Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Folding Simulation in Concurrent Constraint Programming

A protein is identified by a finite sequence of amino acids, each of them chosen from a set of 20 elements. The Protein Structure Prediction Problem is the problem of predicting the 3D native conformation of a protein, when its sequence of amino acids is known. This problem is fundamental for biological and pharmaceutical research. All current mathematical models of the problem are affected by intrinsic computational limits. In particular, simulation-based techniques that handle every chemical interaction between all atoms in the amino acids (and the solvent) are not feasible due to the huge amount of computations involved. These programs are typically written in imperative languages and hard to be parallelized. Moreover, each approach is based on a particular energy function. In the literature there are various proposals and there is no common agreement on which is the most reliable. In this paper we present a novel framework for ab-initio simulations using Concurrent Constraint Programming. We are not aware of any other similar proposals in the literature. Each amino acid of an input protein is viewed as an independent process that communicates with the others. The framework allows a modular representation of the problem and it is easily extensible for further refinements. Simulations at this level of abstraction allow faster calculation. We provide a first preliminary working example in Mozart, to show the feasibility and the power of the method. The code is intrinsically concurrent and thus easy to be parallelized.
Compensatory changes in cortical resource allocation in adults with hearing loss

Hearing loss has been linked to many types of cognitive decline in adults, including an association between hearing loss severity and dementia. However, it remains unclear whether cortical re-organization associated with hearing loss occurs in early stages of hearing decline and in early stages of auditory processing. In this study, we examined compensatory plasticity in adults with mild-moderate hearing loss using obligatory, passively-elicited, cortical auditory evoked potentials (CAEP). High-density EEG elicited by speech stimuli was recorded in adults with hearing loss and age-matched normal hearing controls. Latency, amplitude and source localization of the P1, N1, P2 components of the CAEP were analyzed. Adults with mild-moderate hearing loss showed increases in latency and amplitude of the P2 CAEP relative to control subjects. Current density reconstructions revealed decreased activation in temporal cortex and increased activation in frontal cortical areas for hearing-impaired listeners relative to normal hearing listeners. Participants' behavioral performance on a clinical test of speech perception in noise was significantly correlated with the increases in P2 latency. Our results indicate that changes in cortical resource allocation are apparent in early stages of adult hearing loss, and that these passively-elicited cortical changes are related to behavioral speech perception outcome.
A Novel Vehicle Detection Method With High Resolution Highway Aerial Image

A robust and efficient vehicle detection method from high resolution aerial image is still challenging. In this paper, a novel and robust method for automatic vehicle detection using aerial images over highway was presented. In the method, a GIS road vector map was used to constrain the vehicle detection system to the highway networks. After the morphological structure element was identified, we utilized the grayscale opening transformation and grayscale top-hat transformation to identify hypothesis vehicles in the light or white background, and used the grayscale closing transformation and grayscale bot-hat transformation to identify the hypothesis vehicles in the black or dark background. Then, targets with large size or covering a large area were sieved from the hypothesis vehicles using an area threshold that is much larger than a typical vehicle. Targets, whose width is narrower than the diameter of structure element utilized in the grayscale morphological transformation, were smoothed out from the hypothesis vehicles using binary morphological opening transformation. Finally, the hypothesis vehicles detected in both cases were overlaid. It should be noted that in the detection system, a vehicle could be detected twice by the two approaches. The two identical hypothesis vehicles should be amalgamated into a single one for accuracy assessment subsequently. We tested our system on seventeen highway scenes of aerial images with a spatial resolution of 0.15 × 0.15 m. The experimental results showed that the correctness, completeness, and quality rates of the proposed vehicle detection method were about 98%, 93%, and 92%, respectively. Thus, our proposed approach is robust and efficient to detect vehicles of highway using high resolution aerial images.
Topical Segmentation: a Study of Human Performance and a New Measure of Quality.

In a large-scale study of how people find topical shifts in written text, 27 annotators were asked to mark topically continuous segments in 20 chapters of a novel. We analyze the resulting corpus for inter-annotator agreement and examine disagreement patterns. The results suggest that, while the overall agreement is relatively low, the annotators show high agreement on a subset of topical breaks -- places where most prominent topic shifts occur. We recommend taking into account the prominence of topical shifts when evaluating topical segmentation, effectively penalizing more severely the errors on more important breaks. We propose to account for this in a simple modification of the windowDiff metric. We discuss the experimental results of evaluating several topical segmenters with and without considering the importance of the individual breaks, and emphasize the more insightful nature of the latter analysis.
A secure modular exponential algorithm resists to power, timing, C safe error and M safe error attacks

This paper proposes a method for protecting public key schemes from timing and fault attacks. In general, this is accomplished by implementing critical operations using "branch-less" path routines. More particularly, the proposed method provides a modular exponentiation algorithm without any redundant computation does not have a store operation with non-certain destination so that it can protect the secret key from many known attacks.
The OS* Algorithm: a Joint Approach to Exact Optimization and Sampling

Most current sampling algorithms for high-dimensional distributions are based on MCMC techniques and are approximate in the sense that they are valid only asymptotically. Rejection sampling, on the other hand, produces valid samples, but is unrealistically slow in high-dimension spaces. The OS* algorithm that we propose is a unied approach to exact optimization and sampling, based on incremental renements
Temporal and spectral features of single lead ECG for human identification

The electrocardiogram (ECG) is an electrophysiologic signal that conveys signature biometric data about individuals. While this signal varies across time and with mental state, and is susceptible to noise artifact, this paper presents an approach for classifying individuals that is robust to these signal properties and noise sources. To show maximal information extraction, we take the discrete wavelet transform of a single lead ECG for feature extraction and identify individuals using a multiclass support vector machine. This approach utilizes temporal and spectral information to characterize ECG waveform morphology and timing with low computational cost. To demonstrate the effectiveness of this approach, records from the MIT-BIH normal sinus rhythm database are used to test subject identification, yielding high accuracy and positive predictive value.
Genetic Interactions with Prenatal Social Environment

Numerous studies report gene-environment interactions, suggesting that specific alleles have different effects on social outcomes depending on environment. In all these studies, however, environmental conditions are potentially endogenous to unmeasured genetic characteristics. That is, it could be that the observed interaction effects actually reflect underlying genetic tendencies that lead individuals into certain environments. What is critical to move this literature forward is random environmental variation that we know is not correlated with innate characteristics of subjects. We exploit a natural experiment that randomizes a particular stressor—birth weight discordance within twin pairs—to address this challenge and ask: Do random differences in early environment (prenatal nutrition) moderate genetic effects on depression, delinquency, or GPA? Using Add Health data, the only consistently significant allele–birth weight interaction we reveal works in the opposite direction of Caspi et al.’s classic finding regarding the interaction of maltreatment with genetic variation in the serotonin transporter promoter. Less robust interactions found for DRD2 and MAOA are consistent with this pattern that reverses prior findings. These results do not necessarily overturn existing research but support our methodological point that gene-environment research must address endogeneity.
3D object modelling for entertainment applications

Recent advances in three-dimensional (3D) data acquisition techniques have offered an alternative to the traditional 2D metamorphosis (or morphing) approaches, which gradually change a source object through intermediate objects into a target object. In this paper, we approach 3D metamorphosis via a novel 3D modelling technique, which reconstructs a fairly complex object with a single B-Spline patch. Our object representation is compact - over 90% compression rate can be achieved. Despite such huge amount of data reduction, our method achieves similar rendering result to that using polygonal representation. Our approach also allows a one-to-one mapping from the object space to a common parameter space to be established, to allow automatic correspondence between a pair of objects. This way to establishing object correspondence is advantageous over the common connectivity generation process, with which, if either the source or target object is changed, the whole process of establishing correspondences must be repeated. Several aesthetically pleasing examples of 3D morphing are demonstrated using the proposed method.
Classification of boundaries and accents in spontaneous speech

Das diesem Bericht zugrundeliegende Forschungsvorhaben wurde mit Mitteln des Bundesministers f ur Bildung, Wissenschaft, Forschung und Technologie unter dem F orderkennzeichen 01 IV 102 H/0 und 01 IV 102 F/4 gef ordert. Die Verantwortung f ur den Inhalt dieser Arbeit liegt bei den Autoren.
Domain Speci c Mapping for Solving Graph Problems on Recon gurable Devices ?

Conventional mapping approaches to Recon gurable Computing (RC) utilize CAD tools to perform the technology mapping of a high-level design. In comparison with the execution time on the hardware, extensive amount of time is spent for compilation by the CAD tools. However, the long compilation time is not always considered when evaluating the time performance of RC solutions. In this paper, we propose a domain speci c mapping approach for solving graph problems. The key idea is to alleviate the intervention of the CAD tools at mapping time. High-level designs are synthesized with respect to the speci c domain and are adapted to the input graph instance at run-time. The domain is de ned by the algorithm and the recon gurable target. The proposed approach leads to predictable RC solutions with superior time performance. The time performance metric includes both the mapping time and the execution time. For example, in the case of the single-source shortest path problem, the estimated run-time speed-up is 10 compared with the state-of-the-art. In comparison with software implementations, the estimated run-time speed-up is asymptotically 3:75 and can be improved by further optimization of the hardware design or improvement of the con guration time.
The Parallel Mathematical Libraries Project (PMLP) - A Next Generation Scalable, Sparse, Object-Oriented, Mathematical Library Suite

The Parallel Mathematics Libraries Project (PMLP), a joint e ort of Intel, Lawrence Livermore National Laboratory, the Russian Federal Nuclear Laboratory (VNIIEF), and Mississippi State University (MSU), constitutes a concerted e ort to create a supportable, comprehensive \Sparse Object-Oriented Mathematical Library suite. "With overall design and software validation work at MSU, and most software development and testing at VNIIEF, this international collaboration brings objectoriented programming techniques and C++ to the task of providing linear and nonlinear algebraic-oriented algorithms for scientists and engineers. Language bindings for C, Fortran-77, and C++ are provided, o ering the widest possible applicability. PMLP di ers from other major library e orts in its systematic use of software engineering and design, including e orts to provide high performance, portability, and usability. In addition, important contributions of this e ort, in design principles such as storageformat independence, data-distribution independence etc., which contributes towards the performance, ease-of-use, application interoperability and portability etc., will be highlighted. Finally, we will also provide an initial set of benchmarked results.
Plasma total cysteine, mortality, and cardiovascular disease hospitalizations: the Hordaland Homocysteine Study.

BACKGROUND We have previously reported a positive association between tHcy and mortality and cardiovascular disease (CVD) hospitalizations in the Hordaland Homocysteine Study cohort. Using the same data set, we assessed the relationship between plasma total cysteine (tCys) and mortality from all causes and from cardiovascular and noncardiovascular conditions, and the association between tCys and the risk of hospitalizations from CVD. METHODS We measured plasma tCys in blood samples from 12,595 men and women 40-42 years of age and from 4766 men and women 65-67 years of age, collected as part of the Hordaland Homocysteine Study in the year 1992-1993. Follow-up data on mortality were collected through 1999. Data on CVD hospitalizations were collected from hospital records up to May 31, 1998. RESULTS After a follow-up time of 6.6-7.6 years, there were a total of 610 deaths, of which 243 were cardiovascular deaths and 367 were noncardiovascular deaths. There was no association between tCys and all-cause, cardiovascular, or noncardiovascular mortality. When we used tCys values <247.6 micromol/L (lowest quartile) as the reference category, the adjusted mortality ratio (MR) for all-cause mortality at tCys concentrations of 247.6-270.79, 270.8-295.79, and > or =295.8 micromol/L (highest quartile) were 1.0, 0.9, and 1.0, respectively. The adjusted MRs for cardiovascular mortality were 1.0, 1.1, and 1.1, respectively. There were no associations between tCys and 1275 CVD hospitalizations, except that tCys was significantly associated with hospitalizations from coronary artery bypass grafting. CONCLUSION Plasma tCys is not associated with mortality or CVD hospitalizations.
Study of Resource Utilization in IEEE 802.15.4 Wireless Body Sensor Network, Part I: The Need for Enhancement

The impact of shared frequency spectrum on performance of Radio Frequency (RF) technologies such as Wireless Body Sensor Networks (WBSNs), have recently brought a serious attention among computer scientists. In this study, the impact of channel scarcity on WBSN performance is investigated from various points of view, Spectrum utilization level, orphan scanning duration, packet loss and total energy consumption. We have proposed two schemes called Idealized scheme and Initial-Choice scheme to indicate the channel utilization in "Ideal" and "realistic" manners respectively. A comparison among abovementioned schemes and a simplified version of IEEE 802.15. 4 standard is managed to evaluate the performance of them. Furthermore, to highlight the tangible need of extensive investigation on channel utilization concept is considered as another scope of this study. Eventually, it is revealed that the deployment of IEEE 802.15. 4 standard protocol, could cause the WBSN's performance degradation as the number of WBSNs increases. This is due to sever impact of channel coexistence and WBSNs overlapping active periods while there is still gaps (free slots) available and the channel is not fully utilized.
Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction

This paper presents a method of automatically constructing information extraction patterns on predicate-argument structures (PASs) obtained by full parsing from a smaller training corpus. Because PASs represent generalized structures for syntactical variants, patterns on PASs are expected to be more generalized than those on surface words. In addition, patterns are divided into components to improve recall and we introduce a Support Vector Machine to learn a prediction model using pattern matching results. In this paper, we present experimental results and analyze them on how well protein-protein interactions were extracted from MEDLINE abstracts. The results demonstrated that our method improved accuracy compared to a machine learning approach using surface word/part-of-speech patterns.
The end of handwriting? Using computers in traditional essay examinations

Most of our students complete most of their written assignments using a word processor, but they are still asked to handwrite responses in an examination. It could be argued that they have not practiced this task and the validity of the assessment could thus be questioned. This paper explores the possibility of bringing computers into the traditional essay-examination context, describes an appropriate hardware and software configuration, and provides feedback from initial evaluations with students and their reactions to the idea. Some of the implications and equity concerns that need to be considered before a decision can be made to use computers in essay exams are also discussed.
Direct mechanical stimulation of tip links in hair cells through DNA tethers

Mechanoelectrical transduction by hair cells commences with hair-bundle deflection, which is postulated to tense filamentous tip links connected to transduction channels. Because direct mechanical stimulation of tip links has not been experimentally possible, this hypothesis has not been tested. We have engineered DNA tethers that link superparamagnetic beads to tip links and exert mechanical forces on the links when exposed to a magnetic-field gradient. By pulling directly on tip links of the bullfrog's sacculus we have evoked transduction currents from hair cells, confirming the hypothesis that tension in the tip links opens transduction channels. This demonstration of direct mechanical access to tip links additionally lays a foundation for experiments probing the mechanics of individual channels. DOI: http://dx.doi. org/10.7554/eLife.16041. 001
Human hallucinogen research: guidelines for safety

There has recently been a renewal of human research with classical hallucinogens (psychedelics). This paper first briefly discusses the unique history of human hallucinogen research, and then reviews the risks of hallucinogen administration and safeguards for minimizing these risks. Although hallucinogens are relatively safe physiologically and are not considered drugs of dependence, their administration involves unique psychological risks. The most likely risk is overwhelming distress during drug action ('bad trip'), which could lead to potentially dangerous behaviour such as leaving the study site. Less common are prolonged psychoses triggered by hallucinogens. Safeguards against these risks include the exclusion of volunteers with personal or family history of psychotic disorders or other severe psychiatric disorders, establishing trust and rapport between session monitors and volunteer before the session, careful volunteer preparation, a safe physical session environment and interpersonal support from at least two study monitors during the session. Investigators should probe for the relatively rare hallucinogen persisting perception disorder in follow-up contact. Persisting adverse reactions are rare when research is conducted along these guidelines. Incautious research may jeopardize participant safety and future research. However, carefully conducted research may inform the treatment of psychiatric disorders, and may lead to advances in basic science.
Cosine Similarity Measure According to a Convex Cost Function

In this paper, we describe a new vector similarity measure associated with a convex cost function. Given two vectors, we determine the surface normals of the convex function at the vectors. The angle between the two surface normals is the similarity measure. Convex cost function can be the negative entropy function, total variation (TV) function and filtered variation function. The convex cost function need not be differentiable everywhere. In general, we need to compute the gradient of the cost function to compute the surface normals. If the gradient does not exist at a given vector, it is possible to use the subgradients and the normal producing the smallest angle between the two vectors is used to compute the similarity measure.
Overexpression of Rat Neurons Nitric Oxide Synthase in Rice Enhances Drought and Salt Tolerance

Nitric oxide (NO) has been shown to play an important role in the plant response to biotic and abiotic stresses in Arabidopsis mutants with lower or higher levels of endogenous NO. The exogenous application of NO donors or scavengers has also suggested an important role for NO in plant defense against environmental stress. In this study, rice plants under drought and high salinity conditions showed increased nitric oxide synthase (NOS) activity and NO levels. Overexpression of rat neuronal NO synthase (nNOS) in rice increased both NOS activity and NO accumulation, resulting in improved tolerance of the transgenic plants to both drought and salt stresses. nNOS-overexpressing plants exhibited stronger water-holding capability, higher proline accumulation, less lipid peroxidation and reduced electrolyte leakage under drought and salt conditions than wild rice. Moreover, nNOS-overexpressing plants accumulated less H2O2, due to the observed up-regulation of OsCATA, OsCATB and OsPOX1. In agreement, the activities of CAT and POX were higher in transgenic rice than wild type. Additionally, the expression of six tested stress-responsive genes including OsDREB2A, OsDREB2B, OsSNAC1, OsSNAC2, OsLEA3 and OsRD29A, in nNOS-overexpressing plants was higher than that in the wild type under drought and high salinity conditions. Taken together, our results suggest that nNOS overexpression suppresses the stress-enhanced electrolyte leakage, lipid peroxidation and H2O2 accumulation, and promotes proline accumulation and the expression of stress-responsive genes under stress conditions, thereby promoting increased tolerance to drought and salt stresses.