Miracle-dz/UniFAR-FTUs huggingface dataset:
Attenuation of microvascular reperfusion injury in rat pancreas transplantation by L-arginine.

BACKGROUND Despite improving results, exocrine complications remain a major challenge in clinical pancreas transplantation. The etiology of posttransplantation pancreatitis relates almost certainly to cold ischemia/reperfusion-induced microvascular injury with an imbalance of vasoconstricting and vasodilating mediators due to endothelial dysfunction. We therefore studied the effectiveness of a nitric oxide donor on postischemic microvascular reperfusion injury after pancreas transplantation. METHODS Heterotopic isogeneic pancreaticoduodenal transplantation was performed in spontaneously breathing, chloralhydrate-anesthetized Sprague Dawley rats after 16 hr (n=5) of cold storage of the graft in 4 degrees C histidine-tryptophane-ketoglutarate solution. An additional five animals received L-arginine immediately before (50 mg/kg i.v.) and during the first 30 min of reperfusion (100 mg/kg i.v.). Five animals that did not undergo transplantation served as controls. Intravital fluorescence microscopy was used for analysis of functional capillary density, capillary diameters, and capillary red blood cell velocity in exocrine pancreatic tissue during 120 min of reperfusion. Histology served for quantitative assessment of inflammatory response (leukocytic tissue infiltration) and endothelial disintegration (edema formation). RESULTS In L-arginine-treated animals, functional capillary density of exocrine tissue of pancreatic grafts was found slightly higher after 30 and 60 min, and significantly higher after 120 min of postischemic reperfusion compared with untreated pancreatic grafts. This was accompanied by a significant increase of capillary diameters. In parallel, pancreatic histology revealed significant attenuation of both leukocytic tissue infiltration and edema formation in the L-arginine-treated animals when compared with the nontreated controls. CONCLUSIONS Besides reduction of leukocyte-dependent microvascular injury, L-arginine improves postischemic microvascular reperfusion, supposedly by capillary dilatation. Thus, our results suggest that supplement of nitric oxide during reperfusion is effective in attenuating exocrine microvascular reperfusion injury.
AP-3 and Rabip4’ Coordinately Regulate Spatial Distribution of Lysosomes

The RUN and FYVE domain proteins rabip4 and rabip4’ are encoded by RUFY1 and differ in a 108 amino acid N-terminal extension in rabip4’. Their identical C terminus binds rab5 and rab4, but the function of rabip4s is incompletely understood. We here found that silencing RUFY1 gene products promoted outgrowth of plasma membrane protrusions, and polarized distribution and clustering of lysosomes at their tips. An interactor screen for proteins that function together with rabip4’ yielded the adaptor protein complex AP-3, of which the hinge region in the β3 subunit bound directly to the FYVE domain of rabip4’. Rabip4’ colocalized with AP-3 on a tubular subdomain of early endosomes and the extent of colocalization was increased by a dominant negative rab4 mutant. Knock-down of AP-3 had an ever more dramatic effect and caused accumulation of lysosomes in protrusions at the plasma membrane. The most peripheral lysosomes were localized beyond microtubules, within the cortical actin network. Our results uncover a novel function for AP-3 and rabip4’ in regulating lysosome positioning through an interorganellar pathway.
Characteristics of Social Perception Assessed in Schizophrenia Using Virtual Reality

Impairment in social skills is one of the few criteria that all individuals diagnosed with schizophrenia must meet. Successful social skills require the coordination of many abilities, including social perception, which involves the decoding and interpretation of social cues from others. In this study, we examined the potential for virtual reality (VR) in social skill training. We attempted to determine if VR can be used to measure social skills and social perception, and to determine which VR parameters are related to schizophrenic symptoms. Some of these results have clear clinical relevance, while other observations need further study. The VR system appears to be useful in assessing the social perception of schizophrenics and normal people, and could be more widely used in the future for social training and in the assessment of social problem-solving abilities, assertiveness skills, and general social skills.
Dynamics of social positioning patterns in group-robot interactions

When a mobile robot interacts with a group of people, it has to consider its position and orientation. We introduce a novel study aimed at generating hypotheses on suitable behavior for such social positioning, explicitly focusing on interaction with small groups of users and allowing for the temporal and social dynamics inherent in most interactions. In particular, the interactions we look at are approach, converse and retreat. In this study, groups of three participants and a telepresence robot (controlled remotely by a fourth participant) solved a task together while we collected quantitative and qualitative data, including tracking of positioning/orientation and ratings of the behaviors used. In the data we observed a variety of patterns that can be extrapolated to hypotheses using inductive reasoning. One such pattern/hypothesis is that a (telepresence) robot could pass through a group when retreating, without this affecting how comfortable that retreat is for the group members. Another is that a group will rate the position/orientation of a (telepresence) robot as more comfortable when it is aimed more at the center of that group.
Experimental Study on Concrete Columns Confined with External FRP

It is known that confinement with FRP (fibre reinforced polymer) jackets is a useful reinforcement technique to improve the strength and ductility of concrete columns subjected to axial compression loads, especially in those that have a circular cross section. This strengthening method is less effective for elements with square or rectangular sections in which, unlike the circular ones, the FRP confinement is not uniform. However, concrete columns with non-circular cross section are very common in construction, so it is essential to be able to estimate adequately the ultimate capacity of the reinforced element depending on the shape of the section. Most of the international guidelines for the design and calculation of this type of reinforcements recognize this circumstance and incorporate a shape factor, although there is no unanimity in their proposals. This paper presents the preliminary results of an experimental study on intermediate-sized concrete specimens reinforced with FRP jackets. Special attention is paid to two parameters related to the section shape that have an important impact on the efficiency of the reinforcement on rectangular sections: the aspect ratio of the cross section or relationship between the sides of the concrete section (b/d) and the radius of curvature of the corners (Rc). This work is part of a research project that includes a larger experimental program with full-scale tests.
An Organizational Perspective on the Origins of Instructional Segregation: School Composition and Use of Within-Class Ability Grouping in American Kindergartens

Background This investigation was sparked by research findings on secondary education showing school segregation to be closely associated with homogeneous grouping practices, such as tracking and between-class ability grouping. Research Design We conduct secondary analyses of national data from the Early Childhood Longitudinal Study–Kindergarten Cohort (ECLS-K). Objectives Using these data, we investigate the degree to which the racial and ethnic composition of schools is associated with use of ability grouping practices as early as kindergarten. We focus on within-class ability grouping for reading instruction because it is the most common form of homogeneous grouping for the early grades. Results and Conclusions We find that this form of grouping is practiced by a majority of kindergarten teachers and schools, although frequency of use is quite varied, and some teachers and schools use it only sporadically. The most intensive use of within-class ability grouping exists in schools that serve high proportions of minority students and in schools with high variability in students’ reading readiness. The association between student body composition and use of this instructional practice remains even after variability in student academic skills and other structural characteristics of schools are accounted for. Schools serving primarily minority students that use within-class ability grouping have higher average gains in reading achievement by the end of the school year than comparable schools that do not use this form of grouping. Use of this instructional practice is not associated with increases in average achievement gain scores for schools serving students of diverse or primarily White backgrounds. Our findings provide the foundation for further studies of the structural, cultural, and political features of schools associated with the use of ability grouping at the onset of schooling.
Biofilter as a Functional Annotation Pipeline for Common and Rare Copy Number Burden

Recent studies on copy number variation (CNV) have suggested that an increasing burden of CNVs is associated with susceptibility or resistance to disease. A large number of genes or genomic loci contribute to complex diseases such as autism. Thus, total genomic copy number burden, as an accumulation of copy number change, is a meaningful measure of genomic instability to identify the association between global genetic effects and phenotypes of interest. However, no systematic annotation pipeline has been developed to interpret biological meaning based on the accumulation of copy number change across the genome associated with a phenotype of interest. In this study, we develop a comprehensive and systematic pipeline for annotating copy number variants into genes/genomic regions and subsequently pathways and other gene groups using Biofilter - a bioinformatics tool that aggregates over a dozen publicly available databases of prior biological knowledge. Next we conduct enrichment tests of biologically defined groupings of CNVs including genes, pathways, Gene Ontology, or protein families. We applied the proposed pipeline to a CNV dataset from the Marshfield Clinic Personalized Medicine Research Project (PMRP) in a quantitative trait phenotype derived from the electronic health record - total cholesterol. We identified several significant pathways such as toll-like receptor signaling pathway and hepatitis C pathway, gene ontologies (GOs) of nucleoside triphosphatase activity (NTPase) and response to virus, and protein families such as cell morphogenesis that are associated with the total cholesterol phenotype based on CNV profiles (permutation p-value < 0.01). Based on the copy number burden analysis, it follows that the more and larger the copy number changes, the more likely that one or more target genes that influence disease risk and phenotypic severity will be affected. Thus, our study suggests the proposed enrichment pipeline could improve the interpretability of copy number burden analysis where hundreds of loci or genes contribute toward disease susceptibility via biological knowledge groups such as pathways. This CNV annotation pipeline with Biofilter can be used for CNV data from any genotyping or sequencing platform and to explore CNV enrichment for any traits or phenotypes. Biofilter continues to be a powerful bioinformatics tool for annotating, filtering, and constructing biologically informed models for association analysis - now including copy number variants.
Backchannels revisited from a multimodal perspective

In this study, we analyze the role of several linguistic cues (prosodic units, pitch contours, discourse markers, morphological categories, and gaze direction) in French turn-taking face-to-face interactions. Specifically, we investigate vocal and gestural backchannel signals (BCs) produced by a recipient to show his active listening. We show that some particular pitch contours and discursive markers play a systematic role in inducing both gestural and vocal BCs. Conversely, morphological categories and gestural cues rather play a role for gestural BCs.
Tor Signaling Regulates Transcription of Amino Acid Permeases through a GATA Transcription Factor Gaf1 in Fission Yeast

In the fission yeast, two Tor isoforms, Tor1 and Tor2, oppositely regulate gene expression of amino acid permeases. To elucidate the transcriptional machinery for these regulations, here we have employed the cap analysis of gene expression (CAGE), a method of analyzing expression profiles and identifying transcriptional start sites (TSSs). The loss of Tor1 decreased, and Tor2 inhibition by its temperature sensitive mutation increased, mRNA expression of isp5 +, per1 +, put4 + and SPBPB2B2.01. In contrast, the loss of Tor1 increased, and Tor2 inhibition decreased, the expression of cat1 +. These changes were confirmed by semi-quantitative RT-PCR. These opposite effects by the loss of Tor1 and Tor2 inhibition appeared to occur evenly across multiple TSSs for the respective genes. The motif discovery analysis based on the CAGE results identified the GATA motifs as a potential cis-regulatory element for Tor-mediated regulation. In the luciferase reporter assay, the loss of Tor1 reduced, and Tor2 inhibition and nitrogen depletion increased, the activity of isp5 + promoter as well as that of a GATAAG reporter. One of the GATAAG motifs in isp5 + promoter was critical for its transcriptional activity, and a GATA transcription factor Gaf1 was critical for the activities of isp5 + promoter and the GATAAG reporter. Furthermore, Tor2 inhibition and nitrogen depletion induced nuclear localization of Gaf1 from the cytosol and its dephosphorylation. These results suggest that Tor2 inhibition, which is known to be induced by nitrogen depletion, promotes nuclear localization of Gaf1, thereby inducing isp5 + transcription through Gaf1 binding to the GATAAG motif in its promoter. Since Gaf1 was also critical for transcription of per1 + and put4 +, Tor-Gaf1 signaling may coordinate transcription of multiple amino acid permeases according to nutrient availability.
Association of the Serotonin Receptor 3E Gene as a Functional Variant in the MicroRNA-510 Target Site with Diarrhea Predominant Irritable Bowel Syndrome in Chinese Women

Background/Aims The functional variant (rs56109847) in the 3′-untranslated regions (3′-UTR) of the serotonin receptor 3E (HTR3E) gene is associated with female diarrhea predominant irritable bowel syndrome (IBS-D) in British populations. However, the relationship of the polymorphism both to HTR3E expression in the intestine and to the occurrence of Chinese functional gastrointestinal disorders has yet to be examined. Methods Polymerase chain reaction amplification and restriction fragment length polymorphism analyses were employed to detect polymorphisms among Chinese Han women, particularly 107 patients with IBS-D, 99 patients with functional dyspepsia (FD), 115 patients with mixed IBS and 69 patients with IBS-D + FD. We also assessed microRNA-510 (miR-510) and HTR3E expression in human colonic mucosal tissues with immunohistochemistry and other methods. Dual-luciferase reporter assays were conducted to examine the binding ability of miR-510 and HTR3E 3′-UTR. Results Genotyping data showed the variant rs56109847 was significantly associated with IBS-D, but not with FD, mixed-IBS, or FD + IBS-D. HTR3E was abundantly expressed around the colonic mucosal glands but less expressed in the stroma. miR-510 expression decreased, whereas HTR3E expression increased in the colonic mucosal tissue of patients with IBS-D compared with those in controls. HTR3E expression was significantly higher in patients with the GA genotype than that in patients with the GG genotype. The single-nucleotide polymorphisms disrupted the binding site of miR-510 and significantly upregulated luciferase expression in HEK293 and HT-29 cells. Conclusions The single-nucleotide polymorphisms rs56109847 led to reduced microRNA binding and overexpression of the target gene in intestinal cells, thereby increasing IBS-D risk in the Chinese Han population. The decreased expression of miR-510 might contribute to IBS-D.
Combining a Chinese Thesaurus with a Chinese Dictionary

In this paper, we study the problem of combining a Chinese thesaurus with a Chinese dictionary by linking the word entries in the thesaurus with the word senses in the dictionary, and propose a similar word strategy to solve the problem. The method is based on the definitions given in the dictionary, but without any syntactic parsing or sense disambiguation on them at all. As a result, their combination makes the thesaurus specify the similarity between senses which accounts for the similarity between words, produces a kind of semantic classification of the senses defined in the dictionary, and provides reliable information about the lexical items on which the resources don't conform with each other.
Tracking characteristics of an OBE parameter-estimation algorithm

The tracking properties of a recursive parameter-bounding algorithm, referred to as the Dasgupta-Huang optimal bounding ellipsoid algorithm (DHOBE algorithm) are investigated. Conditions that ensure the existence of these 100% confidence regions in the face of small model-parameter variations are derived. For larger parameter variations, it is shown that the existence of 100% confidence regions is guaranteed asymptotically. A modification that enables the algorithm to track large variations in model parameter is proposed. Simulation results show that in general, the modified algorithm has a tracking performance comparable, and in some cases superior, to that of the exponentially weighted recursive-least-squares (RLS) algorithm. >
Interferon-&ggr; production by natural killer cells and cytomegalovirus in critically ill patients*

Objective:The mechanisms involved in cytomegalovirus reactivation in critically ill patients who were previously immunocompetent are still unknown. The current study was designed to evaluate the possible role of natural killer cells in the reactivation of cytomegalovirus in these patients. Design:Prospective observational. Setting:A medical intensive care unit of a university hospital. Patients:Fifty-one subjects, including 15 patients who experienced cytomegalovirus reactivation (cases) during their intensive care unit stay and 15 patients who matched intensive care unit controls, selected from a cohort of consecutive nonimmunocompromised intensive care unit patients, as well as healthy controls. Interventions:Tests included weekly systematic immunomonitoring and routine screening for cytomegalovirus infection until discharge from the intensive care unit or death. The immunophenotype and functions of natural killer cells were performed by flow cytometry, and serum levels of pro- and anti-inflammatory cytokines were determined by enzyme-linked immunosorbent assay. Measurements and Main Results:The overall occurrence of cytomegalovirus reactivation in the cohort was 27%. No differences of natural killer cell effector functions were observed at admission between cases and controls. Instead, before cytomegalovirus reactivation, the ability of natural killer cells to secrete interferon-&ggr; was significantly reduced in cases as compared with controls upon stimulation with antibody-coated target cells (p = .029) and with K562 cell stimulation (p = .029). No phenotypic or quantitative differences were observed between cases and controls. Cases exhibited higher levels of interleukin 10 (p = .031) and interleukin 15 (p = .021) than controls before cytomegalovirus reactivation. Conclusions:Impaired natural killer cell function with reduced interferon-&ggr; secretion precedes the occurrence of cytomegalovirus reactivation among previously immunocompetent critically ill patients.
Identification and Effects of Choice of Higher versus Lower Preference Assignments for Students at Risk for ED.

A study involving 3 elementary students (ages 8-10) investigated the treatment effects of choice making with academic assignments. Students at risk for emotional disturbance (ED) in a general education setting participated. These were children who exhibited aggressive behaviors and were judged to be achieving below their grade level by their teachers. Interviews with teachers and the students were conducted to identify two higher preference and two lower preference mathematics assignments for each of the three students. A validation assessment was completed to verify that the students engaged in high levels of disruptive behavior. Then, using an ABAB design, and alternating across students, the effects of choice on on-task and disruptive behavior, and academic efficiency was evaluated. First, the effect of student versus teacher choice of lower preference tasks was assessed. Then, the effects of both choice conditions were evaluated for higher preference tasks for one student. Student choice in the lower preference task condition was only associated with a decrease in inappropriate behavior for one student. An increase in engaged behavior or academic efficiency was not observed under low preference choice conditions for any participants. For one student, high preference choice resulted in favorable behavioral changes. (Contains 25 references.) (CR) Reproductions supplied by EDRS are the best that can be made from the original document. Task Preference and Choice 1 Running Head: TASK PREFERENCE AND CHOICE Identification and Effects of Choice of Higher Versus Lower Preference Assignments For Students at Risk for ED Jennifer Coniglio
Childhood Obesity — What We Can Learn From Existing Data on Societal Trends, Part 2

The number of overweight and obese youth has increased in recent decades, yet few data assess how the lives of children have changed during the "obesity epidemic. " Part 1 of this two-part study discussed trends in time use, studying at home, and media use. Part 2 focuses on transportation, physical education, and diet. Walking or biking for transportation can expend a large amount of energy, but active transportation is not a major source of physical activity for youth, averaging eight minutes a day in 2001, with little change over the past few decades. For adolescents, there was no clear trend in physical education during the past decade, but there are no data for after-school and day-care programs, which have become more important as children spend more time away from home. For younger children, time spent in organized sports and outdoor activities increased by 73 minutes per week between 1981 and 1997. Eating as a primary activity declined, suggesting a shift toward snacking or eating as a secondary activity. Statistically significant trends exist for carbohydrate intake, especially for chips/crackers/popcorn/pretzels (intake tripled from the mid-1970s to the mid-1990s) and soft drinks (intake doubled during the same period). Price and income data suggest possible economic reasons for these changes. The percentage of disposable income spent on food has declined continuously, and almost all of the decline has been represented by food consumed at home, yet today's disposable income buys more calories than it has in the past. Relative prices have encouraged shifts across food types. From a baseline of 100 during 1982–84, the price index for fresh fruit and vegetables increased to 258 by 2002 (far exceeding general inflation), whereas the price index for soft drinks increased only to 126 by 2002 (below general inflation).