Miracle-dz/UniFAR-FTUs huggingface dataset:
Serrated polyposis associated with a family history of colorectal cancer and/or polyps: The preferential location of polyps in the colon and rectum defines two molecular entities

Serrated polyposis (SPP) is characterized by the development of multiple serrated polyps and an increased predisposition to colorectal cancer (CRC). In the present study, we aimed to characterize, at a clinical and molecular level, a cohort of SPP patients with or without a family history of SPP and/or polyps/CRC (SPP-FHP/CRC). Sixty-two lesions from 12 patients with SPP-FHP/CRC and 6 patients with sporadic SPP were included. The patients with SPP-FHP/CRC presented with an older mean age at diagnosis (p=0.027) and a more heterogeneous histological pattern of lesions (p=0.032) than the patients with sporadic SPP. We identified two molecular forms of SPP-FHP/CRC, according to the preferential location of the lesions: proximal/whole-colon or distal colon. Mismatch repair (MMR) gene methylation [mutS homolog 6 (MSH6)/mutS homolog 3 (MSH3)] or loss of heterozygosity (LOH) of D2S123 (flanking MSH6) were detected exclusively in the former (p=3.0×10−7), in most early lesions. Proximal/whole-colon SPP-FHP/CRC presented a higher frequency of O-6-methylguanine-DNA methyltransferase (MGMT) methylation/LOH, microsatel-lite instability (MSI) and Wnt mutations (19/29 vs. 7/17; 16/23 vs. 1/14, p=2.2×10−4; 15/26 vs. 2/15, p=0.006; 14/26 vs. 4/20, p=0.02) but a lower frequency of B-raf proto-oncogene, serine/threonine kinase (BRAF) mutations (7/30 vs. 12/20, p=0.0089) than the distal form. CRC was more frequent in cases of Kirsten rat sarcoma viral oncogene homolog (KRAS)-associated proximal/whole-colon SPP-FHP/CRC than in the remaining cases (4/4 vs. 1/8, p=0.01). Thus, SPP-FHP/CRC appears to be a specific entity, presenting two forms, proximal/whole-colon and distal, which differ in the underlying tumor initiation pathways. Early MGMT and MMR gene deficiency in the former may underlie an inherited susceptibility to genotoxic stress.
Do top management performance attribution patterns matter to subsequent organizational outcomes? A two-country study of attribution in economic crisis

Abstract Top management plays a central role in interpreting the organization’s performance and communicating to stakeholders. Management’s performance attributions set the tone for accountability and shape organizational climate. However, prior studies of the relationships between attribution patterns and subsequent performance have been limited and reported mixed results. This study extends this literature stream by examining the relationships of four different types of attribution and subsequent performance concurrently and testing them in a two-country sample. We find a significant positive relationship between positive internal attribution and subsequent performance, and reaffirm prior findings on negative external attribution and performance.
Inferning with High Girth Graphical Models

Unsupervised learning of graphical models is an important task in many domains. Although maximum likelihood learning is computationally hard, there do exist consistent learning algorithms (e.g., psuedo-likelihood and its variants). However, inference in the learned models is still hard, and thus they are not directly usable. In other words, given a probabilistic query they are not guaranteed to provide an answer that is close to the true one. In the current paper, we provide a learning algorithm that is guaranteed to provide approximately correct probabilistic inference. We focus on a particular class of models, namely high girth graphs in the correlation decay regime. It is well known that approximate inference (e.g, using loopy BP) in such models yields marginals that are close to the true ones. Motivated by this, we propose an algorithm that always returns models of this type, and hence in the models it returns inference is approximately correct. We derive finite sample results guaranteeing that beyond a certain sample size, the resulting models will answer probabilistic queries with a high level of accuracy. Results on synthetic data show that the models we learn indeed outperform those obtained by other algorithms, which do not return high girth graphs.
Bitonic-MapReduce : Optimization of MapReduce on the Cell B . E . Architecture with a Bitonic Sort Senior Honors Thesis

The Cell B.E. Architecture is a novel, heterogeneous, multi-core architecture that offers opportunities for significant performance. However, a lack of programmer familiarity with explicitly parallelizing code and difficulty using its unique software-managed memory model make writing programs for the Cell difficult, even for experienced programmers. However, if tools can be made to abstract away the issues that frustrate programmers, then programmers can concentrate on what they do best – coding. MapReduce for the Cell processor is a previously implemented runtime that provides a tool to abstract away these issues from programmers; it explicitly parallelizes the user’s code internally and handles all memory management internally. However, MapReduce for the Cell processor is slowed by a bottleneck in its sorting and grouping phases. This bottleneck is caused by the use of quicksort, which is unable to exploit the data-level parallelism the Cell generates much of its computational power from. In this work, we replace quicksort with Cellsort, an optimized bitonic sort implementation which can better exploit the Cell’s fine-grained and course-grained parallelism. After converting Cellsort to sort (key, value) pairs, a requirement of the MapReduce framework, Cellsort was integrated into MapReduce. Finally, the characteristics of the Cellsort and MapReduce models were studied.
An Examination of a Mindfulness-Based Intervention for Older Adults

Mindfulness-based interventions use meditation and other learning exercises to help individuals become more aware of their current physiological and emotional experiences. Benefits of practicing mindfulness include an increase in positive psychological outcomes (e.g., psychological well-being, emotion regulation) and a decrease in negative psychological outcomes (e.g., anxiety, depression). The vast majority of studies focus on younger rather than older adults—setting the stage for the current study, which involved delivering a five-session mindfulness-based intervention to older adults (i.e., 60 and older). The smaller literature focused on older adults is promising but generally lacks methodological rigor (e.g., lack of no-treatment control groups). The current study added to the existing literature by conducting a longitudinal quasi-experimental delayed treatment trial in a sample of older adults. First, it was hypothesized that there would be an intervention effect on several variables. Specifically, it was hypothesized that participants would experience decreases in depression, anxiety, and stress, as well as increases in the five facets of mindfulness, psychological well-being, and emotional regulation. Second, it was hypothesized that the mindfulness-based
Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.
Linking Spatial Patterns of Groundwater Table Dynamics and Streamflow Generation Processes in a Small Developed Catchment

Knowledge about water flow paths is essential for understanding biogeochemical fluxes in developed agricultural landscapes, i.e., the input of nutrients into surface waters, soil erosion, or pesticide fate. Several methods are available to study rainfall-runoff processes and flux partitioning: hydrometric based approaches, chemical tracers, modeling, and stable isotope applications. In this study a multi-method approach was conducted to gain insights into the hydrological fluxes and process understanding within the complex anthropogenic-influenced catchment of the Vollnkirchener Bach, Germany. Our results indicate that the catchment responds differently to precipitation input signals and dominant runoff-generation processes change throughout the year. Rainfall-induced runoff events during dry periods are characterized by a temporarily active combined sewer overflow. During stormflow, a large contribution of fast event water is observed. At low flow conditions losing and gaining conditions occur in parallel. However, when catchment’s moisture conditions are high, an ephemeral source from clay shale-graywacke dominated forested sites becomes active. The study reveals that the collection of detailed distributed hydrometric data combined with isotopic tracers, provides fundamental information on the complex catchment behavior, which can finally be utilized for conceptualizing water fluxes at a small catchment scale.
The effect of guar gum on the distribution of a radiolabelled meal in the gastrointestinal tract of the rat

1. The effect of addition of guar gum (5 and 10 g/l) to a radiolabelled, homogenized, baked-bean test meal on the distribution of that meal in the gastrointestinal tract was investigated in groups of male rats killed at 25, 50, 100, 200, 300 and 400 min after gavage. 2. Addition of 5 and 10 g guar gum/l significantly increased the proportion of the meal remaining in the stomach at 25 and 50 min after gavage (P <0·01). 3. The heads of the control meal and meals containing guar gum reached the distal small intestine within 25 min after gavage but radioactivity was not observed in the caecum until 100 min after administration of each of the meals. Addition of guar gum (5 and 10 g/l) delayed caecal filling even though the head of each meal reached the caecum at the same time after gavage. 4. The geometric centres of guar-gum-containing meals were proximal to that of the control meal at all times after gavage. 5. The observed delay in the passage of a guar-gum-containing meal through the stomach and small intestine is probably due to the viscous nature of the meal resisting the propulsive and mixing effects of the gastrointestinal contractions, thereby reducing access of the glucose to the absorptive epithelium. This could contribute to the observed reductions in postprandial glycaemia seen in previous studies after incorporating guar gum into a meal.
Dick Feynman—The Guy in the Office Down the Hall

When I think of Richard, I often recall a chilly afternoon in Altadena shortly after his marriage to the charming Gweneth. My late wife, Margaret, and I had returned in September 1960 from a year in Paris, London and East Africa; Richard had greeted me with the news that he was “catching up with me”—he too was to have an English wife and a small brown dog. The wedding soon took place, and it was a delightful occasion. We also met the dog (called Venus, I believe) and found that Richard was going overboard teaching her tricks (leading his mother, Lucille, with her dry wit, to wonder aloud what would become of a child if one came along). The Feynmans and we both bought houses in Altadena, and on the afternoon in question Margaret and I were visiting their place.
Algorithmic Differentiation of Linear Algebra Functions with Application in Optimum Experimental Design (Extended Version)

We derive algorithms for higher order derivative computation of the rectangular QR and eigenvalue decomposition of symmetric matrices with distinct eigenvalues in the forward and reverse mode of algorithmic differentiation (AD) using univariate Taylor propagation of matrices (UTPM). Linear algebra functions are regarded as elementary functions and not as algorithms. The presented algorithms are implemented in the BSD licensed AD tool ALGOPY. Numerical tests show that the UTPM algorithms derived in this paper produce results close to machine precision accuracy. The theory developed in this paper is applied to compute the gradient of an objective function motivated from optimum experimental design:
Genetic Polymorphisms of GSTM1, GSTT1, and GSTP1 with Prostate Cancer Risk: A Meta-Analysis of 57 Studies

Background and Objectives The GSTM1, GSTT1 and GSTP1 polymorphisms might be involved in inactivation of procarcinogens that contribute to the genesis and progression of cancers. However, studies investigating the association between GSTM1, GSTT1 or GSTP1 polymorphisms and prostate cancer (PCa) risk report conflicting results, therefore, we conducted a meta-analysis to re-examine the controversy. Methods Published literature from PubMed, Embase, Google Scholar and China National Knowledge Infrastructure (CNKI) were searched (updated to June 2, 2012). According to our inclusion criteria, studies that observed the association between GSTM1, GSTT1 or GSTP1 polymorphisms and PCa risk were included. The principal outcome measure was the odds ratio (OR) with 95% confidence interval (CI) for the risk of PCa associated with GSTM1, GSTT1 and GSTP1 polymorphisms. Results Fifty-seven studies involving 11313 cases and 12934 controls were recruited. The overall OR, which was 1.2854 (95% CI = 1.1405–1.4487), revealed a significant risk of PCa and GSTM1 null genotype, and the similar results were observed when stratified by ethnicity and control source. Further, the more important is that the present study first reported the high risks of PCa for people who with dual null genotype of GSTM1 and GSTT1 (OR = 1.4353, 95% CI = 1.0345–1.9913), or who with GSTT1 null genotype and GSTP1 A131G polymorphism (OR = 1.7335, 95% CI = 1.1067–2.7152). But no association was determined between GSTT1 null genotype (OR = 1.102, 95% CI = 0.9596–1.2655) or GSTP1 A131G polymorphism (OR = 1.0845, 95% CI = 0.96–1.2251) and the PCa risk. Conclusions Our meta-analysis suggested that the people with GSTM1 null genotype, with dual null genotype of GSTM1 and GSTT1, or with GSTT1 null genotype and GSTP1 A131G polymorphism are associated with high risks of PCa, but no association was found between GSTT1 null genotype or GSTP1 A131G polymorphism and the risk of PCa. Further rigorous analytical studies are highly expected to confirm our conclusions and assess gene-environment interactions with PCa risk.
Resistance to Systemic Oppression by Students of Color in a Diversity Course for Preservice Teachers

In a diversity course for preservice teachers, we explored coursework by students of color to uncover instances in which they resisted the existence systemic oppression in K–12 schools. First, we examined the written responses from 3 students of color (Asian-Indian, Asian immigrant, and Latina) who were largely agreeable to the existence of different forms of oppression presented in the course content. Our work illuminated instances of what we have described as. Students initially referred to narratives of rugged individualism or the American Dream to resist the existence of systemic barriers. As the course progressed, students shifted to deeply entrenched responses that rejected the course content to refute systemic oppression. Second, we developed a case study for one student, a biracial girl that self-identified as White who consistently rejected systemic oppression during class interactions to the point of displaying openly defiant behaviors. The examples of resistance we encountered served as a reminder that students of color, along with their White peers, must be able to critically examine and understand systems of oppression that are pervasive throughout education. Furthermore, the underlying sources of the resistance were closely associated with indoctrination in Whiteness, limited understanding of systemic oppression, deeply held beliefs and understandings, and the lived experiences of individuals. Although we agree that teacher education must recruit and retain more teachers of color for an increasingly diverse US K–12 student population, we add that preparation that meets the needs of teachers of color is essential.
Effects of an extended photoperiod on gonadal function and condition of hair coats in Thoroughbred colts and fillies

ABSTRACT The effects of an extended photoperiod (EP) in Thoroughbreds colts and fillies from winter at one year old to spring at two years old on the gonadal functions, coat condition, and endocrine changes were investigated. Sixty-two Thoroughbreds (31 colts and 31 fillies) reared in the Hidaka Training and Research Center (Hidaka), Japan Racing Association were used. Thirty of them (15 colts and 15 fillies) were reared under EP conditions from December 20 to April 10, and the remaining 32 horses were reared under natural light alone as a control group. For EP, a 100-watt white bulb was set near the ceilings of stalls, and lighting conditions of 14.5-hr light and 9.5-hr dark periods were established. Blood was collected from the jugular vein once a month from October at one year old to February at two years old in both colts and fillies, and then twice a month in colts and weekly in fillies after March, and the coat condition was evaluated in January and April in 56 horses. To investigate endocrine changes, the plasma concentrations of prolactin, luteinizing hormone (LH), follicle-stimulating hormone (FSH), immunoreactive (ir-) inhibin, testosterone, estradiol-17β and progesterone were measured. No significant difference was noted in the coat condition between the two groups in January, but they changed from winter to summer coats (molting of winter coats) in April in the EP group compared with the control group. Regarding endocrine changes, the plasma concentrations of prolactin, FSH, ir-inhibin and testosterone were significantly higher in the EP colts than in the control group from January to April. The plasma concentrations of LH tended to rise in the EP colts from January to April compared with the control group. In the EP fillies, the plasma concentrations of prolactin, LH, ir-inhibin, estradiol-17β and progesterone were significantly higher during January and April, but a significantly high level of FSH was noted in the control than EP group in January. The ovulation day was advanced in the EP fillies compared with the control group. The present study clearly demonstrated that EP treatment during rearing advanced the molting of winter coats in both colts and fillies. These results suggested to be due to the action of prolactin being increased by EP treatment. In addition, EP treatment stimulated the hypothalamus-pituitary-gonadal axis even in yearlings, and advanced ovulation in fillies. Since EP treatment-induced changes in the yearlings were within the physiological range, and the method is safe and simple, EP treatment may be an effective technique in horse husbandry.
Evaluation of intra- and inter-rater reliability and concurrent validity of the Italian version of the Jebsen–Taylor Hand Function Test in adults with rheumatoid arthritis

Introduction In rheumatoid arthritis, a reduction in hand function can lead to a decrease in health, with a consequent limitation of daily life activities and restriction in social participation. Evaluation plays a decisive role in the functional recovery process and in rehabilitation programs. The Jebsen–Taylor Hand Function Test is one of the most widely used non-diagnosis-specific assessment tools in rehabilitation. The aim of the study was to evaluate the intra-rater and inter-rater reliability and concurrent validity of the Italian version of the Jebsen–Taylor Hand Function Test (JTHFT-IT) in a population with rheumatoid arthritis. Methods The test’s reliability and validity were assessed by following international guidelines. Its internal consistency and intra- and inter-rater reliability were examined using Cronbach’s alpha coefficient and the intraclass correlation coefficient, respectively. Its concurrent validity was evaluated using Pearson’s correlation coefficient with a dynamometer instrument. Results The test was given to 108 people with rheumatoid arthritis. Cronbach’s alpha reported a value of 0.91 for the dominant hand and 0.87 for the non-dominant hand. Intra- and inter-rater reliability were evaluated with a subgroup of 30 individuals. Intraclass correlation coefficients ranged from 0.46 to 1.00 in the dominant and non-dominant hands. Pearson’s correlation between subtests and the dynamometer ranged from –0.14 to –0.59. Conclusions The present study supports the use of the JTHFT-IT as a measure of hand functionality in people with rheumatoid arthritis. It is an important tool for Italian professionals and it can be useful both in clinical practice to evaluate improvement after rehabilitation treatments and for research in hand rehabilitation.
THE r-PROCESS IN METAL-POOR STARS AND BLACK HOLE FORMATION

Nucleosynthesis of heavy nuclei in metal-poor stars is generally thought to occur via the r-process because the r-process is a primary process that would have operated early in the Galaxy's history. This idea is strongly supported by the fact that the abundance pattern in many metal-poor stars matches well the inferred solar r-process abundance pattern in the mass range between the second and third r-process abundance peaks. Nevertheless, a significant number of metal-poor stars do not share this standard r-process template. In this Letter, we suggest that the nuclides observed in many of these stars are produced by the r-process, but that it is prevented from running to completion in more massive stars by collapse to black holes before the r-process is completed, creating a “truncated r-process,” or “tr-process. ” We find that the observed fraction of tr-process stars is qualitatively what one would expect from the initial mass function and that an apparent sharp truncation observed at around mass 160 could result from a combination of collapses to black holes and the difficulty of observing the higher mass rare-earth elements. We test the tr-process hypothesis with r-process calculations that are terminated before all r-process trajectories have been ejected. We find qualitative agreement between observation and theory when black hole collapse and observational realities are taken into account.
rt 1 0 / 2 0 0 6 Learning structure illuminates black boxes – an introduction into Estimation of Distribution Algorithms

This chapter serves as an introduction to estimation of distribution algorithms. Estimation of distribution algorithms are a new paradigm in evolutionary computation. State-of-the-art EDAs consistently outperform classical genetic algorithms on a broad range of problems. We review the fundamental principles and algorithms that are necessary to understand EDA research. We focus on EDAs for the discrete and the continuous problem domains and discuss the differences between the two.