Miracle-dz/UniFAR-FTUs huggingface dataset:
Cache-aware sparse matrix formats for Kepler GPU

Scientific simulations often require solving extremely large sparse linear equations, whose dominant kernel is sparse matrix vector multiplication. On modern many-core processors such as GPU or MIC, the operation has been known to pose significant bottleneck and thus would result in extremely poor efficiency, because of limited processor-to-memory bandwidth and low cache hit ratio due to random access to the input vector. Our family of new sparse matrix formats for many-core processors significantly increases the cache hit ratio and thus performance by segmenting the matrix along the columns, dividing the work among the many core up to the internal cache capacity, and aggregating the result later on. Performance studies show that we achieve up to x3.0 speedup in SpMV and x1.68 in multi-node CG, compared to the best vendor libraries and competing new formats that have been recently proposed such as SELL-C-σ.
Cowbird parasitism of Pale-headed Brush-finch Atlapetes pallidiceps: implications for conservation and management

Pale-headed Brush-finch Atlapetes pallidiceps is a restricted-range species that is threatened with extinction due to habitat loss. The total population of 60–80 individuals achieved a reproductive output of only 0.74 young per breeding pair in 2002. Brood parasitism by Shiny Cowbird Molothrus bonariensis was a major factor reducing breeding success, affecting 38.5% of broods. Parasitism rates reached 50% in an ungrazed reserve, but only 14% on an adjacent grazed plot. The resulting difference in breeding success was not, however, attributable to vegetation parameters used to describe microhabitat use. Cowbird parasitism rates therefore seem to be influenced largely by factors operating at the landscape level. These may include grazing scheme, topography, humidity and host availability. It is suggested that lower species diversity and bird abundance rendered the grazed site less attractive to cowbirds. Current parasitism rates are of great conservation concern due to the low population size of Pale-headed Brush-finch, and the initiation of controlling measures is pressing. Management options described from intensive cowbird control programmes in North America are reviewed and evaluated for their applicability here. To combine the possibility of further data collection with commencement of immediate conservation action, we consider two alternative approaches. Nest monitoring and cowbird egg removal would enable the study of the distribution of parasitism in relation to landscape and vegetation variables, whereas cowbird shooting and nest monitoring might provide a larger short-term benefit to reproductive output. Habitat management, resumption of some grazing in the reserve and cowbird removal should be considered for the intermediate future.
Fractal grooves applied to passive micro-mixers

The purpose of the present work is to study on the application of a navel fractal pattern to passives micro-mixers. The SU-8 soft lithography is used to transfer the fractal grooves and the micro channel to PDMS mold on a glass. The authors also used numerical software Fluent to simulate the flow fields of the new passive micro-mixers. The 3 kinds of fractal configurations, three flow conditions (Re=0.64, 6.4, and 64) have been compared with the experimental mixing indices. The simulation results show that the novel fractal pattern do create lateral mass transport to improve mixing. With the same fractal patterns, the lower Reynolds number flow (0.64) has the higher mixing index. The branch with fractal patterns for two times (type III) is also better than other cases with high mixing performance.
Bullying and Mobbing in Academe: Challenges for Distance Education and Social Media Applications.

Bullying and mobbing are migrating to online realms, intensifying the damage involved and increasing the complexities of these issues. Social media (such as Facebook and Twitter) are intensely communal in many senses; they may serve to increase the negative aspects of bullying and mobbing as well as provide community-oriented tools for mitigation. Academic environments such as distance education also introduce intricate dimensions to these concerns, especially involving online freedom of speech and privacy issues. Younger individuals in academic realms may not be aware of the power of words and images to harm, especially in seemingly playful online contexts. Higher education institutions are legally and morally constrained in terms of student and employee privacy and free speech, which can make it difficult to protect victims and control the dissemination of oftendamaging information. Many social media platforms allow for the surveillance and recording of incidents of bullying and mobbing, enabling some mitigation and disciplinary efforts. However, these capabilities also increase the responsibilities of administrators, faculty, and staff in dealing with bullying and mobbing, as well as their legal liabilities.
Improving Program Acceptability Through Source Code Transformations

What does it mean for software to be acceptable? The question has an inherently human element. Unlike functional specifications, security requirements, or performance bounds, which may be documented and measured against that documentation, acceptability is simply a determination of whether the software meets the user’s needs [76]. The latter frequently subsumes the former: if software does not function, it is unlikely to be acceptable. However, acceptability also includes “non-functional properties” [41], both documented and undocumented. This convenient phrase has been defined in a number of ways by a number of authors (Glinz [41] and Chung and Prado Leite [25] have collected several different definitions). In the broadest sense, this category contains any desired program properties beyond the functional specification. The ambiguity of the term belies the very real impact of such properties. For example, safety properties [43] of airline software are responsible for the safety of hundreds of millions of passengers per year in the U.S. alone [9]. Software developers account for 7 out of every 1000 workers in the U.S. [2, 8], each of whom spends an order of magnitude more time reading code than writing it [62]. Data centers may account for over 1% of global energy consumption [58], an amount significantly affected by the efficiency of the applications deployed in those centers [93]. The stunning visuals that contribute to the billions of dollars brought in by 3D movies each year [1] are generated by programs that must balance the competing properties of speed and image quality. Figure 1 demonstrates the need for an acceptable trade-off with a simple program, orders of magnitude smaller than the programs Pixar uses to draw textures [75]. In part because of the range of factors affecting acceptability, researchers have proposed a variety of methods to help evaluate or ensure it. Many of these methods require significant additional effort beyond the challenge of writing acceptable software. For example, one might construct a formal argument for the safety of a system [46] or conduct targeted code reviews for readability [56]. Other approaches increase the effort of developing the software, requiring a particular design to allow performance optimization [39] or
Title: Estimating Selection Intensity on Synonymous Codon Usage in a Non-equilibrium Population Materials and Methods the Effects of a Recent Population Size Change on Methods That Assume Equilibrium

Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation-selection-drift equilibrium. Natural populations, however, frequently deviate from equilibrium, often because of recent demographic changes. Here, we construct a matrix model that includes the effects of a recent change in population size on estimates of selection on preferred versus unpreferred codons. Our results suggest that patterns of synonymous polymorphisms affecting codon usage can be quite erratic after such a change; statistical methods that fail to take demographic effects into account can then give incorrect estimates of important parameters. We propose a new method that can accurately estimate both demographic and codon usage parameters. The method also provides a simple way of testing for the effects of covariates such as gene length and level of gene expression on the intensity of selection, which we apply to a large Drosophila melanogaster polymorphism dataset. Our analyses of twofold degenerate codons reveal that: (i) selection acts in favor of preferred codons (ii) there is mutational bias in favor of unpreferred codons (iii) shorter genes and genes with higher expression levels are under stronger selection (iv) there is little evidence for a recent change in population size in the Zimbabwe population of D. melanogaster. 4 Codons specifying the same amino acid are called synonymous codons. These are often used non-randomly, with some codons appearing more frequently than others. This biased usage of synonymous codons has been found in many organisms such as Drosophila, yeast, 2008). Conventionally, synonymous codons for a given amino acid are divided into two classes: preferred and unpreferred codons (IKEMURA 1985; AKASHI 1994; DURET and MOUCHIROUD 1999). Several observations indicate that codon usage is affected by natural selection. First, in species with codon usage bias, preferred codons generally correspond to the most abundant tRNA species (IKEMURA 1981). Second, highly expressed genes usually have higher codon usage bias than genes with low expression (SHARP and LI 1986; DURET and MOUCHIROUD 1999; HEY and KLIMAN 2002). Third, the synonymous substitution rate of a gene has been shown to be negatively correlated with its degree of codon usage bias (SHARP and LI 1986; BIERNE and EYRE-WALKER 2006). The most commonly cited explanations of the apparent fitness differences between preferred and unpreferred codons are selection for translation efficiency, translational accuracy, and mRNA stability (IKEMURA 1985; been proposed …
Reconstruction of cylindrical metal targets using their monostatic RCS

A simple target reconstruction algorithm has been proposed for cylindrical metal scatterers from the angular Radar Cross Section (RCS) variation. This algorithm is based upon the fact that the monostatic RCS return from a plate has its peak value at the specular reflection angle, and the RCS lobe width in the angular variation is related with its plate width. By assuming the target is a polygonal convex cylinder, sizes of their facets are estimated by the local maxima in the angular RCS variation. Then one may be able to reconstruct the target's shape by connecting all facets in the specular reflection order. Our algorithm for the flat facet case can also extend to handle smooth curved facets. We have applied our reconstruction algorithm for several cylindrical targets from numerically calculated and measured RCS values. Good agreement has been observed to show the validity of our method.
Seven to Eight Hours of Sleep a Night Is Associated with a Lower Prevalence of the Metabolic Syndrome and Reduced Overall Cardiometabolic Risk in Adults

Background Previous studies looking at the relationship between sleep duration and the metabolic syndrome have only used a dichotomous approach (presence/absence) and failed to adjust for important confounding factors. The objective of the present study was to examine the association between self-reported sleep duration and features of the metabolic syndrome in adults. Methods A cross-sectional analysis from the Quebec Family Study (Canada) was conducted on 810 participants aged 18 to 65 years. Participants were categorized as short (≤6 h), adequate (7–8 h) or long (≥9 h) sleepers. The metabolic syndrome was defined according to the American Heart Association/National Heart, Lung, and Blood Institute’s criteria. Results Overall, 24.6% of the sample had the metabolic syndrome. A U-shaped relationship between sleep duration and the prevalence of metabolic syndrome (33.3%, 22.0% and 28.8% in short, adequate and long sleepers, respectively) was observed (P<0.01). Only short sleepers had a significant increase in the odds of having the metabolic syndrome (OR = 1.76, 95% CI = 1.08–2.84) compared to adequate sleepers after adjustment for age, sex, smoking habits, highest education level, total annual family income, alcohol consumption, coffee intake, menopausal status, daily caloric intake, and moderate-to-vigorous physical activity. Likewise, the clustered cardiometabolic risk score (i.e. continuous risk score based on the metabolic syndrome components) was significantly higher in short sleepers compared to adequate sleepers after adjustment for covariates (P<0.05). Conclusion Sleeping ≤6 h per night is associated with an elevated cardiometabolic risk score and an increase in the odds of having the metabolic syndrome after adjusting for possible confounders. These results strongly suggest that short sleep duration is a risk factor for the metabolic syndrome.
Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.
Sensitivity Analysis on Locations of Energy Storage in Power Systems With Wind Integration

The penetration of renewable energy sources, particularly wind energy, into power systems has been rapidly increasing in recent years. However, the integration of wind power has posed many challenges for power system operation. For instance, this type of energy source is relatively variable and unpredictable. The installation of this renewable source might require the grid to transmit power at full capacity and some transmission lines could become congested. As a result, in some operating conditions, wind power could be curtailed, which will drive up costs for system operators. One of the actions that can be taken to support the integration of the wind is using energy storage systems. In this paper, a multiperiod ac optimal power flow problem with battery energy storages (BESs) is formulated and sets of candidate buses for BES installation are identified based on an economic criterion. Tests are carried out on IEEE 14-bus and IEEE 118-bus systems to assess the robustness of storage location on system operation.
Exploiting descriptor distances for precise image search

This report addresses precise image search based on local descriptors. Our approach extends a k-NN voting scheme in several ways. First, we introduce a query-adaptive criterion that is shown effective to weight the descriptor matches. Second, we exploit the distances between SIFT descriptors and the reciprocal neighbors to further refine the similarity measure between descriptors. Each of these two complementary strategies leads to a significant improvement over the usual voting baseline, and significantly outperforms bag-of-features, at the cost of a high computational and memory complexity due to the exact computation of distances and reciprocal nearest neighbors. In order to make our method tractable, we exploit an approximate search method which, in addition to returning nearest neighbors with high probability, provides precise distance estimates without accessing the full raw vectors, which is critical to avoid memory issues. Experimental results show that our method outperforms the state of the art on four challenging datasets. Although our method is not as efficient as bag-of-features, we show that it can handle a database of up to 1 million images with reasonable query times.
Daily energy expenditure and its main components as measured by whole-body indirect calorimetry in athletic and non-athletic adolescents

The objectives of the present study were to determine whether differences in usual physical activity affect BMR, sleeping energy expenditure (EE), and EE during seated activities between athletic and non-athletic adolescents, and to establish individual relationships between heart rate and EE. Adolescents (n 49, four groups of eleven to fifteen boys or girls aged 16–19 years) participated in the study. Body composition was measured by the skinfold-thickness method and maximum O2 consumption (VO2max) by a direct method (respiratory gas exchange) on a cycloergometer. The subjects each spent 36 h in one of two large whole-body calorimeters. They followed a standardized activity programme including two periods of exercise simulating their mean weekly physical activities. Fat-free mass (FFM), VO2max, daily EE and EE during sleep and seated activities were significantly higher in athletic than in non-athletic subjects of both sexes. VO2max, daily EE and EE during exercise adjusted for FFM were higher in athletic than in non-athletic adolescents (P < 0·001), whereas sleeping EE, BMR and EE during seated activities and adjusted for FFM were not significantly different between athletic and non-athletic adolescents. However, sex differences in EE remained significant. Thus, differences in EE between athletic and non-athletic adolescents resulted mainly from differences in FFM and physical exercise. Usual activity did not significantly affect energy utilization of substrates. Finally, individual relationships were computed between heart rate and EE with activity programmes simulating the usual activities of athletic and non-athletic adolescents with the goal of predicting EE of the same subjects in free-living conditions.
A Method to Integrate GMM, SVM and DTW for Speaker Recognition

This paper develops an effective and efficient scheme to integrate Gaussian mixture model (GMM), support vector machine (SVM), and dynamic time wrapping (DTW) for automatic speaker recognition. GMM and SVM are two popular classifiers for speaker recognition applications. DTW is a fast and simple template matching method, and it is frequently seen in applications of speech recognition. In this work, DTW does not play a role to perform speech recognition, and it will be employed to be a verifier for verification of valid speakers. The proposed combination scheme of GMM, SVM and DTW, called SVMGMM-DTW, for speaker recognition in this study is a two-phase verification process task including GMM-SVM verification of the first phase and DTW verification of the second phase. By providing a double check to verify the identity of a speaker, it will be difficult for imposters to try to pass the security protection; therefore, the safety degree of speaker recognition systems will be largely increased. A series of experiments designed on door access control applications demonstrated that the superiority of the developed SVMGMM-DTW on speaker recognition accuracy.
￼Mastering Growth while Bootstrapping Sensorimotor Coordination

The bodily change in infancy due to growth is a fundamental challenge for the bootstrapping of sensorimotor coordination. We argue that learning by doing, and thus a babbling of goals instead of motor commands provides an appealing explanation for the success of infants in that bootstrapping. We show that Goal Babbling allows to bootstrap reaching skills during dierent growth patterns on a robot arm with five degrees of freedom and on the infant like humanoid iCub.
Coping to play : the effect of user-driven innovations on user experience in games

Hänninen, Juha Coping to play: the effect of user-driven innovations on user experience in games Jyväskylä: University of Jyväskylä, 2017, 66 p. Information Systems, Master’s Thesis Supervisor: Rousi, Rebekah This master’s thesis studies how user-driven innovations help players to cope with usability problems in video games. Additionally, the effect of user-driven innovations on the user experience is covered. The topic is important for the game industry, as several game companies have given the opportunity for the players to modify their games with modifications, that can alter the games visual appearance, mechanics and logic, as well as content. Continuing the game development further in the gaming community has become a major part of the gaming culture. Therefore, it is important for the gaming companies to understand the opportunities and threats that lie beneath this phenomenon. The thesis consists of a literature review from the existing literature on coping, usability, user experience and user-driven innovations, and an empirical study. In the empirical study, the methodology for interviewing players is presented, along with the explanation of thematic analysis used for interpreting the interview data. Themes chosen based on the interview data were performance and usability, content, and aesthetics. Each theme is a fundamental part of the gaming experience and their effect on user experience can be further amplified with user-driven innovations. The results of the research indicate that user-driven innovations are often used by the players to cope with usability issues, but also they tend to improve the overall user experience as well. Finally, the thesis concludes with a discussion on the results and their meaning and possible topics for future research are presented.