Miracle-dz/UniFAR-FTUs huggingface dataset:
Shrinkage estimation for robust and efficient screening of single‐SNP association from case‐control genome‐wide association studies

Population‐based case‐control design has become one of the most popular approaches for conducting genome‐wide association scans for rare diseases like cancer. In this article, we propose a novel method for improving the power of the widely used single‐single‐nucleotide polymorphism (SNP) two‐degrees‐of‐freedom (2 d.f.) association test for case‐control studies by exploiting the common assumption of Hardy‐Weinberg Equilibrium (HWE) for the underlying population. A key feature of the method is that it can relax the assumed model constraints via a completely data‐adaptive shrinkage estimation approach so that the number of false‐positive results due to the departure of HWE is controlled. The method is computationally simple and is easily scalable to association tests involving hundreds of thousands or millions of genetic markers. Simulation studies as well as an application involving data from a real genome‐wide association study illustrate that the proposed method is very robust for large‐scale association studies and can improve the power for detecting susceptibility SNPs with recessive effects, when compared to existing methods. Implications of the general estimation strategy beyond the simple 2 d.f. association test are discussed. Genet. Epidemiol. 33:740–750, 2009. Published 2009 Wiley‐Liss, Inc.
Compressive Spectral Clustering

Spectral clustering has become a popular technique due to its high performance in many contexts. It comprises three main steps: create a similarity graph between N objects to cluster, compute the first k eigenvectors of its Laplacian matrix to define a feature vector for each object, and run k-means on these features to separate objects into k classes. Each of these three steps becomes computationally intensive for large N and/or k. We propose to speed up the last two steps based on recent results in the emerging field of graph signal processing: graph filtering of random signals, and random sampling of bandlimited graph signals. We prove that our method, with a gain in computation time that can reach several orders of magnitude, is in fact an approximation of spectral clustering, for which we are able to control the error. We test the performance of our method on artificial and real-world network data.
A REVIEW OF RANGELAND PRIVATISATION AND ITS IMPLICATIONS IN THE TIBETAN PLATEAU, CHINA

The Tibetan plateau of China is one of the world's major pastoral areas, in which rangeland management underwent fundamental changes in the twentieth century. This article reviews the rangeland privatisation process in the Tibetan plateau over the last ten years, examining cases from Hongyuan, Zoige and Maqu Counties in the eastern part of the plateau, Nyima County in the northwestern part and Dingri County in the southwestern part. Rangelands have been allocated to individual households or 'the least contracting unit' starting from 1996, but the process of rangeland privatisation was diverse and is still ongoing in the western part of the Tibetan plateau. Rangeland privatisation has some significant impacts on local people and their environment. First, many rangelands are inequitably allocated due to their highly variable topography, productivity and availability of water resources. Secondly, access to social and economic services has been made more difficult for some, while social conflicts have increased. Thirdly, privatisation of rangeland and sedentarisation of nomads needs matching infrastructure but that is still missing in many places. Meanwhile, privatisation of rangeland has led to increased labour inputs in some places and added more workload onto women and children. The article concludes that rangeland privatisation was intended to stop further rangeland degradation and to provide nomads with better lives. However, more study is needed on managing rangeland in an appropriate way.
Mechanistic Insight into the Relationship between N-Terminal Acetylation of α-Synuclein and Fibril Formation Rates by NMR and Fluorescence

Aggregation of α-synuclein (αSyn), the primary protein component in Lewy body inclusions of patients with Parkinson’s disease, arises when the normally soluble intrinsically disordered protein converts to amyloid fibrils. In this work, we provide a mechanistic view of the role of N-terminal acetylation on fibrillation by first establishing a quantitative relationship between monomer secondary structural propensity and fibril assembly kinetics, and secondly by demonstrating in the N-terminal acetylated form of the early onset A53T mutation, that N-terminal transient helices formed and/or inhibited by N-terminal acetylation modulate the fibril assembly rates. Using NMR chemical shifts and fluorescence experiments, we report that secondary structural propensity in residues 5–8, 14–31, and 50–57 are highly correlated to fibril growth rate. A four-way comparison of secondary structure propensity and fibril growth rates of N-terminally acetylated A53T and WT αSyn with non-acetylated A53T and WT αSyn present novel mechanistic insight into the role of N-terminal acetylation in amyloid fibril formation. We show that N-terminal acetylation inhibits the formation of the “fibrillation promoting” transient helix at residues 14–31 resulting from the A53T mutation in the non-acetylated variant and supports the formation of the “fibrillation inhibiting” transient helix in residues 1–12 thereby resulting in slower fibrillation rates relative to the previously studied non-acetylated A53T variant. Our results highlight the critical interplay of the region-specific transient secondary structure of the N-terminal region with fibrillation, and the inhibitory role of the N-terminal acetyl group in fibril formation.
Towards Understanding Human Mistakes of Programming by Example: An Online User Study

Programming-by-Example (PBE) enables users to create programs without writing a line of code. However, there is little research on people's ability to accomplish complex tasks by providing examples, which is the key to successful PBE solutions. This paper presents an online user study, which reports observations on how well people decompose complex tasks, and disambiguate sub-tasks. Our findings suggest that disambiguation and decomposition are difficult for inexperienced users. We identify seven types of mistakes made, and suggest new opportunities for actionable feedback based on unsuccessful examples, with design implications for future PBE systems.
Bone metabolism and body composition in Japanese patients with active acromegaly

OBJECTIVE Skeletal involvement is a common clinical feature in acromegalic patients. Although several recent reports are available concerning bone mineral density (BMD) in acromegaly, the controversy still exists as to whether BMD of acromegalic patients is increased or not. The present study was performed to examine biochemical bone metabolic indices and BMD as well as body composition in 26 Japanese patients with active acromegaly and 26 control subjects matched for age, sex, race and height in a cross‐sectional study.
Morphology and speech technology

This paper describes a morphological component in a speech recognition architecture for German dealing with the recognition of compounds from their individual constituents. The specification of our morphological model allows for variation in functionality, e. g.  the reconstruction of split compounds, of lexicalised, and of non-lexicalised (unknown) compounds. An implementation and evaluation results for split compounds are presented.
Photography and Children: Auto-driven Photo-elicitation

This Department is devoted to research reports, notes, conference résumés and other significant research events. Two copies of write-ups, not exceeding 3,000 words, may be mailed to the Section Editor, Professor David A. Fetmell, Brock University, St. Catharines, Ontario, Canada L2S 3A1; e-mail. david.fennell@brocku.ca. In all cases, one copy of the report should be mailed to the Chief Editor, TRR.
Layout-Related Stress Effects on Radiation-Induced Leakage Current

The effects of shallow-trench-isolation-induced mechanical stress on radiation-induced off-state leakage current are reported in 90-nm NMOS devices. The radiation-induced leakage current increases with increasing active device-to-isolation spacing. The leakage current also depends on channel width; narrow devices exhibit less leakage before irradiation, but more after irradiation. These geometrical factors affect the mechanical stress in the device, which impact the dopant diffusion and activation and the charge trapping in the STI oxide. The combined effects of these layout-related phenomena affect the sensitivity to radiation-induced charge.
Spotlighting: Emergent Gender Bias in Undergraduate Engineering Education

“Spotlighting” is the singling out of women by gender in ways that make them uncomfortable. It has three forms: Type I is singling out with the intention to harm (overt sexism); Type II is doing so with neutral intentions (tacit sexism); and Type III, a new type of gender bias, is singling out women with the intention to help them. In a longitudinal, qualitative study including three types of schools, undergraduate women engineers named Type III spotlighting due to women in engineering (WIE) programs as the direct or indirect cause of their primary gender‐bias difficulties. Two changes to WIE programs are suggested to reduce Type III spotlighting: (1) offer their benefits either to all students or based on academic, not demographic, criteria, and (2) expand WIE programs to “conduct in engineering” programs that would emphasize pre‐emption of non‐professional behavior, and would be more inclusive of other biases.
Genetic variation underlies temperature tolerance of embryos in the sea urchin Heliocidaris erythrogramma armigera

Ocean warming can alter natural selection on marine systems, and in many cases, the long‐term persistence of affected populations will depend on genetic adaptation. In this study, we assess the potential for adaptation in the sea urchin Heliocidaris erythrogramma armigera, an Australian endemic, that is experiencing unprecedented increases in ocean temperatures. We used a factorial breeding design to assess the level of heritable variation in larval hatching success at two temperatures. Fertilized eggs from each full‐sibling family were tested at 22 °C (current spawning temperature) and 25 °C (upper limit of predicted warming this century). Hatching success was significantly lower at higher temperatures, confirming that ocean warming is likely to exert selection on this life‐history stage. Our analyses revealed significant additive genetic variance and genotype‐by‐environment interactions underlying hatching success. Consistent with prior work, we detected significant nonadditive (sire‐by‐dam) variance in hatching success, but additionally found that these interactions were modified by temperature. Although these findings suggest the potential for genetic adaptation, any evolutionary responses are likely to be influenced (and possibly constrained) by complex genotype‐by‐environment and sire‐by‐dam interactions and will additionally depend on patterns of genetic covariation with other fitness traits.
Energy-Aware Sensor Selection in Field Reconstruction

In this letter, a new sparsity-promoting penalty function is introduced for sensor selection problems in field reconstruction, which has the property of avoiding scenarios where the same sensors are successively selected. Using a reweighted ℓ1 relaxation of the ℓ0 norm, the sensor selection problem is reformulated as a convex quadratic program. In order to handle large-scale problems, we also present two fast algorithms: accelerated proximal gradient method and alternating direction method of multipliers. Numerical results are provided to demonstrate the effectiveness of our approaches.
A Method for Measuring Fishing Effort by Small-scale Fish Aggregating Device (FAD) Fishers from the Commonwealth of Dominica

We used global positioning system (GPS) technology and tracking analysis to measure fishing effort by marine, small-scale, fish aggregating device (FAD) fishers of the Commonwealth of Dominica. FADs are human-made structures designed to float on the surface of the water and attract fish. They are also prone to common pool resource problems. To identify free riders with respect to specific FADs, we need to compare the cost expended for FAD construction versus the benefit fishers extract from their use of the FADs. From August to December 2012, we placed GPS devices on a sample of fishing trips to track movement and measure variation in fishers’ fishing efforts at a set of seven FADs off the Atlantic east coast of central Dominica. The method produces high-resolution data to determine how much time different fishers use different FADs.
Phenotyping, Genotyping, and Selections within Italian Local Landraces of Romanesco Globe Artichoke

Ten Italian globe artichoke clones belonging to the Romanesco typology were characterized in the western coastal area of Italy (Cerveteri, Rome), using a combination of morphological (UPOV descriptors), biochemical (HPLC analysis), and molecular (AFLP, ISSR, and SSR markers) traits. Significant differences among clones were found for many of the quantitative and qualitative morphological traits. Multivariate analyses (Principal Component Analysis) showed that, of the 47 morphological descriptors assessed, four (i.e., plant height, central flower-head weight, earliness, and total flower-head weight) presented a clear grouping of the clones. Biochemical analyses showed that the clones significantly differed in the polyphenolic profiles of the flower-head, with the suggestion that some of these, such as S2, S3, S5, and S18, are more suitable for the fresh market. The clones, clustered by a UPGMA dendrogram based on 393 polymorphic AFLP and ISSR loci, showed that the clones were genetically separated from each other. This highlights the importance of characterizing, evaluating, and conserving autochthonous germplasm for future plant breeding activities. Overall, these studies resulted in the identification of two new clones, selected on the basis of flower-head morphology and earliness. These clones, named Michelangelo and Raffaello, are registered on the Italian National Register of Varieties (DM n. 6135, 3/29/2013 G.U. 91, 18 April 2013).
Emotional ratings of music excerpts in the western art music repertoire and their self-organization in the Kohonen neural network

Suggestions for basic emotional music excerpts in the western art music repertoire were collected through a survey that was sent to about 500 music professionals. A total of 78 music excerpts were then tested in the listening experiments 1 (n = 44) and 2 (n = 55), considering emotional quality and intensity, and the topological organization of the music excerpts in the basic emotion dimensions (i.e. joy, sadness, anger, fear, surprise and disgust) was examined using Kohonen’s neural network. The results suggest that, in general, the basic emotions can be considered as distinct emotional dimensions in music. Joy and sadness seem to be easier to express and recognize than fear, anger and surprise. The participants’ level of music education or other background factors had no effect on emotional or intensity judgments. The results also suggest that the emotional connotations in modern music are not so well established as in music that is more tonal (i.e. Baroque, Classical, and Romantic).
Anxiety Among an Australian Sample of Young Girls Adopted From China

This study aims to contribute to the body of knowledge about post-adoption functioning of international adoptees by examining patterns of anxiety among young children adopted from China by Australian families. The study had two objectives: to examine anxiety in children adopted from China comparing this sample to available normative data and to examine the associations among child anxiety and child (e.g., age at adoption) and parent (e.g., age, education level) factors. Parents of 59 children adopted from China completed online a number of measures of child anxiety, temperament, and parent psychological well-being. Results indicated a high prevalence of anxiety symptoms among the adopted children when compared with available data from normative samples, particularly related to separation contexts. A number of factors, including inhibited temperament and younger age of parents, were associated with child anxiety. Clinical and research implications are discussed.
Is it Seeing or Believing? Exposure, Perceived Realism, and Emerging Adults' Perceptions of Their Own and Others' Attitudes About Relationships

The differential impact hypothesis predicts that media exposure is more likely to influence social-level than personal-level judgments unless individuals identify with media content. An important factor in determining identification is perceived realism. Research in other areas has found, however, that individuals engage in motivated differential perceptions (MDPs) of self and others and that the extent and nature of these MDPs are determined by both motivational and cognitive factors. This study found that emerging adults (N = 282) in both within-subjects and between-subjects conditions engaged in MDPs—rating peers as more likely to endorse recreational attitudes and less likely to endorse relational attitudes than themselves. Exposure was significantly related to social-level perceptions of peers, but not to personal attitudes. Perceived realism reduced MDPs and was significantly related to personal-level attitudes, but not to social-level perceptions. There were important gender differences in the nature of these relationships. For females, increased exposure was related to higher perceptions of peers' agreement with recreational attitudes, but for males exposure was associated with higher perceptions of other's agreement with relational attitudes. A range of entertainment media formats (television, magazines, radio, and Internet sites) were examined.
Feminist Standpoint Theory and the Questions of Social Work Research

This article presents feminist standpoint theory as an alternative epistemology for social work research—an alternative theory of what makes knowledge possible and how to get it—and discusses the outcomes and consequences of a research so transformed. Three issues raised by standpoint theory are used to refocus the questions of social work research: What is the base of the research? What is the purpose of the research? How does this project incorporate researchers' ref lexivity?
Unpacking the role of self-esteem in career uncertainty: A self-determination perspective

The aim of this study is to explain why students with high self-esteem have lower career uncertainty than students with low self-esteem. Based on self-determination theory, students with high self-esteem would have higher efficacy in making decisions, which would encourage them to choose a major for self-concordance, such as interest and ability, and increase their course involvement. Both factors are assumed to be related to lower career uncertainty. Data from a national survey of the Taiwan Higher Education Database within the Survey Research Data Archive from juniors at 92 colleges and universities in Taiwan (N = 7418) were analyzed to examine the model. Results supported the proposed model by showing that students with high self-esteem had lower career uncertainty because they chose a major for self-concordant reasons and had a strong motivation to learn, both of which contribute to lower career uncertainty.
Neighbor Carrier Signal Strength Estimation for Carrier Aggregation in LTE-A

In Advanced Long Time Evolution (LTE-A) mobile wireless communication system, the Carrier Aggregation (CA) technique feature was introduced to support large transmission bandwidth. But due to the capacity limit of UE, to measure all component carriers with low latency and cost has been a challenge. In this paper a solution is presented in which only some reference component carriers need to be measured; the signal strength of others are estimated by utilizing the correlation between these component carriers and reference component carrier. The simulation results show that the estimation error is acceptable.
Performance Analysis of Multicasting in Cloud-Radio Access Networks

Cloud-radio access networks (C-RANs) are considered as energy efficient network architectures. Nevertheless, a dilemma in C-RAN architecture is to simultaneously optimize both spectral efficiency (SE) and energy efficiency (EE). In this paper, the tradeoff between SE and EE are studied considering a downlink multicasting transmission scenario in a C-RAN. In particular, to effectively mitigate the severe interference caused by densely deployed RRHs and improve the energy efficiency, a thinning scheme of RRHs is proposed. With a fixed diluted density of deployed active RRHs, the explicit closed-form expressions for coverage probability, SE and EE are derived by applying stochastic geometry. By using the obtained theoretical result as a utility function, a problem of optimizing the selection radius of RRHs is formulated to make a tradeoff between SE and EE for different preferences. Then, scalarization methods are proposed to give efficient solution. Numerical results validate the correctness and precision of performance analysis and show that the proposed approaches can generate an optimal selection radius of the thinning scheme.