Miracle-dz/UniFAR-FTUs huggingface dataset:
Search Filters for Finding Prognostic and Diagnostic Prediction Studies in Medline to Enhance Systematic Reviews

Background The interest in prognostic reviews is increasing, but to properly review existing evidence an accurate search filer for finding prediction research is needed. The aim of this paper was to validate and update two previously introduced search filters for finding prediction research in Medline: the Ingui filter and the Haynes Broad filter. Methodology/Principal Findings Based on a hand search of 6 general journals in 2008 we constructed two sets of papers. Set 1 consisted of prediction research papers (n = 71), and set 2 consisted of the remaining papers (n = 1133). Both search filters were validated in two ways, using diagnostic accuracy measures as performance measures. First, we compared studies in set 1 (reference) with studies retrieved by the search strategies as applied in Medline. Second, we compared studies from 4 published systematic reviews (reference) with studies retrieved by the search filter as applied in Medline. Next – using word frequency methods – we constructed an additional search string for finding prediction research. Both search filters were good in identifying clinical prediction models: sensitivity ranged from 0.94 to 1.0 using our hand search as reference, and 0.78 to 0.89 using the systematic reviews as reference. This latter performance measure even increased to around 0.95 (range 0.90 to 0.97) when either search filter was combined with the additional string that we developed. Retrieval rate of explorative prediction research was poor, both using our hand search or our systematic review as reference, and even combined with our additional search string: sensitivity ranged from 0.44 to 0.85. Conclusions/Significance Explorative prediction research is difficult to find in Medline, using any of the currently available search filters. Yet, application of either the Ingui filter or the Haynes broad filter results in a very low number missed clinical prediction model studies.
A multiscale method for disease mapping in spatial epidemiology

The effects of spatial scale in disease mapping are well‐recognized, in that the information conveyed by such maps varies with scale. Here we provide an inferential framework, in the context of tract count data, for describing the distribution of relative risk simultaneously across a hierarchy of multiple scales. In particular, we offer a multiscale extension of the canonical standardized mortality ratio (SMR), consisting of Bayesian posterior‐based strategies for both estimation and characterization of uncertainty. As a result, a hierarchy of informative disease and confidence maps can be produced, without the need to first try to identify a single appropriate scale of analysis. We explore the behaviour of the proposed methodology in a small simulation study, and we illustrate its usage through an application to data on gastric cancer in Tuscany. Copyright © 2005 John Wiley & Sons, Ltd.
Generalized network community detection

Community structure is largely regarded as an intrinsic property of complex real-world networks. However, recent studies reveal that networks comprise even more sophisticated modules than classical cohesive communities. More precisely, real-world networks can also be naturally partitioned according to common patterns of connections between the nodes. Recently, a propagation based algorithm has been proposed for the detection of arbitrary network modules. We here advance the latter with a more adequate community modeling based on network clustering. The resulting algorithm is evaluated on various synthetic benchmark networks and random graphs. It is shown to be comparable to current state-of-the-art algorithms, however, in contrast to other approaches, it does not require some prior knowledge of the true community structure. To demonstrate its generality, we further employ the proposed algorithm for community detection in different unipartite and bipartite real-world networks, for generalized community detection and also predictive data clustering.
The conservation genetics juggling act: integrating genetics and ecology, science and policy

The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has ‘grown up’ with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de‐list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.
A New Stabilization of Adaptive Step Trapezoid Rule Based on Finite Difference Interrupts

The adaptive step trapezoid rule (TR) is a generally effective numerical integrator, but it is prone to ringing instability and solution stall. We introduce a new stabilization algorithm based on finite difference interrupts (FDI) that reduces ringing and prevents stall. Unlike previously reported stabilization schemes, our algorithm achieves stability and second order accuracy without incurring significant computational cost or spurious diffusion. TR with FDI is at least as stable and accurate as existing methods when solving the prototypical scalar problem. We demonstrate that it has better stability, accuracy, and cost when solving the tightly coupled system describing free surface flows of viscoelastic liquids. Though we demonstrate TR with FDI in the context of a finite element method-of-lines, it is applicable to any TR-based algorithm.
Multiple Polymorphisms Affect Expression and Function of the Neuropeptide S Receptor (NPSR1)

Background neuropeptide S (NPS) and its receptor NPSR1 act along the hypothalamic-pituitary-adrenal axis to modulate anxiety, fear responses, nociception and inflammation. The importance of the NPS-NPSR1 signaling pathway is highlighted by the observation that, in humans, NPSR1 polymorphism associates with asthma, inflammatory bowel disease, rheumatoid arthritis, panic disorders, and intermediate phenotypes of functional gastrointestinal disorders. Because of the genetic complexity at the NPSR1 locus, however, true causative variations remain to be identified, together with their specific effects on receptor expression or function. To gain insight into the mechanisms leading to NPSR1 disease-predisposing effects, we performed a thorough functional characterization of all NPSR1 promoter and coding SNPs commonly occurring in Caucasians (minor allele frequency >0.02). Principal Findings we identified one promoter SNP (rs2530547 [−103]) that significantly affects luciferase expression in gene reporter assays and NPSR1 mRNA levels in human leukocytes. We also detected quantitative differences in NPS-induced genome-wide transcriptional profiles and CRE-dependent luciferase activities associated with three NPSR1 non-synonymous SNPs (rs324981 [Ile107Asn], rs34705969 [Cys197Phe], rs727162 [Arg241Ser]), with a coding variant exhibiting a loss-of-function phenotype (197Phe). Potential mechanistic explanations were sought with molecular modelling and bioinformatics, and a pilot study of 2230 IBD cases and controls provided initial support to the hypothesis that different cis-combinations of these functional SNPs variably affect disease risk. Significance these findings represent a first step to decipher NPSR1 locus complexity and its impact on several human conditions NPS antagonists have been recently described, and our results are of potential pharmacogenetic relevance.
Multi-channel design for iterative learning control

In this paper, a multi-channel method is proposed for design of iterative learning control. This novel design method uses multiple channels to widen the learning frequency range that can be achieved by a single channel. The application of the multi-channel method to the anticipatory learning control design is analyzed in details. The design procedure and effectiveness of the multi-channel method are demonstrated via an example and simulations. Comparisons of the multi-channel learning control with the conventional single channel learning control highlight the application prospect of the multi-channel design method.
Problems reported by parents of children in multiple cultures: the Child Behavior Checklist syndrome constructs.

OBJECTIVE The purpose of this study was to compare syndromes of parent-reported problems for children in 12 cultures. METHOD Child Behavior Checklists were analyzed for 13,697 children and adolescents, ages 6 through 17 years, from general population samples in Australia, Belgium, China, Germany, Greece, Israel, Jamaica, the Netherlands, Puerto Rico, Sweden, Thailand, and the United States. RESULTS Comparisons of nine cultures for subjects ages 6 through 17 gave medium effect sizes for cross-cultural variations in withdrawn and social problems and small effect sizes for somatic complaints, anxious/depressed, thought problems, attention problems, delinquent behavior, and aggressive behavior. Scores of Puerto Rican subjects were the highest, whereas Swedish subjects had the lowest scores on almost all syndromes. With great cross-cultural consistency, girls obtained higher scores than boys on somatic complaints and anxious/depressed but lower scores on attention problems, delinquent behavior, and aggressive behavior. Although remarkably consistent across cultures, the developmental trends differed according to syndrome. Comparison of the 12 cultures across ages 6 through 11 supported these results. CONCLUSIONS Empirically based assessment in terms of Child Behavior Checklist syndromes permits comparisons of problems reported for children from diverse cultures.
ESTIMATING THE DETERMINANTS OF TAXPAYER COMPLIANCE WITH EXPERIMENTAL DATA

The fundamental difficulty in empirical work on taxpayer compliance is the absence of detailed and reliable information on individual compliance choices. This paper uses data from laboratory experiments to estimate individual responses to tax, penalty, and audit rate changes, as well as to changes in government expenditures. The empirical results confirm some (although not all) theoretical predictions, and compare quantitatively with other empirical work. Taxpayer reporting increases with greater audit and penalty rates; however, these responses are not large. Compliance is also greater when individuals face a lower tax rate and when they receive something for their taxes.
PERSISTENT ASYMMETRIC STRUCTURE OF SAGITTARIUS A* ON EVENT HORIZON SCALES

The Galactic Center black hole Sagittarius A* (Sgr A*) is a prime observing target for the Event Horizon Telescope (EHT), which can resolve the 1.3 mm emission from this source on angular scales comparable to that of the general relativistic shadow. Previous EHT observations have used visibility amplitudes to infer the morphology of the millimeter-wavelength emission. Potentially much richer source information is contained in the phases. We report on 1.3 mm phase information on Sgr A* obtained with the EHT on a total of 13 observing nights over four years. Closure phases, which are the sum of visibility phases along a closed triangle of interferometer baselines, are used because they are robust against phase corruptions introduced by instrumentation and the rapidly variable atmosphere. The median closure phase on a triangle including telescopes in California, Hawaii, and Arizona is nonzero. This result conclusively demonstrates that the millimeter emission is asymmetric on scales of a few Schwarzschild radii and can be used to break 180° rotational ambiguities inherent from amplitude data alone. The stability of the sign of the closure phase over most observing nights indicates persistent asymmetry in the image of Sgr A* that is not obscured by refraction due to interstellar electrons along the line of sight.
Validation of a Food Frequency Questionnaire in Preschool Children

Background. Support for the validity of food frequency questionnaires (FFQ) in preschool children using parental report is limited. Methods. We obtained dietary information for 68 children age 1–3 years using three or four 24-hour recalls and a FFQ regarding the child’s diet covering one year from families in Denver, CO from 1997 to 1999. FFQs were completed by the parents, and recalls were collected via interviews with the parents and alternate caregivers, where applicable. Nutrient biomarkers were measured in the plasma of 38 of the children. All nutrients were adjusted for energy intake using residuals, and log-transformed where necessary. Results. Correlations (Pearson r) between the FFQ and the average of the recalls were 0.33 for protein, 0.41 for carbohydrate, 0.39 for fat, 0.42 for vitamin C, 0.27 for alpha-tocopherol, and 0.08 for total energy intake. We found no substantial changes in these correlations after stratification by whether or not meals and snacks were provided by caregivers other than the parents. The highest correlations (Spearman r) with biological measures were 0.51 between plasma ascorbic acid and FFQ vitamin C, and 0.48 between plasma and FFQ alpha-tocopherol. Conclusions. The FFQ shows mostly good agreements with multiple 24-hour recalls and biomarkers in preschool children. In addition, the validity of the FFQ using parental report does not appear to be compromised when there are meal providers in addition to the parents.
Examining the Validity of the Academic Motivation Scale by Comparing Scale Construction to Self-Determination Theory

This study examined the construct validity of the Academic Motivation Scale. Specifically, subscale correlations were examined to assess whether support for a continuum of self-determination would be provided. The three types of Intrinsic Motivation were significantly and positively correlated with each other . 67, . 62, and . 58, while the three types of Extrinsic Motivation were significantly and positively intercorrelated . 50, . 49, and . 45. The former subscales, however, correlated higher with Introjected Regulation than Identified Regulation, suggesting that Introjected Regulation may be indicative of more self-determined behavior than has previously been believed. Also, the Intrinsic Motivation To Accomplish subscale had a stronger relationship with two of the Extrinsic Motivation subscales, Identified Regulation and Introjected Regulation, than did the Extrinsic Motivation subscales with each other. This suggests that the differences between Extrinsic and Intrinsic Motivation are not as obvious as has been believed. Also, contrary to self-determination theory, Amotivation had a stronger negative correlation with Identified Regulation (r = −.31) than with any of the Intrinsic Motivation subscales (rs = −.27, −.19, and –.11).
Evaluating communication training for paid carers of people with traumatic brain injury

Primary objective: To evaluate the effectiveness of a communication training programme for paid carers to improve their conversational interactions with people with TBI. Research design: Single blinded randomized controlled study. Methods and procedures: Ten paid carers were randomly selected from a post-acute residential rehabilitation programme and allocated to either a training or control group. Training comprised a 17-hour programme (across 8 weeks) with conversational interactions (i.e. structured and casual) between paid carers and people with TBI videotaped pre-training, post-training and at 6-months follow-up. Interactions were rated on the Adapted Measure of Support in Conversation (MSC), Adapted Measure of Participation in Conversation (MPC) and Global Impression Scales of conversation. Main outcomes and results: Trained paid carers were more able to acknowledge and reveal the competence of people with TBI. Conversations were perceived as more appropriate, interesting and rewarding compared to the control group. Improvements were confined to the structured conversation and were maintained for 6 months. Conclusions: Training paid carers has a positive effect on improving conversational interactions with people with TBI in a long-term care facility. These improvements can help to foster increased independence for the person with TBI in the home and community.
Creatinine, Diet, Micronutrients, and Arsenic Methylation in West Bengal, India

Background: Ingested inorganic arsenic (InAs) is methylated to monomethylated (MMA) and dimethylated metabolites (DMA). Methylation may have an important role in arsenic toxicity, because the monomethylated trivalent metabolite [MMA(III)] is highly toxic. Objectives: We assessed the relationship of creatinine and nutrition—using dietary intake and blood concentrations of micronutrients—with arsenic metabolism, as reflected in the proportions of InAS, MMA, and DMA in urine, in the first study that incorporated both dietary and micronutrient data. Methods: We studied methylation patterns and nutritional factors in 405 persons who were selected from a cross-sectional survey of 7,638 people in an arsenic-exposed population in West Bengal, India. We assessed associations of urine creatinine and nutritional factors (19 dietary intake variables and 16 blood micronutrients) with arsenic metabolites in urine. Results: Urinary creatinine had the strongest relationship with overall arsenic methylation to DMA. Those with the highest urinary creatinine concentrations had 7.2% more arsenic as DMA compared with those with low creatinine (p < 0.001). Animal fat intake had the strongest relationship with MMA% (highest tertile animal fat intake had 2.3% more arsenic as MMA, p < 0.001). Low serum selenium and low folate were also associated with increased MMA%. Conclusions: Urine creatinine concentration was the strongest biological marker of arsenic methylation efficiency, and therefore should not be used to adjust for urine concentration in arsenic studies. The new finding that animal fat intake has a positive relationship with MMA% warrants further assessment in other studies. Increased MMA% was also associated, to a lesser extent, with low serum selenium and folate.
Accounting for Expenditure on Intangibles

In search of a unifying measurement feature on which to base a more systematic and potentially comprehensive analysis of intangibles, this paper first analyses the economic and accounting properties of intangibles, and second, empirically evaluates managerial practices for measuring and analysing expenditure on intangibles. We present evidence from a survey of 614 large Australian firms that suggests gaps in the extent with which firms plan, monitor, record, analyse, and report on intangibles. Third, we evaluate the implications of our analysis and survey for accounting practice. Our evidence suggests GAAP has a role to provide guidance that helps firms identify and classify their expenditure on intangibles in ways that elucidate the strategic implications of the different types of intangibles for future output. A secondary step for accountants, after identifying and classifying the expenditure on intangibles, is to apply a capitalization test to distinguish expenses from assets. The current asymmetric treatment of expenditure on purchased versus internally generated intangibles is not supportable on economic grounds. However, economists identify weak property rights as a major cause of uncertainty associated with the outcomes from expenditure on intangibles, suggesting verifiable property rights is a unifying measurement feature on which to base a capitalization test for intangible assets.
Characterization of 1′-Hydroxymidazolam Glucuronidation in Human Liver Microsomess⃞

Midazolam is a potent benzodiazepine derivative with sedative, hypnotic, anticonvulsant, muscle-relaxant, and anxiolytic activities. It undergoes oxidative metabolism catalyzed almost exclusively by the CYP3A subfamily to a major metabolite, 1′-hydroxymidazolam, which is equipotent to midazolam. 1′-Hydroxymidazolam is subject to glucuronidation followed by renal excretion. To date, the glucuronidation of 1′-hydroxymidazolam has not been evaluated in detail. In the current study, we identified an unreported quaternary N-glucuronide, as well as the known O-glucuronide, from incubations of 1′-hydroxymidazolam in human liver microsomes enriched with uridine 5′-diphosphoglucuronic acid (UDPGA). The structure of the N-glucuronide was confirmed by nuclear magnetic resonance analysis, which showed that glucuronidation had occurred at N-2 (the imidazole nitrogen that is not a part of the benzodiazepine ring). In a separate study, in which midazolam was used as the substrate, an analogous N-glucuronide also was detected from incubations with human liver microsomes in the presence of UDPGA. Investigation of the kinetics of 1′-hydroxymidazolam glucuronidation in human liver microsomes indicated autoactivation kinetics (Hill coefficient, n = 1.2–1.5). The apparent S50 values for the formation of O- and N-glucuronides were 43 and 18 μM, respectively, and the corresponding apparent Vmax values were 363 and 21 pmol/mg of microsomal protein/min. Incubations with recombinant human uridine diphosphate glucuronosyltransferases (UGTs) indicated that the O-glucuronidation was catalyzed by UGT2B4 and UGT2B7, whereas the N-glucuronidation was catalyzed by UGT1A4. Consistent with these observations, hecogenin, a selective inhibitor of UGT1A4, selectively inhibited the N-glucuronidation, whereas diclofenac, a potent inhibitor of UGT2B7, had a greater inhibitory effect on the O-glucuronidation than on the N-glucuronidation. In summary, our study provides the first demonstration of N-glucuronidation of 1′-hydroxymidazolam in human liver microsomes.
Inhibition of BACE2 counteracts hIAPP‐induced insulin secretory defects in pancreatic β‐cells

BACE2 (β‐site APP‐cleaving enzyme 2) is a protease localized in the brain, where it appears to play a role in the development of Alzheimer disease (AD). It is also found in the pancreas, although its biologic function is not fully known. Amyloidogenic diseases, including AD and type 2 diabetes mellitus (T2D), share the accumulation of abnormally folded and insoluble proteins that interfere with cell function. Islet amyloid polypeptide (IAPP) deposits are a key pathogenic feature of T2D. Within this context, we found by global gene expression profiling that BACE2 was up‐regulated in the rat pancreatic β‐cell line INS1E stably transfected with human IAPP gene (hIAPP‐INS1E). Glucose‐stimulated insulin secretion (GSIS) in hIAPP‐INS1E cells was 30% lower than in INS1E cells. Additionally, INS1E cells transfected with a transient overexpression of BACE2 showed a 60% decrease in proliferation, a 3‐fold increase in reactive oxygen species production, and a 25% reduction in GSIS compared to control cells. Remarkably, silencing of endogenous BACE2 in hIAPP‐INS1E cells resulted in a significant improvement in GSIS (3‐fold increase vs. untransfected cells), revealing the significant role of BACE2 expression in β‐cell function. Thus, BACE2 inhibition may be useful to recover insulin secretion in hIAPP‐INS1E defective cells and may be proposed as a therapeutic target for T2D. ‐ Montane, J., Servitja, J.‐M. , Novials, A. Inhibition of BACE2 counteracts hIAPP‐induced insulin secretory defects in pancreatic β‐cells. FASEB J. 29, 95–104 (2015). www.fasebj. org