Miracle-dz/UniFAR-FTUs huggingface dataset:
A fast Bayesian change point analysis for the segmentation of microarray data

MOTIVATION The ability to detect regions of genetic alteration is of great importance in cancer research. These alterations can take the form of large chromosomal gains and losses as well as smaller amplifications and deletions. The detection of such regions allows researchers to identify genes involved in cancer progression, and to fully understand differences between cancer and non-cancer tissue. The Bayesian method proposed by Barry and Hartigan is well suited for the analysis of such change point problems. In our previous article we introduced the R package bcp (Bayesian change point), an MCMC implementation of Barry and Hartigan's method. In a simulation study and real data examples, bcp is shown to both accurately detect change points and estimate segment means. Earlier versions of bcp (prior to 2.0) are O(n(2)) in speed and O(n) in memory (where n is the number of observations), and run in approximately 45 min for a sequence of length 10 000. With the high resolution of newer microarrays, the number of computations in the O(n(2)) algorithm is prohibitively time-intensive. RESULTS We present a new implementation of the Bayesian change point method that is O(n) in both speed and memory; bcp 2.1 runs in approximately 45 s on a single processor with a sequence of length 10,000--a tremendous speed gain. Further speed improvements are possible using parallel computing, supported in bcp via NetWorkSpaces. In simulated and real microarray data from the literature, bcp is shown to quickly and accurately detect aberrations of varying width and magnitude. AVAILABILITY The R package bcp is available on CRAN (R Development Core Team, 2008). The O(n) version is available in version 2.0 or higher, with support for NetWorkSpaces in versions 2.1 and higher.
Articular cartilage segmentation in noisy MR images of human knee

The segmentation of MR images is of great interests in automatic medical diagnosis. However, such images are corrupted by Rician noise and with fuzzy edges. The non-additive and intensity dependant features of Rician noise make image processistandardng very challenging. In this paper, a combination of techniques are carefully selected, tailored, and organized to improve the image quality for automatic segmentation of the articular cartilage from noisy MR images. A prototype software procedure is developed based on that. First, the Rician noise, known as the major factor contributing to corrupt the magnitude MR images, is investigated. A method based on the least squares approach is employed to estimate the noise standard deviation from the background mode of the image. Then, a total variation noise removal algorithm using iterative scheme is applied to remove the noise. After that, the vector field convolution active contour method is applied to the resultant image for cartilage segmentation. Two different approaches are proposed to define the initial contour to avoid local optimization traps. A test set MR images on 62 slices of human knee is used to illustrate the proposed system. Effectiveness of the proposed procedure is demonstrated using computational experiments in comparison to some existing methods.
Chasing the Mythical Ten Percent: Parental Hearing Status of Deaf and Hard of Hearing Students in the United States

This article investigates the basis for the frequently reported statement that ten percent of deaf persons are born to families with one or more deaf parents. The prevalence of deaf children born to deaf parents (deaf-of-deaf) is important because it is often cited when describing linguistic and educational advantages, along with social and cultural differences, associated with deaf children born to deaf parents compared to deaf children of hearing parents. This analysis provides a current estimate for the distribution of parental hearing status among deaf and hard of hearing students in United States using data from the Annual Survey of Deaf and Hard of Hearing Children and Youth (1999–2000). This is the first national estimate that fully utilizes the distinction between children having deaf parents and hard of hearing parents, as well as hearing parents. The authors propose that the key demographic to report, other than that the overwhelming majority of deaf and hard of hearing students have hearing parents, is whether the child has one or two deaf parents. The annual survey findings indicate that less than five percent of deaf and hard of hearing students receiving special education are known to have at least one deaf parent, which is less than half of the presumed ten percent. Reasons for the difference between the present and previous estimates are suggested.
Risk Perception, Rape, and Sexual Revictimization: A Prospective Study of College Women

Risk perception was examined in relation to sexual victimization among 262 college women. Participants were presented with written vignettes that described hypothetical situations with a stranger and with an acquaintance. Participants' hypothetical decision to leave a potentially risky situation with an acquaintance predicted rape and revictimization during an 8-month follow-up period. Revictimized participants had significantly delayed responses compared to previously victimized respondents who were not revictimized. Multivariate models indicated that prior victimization and delayed risk response increased vulnerability for rape and other forms of sexual victimization. Results highlight the need to assess multiple aspects of risk perception, including threat identification and behavioral responses to hypothetical or real situations. Findings suggest that delayed response to danger cues might be one factor that increases vulnerability for revictimization by acquaintances.
NEURAL CORRELATES OF MARITAL SATISFACTION AND WELL-BEING: REWARD, EMPATHY, AND AFFECT

Numerous studies suggest that marital satisfaction is associated with psychological and physical health. Using fMRI, the present study explored the neural correlates of marital satisfaction to investigate the physiological markers potentially mediating these health effects. Seventeen middle-aged individuals (M= 52.85 years) in happy, stable, longterm, heterosexual pair-bonds (Mean length of marriage = 21.4 years) were scanned while viewing facial images of their spouses, as well as facial images of a familiar acquaintance and a close friend (to control for familiarity and social bonding). Participants’ marital satisfaction scores (assessed with the Relationship Assessment Scale; Hendrick 1988) were correlated with brain activity in response to all of these facial images. Greater marital satisfaction (after controlling for Passionate Love Scale scores) was positively correlated with activation in several neural regions, including the ventral tegmental area (reflecting reward and motivation); the orbitofrontal cortex (associated with the evaluation of rewards); the anterior insula (associated with empathy); the inferior frontal gyrus (associated with the mirror system), the bed nucleus of the stria terminalis (associated with stress control); and the prefrontal cortex (associated with affective regulation). Greater marital satisfaction was also associated with decreased activation of the subcallosal cingulate gyrus, an area whose high activity is implicated in severe depression. These findings highlight key neural sites that may mediate the link between relationship quality with psychological and physical well-being and health.
Dolphin Signature Rhythms and the Non-Cacophonous Coyote: Rhythm, cognition and the animal umwelt

Merlin Donald claims that "Rhythm is a uniquely human attribute; no other creature spontaneously tracks and imitates rhythms in the way humans do, without training. "(Donald 1991: 186). This paper marshals a defense of animal cognitive capacity for rhythm, especially as it manifests in communicative acts. The conclusions is that some animals, specifically, coyotes {cants latrans) and bottlenose dolphins (tumops truncatus) do exhibit much of what Donald demands of naturally rhythmic creatures, and as such, they manifest the precursors of more sophisticated conceptual-linguistic understanding.
Current Implant Surface Technology: An Examination of Their Nanostructure and Their Influence on Fibroblast Alignment and Biocompatibility

Systematic reviews indicate that breast implant texture confers a protective effect on capsular contracture. Fibroblasts are affected by micro- and nanotopographies. Few previous studies have investigated the inherent topographies of existing breast implants and the surfaces with which body tissue is exposed. Aims: To examine currently available breast implant surfaces at high resolution and evaluate features within their surface that have been demonstrated to influence fibroblast alignment. Methods: Using scanning electron and light microscopy, 5 distinct smooth and textured silicone implants including the Mentor Siltex® (Mentor Corporation, Santa Barbara, Calif) and Allergan Biocell® (Allergan Medical Corporation, Santa Barbara, Calif) surfaces were investigated at high magnification to illustrate their intrinsic surface topographies. Results: The images obtained illustrate remarkable micro- and nanoscale topographies. Each surface produced a distinctive microenvironment capable of influencing cell shape and thus biointegration. These features are illustrated by our unique, high-magnification images. The smooth surface exhibits a shallow, regular, 5-µm period rippled texture that may explain higher reported contracture rates, while the Biocell and Siltex surfaces show 100- to 200-µm deep but random features that have been shown to anchor the implant to breast tissue and reduce contracture. Results allow a cell's eye view of these implants, with an explanation of why these types of topographies influence the success of these implants. Conclusions: We assessed commonly available silicone implants and offer a unique overview into their surface topographies and how they are manufactured. We conclude that these surfaces require modernization. Our findings provide further insight into potential interactions between cellular assemblies and artificial surfaces and may contribute to the development of improved implant surfaces.
Constructing and sampling directed graphs with given degree sequences

The interactions between the components of complex networks are often directed. Proper modeling of such systems frequently requires the construction of ensembles of digraphs with a given sequence of in- and out-degrees. As the number of simple labeled graphs with a given degree sequence is typically very large even for short sequences, sampling methods are needed for statistical studies. Currently, there are two main classes of methods that generate samples. One of the existing methods first generates a restricted class of graphs and then uses a Markov chain Monte-Carlo algorithm based on edge swaps to generate other realizations. As the mixing time of this process is still unknown, the independence of the samples is not well controlled. The other class of methods is based on the configuration model that may lead to unacceptably many sample rejections due to self-loops and multiple edges. Here we present an algorithm that can directly construct all possible realizations of a given bi-degree sequence by simple digraphs. Our method is rejection-free, guarantees the independence of the constructed samples and provides their weight. The weights can then be used to compute statistical averages of network observables as if they were obtained from uniformly distributed sampling or from any other chosen distribution.
Non-mitochondrial coenzyme Q.

The key role of coenzyme Q (ubiquinone or Q) is in mitochondrial and prokaryotic energetics. Less well investigated is the basis for its presence in eukaryotic membrane locations other than mitochondria and in plasma where both antioxidant and potentially more targeted roles are indicated. Included in the latter is that of a lipid-soluble electron transfer intermediate that serves as the transmembrane component of plasma membrane and Golgi apparatus electron transport, which regulates cytosolic NAD(+) /NADH ratios and is involved in vectorial membrane displacements and in the regulation of cell growth. Important protective effects on circulating lipoproteins and in the prevention of coronary artery disease ensue not only from the antioxidant role of CoQ(10) but also from its ability to directly block protein oxidation and superoxide generation of the TM-9 family of membrane proteins known as age-related NADH oxidase or arNOX (ENOX3) and their shed forms that appear after age 30 and some of which associate specifically with low-density lipoprotein particles to catalyze protein oxidation and crosslinking.
Childrearing Discussions in Families of Nonproblem Children and ADHD Children With Higher and Lower Levels of Aggresive-Defiant Behavior

The authors examined childrearing discussions in 14 couples with nonproblem children (NO), 14 couples with ADHD children with relatively little aggressive-defiant behavior (ADHD-LAD), and 14 couples with ADHD children with more aggressive-defiant behavior (ADHD-HAD). Discussions foucsed on attention deficit, oppositional, and conduct problem child behaviors. Couples' discussions were coded for the childrearing strategies suggested and the communication style. The groups did not differ in their suggested strategies, although more punishing responses were elicited by conduct problems and more proactive, preventive strategies by attention deficit behaviors. Couples in both ADHD groups were less positive in discussions of all behaviors and more negative in discussions of conduct problems than the NO couples. Couples with aggressize-defiant ADHD children were more negative than either the NO or ADHD-LAD group in disuccsions of ADHD behaviors. The implications for understanding interactions in families of ADHD children are discussed, as are suggestions for interventions designed to enhance couples' collaborative childrearing efforts.
[Prevalence of vitamin a deficiency and anemia in children under five years of age in Peru].

OBJECTIVES To determine the prevalence of vitamin A deficiency (VAD) and nutritional anemia (NA) in children under five in Peru. MATERIALS AND METHODS Cross-sectional study with a stratified and multi-staged probabilistic sample conducted between November 2007 and April 2010.2,736 children were included for NA and 1,465 children for VAD. NA was defined as Hb<11 g/dL.VAD was identified by serum retinol levels <20 µg/dL. Sociodemographic variables related to the child and the mother were studied in addition to their participation in growth control and development programs, integrated nutrition program and supplementation with iron and vitamin A. Analysis of complex samples was performed, descriptive statistics and logistic regression with 95% confidence intervals and a significance level of p<0.05 were calculated. RESULTS The prevalence of VAD was 11.7% (95% CI: 9.4 to 14.4). The highest prevalences were in children under five months (44.6%) and those living in rural areas (19.5%). The prevalence of NA was 33% (95% CI: 29.9 to 36.1) and was higher in children under 11 months (68.2%) and children of mothers aged 13-19 years old (55.4 %). CONCLUSIONS VAD is a public health problem that remains, with the most affected children living in rural areas and in the jungle. The prevalence of NA shows a slight improvement. It is necessary to improve the efficiency and impact of programs that include supplementation of vitamin A and iron.
Selection Mapping of Loci for Quantitative Disease Resistance in a Diverse Maize Population

The selection response of a complex maize population improved primarily for quantitative disease resistance to northern leaf blight (NLB) and secondarily for common rust resistance and agronomic phenotypes was investigated at the molecular genetic level. A tiered marker analysis with 151 simple sequence repeat (SSR) markers in 90 individuals of the population indicated that on average six alleles per locus were available for selection. An improved test statistic for selection mapping was developed, in which quantitative trait loci (QTL) are identified through the analysis of allele-frequency shifts at mapped multiallelic loci over generations of selection. After correcting for the multiple tests performed, 25 SSR loci showed evidence of selection. Many of the putatively selected loci were unlinked and dispersed across the genome, which was consistent with the diffuse distribution of previously published QTL for NLB resistance. Compelling evidence for selection was found on maize chromosome 8, where several putatively selected loci colocalized with published NLB QTL and a race-specific resistance gene. Analysis of F2 populations derived from the selection mapping population suggested that multiple linked loci in this chromosomal segment were, in part, responsible for the selection response for quantitative resistance to NLB.
Effects of interventions in pregnancy on maternal weight and obstetric outcomes: meta-analysis of randomised evidence

Objective To evaluate the effects of dietary and lifestyle interventions in pregnancy on maternal and fetal weight and to quantify the effects of these interventions on obstetric outcomes. Design Systematic review and meta-analysis. Data sources Major databases from inception to January 2012 without language restrictions. Study selection Randomised controlled trials that evaluated any dietary or lifestyle interventions with potential to influence maternal weight during pregnancy and outcomes of pregnancy. Data synthesis Results summarised as relative risks for dichotomous data and mean differences for continuous data. Results We identified 44 relevant randomised controlled trials (7278 women) evaluating three categories of interventions: diet, physical activity, and a mixed approach. Overall, there was 1.42 kg reduction (95% confidence interval 0.95 to 1.89 kg) in gestational weight gain with any intervention compared with control. With all interventions combined, there were no significant differences in birth weight (mean difference −50 g, −100 to 0 g) and the incidence of large for gestational age (relative risk 0.85, 0.66 to 1.09) or small for gestational age (1.00, 0.78 to 1.28) babies between the groups, though by itself physical activity was associated with reduced birth weight (mean difference −60 g, −120 to −10 g). Interventions were associated with a reduced the risk of pre-eclampsia (0.74, 0.60 to 0.92) and shoulder dystocia (0.39, 0.22 to 0.70), with no significant effect on other critically important outcomes. Dietary intervention resulted in the largest reduction in maternal gestational weight gain (3.84 kg, 2.45 to 5.22 kg), with improved pregnancy outcomes compared with other interventions. The overall evidence rating was low to very low for important outcomes such as pre-eclampsia, gestational diabetes, gestational hypertension, and preterm delivery. Conclusions Dietary and lifestyle interventions in pregnancy can reduce maternal gestational weight gain and improve outcomes for both mother and baby. Among the interventions, those based on diet are the most effective and are associated with reductions in maternal gestational weight gain and improved obstetric outcomes.
The Cognitive and Behavioural Dimensions of Organizational Learning in a Merger: An Empirical Study

This paper addresses the links between cognitive and behavioural learning at both a theoretical and empirical level. An integrative model is developed which identifies a number of conceptually distinct learning modes and which incorporates the tacit aspect of knowledge. An empirical illustration of this model is provided in the form of a case study of a merger of two companies in the BSN‐Danone Group. Mergers provide firms with opportunities for shared learning but this study also identifies several barriers to learning. The managerial implications of an integrated approach to organizational learning are also discussed.
Katherine: A Long, Hard Case

This article memorializes my long-term therapeutic relationship with Katherine. In reconstructing our work, some general ideas about long-term therapy became clear. Most important, as life contexts and needs changed for both patient and analyst, so, too, did the therapeutic work. As our respective contexts shifted and interacted, new therapies emerged unbidden, complete with new players, new roles, and affective responses and altered therapeutic tasks. It turned out that, in this work, flexibility with theory and clinical procedure was a frequent challenge and necessity. As Katherine's and my relationship deepened over time, achieving what I call “analytic intimacy,” my personal bond with and sense of responsibility to Katherine also intensified. This long relationship, then, raised this question for me: What is the therapist's relationship—affectively, practically, and morally—to her patients' suffering?
Forest Transitions and Rural Livelihoods: Multiple Pathways of Smallholder Teak Expansion in Northern Laos

Smallholder teak ( Tectona grandis ) plantations have been identified as a potentially valuable component of upland farming systems in northern Laos that can contribute to a “livelihood transition” from subsistence-oriented swidden agriculture to a more commercially-oriented farming system, thereby bringing about a “forest transition” at the landscape scale. In recent years, teak smallholdings have become increasingly prominent in the province of Luang Prabang, especially in villages close to Luang Prabang City. In this paper, we draw on a household survey conducted in five teak-growing villages and case studies of different household types to explore the role that small-scale forestry has played in both livelihood and land-use transitions. Drawing on a classification of forest transitions, we identify three transition pathways that apply in the study villages—the “economic development” pathway, the “smallholder, tree-based, land-use intensification” pathway, and the “state forest policy” pathway. The ability of households to integrate teak into their farming system, manage the woodlots effectively, and maintain ownership until the plantation reaches maturity varies significantly between these pathways. Households with adequate land resources but scarce labor due to the effects of local economic development are better able to establish and hold onto teak woodlots, but less able to adopt beneficial management techniques. Households that are land-constrained are motivated to follow a path of land-used intensification, but need more productive agroforestry systems to sustain incomes over time. Households that are induced to plant teak mainly by land-use policies that threaten to deprive them of their land, struggle to efficiently manage or hold on to their woodlots in the long term. Thus, even when it is smallholders driving the process of forest transition via piecemeal land-use changes, there is potential for resource-poor households to be excluded from the potential livelihood benefits or to be further impoverished by the transition. We argue that interventions to increase smallholder involvement in the forestry sector need to take explicit account of the initial variation in livelihood platforms and in alternative transition pathways at the household scale in order to pursue more inclusive “forest-and-livelihood” transitions in rural areas.