Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between reactive oxygen species production in human semen and sperm DNA damage assessed by Sperm Chromatin Structure Assay.

AIM The aim of this prospective study was to find possible relationship between ROS production measured by chemiluminescence and flow cytometry in human semen and sperm DNA damage estimated by Sperm Chromatin Structure Assay. METHODS Study included 39 men from infertile couples and 23 fertile volunteers who served as a control group. Aliquot of neat semen was used for ROS detection by chemiluminescence. Aliquot of sperm suspension in phosphate buffered saline was used for the detection of ROS by flow cytometry. Another aliquot of sperm suspension was used for SCSA to measure DNA fragmentation index and High DNA stainability. RESULTS DNA fragmentation index correlated negatively with sperm morphology and motility. High DNA stainability correlated positively with ROS production and negatively with sperm morphology and concentration. Although there were similar trends of rising DNA fragmentation index and ROS production among the three groups of men, the relationship did not reach statistical significance. CONCLUSIONS Higher values of DNA fragmentation index and high DNA stainability may also reflect developmental and/or environmental problems and not only oxidative stress.
The Client’s Intervention Priorities (CIP)©: A person-centered tool to support goal setting during interdisciplinary neurorehabilitation

Abstract Evidence-based neurorehabilitation must be informed by the values, expectations, and goals of individuals with acquired brain injury (ABI). The Client’s Intervention Priorities (CIP)© is a person-centered tool for defining rehabilitation priorities according to self-perceived functioning. The use of the CIP tool is encouraged to promote self-determination and optimal involvement of individuals with ABI in interdisciplinary neurorehabilitation. The objective of this study was to determine the reliability (internal consistency, temporal stability) and content validity (expert agreement) of the CIP tool. Thirty individuals with ABI (66.7% with traumatic brain injury, 33.3% with stroke) with a mean age of 44.8 (SD = 12.6) years were administered the CIP twice at a test-retest interval of 2.3 (SD = 0.7) weeks. An expert panel of 17 neurorehabilitation clinicians and researchers participated in the validation. The CIP tool showed excellent (total score α = .90) and good (CIP subscales α = .83-.87) internal consistencies, with excellent temporal stability (intraclass correlation coefficients = .78-.90). Experts agreed that the CIP items reflect the Disability Creation Process model (89.4% scored as having high to very high correspondence) and were comprehensibly stated (98% rated as clear to absolutely clear). The CIP is a valid and reliable self-assessment tool to assist professionals and their clients in developing and prioritizing rehabilitation goals.
MPI Overlap: Benchmark and Analysis

In HPC applications, one of the major overhead compared to sequential code, is communication cost. Application programmers often amortize this cost by overlapping communications with computation. To do so, they post a non-blocking MPI request, perform computation, and wait for communication completion, assuming MPI communication will progress in background. In this paper, we propose to measure what really happens when trying to overlap non-blocking point-to-point communications with computation. We explain how background progression works, we describe relevant test cases, we identify challenges for a benchmark, then we propose a benchmark suite to measure how much overlap happen in various cases. We exhibit overlap benchmark results on a wide panel of MPI libraries and hardware platforms. Finally, we classify, analyze, and explain the results using low-level traces to reveal the internal behavior of the MPI library.
CROP GROUND COVER FRACTION AND CANOPY CHLOROPHYLL CONTENT MAPPING USING RAPIDEYE IMAGERY

Remote sensing is a suitable tool for estimating the spatial variability of crop canopy characteristics, such as canopy chlorophyll content (CCC) and green ground cover (GGC%), which are often used for crop productivity analysis and site-specific crop management. Empirical relationships exist between different vegetation indices (VI) and CCC and GGC% that allow spatial estimation of canopy characteristics from remote sensing imagery. However, the use of VIs is not suitable for an operational production of CCC and GGC% maps due to the limited transferability of derived empirical relationships to other regions. Thus, the operational value of crop status maps derived from remotely sensed data would be much higher if there was no need for reparametrization of the approach for different situations. This paper reports on the suitability of high-resolution RapidEye data for estimating crop development status of winter wheat over the growing season, and demonstrates two different approaches for mapping CCC and GGC%, which do not rely on empirical relationships. The final CCC map represents relative differences in CCC, which can be quickly calibrated to field specific conditions using SPAD chlorophyll meter readings at a few points. The prediction model is capable of predicting SPAD readings with an average accuracy of 77%. The GGC% map provides absolute values at any point in the field. A high R² value of 80% was obtained for the relationship between estimated and observed GGC%. The mean absolute error for each of the two acquisition dates was 5.3% and 8.7%, respectively.
National Conference of Commissioners on Uniform State Laws

The ideas and conclusions set forth in this draft, including the proposed statutory language and any comments or reporter=s notes, have not been passed upon by the National Conference of Commissioners on Uniform State Laws or the Drafting Committee. They do not necessarily reflect the views of the Conference and its Commissioners and the Drafting Committee and its Members and Reporter. Proposed statutory language may not be used to ascertain the intent or meaning of any promulgated final statutory proposal.
Reusability assessment of test collections with multi-levels of judgments

Constructing good test collection is an expensive and time-consuming process. Traditionally, test collections contain binary judgments. In recent years, however, there has been increasingly interest in test collections with Multi-levels judgments and of certain qualities. Such collections are even more expensive to construct. Therefore, ability to reuse test collections can not only save construction costs, but also boosts our confidence in their quality. This paper proposes a method for assessing reusability of a test collection with multi-level judgments. The proposed method can help IR researchers to determine whether an existing test collection with a set of multi-level judgments is suitable for evaluating a new IR system or not. Results of our experiments (on MAHAK test collection) suggest that this method can help assessing reusability of a test collection.
Modeling and Identification of Worst-Case Cascading Failures in Power Systems

Cascading failures in power systems normally occur as a result of initial disturbance or faults on electrical elements, closely followed by errors of human operators. It remains a great challenge to systematically trace the source of cascading failures in power systems. In this paper, we develop a mathematical model to describe the cascading dynamics of transmission lines in power networks. In particular, the direct current (DC) power flow equation is employed to calculate the transmission power on the branches. By regarding the disturbances on the elements as the control inputs, we formulate the problem of determining the initial disturbances causing the cascading blackout of power grids in the framework of optimal control theory, and the magnitude of disturbances or faults on the selected branch can be obtained by solving the system of algebraic equations. Moreover, an iterative search algorithm is proposed to look for the optimal solution leading to the worst case of cascading failures. Theoretical analysis guarantees the asymptotic convergence of the iterative search algorithm. Finally, numerical simulations are carried out in IEEE 9 Bus System and IEEE 14 Bus System to validate the proposed approach.
Comparison of the therapeutic dose of warfarin in HIV-infected and HIV-uninfected patients: a study of clinical practice

Background People infected with HIV are prone to venous thrombosis. Treatment of thrombosis is primarily with warfarin. No studies have addressed the effects of HIV infection on warfarin dose. The aims of this study were to determine whether the therapeutic dose of warfarin and induction time to therapeutic dose in HIV-infected patients differ from that in HIV-uninfected patients. Methods A prospective and retrospective descriptive study of induction time to therapeutic warfarin dose, as well as of ambulant therapeutic warfarin dose, was performed. HIV-infected and HIV-uninfected patients being treated after deep venous thrombosis with or without pulmonary embolism were compared. Sex and use of antiretroviral drugs (ARVs) were also compared in the groups. Results 234 patients were entered into the study. Induction time to therapeutic warfarin dose did not differ between the 2 groups. The mean therapeutic dose of warfarin was higher in the HIV-infected than the HIV-uninfected group: 6.06 vs 5.72 mg/day, but this was not statistically significant (p=0.29). There was no difference in therapeutic warfarin dose between ARV-naïve groups—HIV-uninfected and HIV-infected patients not on ARVs. Conclusions There appears to be little effect of HIV infection on warfarin dosing. Warfarin therapy should be administered conventionally in HIV-infected patients.
Proteolysis of the Docking Protein HEF1 and Implications for Focal Adhesion Dynamics

ABSTRACT The dynamic regulation of focal adhesions is implicated in cellular processes of proliferation, differentiation, migration, and apoptosis. The focal adhesion-associated docking protein HEF1 is cleaved by caspases during both mitosis and apoptosis. Common to both of these cellular processes is the loss of focal adhesions, transiently during mitosis and permanently during apoptosis. The proteolytic processing of HEF1 during both mitosis and apoptosis therefore posits a general role for HEF1 as a sensor of altered adhesion states. In this study, we find that HEF1 undergoes proteolytic processing specifically in response to cellular detachment, while HEF1 proteolysis is prevented by specific integrin receptor ligation and focal adhesion formation. We show that overexpression of a C-terminal caspase-derived 28-kDa HEF1 peptide causes cellular rounding that is demonstrably separable from apoptosis. Mutation of the divergent helix-loop-helix motif found in 28-kDa HEF1 significantly reduces the induction of apoptosis by this peptide, while deletion of the amino-terminal 28 amino acids of 28-kDa HEF1 completely abrogates the induction of apoptosis. Conversely, these mutations have no effect on the rounding induced by 28-kDa HEF1. Finally, we detect a novel focal adhesion targeting domain located in the C terminus of HEF1 and show that this activity is necessary for HEF1-induced cell spreading. Together, these data suggest that proteolytic and other posttranslational modifications of HEF1 in response to loss of adhesion serve to modulate the disassembly of focal adhesions.
Algorithmic Robustness for Learning via $(\epsilon, \gamma, \tau)$-Good Similarity Functions

The notion of metric plays a key role in machine learning problems such as classification, clustering or ranking. However, it is worth noting that there is a severe lack of theoretical guarantees that can be expected on the generalization capacity of the classifier associated to a given metric. The theoretical framework of $(\epsilon, \gamma, \tau)$-good similarity functions (Balcan et al., 2008) has been one of the first attempts to draw a link between the properties of a similarity function and those of a linear classifier making use of it. In this paper, we extend and complete this theory by providing a new generalization bound for the associated classifier based on the algorithmic robustness framework.
Integration of perception, control and injury knowledge for safe human-robot interaction

In the past few years the need for more flexibility in industrial production has implied a growing attention towards scenarios where humans work directly in touch with robots. In order to allow safe human-robot interaction, a methodology to evaluate the severity of an impact between a human worker and an industrial robot, based on related work on injury knowledge in human-robot contacts and relying on information coming from different exteroceptive sensors, has been developed in this paper. On the basis of this severity evaluation, the robot controller enforces a suitable safety-oriented strategy, ranging from on-path speed reduction to task-consistent evasive motion and protective stop. The safety evaluation methodology has been implemented in a dedicated software component, integrated with a video surveillance system and with the real time robot controller to obtain a complete HW/SW architecture named “Safety Controller”. The system has been validated on an ABB IRB140 robot.
Effect of added inertia on the pelvis on gait

Gait-training robots must display a low inertia in order to allow normal-looking walking. We studied the effect of inertia added to the pelvis during walking. We attached subjects to a mechanism that displays inertia to the pelvis in the anterior/posterior (AP) direction and the lateral direction independently. During walking we measured EMG, metabolic rate and kinematics of nine subjects. We found that inertias up to 5.3 kg added in lateral direction had no significant effect on gait. We found that 4.3 kg added in the AP direction had a significant but not relevant effect on the range of motion (RoM) of pelvis AP displacement and acceleration, and on hip flexion. 10.3 kg caused a significant and relevant difference in pelvis acceleration RoM. 6 kg is estimated as the maximum inertia that gait-training robots can add to the pelvis, without affecting the gait.
The action potential‐evoked sarcoplasmic reticulum calcium release is impaired in mdx mouse muscle fibres

The mdx mouse, a model of the human disease Duchenne muscular dystrophy, has skeletal muscle fibres which display incompletely understood impaired contractile function. We explored the possibility that action potential‐evoked Ca2+ release is altered in mdx fibres. Action potential‐evoked Ca2+‐dependent fluorescence transients were recorded, using both low and high affinity Ca2+ indicators, from enzymatically isolated fibres obtained from extensor digitorum longus (EDL) and flexor digitorum brevis (FDB) muscles of normal and mdx mice. Fibres were immobilized using either intracellular EGTA or N‐benzyl‐p‐toluene sulphonamide, an inhibitor of the myosin II ATPase. We found that the amplitude of the action potential‐evoked Ca2+ transients was significantly decreased in mdx mice with no measured difference in that of the surface action potential. In addition, Ca2+ transients recorded from mdx fibres in the absence of EGTA also displayed a marked prolongation of the slow decay phase. Model simulations of the action potential‐evoked transients in the presence of high EGTA concentrations suggest that the reduction in the evoked sarcoplasmic reticulum Ca2+ release flux is responsible for the decrease in the peak of the Ca2+ transient in mdx fibres. Since the myoplasmic Ca2+ concentration is a critical regulator of muscle contraction, these results may help to explain the weakness observed in skeletal muscle fibres from mdx mice and, possibly, Duchenne muscular dystrophy patients.
CEGA—a catalog of conserved elements from genomic alignments

By identifying genomic sequence regions conserved among several species, comparative genomics offers opportunities to discover putatively functional elements without any prior knowledge of what these functions might be. Comparative analyses across mammals estimated 4–5% of the human genome to be functionally constrained, a much larger fraction than the 1–2% occupied by annotated protein-coding or RNA genes. Such functionally constrained yet unannotated regions have been referred to as conserved non-coding sequences (CNCs) or ultra-conserved elements (UCEs), which remain largely uncharacterized but probably form a highly heterogeneous group of elements including enhancers, promoters, motifs, and others. To facilitate the study of such CNCs/UCEs, we present our resource of Conserved Elements from Genomic Alignments (CEGA), accessible from http://cega.ezlab. org. Harnessing the power of multiple species comparisons to detect genomic elements under purifying selection, CEGA provides a comprehensive set of CNCs identified at different radiations along the vertebrate lineage. Evolutionary constraint is identified using threshold-free phylogenetic modeling of unbiased and sensitive global alignments of genomic synteny blocks identified using protein orthology. We identified CNCs independently for five vertebrate clades, each referring to a different last common ancestor and therefore to an overlapping but varying set of CNCs with 24 488 in vertebrates, 241 575 in amniotes, 709 743 in Eutheria, 642 701 in Boreoeutheria and 612 364 in Euarchontoglires, spanning from 6 Mbp in vertebrates to 119 Mbp in Euarchontoglires. The dynamic CEGA web interface displays alignments, genomic locations, as well as biologically relevant data to help prioritize and select CNCs of interest for further functional investigations.
Correlated gravitational lensing of the CMB

Cosmological inhomogeneities gravitationally deflect radiation propagating from distant sources, transforming the spatial and angular correlation functions of intrinsic source properties. For a gaussian distribution of deflections (e.g. from a primordial gaussian density perturbation spectrum or from the central limit theorem) we calculate the probability distributions for geodesic deviations. If the intrinsic variable is also gaussian, e.g. the large scale velocity flow field or cosmic microwave background temperature anisotropies, then distributions and correlation functions of the observed image sky properties can be obtained. Specialising to CMB temperature fluctuations we rederive simply the influence of independent gravitational lensing on the anisotropy angular correlation function and calculate the new effect of lensing correlated with the anisotropies, e.g. arising from the same primordial gravitational perturbation field. Characteristic magnitudes and scales are given in terms of the density power spectrum. The correlated deflection-temperature effect is shown to be negligible.
RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria

Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.
New stemming for arabic text classification using feature selection and decision trees

In this paper we conduct a comparative study between two stemming algorithms: khoja stemmer and our new stemmer for Arabic text classification (categorization), using Chisquare statistics as feature selection and focusing on decision tree classifier. Evaluation used a corpus that consists of 5070 documents independently classified into six categories: sport, entertainment, business, middle east, switch and world, on WEKA toolkit. The recall measure is used to compare the performance of these methods. Results show that text classification using our new stemmer outperforms classification using Khoja stemmer. Keywords—Arabic Text classification; Stemming; Decision tree; Chi-square;
Time compression characteristics of the Augmented Prototyping Pipeline

1. Introduction Current rapid prototyping techniques are of limited use in the early phases of design. In order to establish a more dynamic and effective means, the concept of augmented prototyping recently gained interest [Stork et al., 2002][Verlinden et al., 2003]. The concept of Augmented Prototyping combines Rapid Prototyping techniques to obtain 3D physical objects (e.g. Stereo lithography, NC milling), with Augmented Reality systems. For example, Figure 1 shows a NC milled foam model of a car on which a video projector directly beams digital 3D perspective renderings. In such a combination of physical and virtual prototyping, only a rough, global physical shape has to be manufactured, while
Hardware based algorithm for conflict diagnosis in SAT solver

The Boolean satisfiability problem (SAT) is an NP-complete problem so software SAT's solving algorithm execution time influences the performance of SAT- based CAD tools. In this paper, we present a new approach for implementing conflict analysis based on a conflicting variables accumulator and priority encoder to determine backtrack level Using this approach, we implement an FPGA-based SAT solver performing depth- first search with conflict directed nonchronological backtracking. We compare our SAT solver with other SAT solvers through instances from DIMACS benchmarks suite.
Guided Parsing of Range Concatenation Languages

The theoretical study of the range concatenation grammar [RCG] formalism has revealed many attractive properties which may be used in NLP. In particular, range concatenation languages [RCL] can be parsed in polynomial time and many classical grammatical formalisms can be translated into equivalent RCGs without increasing their worst-case parsing time complexity. For example, after translation into an equivalent RCG, any tree adjoining grammar can be parsed in O(n6) time. In this paper, we study a parsing technique whose purpose is to improve the practical efficiency of RCL parsers. The non-deterministic parsing choices of the main parser for a language L are directed by a guide which uses the shared derivation forest output by a prior RCL parser for a suitable superset of L. The results of a practical evaluation of this method on a wide coverage English grammar are given.