Miracle-dz/UniFAR-FTUs huggingface dataset:
Scala: A Performance System for Scalable Computing

Summary Lack of effective performance-evaluation environments is a major barrier to the broader use of high performance computing. Conventional performance environments are based on profiling and event instrumentation. It becomes problematic as parallel systems scale to hundreds of nodes and beyond. A framework of developing an integrated performance modeling and prediction system, SCALability Analyzer (SCALA), is presented in this study. In contrast to existing performance tools, the program performance model generated by SCALA is based on scalability analysis. SCALA assumes the availability of modern compiler technology, adopts statistical and symbolic methodologies, and has the support of browser interface. These technologies, together with anew approach of scalability analysis, enable SCALA to provide the user with a more intuitive level of performance analysis for scalable computing. A prototype SCALA system has been implemented. Initial experimental results show that SCALA is unique in its ability of revealing the scaling properties of a computing system.
Pharmaco-Electrophysiology of Isolated Perfused Rat Heart Assessed with Flexible Microelectrode Arrays

Background: Heart slices and enzymatically dissociated cardiomyocytes are used in cardiac safety pharmacology for extracellular recording using microelectrode array (MEA). The aim of this study was to set up and validate a vitro cardiac surface mapping system for studies pharmaco-electrophysiology effects in Langendorff perfused rat hearts by flexible MEA. Materials and Methods: Hearts isolated from Sprague-Dawley (SD) male rat of either sex weighing 200-250 g were perfused by the Langendorff method with Tyrode’s solution. A cardiac surface mapping system suitable for recordings from Langendorff-perfused rat hearts using the Class III antiarrhythmic agents has been developed. In 48 Langendorff-perfused rat hearts, after obtaining baseline data, ibutilide, amiodarone or dofetilide were infused. The field potentials (FP) and heart rhythm by Multi-channel flexible MEA were monitored throughout the experiments. Results: Langendorff perfusion enabled the autorhythmicity of the rats’ heart last about 240 min. Simultaneous 64 channels FP graphs could be recorded stably. FP duration revealed significant, dose-dependent prolongation more than 2 fold upon administration of three drugs, but present a different proarrhythmic properties (dofetilide> ibutilide>amiodarone). Dofetilide and ibutilide lead to early afterdepolarizations (EAD) and ventricular tachycardia (VT) but not amiodarone. Amiodarone led to atrial ventricular block, atrial flutter and junctional escape rhythm, in the presence of ibutilide or dofetilide, neither EAD nor VT occur. Conclusion: Our model with isolated rat heart and flexible MEA represents a novel and reliable tool for application in cardiac safety pharmacology and preclinical studies of electrophysiological effects of various pathophysiological concepts.
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

Mutations create the genetic diversity on which selective pressures can act, yet also create structural instability in proteins. How, then, is it possible for organisms to ameliorate mutation-induced perturbations of protein stability while maintaining biological fitness and gaining a selective advantage? Here we used site-specific chromosomal mutagenesis to introduce a selected set of mostly destabilizing mutations into folA—an essential chromosomal gene of Escherichia coli encoding dihydrofolate reductase (DHFR)—to determine how changes in protein stability, activity, and abundance affect fitness. In total, 27 E. coli strains carrying mutant DHFR were created. We found no significant correlation between protein stability and its catalytic activity nor between catalytic activity and fitness in a limited range of variation of catalytic activity observed in mutants. The stability of these mutants is strongly correlated with their intracellular abundance, suggesting that protein homeostatic machinery plays an active role in maintaining intracellular concentrations of proteins. Fitness also shows a significant correlation with intracellular abundance of soluble DHFR in cells growing at 30 °C. At 42 °C, the picture was mixed, yet remarkable: A few strains carrying mutant DHFR proteins aggregated, rendering them nonviable, but, intriguingly, the majority exhibited fitness higher than wild type. We found that mutational destabilization of DHFR proteins in E. coli is counterbalanced at 42 °C by their soluble oligomerization, thereby restoring structural stability and protecting against aggregation.
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment

MOTIVATION Non-coding RNA genes and RNA structural regulatory motifs play important roles in gene regulation and other cellular functions. They are often characterized by specific secondary structures that are critical to their functions and are often conserved in phylogenetically or functionally related sequences. Predicting common RNA secondary structures in multiple unaligned sequences remains a challenge in bioinformatics research. METHODS AND RESULTS We present a new sampling based algorithm to predict common RNA secondary structures in multiple unaligned sequences. Our algorithm finds the common structure between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures and subsequently recalculates stem conservation using the updated probabilities. The iterative process terminates upon convergence of the sampled structures. We extend the algorithm to multiple sequences by a consistency-based method, which iteratively incorporates and reinforces consistent structure information from pairwise comparisons into consensus structures. The algorithm has no limitation on predicting pseudoknots. In extensive testing on real sequence data, our algorithm outperformed other leading RNA structure prediction methods in both sensitivity and specificity with a reasonably fast speed. It also generated better structural alignments than other programs in sequences of a wide range of identities, which more accurately represent the RNA secondary structure conservations. AVAILABILITY The algorithm is implemented in a C program, RNA Sampler, which is available at http://ural.wustl. edu/software.html
Quality of life of post–stroke patients and their caregivers

With improvements in health care, more people survive stroke but many have to cope with the physical, psychological, social and functional sequelae, resulting in increased personal and public costs. Cerebral stroke causes a significant deterioration of the patient's functioning and worsening of her/his quality of life. Long–term disability caused by stroke is a common problem in all countries and its incidence increases markedly with advancing age. The assessment of the Quality of Life could be as well the evaluator of sequelae of stroke as an indicator of the effectiveness of the post–stroke rehabilitation. In this review article, the contemporary state of art in assessment of the post–stroke Quality of Life has been presented. The emphasis was placed on participation in terms of personal factors and environmental factors of post–stroke persons and their caregivers.
An Evaluation and Design Support System for Urban Walkability

We present an operational proposal for the evaluation of walkability. Its distinguishing characteristic in conceptualising walkability is to take into account and combine three distinct elements in a multicriteria evaluation model: the availability of attractive destinations, their effective distances along a detailed representation of the street network and the qualities relevant to walkability of the potential paths leading to these destinations. In other words, our construction of the walkability score does not reflect only how a place is per se walkable, but rather what is the walkability that place is endowed with. We further present examples and use cases of how such an operational approach may be used (1) for the evaluation of walkability of an urban area; (2) as a "conventional" planning and decision support system, through comparing the effects of urban projects on the walkability of the area; and finally (3) as a design support system, with having the system itself attempt to devise possible designs and projects, given a userdefined objective to raise the walkability of an urban area. _______________________________________________________ I. Blecic (Corresponding author) • Arnaldo Cecchini • Francesco Fancello Giovanna Fancello • Giuseppe A. Trunfio Department of Architecture, Design and Planning, University of Sassari, Palazzo Pou Salut, Piazza Duomo 6, 07041 Alghero, Italy Emails: ivan@uniss.it • cecchini@uniss.it • francesco-fancello@hotmail.it • giannina.fancello@gmail.com • trunfio@uniss.it CUPUM 2015 138-Paper
POSTECH machine translation system for IWSLT 2008 evaluation campaign.

In this paper, we describe POSTECH system for IWSLT 2008 evaluation campaign. The system is based on phrase based statistical machine translation. We set up a baseline system using well known freely available software. A preprocessing method and a language modeling method have been applied to the baseline system in order to improve machine translation quality. The preprocessing method is to identify and remove useless tokens in source texts. And the language modeling method models phrase level n-gram. We have participated in the BTEC tasks to see the effects of our methods.
PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor. org/PredPPCrys.
The SkinBase Project: Providing 3D Virtual Access to Indigenous Skin Clothing Collections from the Circumpolar Area

In 2014, the National Museum of Denmark (NMD), in conjunction with the Greenland National Museum and Archives (Nunatta Katersugaasivia Allagaateqarfialu [NKA]), as well as the Museum of Cultural History, Oslo, launched the website Skin Clothing Online. The site presents the NMD’s total collection of 2,170 historic skin clothing items, dating from circa 1830 to 1950, from the circumpolar area. The clothing can be studied in minute detail due to high-resolution photos; 100 complete suits were photographed from all sides. Furthermore, 107 items of clothing were measured by means of 3D technology, which can be used to draw precise two-dimensional patterns. The documentation is made accessible to the public through a website, in compliance with creative commons licenses: CC-BY-SA for the photos and CC-BY-SA-NC for the patterns. The website uses content from the database SkinBase. Since 2017 parts of the NKA’s collection of archeological skin clothing from Qilakitsoq (circa 1475 AD), as well as historical garments and contemporary fashions, have also been made accessible, in keeping with the same copyright rules for photos. The NKA staff entered the items into the database without difficulty using a Virtual Private Connection (VPN). The Danish and Greenlandic national museums encourage international partners to contribute items to the website. The aim is to create a collaborative open forum for information and research with easy access for everybody to unique, fragile pieces of circumpolar cultural heritage. With clothing from Arctic peoples and clothing used on expeditions to Antarctica, the Polar Museum in Cambridge will be the next museum to contribute to the website.
Environmental toxicology and chemistry in Latin America

Fil: Carriquiriborde, Pedro. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Quimica. Centro de Investigaciones del Medio Ambiente; Argentina
Semi-definite programming and functional inequalities for distributed parameter systems

We study one-dimensional integral inequalities on bounded domains, with quadratic integrands. Conditions for these inequalities to hold are formulated in terms of function matrix inequalities which must hold in the domain of integration. For the case of polynomial function matrices, sufficient conditions for positivity of the matrix inequality and, therefore, for the integral inequalities are cast as semi-definite programs. The inequalities are used to study stability of linear partial differential equations.
Sensitivity of bronchial responsiveness measurements in young infants.

OBJECTIVES There is limited evidence on the preferred methods for evaluating lung function in infancy. The objective of this study was to compare sensitivity and repeatability of indexes of lung function in young infants during induced airway obstruction. METHODS The study population consisted of 402 infants (median age, 6 weeks). Forced flow-volume measurements were obtained by the raised volume rapid thoracoabdominal compression technique and were compared with indexes of tidal breathing, measurements of transcutaneous oxygen (Ptco(2)), and auscultation during methacholine challenge testing. RESULTS Ptco(2) was the most sensitive parameter to detect increasing airway obstruction during methacholine challenge, followed by forced expiratory volume at 0.5 s (FEV(0.5)). Both were superior to other indexes of forced spirometry as well as tidal breathing indexes and auscultation. Coefficients of variations for Ptco(2) and FEV(0.5) were 4% and 7%, respectively. CONCLUSIONS Ptco(2) and FEV(0.5) are the most sensitive parameters for measurement of bronchial responsiveness in young infants. Measurements of baseline lung function should preferably be made using FEV(0.5.) Measurements of bronchial responsiveness are best assessed using Ptco(2), which may be performed in nonsedated infants and improve feasibility of future studies on lung function in infancy.
Tapping Mode. Optical Micrographs Were Recorded with Polarized Visualizing Ion Currents in Conjugated Polymers**

light microscopy (Zeiss LM Axioplan) equipped with digital camera. The cell thickness was determined by UV-visible spectroscopy (Shimadzu UV-3102 PC). Electro-Optical Characterization: The electro-optical characteristics were investigated using DMS 703 display measuring system (Autronic-Melchers GmbH). A square wave was used in order to drive the cells for the dynamic response measurements. In numerous technologically important materials, electro-chemical reactions are accompanied by the mass transport of charged particles. For example, ion ingress and egress during 1605 Figure 6. Shows the conoscopic images a) polyimide by conventional rubbing, anti-parallel cells (18 lm), b) l-rubbed, anti-parallel cells.
Microsatellite loci within sixgill sharks, Hexanchus griseus

Novel sixgill shark (Hexanchus griseus) microsatellite loci were developed and tested on five shark species. A suite of microsatellite loci previously developed for lemon sharks (Negaprion brevirostris) was also tested. Data on 15 microsatellites are presented including primer sequences, number of alleles (a), observed (HO) and expected heterozygosities (HE), and FIS values for sixgill sharks (a = 10–69, HO = 0.24–1.00, HE = 0.76–0.96 and FIS = –0.21–0.60), sevengill sharks (Notorynchus cepedianus) (a = 6–40, HO = 0.20–0.73, HE = 0.59–0.94 and FIS = –0.47–0.58), Pacific spiny dogfish (Squalus acanthias) (a = 3–13, HO = 0.00–0.96, HE = 0.24–0.93 and FIS =–0.52–1.00), angle sharks (Squatina californica) (a = 1–4, HO = 0.00–1.00, HE = 0.60–1.00 and FIS =–1.00–0.25), and leopard sharks (Triakis semifasciata) (a = 3–16, HO = 0.20–1.00, HE = 0.53–0.92 and FIS = –0.57–1.00). A final suite of 14 microsatellites (13 developed from sixgill sharks and one from lemon sharks) were found to be polymorphic and conform to Hardy–Weinberg equilibrium within sixgill sharks.
Dynamic scheduling strategies for shared-memory multiprocessors

Efficiently scheduling parallel tasks on to the processors of a shared-memory multiprocessor is critical to achieving high performance. Given perfect information at compile-time, a static scheduling strategy can produce an assignment of tasks to processors that ideally balances the load among the processors while minimizing the run-time scheduling overhead and the average memory referencing delay. Since perfect information is seldom available, however, dynamic scheduling strategies distribute the task assignment function to the processors by having idle processors allocate work to themselves from a shared queue. While this approach can improve the load balancing compared to static scheduling, the time required to access the shared work queue adds directly to the overall execution time. To overlap the time required to dynamically schedule tasks with the execution of the tasks, we examine a class of self-adjusting dynamic scheduling (SADS) algorithms that centralizes the assignment of tasks to processors. These algorithms dedicate a single processor of the multiprocessor to perform a novel on-line branch-and-bound technique that dynamically computes partial schedules based on the loads of the other processors and the memory locality (affinity) of the tasks and the processors. Our simulation results show that this centralized scheduling outperforms self-scheduling algorithms even when using only a small number of processors.
New all digital frequency divider and phase shifter

In this paper, a counter based all digital frequency divider is presented. The architecture is based on a counter and a control logic which controls the division ratio. Depending on the control logic circuitry, phase shifting of divided clock signal is also possible. By utilizing both divided signal and shifted signal, fractional ratios are implemented. Phase shifting relies on division factor. Key circuit of the architecture is counter that consumes more power than control logic. Depending on circuitry of the counter, power consumption could be optimized. Multiple division ratios are possible to be implemented by utilizing an appropriate control structure. The circuits were simulated in standard TSMC 0.18 um CMOS technology with nominal power supply of 1.8v.
Spatial Analysis Model for Estimation of Population and Other Census Data in India for Forecasts in Demographic, Social and Economic Arena

In general, Population and other forms of data for different states and times in India are taken from census data which will be taken for every 10 years. This data may have spatial autocorrelation which is characterized by a correlation in a signal among nearby locations in space. Spatial autocorrelation is more complex than onedimensional autocorrelation because spatial correlation is multi-dimensional and multi-directional. Thus in this work a model is being used to study population data for its spatial and temporal characteristics. Before the model being considered, the data will be initially studied for its relevance in spatial analysis problem. Once the problem is satisfied for its spatial autocorrelation characteristics, the model is used to generate coefficients from available census data, which will be used to generate data within 10 years span and for future predictions.
Linguistic Markers of Influence in Informal Interactions

There has been a long standing interest in understanding ‘Social Influence’ both in Social Sciences and in Computational Linguistics. In this paper, we present a novel approach to study and measure interpersonal influence in daily interactions. Motivated by the basic principles of influence, we attempt to identify indicative linguistic features of the posts in an online knitting community. We present the scheme used to operationalize and label the posts as influential or non-influential. Experiments with the identified features show an improvement in the classification accuracy of influence by 3.15%. Our results illustrate the important correlation between the structure of the language and its potential to influence others.
Supplementing Exposure to Hypoxia with a Copper Depleted Diet Does Not Exacerbate Right Ventricular Remodeling in Mice

Background Pulmonary hypertension and subsequent right ventricular (RV) failure are associated with high morbidity and mortality. Prognosis is determined by occurrence of RV failure. Currently, adequate treatment for RV failure is lacking. Further research into the molecular basis for the development of RV failure as well as the development of better murine models of RV failure are therefore imperative. We hypothesize that adding a low-copper diet to chronic hypoxia in mice reinforces their individual effect and that the combination of mild pulmonary vascular remodeling and capillary rarefaction, induces RV failure. Methods Six week old mice were subjected to normoxia (N; 21% O2) or hypoxia (H; 10% O2) during a period of 8 weeks and received either a normal diet (Cu+) or a copper depleted diet (Cu-). Cardiac function was assessed by echocardiography and MRI analysis. Results and Conclusion Here, we characterized a mouse model of chronic hypoxia combined with a copper depleted diet and demonstrate that eight weeks of chronic hypoxia (10%) is sufficient to induce RV hypertrophy and subsequent RV failure. Addition of a low copper diet to hypoxia did not have any further deleterious effects on right ventricular remodeling.