Miracle-dz/UniFAR-FTUs huggingface dataset:
PyCUDA: GPU Run-Time Code Generation for High-Performance Computing

High-performance scientic computing has recently seen a surge of interest in heterogeneous systems, with an emphasis on modern Graphics Processing Units (GPUs). These devices oer tremendous potential for performance and eciency in important large-scale applications of computational science. However, exploiting this potential can be challenging, as one must adapt to the specialized and rapidly evolving computing environment currently exhibited by GPUs. One way of addressing this challenge is to embrace better techniques and develop tools tailored to their needs. This article presents one simple technique, GPU run-time code generation (RTCG), and PyCUDA, an open-source toolkit that supports this technique. In introducing PyCUDA, this article proposes the combination of a dynamic, high-level scripting language with the massive performance of a GPU as a compelling two-tiered computing platform, potentially oering signicant performance and productivity advantages over conventional single-tier, static systems. It is further observed that, compared to competing techniques, the eort required to create codes using run-time code generation with PyCUDA grows more gently in response to growing needs. The concept of RTCG is simple and easily implemented using existing, robust tools. Nonetheless it is powerful enough to support (and encourage) the creation of custom application-specic tools by its users. The premise of the paper is illustrated by a wide range of examples where the technique has been applied with considerable success.
Interactive knowledge externalization and combination for SECI model

One of the subjects in knowledge management is knowledge externalization and combination in which people express their tacit knowledge and formulate it. Communication among people is important for this process. This paper proposes a model that helps two users to have a discussion for knowledge externalization and combination. In this model, the computer verifies the consistency between the knowledge generated by inductive learning from cases and the two user's knowledge sets expressed by themselves. From the result of this verification, it provides the point at issue for the discussion to improve the knowledge. We conducted a user experiment in the domain of gure-fishing where real experts had participated in. We confirmed the effectiveness in activating people's communication and also in improving the quality of their knowledge.
Computational auditory scene analysis by using statistics of high-dimensional speech dynamics and sound source direction

A main task for computational auditory scene analysis (CASA) is to separate several concurrent speech sources. From psychoacoustics it is known that common onsets, common amplitude modulation and sound source direction are among the important cues which allow the separation for the human auditory system. A new algorithm is presented here, that performs statistical estimation of different sources by a state-space approach which integrates temporal and frequency-specific features of speech. It is based on a Sequential Monte Carlo (SMC) scheme and tracks magnitude spectra and direction on a frame-by-frame basis. First results for estimating sound source direction and separating the envelopes of two voices are shown. The results indicate that the algorithm is able to localize two superimposed sound sources in a time scale of 50 ms. This is achieved by integrating measured high-dimensional statistics of speech. Also, the algorithm is able to track the short-time envelope and the short-time magnitude spectra of both voices on a time scale of 10 -4 0 ms. The algorithm presented in this paper is developed for but not restricted to use in binaural hearing aid applications, as it is based on two head-mounted microphone signals as input. It is conceptionally able to separate more than two voices and integrate additional cues.
Signal Transduction Pathways That Regulate Eukaryotic Protein Synthesis*

The last several years have witnessed an explosion in the published literature on two topics, the pathways that transduce extracellular signals to their intracellular targets and modification of the core translational apparatus in response to these signals. Most of these pathways result in cell growth and cell division. Synthesis of the entire complement of proteins is necessary to double the cell size, but synthesis of the so-called “growth-regulated” proteins (1) is needed for cell division. This article summarizes recent advances in our understanding of how a single mitogenic stimulus can simultaneously lead to an increase in both global and growth-regulated protein synthesis.
Synchrotron radiation: Micrometer‐sized x‐ray beams as fine tools for macromolecular crystallography

Structural data play a central role in understanding biological function at the molecular level. At present, the majority of high‐resolution structural data about biological macromolecules and their complexes originates from crystallography. In crystal structure determination, the major hurdle to overcome is the production of crystals of sufficient size and quality. High‐flux x‐ray beams with diameters of a few micrometers or less help to alleviate this problem as small beams allow the use of small crystals or scanning of large crystals for regions of acceptable diffraction. Using sophisticated x‐ray optics and mechanics with submicrometer precision, Riekel et al. [Acta Crystallogr. , Sect. D: Biol. Crystallogr. , 64, 158–166 (2008)], have recently demonstrated that an x‐ray beam of 1 μm can be used to determine the crystal structure of a protein to a resolution of 1.5 Å. The smallest volume from which usable diffraction data were collected amounted to 20 μm3, corresponding to not more than 2×108 unit cells. In a diffraction volume of micrometer dimensions, radiation damage is expected to be reduced with respect to large volumes as a significant fraction of the photoelectrons produced by the incident radiation escapes from the diffracting volume before dissipating their energy. The possibility to make use of small and/or inhomogeneous crystals in combination with a possible reduction in radiation damage due to size effects has the potential to make many more systems amenable to crystal structure analysis.
Olfaction: Smelling the Content of Consciousness

Olfaction: Smelling the Content of Consciousness. by Benjamin D. Young Adviser: Jesse Prinz Scientific research on the sense of smell has blossomed over the past two decades, yet a comprehensive philosophical treatment of olfaction is nonexistent. My dissertation remedies this neglect by showing how the anatomical structure, functional circuitry, and sensory states of the olfactory system, call into question the reigning theories of cognition and consciousness. Specifically, olfaction provides new insight about the nature of object perception, the structure of our thoughts, consciousness, and the qualitative character of our experiences. The object of our olfactory experience and what constitutes its olfactory quality, is the chemical structure of molecular compounds, which are unlike those of the other perceptual modalities. Additionally, the content of olfactory experience is represented in a format that is unlike the system of representations posited by Language of Thought Theorists, thus creating a new game in-town. The olfactory systemʼs implementation of a functionally compositional system of representations allows for a new treatment of nonconceptual content as an issue of the representational format that a system employs. Formative nonconceptual content resuscitates the ʻRichness of Experienceʼ argument by showing that our
Contaminated Small Drinking Water Supplies and Risk of Infectious Intestinal Disease: A Prospective Cohort Study

Background This study sought to identify whether elevated risk of infectious intestinal disease (IID) exists in contaminated small water supply consumers compared with consumers drinking from small supplies complying with current standards and whether this effect is modified by age. Methodology and Principal Findings A prospective cohort study of 611 individuals receiving small supplies in England was conducted. Water supplies received sanitary inspection and examination for indicator bacteria and participants maintained a daily record of IID. Regression modeling with generalized estimating equations that included interaction terms between age and indicators of fecal pollution was performed. Crude IID prevalence was 9·3 days with symptoms/1000 person days (95%CI: 8·4, 10·1) and incidence was 3·2 episodes/1000 person days (95%CI, 2·7, 3·7) or 1·2 episodes per person year. Although there was no overall association between IID risk and indicator presence, there was strong interaction between age and indicator presence. In children under ten, relative risk (RR) of IID in those drinking from enterococci contaminated supplies was 4.8 (95%CI: 1.5, 15.3) for incidence and 8.9 (95%CI: 2.8, 27.5) for prevalence. In those aged 10 to 59, IID risk was lower but not statistically significant. Conclusions Contaminated small water supplies pose a substantial risk of IID to young children who live in homes reliant on these supplies. By contrast older children and adults do not appear to be at increased risk. Health care professionals with responsibility for children living in homes provided by very small water supplies should make parents aware of the risk.
Systematic comparison of the human saliva and plasma proteomes

The proteome of human salivary fluid has the potential to open new doors for disease biomarker discovery. A recent study to comprehensively identify and catalog the human ductal salivary proteome led to the compilation of 1166 proteins. The protein complexity of both saliva and plasma is large, suggesting that a comparison of these two proteomes will provide valuable insight into their physiological significance and an understanding of the unique and overlapping disease diagnostic potential that each fluid provides. To create a more comprehensive catalog of human salivary proteins, we have first compiled an extensive list of proteins from whole saliva (WS) identified through MS experiments. The WS list is thereafter combined with the proteins identified from the ductal parotid, and submandibular and sublingual (parotid/SMSL) salivas. In parallel, a core dataset of the human plasma proteome with 3020 protein identifications was recently released. A total of 1939 nonredundant salivary proteins were compiled from a total of 19 474 unique peptide sequences identified from whole and ductal salivas; 740 out of the total 1939 salivary proteins were identified in both whole and ductal saliva. A total of 597 of the salivary proteins have been observed in plasma. Gene ontology (GO) analysis showed similarities in the distributions of the saliva and plasma proteomes with regard to cellular localization, biological processes, and molecular function, but revealed differences which may be related to the different physiological functions of saliva and plasma. The comprehensive catalog of the salivary proteome and its comparison to the plasma proteome provides insights useful for future study, such as exploration of potential biomarkers for disease diagnostics.
Optimization of the efficiency and reliability of reverse-fabricated CMUT arrays

The electromechanical conversion efficiency and the long-term reliability of Capacitive Micromachined Ultrasonic Transducers (CMUT) are mainly limited by the parasitic capacitance and by charge injection phenomena, which are generated the first, by the portions of the CMUT electrodes used for interconnection, and the second, by the low dielectric strength of the in-cavity passivation materials. Reverse Fabrication Process (RFP) [doi: 10.1088/0960-1317/25/1/015012] is a sacrificial-release low-temperature CMUT technology that employs ultra-low-stress Silicon Nitride (SixNy) dielectrics and Titanium-Aluminum-Titanium metals. In this paper, we investigated the possibility of reducing both the parasitic capacitance, by acting on the electrodes layout, and the charge injection phenomena, by introducing Silicon Oxide (SiO2) buffer layers between the electrodes and the in-cavity passivation layers.
A robust defense against Content-Sniffing XSS attacks

Many Web sites such as MySpace, Facebook and Twitter allow their users to upload files. However when a Web site's Content-Sniffing algorithm differs from a browser's Content-Sniffing algorithm, an attacker can often mount a Content-Sniffing XSS attack on the visitor. That is, by carefully embedding HTML code containing malicious script into a non-HTML file and uploading this file to the Web site, an attacker can deceive the visitor's browser into assuming the file as HTML file and run the script code. However Content-Sniffing XSS attack can be avoided if files uploaded on the server are checked for HTML codes. In this paper we propose a server-side ingress filter that aims to protect vulnerable browsers which may treat non-HTML files as HTML files. Our filter examines user-uploaded files against a set of potentially dangerous HTML elements (a set of regular expressions). The results of our experiment show that the proposed automata-based scheme is highly efficient and more accurate than existing signature-based approach.
Serum sclerostin in alcoholics: a pilot study.

AIMS Sclerostin is an endogenous inhibitor of the Wnt/β-catenin pathway secreted by osteocytes, which inhibits osteoblast function, differentiation and survival. As a consequence, sclerostin tends to decrease bone mass. Alcoholics frequently present osteoporosis, mainly due to decreased bone synthesis. The behaviour of sclerostin in these patients is unknown. The aim of this work was to analyse the relationship between serum sclerostin levels and bone mineral density (BMD), ethanol consumption, nutritional status, liver function derangement and biomarkers of bone homeostasis in alcoholic patients. METHODS We included 31 alcoholic patients, of whom 11 were infected with Hepatitis C virus (HCV) and 7 age and sex-matched controls. All underwent densitometry, and serum sclerostin, osteocalcin, collagen telopeptide, parathyroid hormone (PTH), vitamin D, cortisol and testosterone were determined. RESULTS Sclerostin levels were significantly higher in patients (30.95 ± 18.91 pmol/l) than controls (t = 4.4; P < 0.001), especially in non-HCV patients; they showed an inverse correlation with osteocalcin, prothrombin activity and serum albumin, and a direct correlation with bilirubin and telopeptide, but not with BMD, nutritional status or ethanol intake. CONCLUSIONS Serum sclerostin was raised in alcoholic patients, and it correlated with decreased markers of bone synthesis and increased markers of bone breakdown. The elevation in sclerostin levels was clearly related with liver function, but not with ethanol intake, nutritional status or concomitant HCV infection.
Signal Representation Attribute Extraction and the Use Distinctive Features for Phonetic Classification

The study reported in this paper addresses three issues related to phonetic classification: 1) whether it is important to choose an appropriate signal representation, 2) whether there are any advantages in extracting acoustic attributes over directly using the spectral information, and 3) whether it is advantageous to introduce an intermediate set of linguistic units, i.e. distinctive features. To restrict the scope of our study, we focused on 16 vowels in American English, and investigated classification performance using an artificial neural network with nearly 22,000 vowels tokens from 550 speakers excised from the TIMIT corpus. Our results indicate that 1) the combined outputs of Seneff's auditory model outperforms five other representations with both undegraded and noisy speech, 2) acoustic attributes give similar performance to raw spectral information, but at potentially considerable computational savings, and 3) the distinctive feature representation gives similar performance to direct vowel classification, but potentially offers a more flexible mechanism for describing context dependency.
Finite-Horizon Approximate Optimal Guaranteed Cost Control of Uncertain Nonlinear Systems With Application to Mars Entry Guidance

This paper studies the finite-horizon optimal guaranteed cost control (GCC) problem for a class of time-varying uncertain nonlinear systems. The aim of this problem is to find a robust state feedback controller such that the closed-loop system has not only a bounded response in a finite duration of time for all admissible uncertainties but also a minimal guaranteed cost. A neural network (NN) based approximate optimal GCC design is developed. Initially, by modifying the cost function to account for the nonlinear perturbation of system, the optimal GCC problem is transformed into a finite-horizon optimal control problem of the nominal system. Subsequently, with the help of the modified cost function together with a parametrized bounding function for all admissible uncertainties, the solution to the optimal GCC problem is given in terms of a parametrized Hamilton-Jacobi-Bellman (PHJB) equation. Then, a NN method is developed to solve offline the PHJB equation approximately and thus obtain the nearly optimal GCC policy. Furthermore, the convergence of approximate PHJB equation and the robust admissibility of nearly optimal GCC policy are also analyzed. Finally, by applying the proposed design method to the entry guidance problem of the Mars lander, the achieved simulation results show the effectiveness of the proposed controller.
Constant Velocity High Force Microactuator for Stick-Slip Testing of Micromachined Interfaces

A chevron thermal actuator has been implemented as a constant velocity puller in a multiasperity frictional test platform. This platform enables a wide variation of puller velocity (1-3100 μm/s, 3.5 decades), normal load (2-4500 μN, 3.4 decades), and spring constant (0.06-100 μN/μm, 3.2 decades). These characteristics are achieved by leveraging the actuator thermal time constant, which is long compared with the mechanical time constant, in combination with iterative learning control. Good thermal isolation between the actuator and the friction block is achieved by shunting heat to the substrate. Uncoated and FOTAS [tridecafluorotris(dimethylamino)silane, CF3(CF2)5(CH2)2Si(N(CH3)2)3]-coated devices were tested, and normal load induced a transition from steady sliding to stick-slip. This platform could have several important uses for mapping microscale kinetic friction phase diagrams, including determining the stick-slip to steady sliding bifurcation line, performing startstop tests and instantaneous velocity change tests, and inferring information on wear performance of coatings as a function of load and velocity.
ASC, TBS, and the power of ALTS.

In this issue of the Journal, Lee and colleagues 1 from Hong Kong describe their assessment of the impact of the 2001 Bethesda System (TBS) revisions on their cytology practice. The primary focus of the study was to assess the impact of the conversion from TBS 1991 to the 2001 version on the frequency of atypical squamous cells (ASC) diagnoses. As noted in prior commentaries, ASC is not a diagnosis. ASC is a poorly reproducible mixture of reactive and inflammatory changes that mimic squamous intraepithelial lesion (SIL) in a group of patients who have SIL, mostly low grade (ASC-US [undetermined significance]) but perhaps 5% to 10% high grade (ASC-H). 2-6 So, can changes in classification terminology and criteria impact how much we equivocate? Let's see. Cases of ASC were retrospectively correlated within their computerized database for higher-grade end points including low-grade SIL (LSIL)/cervical intraepithelial neoplasia (CIN) 1, HSIL/CIN 2 or 3, or carcinoma based on routine practice. Fourteen cytopathologists and an undetermined number of cytotechnologists were involved in this study, which basically compared 28,000 cases from July 2000 to June 2002 when TBS 1991 was used with a similar number of cases in the 2-year period from July 2002 to June 2004. The major conclusion in this study was that the conversion to TBS 2001 led to a small but statistically significant increase in the specificity of the ASC diagnostic category and virtually all other diagnostic rates were unchanged. Is this really an important finding? And does it support the conversion to TBS 2001 as an important advance, as the authors suggest? Unfortunately, the comparisons in this article are confounded by multiple variables. The terminology conversion undoubtedly had a learning curve such that the application of the revised criteria early in the second observation period may have yielded different rates compared with when the operators were more familiar with the criteria later in the study. Regrettably, few time trend data are included. It is important to note that the terminology conversion was also associated with the implementation and partial conversion from conventional spray-fixed Papanicolaou smears to liquid-based cytol-ogy preparations. In the detail of the report it is also noted that the collection devices used for conventional cytology included only the spatula and no endocervical sampling device compared with the broom device used for liquid-based cytology preparations. In addition, the period of study was associated with a region-wide campaign to increase …
Comparative analysis of unsupervised eye center localization approaches

The paper focuses on the comparative analysis of the latest and the most effective techniques for automatic eye center localization developed in recent years. The basic aim of the work is to identify the most accurate and efficient technique for eye center detection based upon an unsupervised approach. These techniques are developed using basic principles laid down by the various researchers without any optimizations, pre-processing or post processing steps and are explored over the periocular images extracted from standard database. The study showed varying processing times of these basic techniques for automatic detection of eye pupil over similar image dataset. The aim of this work is to show the significant and efficient unsupervised technique for eye center localization. The results of this study may be useful for the development of efficient and accurate approaches for eye center localization in eye gaze tracking applications.
Effects of dark rearing on phosphorylation of neurotrophin Trk receptors

Total lack of visual experience (dark rearing, DR) is known to affect development of mammalian visual cortex (VC) and to prolong the critical period of visual cortical plasticity. Neurotrophins (NTs) have been proposed to play a relevant role in activity dependent processes important for the final shaping of cortical visual connections. Neurotrophin supply or antagonism of endogenous NT action profoundly affect visual cortical development and plasticity; in particular, exogenous supply of NTs counteracts DR effects on VC development. However, the effects of DR on NT expression are still debated and mounting evidence reports a mismatch between BDNF mRNA and protein expression in DR animals. To gain insight into the effects of DR on expression of nerve growth factor (NGF) and the functional state of NT signalling pathways, we assessed the phosphorylation state of Trk receptors in light‐reared animals (LR), in dark‐reared animals (DR), in DR animals briefly exposed to light and in DR animals with exogenous supply of NTs [NGF, brain‐derived neurotrophic factor (BDNF) and NT‐4] in the VC. We report that DR increases the expression of NGF but reduces the phosphorylation of TrkA and TrkB receptors with respect to LR; normal phosphorylation is rapidly rescued by a brief exposure to light. Exogenous supply of NGF, BDNF or NT4 in DR animals also rescues the phosphorylation of their receptors.