Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast and accurate inference of local ancestry in Latino populations

MOTIVATION It is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease loci, to understand recombination rate variation and to detect recent selection events. The utility of such studies crucially depends on accurate and unbiased estimation of the ancestry at every genomic locus in recently admixed populations. Although various methods have been proposed and shown to be extremely accurate in two-way admixtures (e.g. African Americans), only a few approaches have been proposed and thoroughly benchmarked on multi-way admixtures (e.g. Latino populations of the Americas). RESULTS To address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos.
Gradual fuzzy decision trees to help medical diagnosis

In this paper, we consider the problem of the construction of fuzzy decision trees when there exists a graduality between the values of attributes and values of the class. We propose a new measure, extended from the measure of classification ambiguity, that takes into account both discrimination power and graduality with regards to the class. To highlight the importance of that kinds of measures, Medical applications is presented in which often the values of the class are symbolic and ordered and in which the discovery of gradual links between descriptive attributes and the class are seek for.
Cognitive behavioral therapy for insomnia in posttraumatic stress disorder: a randomized controlled trial.

STUDY OBJECTIVES Examine whether cognitive behavioral therapy for insomnia (CBT-I) improves sleep in posttraumatic stress disorder (PTSD) as well as nightmares, nonsleep PTSD symptoms, depression symptoms, and psychosocial functioning. DESIGN RANDOMIZED CONTROLLED TRIAL WITH TWO ARMS: CBT-I and monitor-only waitlist control. SETTING Department of Veterans Affairs (VA) Medical Center. PARTICIPANTS Forty-five adults (31 females: [mean age 37 y (22-59 y)] with PTSD meeting research diagnostic criteria for insomnia, randomly assigned to CBT-I (n = 29; 22 females) or monitor-only waitlist control (n = 16; nine females). INTERVENTIONS Eight-session weekly individual CBT-I delivered by a licensed clinical psychologist or a board-certified psychiatrist. MEASUREMENTS AND RESULTS Measures included continuous monitoring of sleep with diary and actigraphy; prepolysomnography and postpolysomnography and Clinician-Administered PTSD Scale (CAPS); and pre, mid, and post self-report questionnaires, with follow-up of CBT-I participants 6 mo later. CBT-I was superior to the waitlist control condition in all sleep diary outcomes and in polysomnography-measured total sleep time. Compared to waitlist participants, CBT-I participants reported improved subjective sleep (41% full remission versus 0%), disruptive nocturnal behaviors (based on the Pittsburgh Sleep Quality Index-Addendum), and overall work and interpersonal functioning. These effects were maintained at 6-mo follow-up. Both CBT-I and waitlist control participants reported reductions in PTSD symptoms and CAPS-measured nightmares. CONCLUSIONS Cognitive behavioral therapy for insomnia (CBT-I) improved sleep in individuals with posttraumatic stress disorder, with durable gains at 6 mo. Overall psychosocial functioning improved following CBT-I. The initial evidence regarding CBT-I and nightmares is promising but further research is needed. Results suggest that a comprehensive approach to treatment of posttraumatic stress disorder should include behavioral sleep medicine. CLINICAL TRIAL INFORMATION TRIAL NAME: Cognitive Behavioral Treatment Of Insomnia In Posttraumatic Stress Disorder. URL: http://clinicaltrials.gov/ct2/show/NCT00881647. REGISTRATION NUMBER NCT00881647.
Testing of 3D-stacked ICs with hard- and soft-dies - a Particle Swarm Optimization based approach

This paper presents a test architecture optimization and test scheduling strategy for TSV based 3D-Stacked ICs (SICs). A test scheduling heuristic, that can fit in both session-based and session-less test environments, has been used to select the test concurrency between the dies of the stack. The proposed method minimizes the overall test time of the stack, without violating the system level resource and TSV limits. Particle Swarm Optimization (PSO) based meta search technique has been used to select the resource allocation of individual dies and also their internal test schedules. Incorporation of PSO in two stages of optimization produces a notable reduction in the overall test time of SIC. Experimental results show that upto 51% reduction in test time can be achieved using our strategy, over the existing techniques.
Can a physicalist notion of color provide any insight into the nature of color perception?

Abstract Byrne & Hilbert (B&H) conceive of color perception as the representation of a physical property “out there. ” In our view, their approach does not only have various internal problems, but is also apt to becloud both the intricate and still poorly understood role that “color” plays within perceptual architecture, and the complex coupling to the “external world” of the perceptual system as an entirety. We propose an alternative perspective, which avoids B&H's misleading dichotomy between a purely subjective and a realist conception of “color. ”
Coccolithophore bloom size variation in response to the regional environment of the subarctic North Atlantic

Several environmental/physical variables derived from satellite and in situ data sets were used to understand the variability of coccolithophore abundance in the subarctic North Atlantic. The 7‐yr (1997‐2004) time‐series analysis showed that the combined effects of high solar radiation, shallow mixed layer depth (>20 m), and increased temperatures explained >89% of the coccolithophore variation. The June 1998 bloom, which was associated with high light intensity, unusually high sea‐surface temperature, and a very shallow mixed layer, was found to be one of the most extensive (>995,000 km2) blooms ever recorded. There was a pronounced sea‐surface temperature shift in the mid‐1990s with a peak in 1998, suggesting that exceptionally large blooms are caused by pronounced environmental conditions and the variability of the physical environment strongly affects the spatial extent of these blooms. Consequently, if the physical environment varies, the effects of these blooms on the atmospheric and oceanic environment will vary as well.
Research Report—Skill Loss, Part II:: An Experiment with Engineering Apprentices

In the first of our two articles on skill loss we concentrated on two kinds of investigation, surveys of the opinions of experienced individuals and controlled, but often highly artificial, experiments. In this the second article we shall describe the results of some studies using the “natural experiment” technique. Carrying out a natural experiment is rather like studying an eclipse or an earthquake. There is nothing the scientist can do about arranging the events, as is the rule in the classic laboratory experiment; one simply takes things as they come but hopefully with telescopes, seismographs or whatever appropriate measuring devices suitably deployed to record the events for subsequent analysis.
A genetic approach to dynamic load balancing in a distributed computing system

Presents an efficient dynamic load balancing scheme based on a genetic algorithm (GA) which includes an evaluation mechanism of fitness values in a changing environment. Sender-initiated task migration algorithms continue to send unnecessary requests for a task migration while the system load is heavy, which yields inefficient inter-processor communication and much overhead until the migration is actually performed. In the proposed GA-based load balancing scheme, a subset of processors to which the requests are sent is adaptively determined by a learning procedure to reduce unnecessary requests. The learning procedure consists of standard genetic operations, such as selection, crossover and mutation, applied to a population of binary strings, each of which stands for a list of processors to which the migration requests are sent. Each processor has its own population, and the fitness of a string depends on how efficiently the destination of a migration is found. From the viewpoint of the mean response time of the whole system, we show the effectiveness of our approach through empirical investigations. <<ETX>>
National Survey of Radiation Doses of Pediatric Chest Radiography in Korea: Analysis of the Factors Affecting Radiation Doses

Objective To investigate radiation doses in pediatric chest radiography in a national survey and to analyze the factors that affect radiation doses. Materials and Methods The study was based on the results of 149 chest radiography machines in 135 hospitals nationwide. For each machine, a chest radiograph was obtained by using a phantom representing a 5-year-old child (ATOM® dosimetry phantom, model 705-D, CIRS, Norfolk, VA, USA) with each hospital's own protocol. Five glass dosimeters (M-GD352M, Asahi Techno Glass Corporation, Shizuoka, Japan) were horizontally installed at the center of the phantom to measure the dose. Other factors including machine's radiography system, presence of dedicated pediatric radiography machine, presence of an attending pediatric radiologist, and the use of automatic exposure control (AEC) were also evaluated. Results The average protocol for pediatric chest radiography examination in Korea was 94.9 peak kilovoltage and 4.30 milliampere second. The mean entrance surface dose (ESD) during a single examination was 140.4 microgray (µGy). The third quartile, median, minimum and maximum value of ESD were 160.8 µGy, 93.4 µGy, 18.8 µGy, and 2334.6 µGy, respectively. There was no significant dose difference between digital and non-digital radiography systems. The use of AEC significantly reduced radiation doses of pediatric chest radiographs (p < 0.001). Conclusion Our nationwide survey shows that the third quartile, median, and mean ESD for pediatric chest radiograph is 160.8 µGy, 93.4 µGy, and 140.4 µGy, respectively. No significant dose difference is noticed between digital and non-digital radiography systems, and the use of AEC helps significantly reduce radiation doses.
An Ability Traitor at Work: A Treasonous Call to Subvert Writing From Within

In questioning conventional qualitative research methods, St. Pierre asked, “What else might writing do except mean? ” The author answers, it oppresses. Co-opting the race traitor figurative, she calls on qualitative researchers to become “ability traitors” who interrogate how a valuable coinage of their trade—the written word—is used to rank and categorize individuals with troubling effects. In this article, she commits three betrayals: (a) multigenre writing that undermines the authoritative text; (b) assemblage as a method of analysis that deprivileges the written word; and(c) a gesture toward a dis/ comfort text intended to take up Lather’s example of challenging the “usual ways of making sense”. In committing these betrayals, the author articulates her “traitorous agenda” designed to interrogate assumptions about inquiry, power, equity, and writing as practice-as-usual.
Towards mapping the field of non-photorealistic rendering

Non-photorealistic rendering (NPR) as a field of research is generally described by what it is not and as a result it is often hard to embrace the strengths of non-photorealistic rendering as a discipline beyond digitizing or replicating traditional artistic techniques. Towards generating more discussion within the discipline, this paper provides a simple theory of NPR as a way of mapping perceived changes in a scene to perceived changes in a display. One can think of a photorealistic image as one that preserves a one-to-one mapping, such that parameters such as color, intensity, texture, edges, etc. in a scene are mapped to the same parameters in the display. NPR mappings are not one-to-one. For example edges in a scene may be mapped to black lines to generate a cartoon effect. Within this framework of mappings, a partial listing of previous techniques within the discipline is provided. The aim of this paper is to provide a type of road map to stimulate the future growth of the area of non-photorealistic rendering.
Men's Work–life Conflict: Career, Care and Self‐realization: Patterns of Privileges and Dilemmas

This article aims at contributing to a better understanding of men's work–life reconciliation by developing a typology of work and care adaptations drawing on a sample of 102 European men, aged 21–64, working in different work organizations. The article combines qualitative and quantitative data. Multiple correspondence analysis is used to investigate the men's actual adaptations to work, care and self-realization. ‘Volume of work’ and ‘volume of care’ constitutes separate dimensions that render visible the traditional gendered opposition between a high amount of care combined with low amount of work and vice versa. However, two more untraditional adaptations (low–low and high–high) are identified. Additional analyses show that, even within this all male sample, the distribution of working life privileges corresponds with a high amount of paid work and a low amount of care responsibilities. The structure of the gendered division of labour, status and material privileges is correspondingly rediscovered. A typology of four different positions is derived: the ‘career' position', the care’ position the ‘care and career’ position and the ‘patchwork career’ position. These positions are further investigated utilizing in-depth interviews, discussing dilemmas and advantages of dilemmas and the advantages of each position. The article concludes that even if the number of available work–life adaptations open to men rise, this change will not necessarily contribute to alter the hierarchical distribution of career and care, privileges and costs in society.
Competitive Disadvantage Makes Attitudes towards Rape Less Negative

Evolutionary theorists have argued that perceived competitive disadvantage may lead to more positive evaluation of, and greater likelihood of engaging in, risky and antisocial behavior. However, experimental studies have not yet examined the effects of competitive disadvantage on perceptions of rape. In the current study, we created a manipulation of perceived competitive status to test its effects on beliefs about rape. In one condition, participants were made to feel disadvantaged relative to male peers in terms of financial, physical, and intellectual power, whereas in the other condition they were made to feel advantaged. Participants were 120 heterosexual male undergraduate students. The manipulation was effective; compared to participants in the advantage condition, those in the disadvantage condition rated themselves as significantly worse off financially, shorter, in worse physical shape, and as having lower course marks than the average male student at the university. Compared to perceived competitive advantage, perceived disadvantage led to less negative attitudes towards rape. However, perceived competitive status did not significantly affect justifications and excuses for rape. Future studies using similar experimental manipulations can complement correlational studies and may contribute to greater clarity, precision, and sophistication of research and theory on the role of competitive disadvantage in rape.
Combined QTL and Selective Sweep Mappings with Coding SNP Annotation and cis-eQTL Analysis Revealed PARK2 and JAG2 as New Candidate Genes for Adiposity Regulation

Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
Indicators of Usefulness of Test Scores

Current thinking on validity suggests that educational institutions and individuals should evaluate their uses of test scores in the context of their fundamental goals. Regression coefficients and other traditional criterion-related validity statistics provide relevant information, but often do not, by themselves, address the fundamental reasons for using test scores. Formal decision theory models provide a logically rigorous way to do this, but they are difficult to implement in practice. This article considers a simplification of formal decision theory models, in which one estimates the proportion of examinees for whom positive outcomes result from a use of test scores. For uses involving selection, the proportion of examinees with positive outcomes can be calculated by applying traditional regression coefficients to the marginal distribution of scores in the unselected population. The incremental usefulness of using a particular variable can be judged by comparing its proportion to that associated with no selection and to that associated with using another variable, either alone or jointly. Examples, related to college admission and retention, are given to illustrate these ideas.
Evolution of a cichlid fish in a Lake Malawi satellite lake

Allopatric divergence in peripheral habitats may lead to rapid evolution of populations with novel phenotypes. In this study we provide the first evidence that isolation in peripheral habitats may have played a critical role in generation of Lake Malawi's cichlid fish diversity. We show that Lake Chilingali, a satellite lake 11.5 km from the shore of Lake Malawi, contains a breeding population of Rhamphochromis, a predatory genus previously thought to be restricted to Lake Malawi and permanently connected water bodies. The Lake Chilingali population is the smallest known Rhamphochromis, has a unique male nuptial colour pattern and has significant differentiation in mitochondrial DNA from Lake Malawi species. In laboratory mate choice trials with a candidate sister population from Lake Malawi, females showed a strong tendency to mate assortatively indicating that they are incipient biological species. These data support the hypothesis that isolation and reconnection of peripheral habitats due to lake level changes have contributed to the generation of cichlid diversity within African lakes. Such cycles of habitat isolation and reconnection may also have been important in evolutionary diversification of numerous other abundant and wide-ranging aquatic organisms, such as marine fishes and invertebrates.
Free-living and aggregate-associated Planctomycetes in the Black Sea.

We examined the distribution of uncultured Planctomycetes phylotypes along depth profiles spanning the redox gradient of the Black Sea suboxic zone to gain insight into their respective ecological niches. Planctomycetes phylogeny correlated with depth and chemical profiles, implying similar metabolisms within phylogenetic groups. A suboxic zone sample was split into > 30 and < 30 μm fractions to examine putative aggregate-attached and free-living Planctomycetes. All identified Planctomycetes were present in the > 30 μm fraction except for members of the Scalindua genus, which were apparently free-living. Sequences from Candidatus Scalindua, known to carry out the anammox process, formed two distinct clusters with nonoverlapping depth ranges. One cluster, only 97.1% similar to the named species, was present at high nitrite/nitrate and low ammonium concentrations in the upper suboxic zone. We propose this sequence type be named 'Candidatus Scalindua richardsii'. A second cluster, containing sequences more similar to 'Candidatus Scalindua sorokinii', was present at high ammonium and low nitrite conditions in the lower suboxic zone. Sequences obtained from the sulfidic zone (1000 m depth) yielded Planctomycetes from two uncharacterized Planctomycetacia clusters and three potentially new genera as well as sequences from the uncultured OP3 phylum.
Designing for peer involvement in weight management

The problems of obesity and overweight are commonly cited as the motivation behind recent efforts to develop technology that promotes physical activity. Prompted by the social nature of many of the emerging applications, this paper presents our investigation of the sociality of weight management as experienced by a broad demographic of individuals. Our findings highlight the broad scope of peer involvement, and provide insight into the context and mechanics of related interaction that may prove valuable in informing the next generation of peer-based weight management technology for use in everyday life.