression at the postnatal period. Together, these data suggest that renal Cn isoforms are subject to normal developmental regulation and they may play a role in postnatal kidney development via interaction with COX-2.
Improving MRI-based diagnosis of Alzheimer's disease via an ensemble privileged information learning algorithm

In clinical practice, the magnetic resonance imaging (MRI) is a prevalent neuroimaging technique for Alzheimer's disease (AD) diagnosis. As a learning using privileged information (LUPI) algorithm, SVM+ has shown its effectiveness on the classification of brain disorders, with single-modal neuroimaging samples for testing but multimodal neuroimaging samples for training. In this work, we propose to apply the multimodal restricted Boltzmann machines (RBM) as an LUPI algorithm for feature learning so as to form an RBM+ algorithm. Furthermore, an ensemble LUPI algorithm is developed, integrating SVM+ and RBM+ by the multiple kernel boosting based strategy. The experimental results demonstrate that the proposed RBM+ works well as an LUPI algorithm for feature learning, and the ensemble LUPI algorithm is superior to the traditional predictive models for the MRI-based AD diagnosis using the positron emission tomography as the privileged information.
Theta-Burst Stimulation-Induced Plasticity over Primary Somatosensory Cortex Changes Somatosensory Temporal Discrimination in Healthy Humans

Background The somatosensory temporal discrimination threshold (STDT) measures the ability to perceive two stimuli as being sequential. Precisely how the single cerebral structures contribute in controlling the STDT is partially known and no information is available about whether STDT can be modulated by plasticity-inducing protocols. Methodology/Principal Findings To investigate how the cortical and cerebellar areas contribute to the STDT we used transcranial magnetic stimulation and a neuronavigation system. We enrolled 18 healthy volunteers and 10 of these completed all the experimental sessions, including the control experiments. STDT was measured on the left hand before and after applying continuous theta-burst stimulation (cTBS) on the right primary somatosensory area (S1), pre-supplementary motor area (pre-SMA), right dorsolateral prefrontal cortex (DLPFC) and left cerebellar hemisphere. We then investigated whether intermittent theta-burst stimulation (iTBS) on the right S1 improved the STDT. After right S1 cTBS, STDT values increased whereas after iTBS to the same cortical site they decreased. cTBS over the DLPFC and left lateral cerebellum left the STDT statistically unchanged. cTBS over the pre-SMA also left the STDT statistically unchanged, but it increased the number of errors subjects made in distinguishing trials testing a single stimulus and those testing paired stimuli. Conclusions/Significance Our findings obtained by applying TBS to the cortical areas involved in processing sensory discrimination show that the STDT is encoded in S1, possibly depends on intrinsic S1 neural circuit properties, and can be modulated by plasticity-inducing TBS protocols delivered over S1. Our findings, giving further insight into mechanisms involved in somatosensory temporal discrimination, help interpret STDT abnormalities in movement disorders including dystonia and Parkinson's disease.
Underdetermined blind separation for speech in real environments with sparseness and ICA

In this paper, we propose a method for separating speech signals when there are more signals than sensors. Several methods have already been proposed for solving the underdetermined problem, and some of these utilize the sparseness of speech signals. These methods employ binary masks to extract the signals, and therefore, their extracted signals contain loud musical noise. To overcome this problem, we propose combining a sparseness approach and independent component analysis (ICA). First, using sparseness, we estimate the time points when only one source is active. Then, we remove this single source from the observations and apply ICA to the remaining mixtures. Experimental results show that our proposed sparseness and ICA (SPICA) method can separate signals with little distortion even in reverberant conditions of T/sub R/=130 and 200 ms.
Knowledge based Semantic Annotation Generation of Music

storage capacity and the cost of the storage devises gives raise to voluminous music collection management. Various MIR techniques exist, but getting the required songs from large collection of music files, is still a challenging problem. Getting the required songs from voluminous collection with good recall and precision depends on good annotation, indexing and retrieval techniques. Among this annotation plays a vital role in developing an efficient and effective retrieval system. Tag bases annotation or the low level feature based annotations retrieval systems performance is very poor, though the processing is very simple. Semantic concept based annotation, indexing and retrieval techniques are trying to fill the gap between the machine understanding and the human preferences. This raises the need for semantic based annotation of film songs. Ontology plays a major role in semantic web and information retrieval. This raises the need for an ontology based annotation generation tool for film songs. The current research designs and implements a tool M- SAGT -Music Semantic Annotation Generation Tool. Which is flexible, user friendly and ontology based semantic annotations can be generated and stored in RDF/XML format. The generated semantic annotations can be used in semantic indexing and retrieval, which will enhance the performance of the retrieval system.
Detection of human parechovirus in stool samples collected from children with acute gastroenteritis in Japan during 2007–2008

Of 477 stool specimens, which had been screened for rotavirus, adenovirus, norovirus, sapovirus and astrovirus, collected from infants and children with acute gastroenteritis in pediatric clinics encompassing five localities (Sapporo, Tokyo, Maizuru, Osaka, and Saga) in Japan from July 2007 to June 2008, 247 negative samples (51.7%) were subjected to screening for human parechovirus. Human parechovirus (HPeV) was detected by RT‐PCR using a primer pair to amplify 5′UTR region of its genome and was genotyped by sequencing of the VP1 gene. HPeV was detected in 20 of 247 specimens tested, and the detection rate was found to be 8.1%. Seventeen of the 20 strains that tested positive for HPeV were sequenced successfully the VP1 gene. The majority of the HPeV strains (n = 15) could be identified as HPeV1, and the remaining 2 strains could be typed as HPeV3. By phylogenetic and identical matrix analyses of HPeV VP1 sequences, HPeV1 should be divided into two lineages, and all of the Japanese studied HPeV1 strains belong to the lineage 2 accordingly. This is the first report of the circulation of HPeV, especially HPeV1 in Japan. J. Med. Virol. 83:331–336, 2011. © 2010 Wiley‐Liss, Inc.
Recursive speech enhancement using the EM algorithm with initial conditions trained by HMM's

This paper considers speech enhancement where the speech signal is modeled with hidden filter models (HFMs), when only noisy speech signal are available. The HFM is a parametric approach for representing the speech waveform in the time domain. We apply the nested EM algorithm for jointly estimating the clean signal and the parameters of HFM and noise model. A computationally efficient implementation of the algorithm is developed by the log-likelihood gradient based on the Kalman filter output in the estimation process. The resulting algorithm does not need framing and may be viewed in the time domain context.
Safe Evolution Patterns for Software Product Lines

Despite a global recognition of the problem, and massive investment from researchers and practitioners, the evolution of complex software systems is still a major challenge for today's architects and developers. In the context of product lines, or highly configurable systems, variability in the implementation and design makes many of the pre-existing challenges even more difficult to tackle. Many approaches and tools have been designed, but developers still miss the tools and methods enabling safe evolution of complex, variable systems. In this paper, we present our research plans toward this goal: making the evolution of software product lines safer. We show, by use of two concrete examples of changes that occurred in Linux, that simple heuristics can be applied to facilitate change comprehension and avoid common mistakes, without relying on heavy tooling. Based on those observations, we present the steps we intend to take to build a framework to regroup and classify changes, run simple checks, and eventually increase the quality of code deliveries affecting the variability model, mapping and implementation of software product lines.