Miracle-dz/UniFAR-FTUs huggingface dataset:
Characteristics Desired in Clinical Data Warehouse for Biomedical Research

Objectives Due to the unique characteristics of clinical data, clinical data warehouses (CDWs) have not been successful so far. Specifically, the use of CDWs for biomedical research has been relatively unsuccessful thus far. The characteristics necessary for the successful implementation and operation of a CDW for biomedical research have not clearly defined yet. Methods Three examples of CDWs were reviewed: a multipurpose CDW in a hospital, a CDW for independent multi-institutional research, and a CDW for research use in an institution. After reviewing the three CDW examples, we propose some key characteristics needed in a CDW for biomedical research. Results A CDW for research should include an honest broker system and an Institutional Review Board approval interface to comply with governmental regulations. It should also include a simple query interface, an anonymized data review tool, and a data extraction tool. Also, it should be a biomedical research platform for data repository use as well as data analysis. Conclusions The proposed characteristics desired in a CDW may have limited transfer value to organizations in other countries. However, these analysis results are still valid in Korea, and we have developed clinical research data warehouse based on these desiderata.
Utilisation d'ontologies pour la quête de vérité : une étude expérimentale

L'objectif principal des methodes de recherche de verite (truth-finding en anglais) consiste a determiner les valeurs les plus fiables et dignes de confiance parmi celles qui sont associees a un ensemble de faits. La plupart des methodes actuelles supposent qu'il n'existe qu'une seule valeur 'vraie', ce qui les rend inappropriees pour des applications reelles ou plusieurs valeurs peuvent etre considerees comme vraies simultanement : Paris est une capitale, mais egalement une ville ou meme un departement… Cet article propose une extension de la formalisation habituellement utilisee dans la litterature, afin de prendre en compte les relations entre les valeurs candidates definies au sein d'une ontologie de domaine et ainsi determiner les valeurs qui entrent en conflit et celles qui peuvent etre 'vraies' simultanement. Notre approche s'inspire des fonctions de croyance afin de propager une valeur de confiance a ces valeurs candidates en fonction de l'ordre partiel etabli par l'ontologie. L’evaluation de notre approche, tenant compte de faits extraits de DBpedia, demontre son efficacite par rapport aux approches classiques – au travers notamment d’une diminution du taux d'erreur pouvant aller de 16 a 30%.
Effected Brewing Time and Temperature of Centella Asiatica Tea on Antioxidant Activity and Consumer Acceptance

Centella asiatica has known as medical plant that used for treating bruises and reducing swelling. From the previous research lately, it reported that C.asiatica has properties to improve memory recognition and promote healthy skin. C.asiatica is herbal plant that available in the market, it has been developed to enhance the amount of antioxidant. Therefore, this study was aimed to determine the most effective brewing process of C.asiatica tea and study the amount of antioxidant activities. The temperature was vary with 80°C, 85°C, and 90°C and time was 2, 3, 4, and 5 minutes. The formation of consuming tea was determined by 30 target panelists. The result showed that there was no significant difference among all temperature and time that were determined. The best temperature and time for brewing is 80°C at 5 minutes because it saves energy and can extract the highest amount of antioxidant from herbal tea.
Classical Cut-elimination in the π-calculus

We define a calculus LK a variant of the calculus X that enjoys the Curry-Howard correspondence for Gentzen’s calculus LK; the variant consists of allowing arbitrary progress of cut over cut . We study the π-calculus enriched with pairing, for which we define a notion of implicative type assignment, translate the terms of LK into this variant of π, and show that reduction and assignable types are preserved. This implies that all proofs in LK have a representation in π, and cut-elimination is effectively simulated by π’s synchronisation, congruence, and equivalence between processes. We present two interpretations for which we show soundness results, as well as type preservation. Using the second, we show that we preserve Gentzen’s Hauptsatz result, and prove completeness. We then enrich the logic with the connector ¬, and show that this also can be represented in π, whilst preserving the results.
Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting

Stereologic cell counting has had a major impact on the field of neuroscience. A major bottleneck in stereologic cell counting is that the user must manually decide whether or not each cell is counted according to three-dimensional (3D) stereologic counting rules by visual inspection within hundreds of microscopic fields-of-view per investigated brain or brain region. Reliance on visual inspection forces stereologic cell counting to be very labor-intensive and time-consuming, and is the main reason why biased, non-stereologic two-dimensional (2D) “cell counting” approaches have remained in widespread use. We present an evaluation of the performance of modern automated cell detection and segmentation algorithms as a potential alternative to the manual approach in stereologic cell counting. The image data used in this study were 3D microscopic images of thick brain tissue sections prepared with a variety of commonly used nuclear and cytoplasmic stains. The evaluation compared the numbers and locations of cells identified unambiguously and counted exhaustively by an expert observer with those found by three automated 3D cell detection algorithms: nuclei segmentation from the FARSIGHT toolkit, nuclei segmentation by 3D multiple level set methods, and the 3D object counter plug-in for ImageJ. Of these methods, FARSIGHT performed best, with true-positive detection rates between 38 and 99% and false-positive rates from 3.6 to 82%. The results demonstrate that the current automated methods suffer from lower detection rates and higher false-positive rates than are acceptable for obtaining valid estimates of cell numbers. Thus, at present, stereologic cell counting with manual decision for object inclusion according to unbiased stereologic counting rules remains the only adequate method for unbiased cell quantification in histologic tissue sections.
Meeting Report: Structural Determination of Environmentally Responsive Proteins

The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein–protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health.
Obesity and recurrent intervertebral disc prolapse after lumbar microdiscectomy.

INTRODUCTION The primary aim of this study was to investigate the relationship between obesity and recurrent intervertebral disc prolapse (IDP) following lumbar microdiscectomy. METHODS A retrospective review of case notes from 2008 to 2012 was conducted for all patients who underwent single level lumbar microdiscectomy performed by a single surgeon. All patients were followed up at two weeks and six weeks following surgery, and given an open appointment for a further six months. RESULTS A total of 283 patients were available for analysis: 190 (67%) were in the non-obese group and 93 (32.9%) in the obese group. There was no statistical difference in postoperative infection, dural tear or length of stay between the non-obese and obese groups. Recurrent symptomatic IDP was seen in 27 patients (9.5%) confirmed by magnetic resonance imaging. Nineteen (10.0%) were in the non-obese group and eight (8.6%) in the obese group (p>0.8). CONCLUSIONS In our study, obesity was not a predictor of recurrent IDP following lumbar microdiscectomy. Our literature review confirmed that this study reports the largest series to date analysing the relationship between obesity and recurrent IDP following lumbar microdiscectomy in the British population.
PHYLOGEOGRAPHY OF THE TRUMPETFISHES (AULOSTOMUS): RING SPECIES COMPLEX ON A GLOBAL SCALE

Abstract The distribution of circumtropical marine species is limited by continental boundaries, cold temperate conditions, and oceanic expanses, but some of these barriers are permeable over evolutionary time scales. Sister taxa that evolved in separate ocean basins can come back into contact, and the consequences of this renewed sympatry may be a key to understanding evolutionary processes in marine organisms. The circumtropical trumpetfishes (Aulostomus) include a West Atlantic species (A. maculatus), an Indian-Pacific species (A. chinensis), and an East Atlantic species (A. strigosus) that may be the product of a recent invasion from the Indian Ocean. To resolve patterns of divergence and speciation, we surveyed 480 bp of mitochondrial DNA cytochrome b in 196 individuals from 16 locations. Based on a conventional molecular clock of 2% sequence divergence per million years, the deepest partitions in a neighbor-joining tree (d = 0.063–0.082) are consistent with separation of West Atlantic and Indian-Pacific species by the Isthmus of Panama, 3–4 million years ago. By the same criteria, trumpetfish in the East Atlantic were isolated from the Indian Ocean about 2.5 million years ago (d = 0.044–0.054), coincident with the advent of glacial cycles and cold-water upwelling around South Africa. Continental barriers between tropical oceans have only rarely been surmounted by trumpetfishes, but oceanic barriers do not appear to be substantial, as indicated by weak population partitioning (ϕST = 0.093) in A. chinensis across the Indian and Pacific Oceans. Finally, morphological and mitochondrial DNA data indicate hybridization of A. strigosus and A. maculatus in Brazil. After 3–4 million years and a globe-spanning series of vicariant and dispersal events, trumpetfish lineages have come back into contact in the southwest Atlantic and appear to be merging. This ring species phenomenon may occur in a broad array of marine organisms, with clear implications for the production and maintenance of biodiversity in marine ecosystems. Corresponding Editor: L. Bernatchez
Neuropeptide Y and regulation of the cardiovascular system.

UNLABELLED CONTROL OF CARDIOVASCULAR SYSTEM: Neuropeptide Y has three major activities which are important in the modulation of blood pressure homeostasis. When released from sympathetic neurons innervating the cardiovascular system, this peptide causes direct long-lasting vasoconstriction, inhibits the release of noradrenaline and other neurotransmitters and potentiates the action of noradrenaline and other pressor agents. RECEPTOR SUBTYPE DIVERSITY At least two major subtypes of neuropeptide Y receptor have been defined by pharmacological criteria, and the major subtype involved in the control of blood pressure (Y1) has been isolated by molecular cloning. Analysis of the cloned DNA sequence has confirmed that the receptor is a member of the G protein-coupled receptor superfamily and when expressed in various cell lines can couple to both the inhibition of adenylate cyclase and the elevation of intracellular calcium. NEUROPEPTIDE Y ANTAGONISTS: A specific neuropeptide Y antagonist has been developed which significantly lowers the dose-dependent neuropeptide Y-induced pressor response in normal rats. The inhibition is specific for the peptide and also selective for the postsynaptic Y1 receptor-mediated vasoconstrictor activity. Administration of this specific and selective inhibitor significantly reduces resting arterial blood pressure, which remains depressed for up to 4 h in normal and spontaneously hypertensive rats. CONCLUSIONS Inhibition of endogenous neuropeptide Y activity demonstrates that this peptide makes a significant contribution to the control of blood pressure and indicates the therapeutic potential of neuropeptide Y inhibitors as a new class of antihypertensive agent. The molecular cloning of the neuropeptide Y receptor subtype responsible for both the direct vasoconstrictor activity of the peptide and the potentiation of the action of other pressor agents represents an important advance in our understanding of the molecular basis of neuropeptide Y action and will help in the development of selective neuropeptide Y antagonists.
Motion perception in schizophrenia.

BACKGROUND Eye-tracking dysfunction has been found in many patients with schizophrenia and in about 40% of their first-degree biological relatives. We hypothesized that a deficit in motion processing is associated with eye-tracking dysfunction because both motion signals and the brain regions responsible for processing motion signals are implicated in the generation of smooth pursuit. We examined several aspects of visual perception, including motion perception, in patients with schizophrenia. METHODS To evaluate motion perception, contrast sensitivity for velocity discrimination was measured in patients with schizophrenia (n=15) and normal control subjects (n=18). Contrast sensitivities for orientation discrimination and contrast detection were measured as control tasks. RESULTS Patients with schizophrenia showed significantly lower contrast sensitivity (ie, higher thresholds) than normal controls for the discrimination of small velocity differences (eg, 11 vs 9 degrees/s). This reduction in contrast sensitivity was severe (up to 10-fold) in about 40% of the patients. No group differences were found on the other tasks. CONCLUSION The discrimination of small velocity differences is impaired in a subgroup of patients with schizophrenia.
Relation of Emotional Intelligence to Emotional Recognition and Mood Management

This study replicated Petrides and Furnham's 2000 test of the multidimensional nature of the Emotional Intelligence Scale by Schutte, et al. A survey of 153 college students (M age = 25.0, SD = 4.4, 54.2% women) was performed. Four factors which closely resembled previous ones were found although there were some differences in item loadings. The factors were Optimism, Mood Management, Nonverbal, and Empathy. Then, the total and factor scores were examined for their relationship to scores on the Emotional Recognition and Mood Management Inventories developed by Wells and Hakanen in 1991 for the purpose of testing predictive validity and developing measures with high internal validity.
Intra-system reliability of SICS: video-tracking system (Digital.Stadium®) for performance analysis in soccer.

BACKGROUND The correct evaluation of external load parameters is a key factor in professional soccer. The instrumentations usually utilised to quantify the external load parameters during official matches are video-tracking systems (VTS). VTS is a technology that records two-dimensional position data (x and y) at high sampling rates (over 25 Hz). The aim of this study was to evaluate the intra-system reliability of Digital.Stadium® VTS. METHODS Twenty-eight professional male soccer players taking part in the Italian Serie A (age 24±6 years, body mass 79.5±7.8 kg, stature 1.83±0.05 m) during the 2015/16 season were enrolled in this study (team A and team B). Video-analysis was done during an official match and data analysis was performed immediately after the game ended and then replicated a week later. RESULTS This study reported a near perfect relationship between the initial analysis (analysis 1) and the replicated analysis undertaken a week later (analysis 2). R2 coefficients were highly significant for each of the performance parameters, P<0.001. This study reported a mean TD=8095±3271 and 8073±3263 m in analysis 1 and analysis 2, respectively. Players reported a mean distance covered over 25 w kg-1 equivalent to 1304±673 m and 1294±672 m, and they reported a mean metabolic power of 9.65±1.64 w kg-1 and 9.58±1.61 w kg-1, in analysis 1 and analysis 2, respectively. CONCLUSIONS The findings reported in this study underlined that all data reported by Digital.Stadium® VTS showed high levels of absolute and relative reliability.
Isosurface construction in any dimension using convex hulls

We present an algorithm for constructing isosurfaces in any dimension. The input to the algorithm is a set of scalar values in a d-dimensional regular grid of (topological) hypercubes. The output is a set of (d-1)-dimensional simplices forming a piecewise linear approximation to the isosurface. The algorithm constructs the isosurface piecewise within each hypercube in the grid using the convex hull of an appropriate set of points. We prove that our algorithm correctly produces a triangulation of a (d-1 )-manifold with boundary. In dimensions three and four, lookup tables with 2/sup 8/ and 2/sup 16/ entries, respectively, can be used to speed the algorithm's running time. In three dimensions, this gives the popular marching cubes algorithm. We discuss applications of four-dimensional isosurface construction to time varying isosurfaces, interval volumes, and morphing.
Why is the Corporation Tax Not Neutral?. Anticipated Tax Reform, Investment Spurts and Corporate Borrowing

The paper shows that a corporate tax policy which is thought to be neutral may have significant incentive effects. This result is established in a model with tax advantage to debt and expectations about a forthcoming tax reform. Investment spurt effects are established and compared to those of a firm with equity finance. A tax-cut cum base-broadening tax reform which leaves the long-run investment incentives of an all-equity firm unaffected is shown to cause a substantial short run investment hike. The findings are illustrated by numerical simulations indicating the magnitudes of the spurt effects.
Measurement of condom use self-efficacy and outcome expectancies in a geographically diverse group of STD patients.

The aim of this project was to conduct an initial evaluation among sexually transmitted disease (STD) patients of the psychometric properties of two instruments: the National Institute of Mental Health (NIMH) multisite condom use self-efficacy scale and the NIMH multisite condom use outcome expectancy scale. The condom use self-efficacy scale was designed to measure one's degree of confidence in various aspects of condom use, whereas the outcome expectancy scale was designed to measure one's belief about the consequences of using condoms. Using a sample of 641 patients from five geographically diverse STD clinics in the eastern United States, initial reliability coefficients were computed. The alpha coefficient for the self-efficacy scale was . 91 and for the outcome expectancy scale . 88, indicating high internal consistency for both scales. Both scales were analyzed using common factor analytic procedures. Five factors emerged from the analysis of the self-efficacy scale and six factors from the analysis of the outcome expectancy scale. Reliability coefficients for the individual factors ranged from . 76 to . 86. Construct validity of each scale was assessed by hypothesis testing. As predicted, participants with higher levels of self-efficacy and more positive outcome expectancies were more likely to use condoms.
Adjuvant Epidermal Growth Factor Receptor Inhibitors in Non-Small Cell Lung Cancer.

Nonrandomized studies have suggested a potential benefit with use of an EGFR tyrosine kinase inhibitor in the adjuvant setting in patients with EGFR-mutated non-small cell lung cancer. These nonrandomized studies cannot substitute for well-conducted, adequately powered, prospectively randomized phase III trials. Such trials are under way, and their results are eagerly anticipated.
Progressive Deafness and Altered Cochlear Innervation in Knock-Out Mice Lacking Prosaposin

After a yeast two-hybrid screen identified prosaposin as a potential interacting protein with the nicotinic acetylcholine receptor (nAChR) subunit α10, studies were performed to characterize prosaposin in the normal rodent inner ear. Prosaposin demonstrates diffuse organ of Corti expression at birth, with gradual localization to the inner hair cells (IHCs) and its supporting cells, inner pillar cells, and synaptic region of the outer hair cells (OHCs) and Deiters' cells (DCs) by postnatal day 21 (P21). Microdissected OHC and DC quantitative reverse transcriptase-PCR and immunohistology localizes prosaposin mRNA to DCs and OHCs, and protein predominantly to the apex of the DCs. Subsequent studies in a prosaposin knock-out (KO) (−/−) mouse showed intact but slightly reduced hearing through P19, but deafness by P25 and reduced distortion product otoacoustic emissions from P15 onward. Beginning at P12, the prosaposin KO mice showed histologic organ of Corti changes including cellular hypertrophy in the region of the IHC and greater epithelial ridge, a loss of OHCs from cochlear apex, and vacuolization of OHCs. Immunofluorescence revealed exuberant overgrowth of auditory afferent neurites in the region of the IHCs and proliferation of auditory efferent neurites in the region of the tunnel of Corti. IHC recordings from these KO mice showed normal I–V curves and responses to applied acetylcholine. Together, these results suggest that prosaposin helps maintain normal innervation patterns to the organ of Corti. Furthermore, prosaposin's overlapping developmental expression pattern and binding capacity toward the nAChR α10 suggest that α10 may also play a role in this function.