bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance tests in clinical research—Challenges and pitfalls
Authors: Skovlund Eva 
Published: August 2013

Abstract

Background
Statistical analyses are used to help understand the practical significance of the findings in a clinical study. Many clinical researchers appear to have limited knowledge onhowto perform appropriate statistical analysis as well as understanding what the results in fact mean.

Methods
This focal review is based on long experience in supervising clinicians on statistical analysis and advising editors of scientific journals on the quality of statistical analysis applied in scientific reports evaluated for publication.

Results
Basic facts on elementary statistical analyses are presented, and common misunderstandings are elucidated. Efficacy estimates, the effect of sample size, and confidence intervals for effect estimates are reviewed, and the difference between statistical significance and clinical relevance is highlighted. The weaknesses of p-values and misunderstandings in how to interpret them are illustrated with practical examples.

Conclusions and recommendations
Some very important questions need to be answered before initiating a clinical trial. What is the research question? To which patients should the result be generalised? Is the number of patients sufficient to draw a valid conclusion? When data are analysed the number of (preplanned) significance tests should be kept small and post hoc analyses should be avoided. It should also be remembered that the clinical relevance of a finding cannot be assessed by the p-value. Thus effect estimates and corresponding 95% confidence intervals should always be reported.
Intense bed-load due to a sudden dam-break
Authors: Spinewine Benoit , Capart Hervé 
Published: August 2013

AbstractIntense bed-load, or sheet flow, occurs when a free-surface flow of water drives a thick, rapidly sheared layer of water and grains over an erodible granular bed. We examine here the transient case where flow is induced by a sudden dam-break. Aiming for greater detail than achieved previously, we investigate this case using experiment and theory. The experiments combine particle tracking velocimetry (PTV) with a novel method of concentration measurement based on recording the penetration depth of a laser light sheet. The theory incorporates more vertical detail into the shallow water equations by using piecewise linear profiles of velocity and granular concentration, constrained by constitutive relations proposed recently for intense bed-load. These relations account for Coulomb yield at the bed, immersed granular collisions at the base, and equilibration of shear rate and density stratification across the bed-load layer. Using these approaches, both experiment and theory yield time- and depth-resolved profiles of velocity and granular concentration in addition to longitudinal wave profiles. Without any parameter adjustment, the theoretical predictions are in good agreement with the experimental measurements.
Capsaicin-induced metabolic and cardiovascular autonomic improvement in an animal model of the metabolic syndrome
Authors: Tremarin Camila da Silva , Casali Karina Rabello , Meurer Luise , Schaan Beatriz D'Agord 
Published: August 2013

The metabolic syndrome (MetS) is associated with an increased risk of cardiac mortality, as it is characterised by the clustering of multiple cardiovascular risk factors. Studies have shown that capsaicin (red pepper) may be useful as a nutraceutical, ameliorating metabolic profile and cardiovascular function. The aim of the present study was to investigate the cardiovascular and metabolic effects of orally administered capsaicin in rats with the MetS. Neonate spontaneously hypertensive rats were injected with monosodium glutamate and subjected to one of the following three treatments by oral administration for 14 d, between 27 and 30 weeks: low-dose capsaicin (CAP05,n18, synthetic capsaicin powder diluted in a vehicle (10 % ethyl alcohol) plus 0·5 mg/kg body weight (BW) of capsaicin); high-dose capsaicin (CAP1,n19, synthetic capsaicin powder diluted in a vehicle (10 % ethyl alcohol) plus 1 mg/kg BW of capsaicin); control (C,n18, vehicle). Lee's index, lipid/metabolic profile, and cardiovascular parameters with the rats being conscious, including arterial pressure (AP) and heart rate (HR) variability, as well as aortic wall thickness (haematoxylin and eosin staining) and CD68 (cluster of differentiation 68) antibody levels (monocyte/macrophage immunostaining) were evaluated. Weight, Lee's index, and lipid and metabolic parameters, as well as AP and HR and aortic wall thickness, were similar between the groups. Capsaicin determined HR variability improvement (16·0 (sem9·0), 31·0 (sem28·2) and 31·3 (sem19·0) ms2for the C, CAP05 and CAP1 groups, respectively,P= 0·003), increased vascular sympathetic drive (low-frequency component of systolic AP variability: 3·3 (sem2·8), 8·2 (sem7·7) and 12·1 (sem8·8) mmHg2for the C, CAP05 and CAP1 groups, respectively,P< 0·001) and increased α-index (spontaneous baroreflex sensitivity). The present data show that capsaicin did not improve lipid and glucose abnormalities in rats with the MetS. However, beneficial cardiovascular effects were observed with this nutraceutical.
Diet quality from pre-school to school age in Brazilian children: a 4-year follow-up in a randomised control study
Authors: Rauber Fernanda , Hoffman Daniel J. , Vitolo Márcia Regina 
Published: August 2013

A previous study demonstrated that dietary counselling for mothers during the first year of life improved overall diet quality of children at pre-school age in a low-income population. Thus, the objective of the present study was to assess the long-term effect of this intervention on diet quality of children at school age and examine the tracking of dietary intake throughout childhood. The present study was a follow-up of a randomised controlled trial with children who were assessed at 3–4 years (n 345) and 7–8 years (n 307) of age. We collected two 24 h dietary recalls and assessed diet quality using the Healthy Eating Index (HEI). Analyses were performed by group using a paired t test and a Student's t test for independent samples. Diet quality did not differ between the intervention and control groups at 7–8 years of age (HEI score 65·2 (sd 9·5) v. 64·9 (sd 8·5)). Regarding changes in diet quality from pre-school to school age, we observed the tracking of diet quality in the control group and the loss of the intervention effect in the intervention group. In both groups, the score for fruit and milk intake decreased, while that for saturated fat and dietary variety intake increased. The score for the intakes of grains, meat and legumes, and total fat remained constant for all children. The present data provide evidence that diet quality tracks during childhood since the total HEI score did not differ over time in the control group. The decrease in score for some HEI components did not affect the overall diet quality due to the increase in score for other HEI components.
Graphis koreana (Graphidaceae, Ostropales), a new species from South Korea
Authors: JOSHI Santosh , KOH Young Jin , LÖKÖS László , JAYALAL Udeni , HUR Jae-Seoun 
Published: August 2013

AbstractA saxicolous Graphis discovered in the southern part of South Korea is described as new to science. The new species, Graphis koreana sp. nov., is characterized by a green to brownish green, thick, rimose thallus, completely carbonized proper exciple, trans-septate to submuriform ascospores and the presence of norstictic acid.
Genetic diversity and species delimitation of the zeorin-containing red-fruitedCladoniaspecies (lichenized Ascomycota) assessed with ITS rDNA and β-tubulin data
Authors: STEINOVÁ Jana , STENROOS Soili , GRUBE Martin , ŠKALOUD Pavel 
Published: August 2013

AbstractZeorin-containing red-fruitedCladoniaspecies, the so-calledC. cocciferagroup, are widespread terrestrial lichens which share most of their secondary substances but differ morphologically. The main objective of this study was to explore whether the current delimitation of these species is supported by molecular data. A total of 52 European and North American specimens ofC. coccifera,C. deformis,C. diversa, andC. pleurotawere examined. The internal transcribed spacer regions of the nuclear ribosomal DNA and the β-tubulin gene loci were sequenced for phylogenetic analyses. Traditional morphological species circumscriptions in zeorin-containing members of theC. cocciferagroup are not supported by molecular data.Cladonia coccifera,C. deformis, andC. pleurotawere recovered as polyphyletic in both gene topologies;C. diversaformed a lineage in the ITS phylogeny but this was not statistically supported. We detected chemical patterns of the presence/absence of porphyrilic and/or isousnic acid which may help to characterize two lineages. Our results also show incongruence between the two molecular markers studied. Therefore, we focused on possible explanations of this phenomenon. Five major evolutionary mechanisms can potentially result in phylogenetic discordance between genes: presence of pseudogenes, horizontal gene transfer, gene paralogy, incomplete lineage sorting, and hybridization. These mechanisms are briefly discussed. We consider incomplete lineage sorting and/or hybridization to best explain the incongruence.
Two new Crypthonia species and a new Syncesia from Chapada do Araripe, Ceará, NE Brazil (Ascomycota: Arthoniales), with a key to Crypthonia
Authors: MENEZES Aline Anjos , XAVIER-LEITE Amanda Barreto , de JESUS Katia Almeida , APTROOT André , CÁCERES Marcela Eugenia da Silva 
Published: August 2013

AbstractTwo new species of the small genus Crypthonia are described from the Chapada do Araripe, an isolated table mountain in the state of Ceará, in NE Brazil. Both share the thallus and ascoma organization with the other known species of the genus, and are mainly characterized by differences in ascospores and chemistry. Crypthonia lichexanthonica A. A. Menezes, M. Cáceres & Aptroot has 7-septate ascospores and contains lichexanthone in the thallus, and C. submuriformis A. A. Menezes, M. Cáceres & Aptroot has (sub)muriform ascospores and also contains lichexanthone, but only in the ascigerous areas. A key to all known species of the genus Crypthonia is provided, in which Crypthonia olivacea Frisch & G. Thor is newly reported from Argentina. The new species Syncesia byssolomoides A. A. Menezes, M. Cáceres & Aptroot is described from the same area. It also has a thin byssoid thallus, but differs by the narrowly fusiform ascospores and by containing psoromic acid. It differs from all Syncesia species by the absence of carbonization and the presence of psoromic acid. The epiphytic lichen flora in this Caatinga forest area is dominated by crustose lichens, with Graphis and Polymeridium as the most speciose genera.
Effect of amplified spontaneous emission and parasitic oscillations on the performance of cryogenically-cooled slab amplifiers
Authors: Sawicka Magdalena , Divoky Martin , Lucianetti Antonio , Mocek Tomas 
Published: August 2013

AbstractWe present a three-dimensional code for the optimization of energy storage, heat deposition, and amplification in square-shaped laser slabs and multi-slab laser amplifiers. The influence of the slab dimensions, slab face and edge reflectivities, pump parameters, and operating temperature on amplified spontaneous emission and stored energy has been investigated. The multi-slab and single-slab configurations are compared, analyzing in detail the influence of the absorption cladding for the suppression of amplified spontaneous emission radiation.
Retinocollicular mapping explained?
Authors: STERRATT DAVID C. , HJORTH J.J. JOHANNES 
Published: August 2013

AbstractWe review and comment on the recent model of Grimbert and Cang of the development of topographically ordered maps from the retina to the superior colliculus. This model posits a phase in which arbors are created in zones permitted by Eph and ephrin signaling, followed by a phase in which activity-dependent synaptic plasticity refines the map. We show that it is not possible to generate the arborization probability functions used in the simulations of Grimbert and Cang using gradients of Ephs and ephrins and the interaction mechanism that Grimbert and Cang propose in their results. Furthermore, the arborization probabilities we do generate are far less sharp than we imagine truly “permissive” ones would be. It remains to be seen if maps can be generated from the nonpermissive arborization probabilities generated from gradients.
Enzyme activity effects of N-terminal His-tag attached to catalytic sub-unit of phosphoinositide-3-kinase
Authors: Dickson James M. J. , Lee Woo-Jeong , Shepherd Peter R. , Buchanan Christina M. 
Published: August 2013

NTT (N-terminal tags) on the catalytic (p110) sub-unit of PI 3-K (phosphoinositol 3-kinase) have previously been shown to increase cell signalling and oncogenic transformation. Here we test the impact of an NT (N-terminal) His-tag on in vitro lipid and protein kinase activity of all class-1 PI 3-K isoforms and two representative oncogenic mutant forms (E545K and H1047R), in order to elucidate the mechanisms behind this elevated signalling and transformation observed in vivo. Our results show that an NT His-tag has no impact on lipid kinase activity as measured by enzyme titration, kinetics and inhibitor susceptibility. Conversely, the NT His-tag did result in a differential effect on protein kinase activity, further potentiating the elevated protein kinase activity of both the helical domain and catalytic domain oncogenic mutants with relation to p110 phosphorylation. All other isoforms also showed elevated p110 phosphorylation (although not statistically significant). We conclude that the previously reported increase in cell signalling and oncogenic-like transformation in response to p110 NTT is not mediated via an increase in the lipid kinase activity of PI 3-K, but may be mediated by increased p110 autophosphorylation and/or other, as yet unidentified, intracellular protein/protein interactions. We further observe that tagged recombinant protein is suitable for use in in vitro lipid kinase screens to identify PI 3-K inhibitors; however, we recommend that in vivo (including intracellular) experiments and investigations into the protein kinase activity of PI 3-K should be conducted with untagged constructs.
Protrudin binds atlastins and endoplasmic reticulum-shaping proteins and regulates network formation
Authors: Chang Jaerak , Lee Seongju , Blackstone Craig 
Published: August 2013

Significance
In this study, we have identified a type of protein that participates in the formation of the tubular endoplasmic reticulum. This protein, protrudin, harbors hydrophobic hairpins that generate high curvature in endoplasmic reticulum tubules, as well as several domains that may link the tubular endoplasmic reticulum to the plasma membrane or other organelles.
Microscopy ambient ionization top-down mass spectrometry reveals developmental patterning
Authors: Hsu Cheng-Chih , White Nicholas M. , Hayashi Marito , Lin Eugene C. , Poon Tiffany , Banerjee Indroneal , Chen Ju , Pfaff Samuel L. , Macagno Eduardo R. , Dorrestein Pieter C. 
Published: August 2013

Significance
To improve targeted molecular characterization of biological samples, we have interfaced a light microscope with ambient ionization MS to perform microscopy-guided targeted mass spectrometric analysis. This tool was used to characterize a diverse set of biomolecules ranging from lipids, sugars, peptides to proteins with molecular masses ranging from ∼300 Da to 16 kDa. Each of these entities could be characterized using top-down analysis directly on developing mouse spinal cords. This technology will be applicable in diverse fields ranging from chemical biology, pathology, and microbiology to neuroscience, medicine, and agriculture.
Effects of Contact Precautions on Patient Perception of Care and Satisfaction: A Prospective Cohort Study
Authors: Mehrotra Preeti , Croft Lindsay , Day Hannah R. , Perencevich Eli N. , Pineles Lisa , Harris Anthony D. , Weingart Saul N. , Morgan Daniel J. 
Published: August 2013

Objective.Contact precautions decrease healthcare worker-patient contact and may impact patient satisfaction. To determine the association between contact precautions and patient satisfaction, we used a standardized interview for perceived issues with care.Design.Prospective cohort study of inpatients, evaluated at admission and on hospital days 3, 7, and 14 (until discharged). At each point, patients underwent a standardized interview to identify perceived problems with care. After discharge, the standardized interview and Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey were administered by telephone. Responses were recorded, transcribed, and coded by 2 physician reviewers.Participants.A total of 528 medical or surgical patients not admitted to the intensive care unit.Results.A total of 528 patients were included in the primary analysis, of whom 104 (20%) perceived some issue with their care. On multivariable logistic regression, contact precautions were independently associated with a greater number of perceived concerns with care (odds ratio, 2.05 [95% confidence interval, 1.31–3.21]; P<.01), including poor coordination of care (P = .02) and a lack of respect for patient needs and preferences (P = .001). Eighty-eight patients were included in the secondary analysis of HCAHPS. Patients under contact precautions did not have different HCAHPS scores than those not under contact precautions (odds ratio, 1.79 [95% confidence interval, 0.64–5.00]; P = .27).Conclusions.Patients under contact precautions were more likely to perceive problems with their care, especially poor coordination of care and a lack of respect for patient preferences.
MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation
Authors: Qu Jianghan , Zhou Meng , Song Qiang , Hong Elizabeth E. , Smith Andrew D. 
Published: August 2013

Abstract
Motivation: The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels.
Results: We present a method to jointly model read counts from bisulfite sequencing, oxidative bisulfite sequencing and Tet-Assisted Bisulfite sequencing, providing simultaneous estimates of 5-hmC and 5-mC levels that are consistent across experiment types.
Availability: http://smithlab.usc.edu/software/mlml
Contact: andrewds@usc.edu
Supplementary information: Supplementary material is available at Bioinformatics online.
Genome compression: a novel approach for large collections
Authors: Deorowicz Sebastian , Danek Agnieszka , Grabowski Szymon 
Published: August 2013

Abstract
Motivation: Genomic repositories are rapidly growing, as witnessed by the 1000 Genomes or the UK10K projects. Hence, compression of multiple genomes of the same species has become an active research area in the past years. The well-known large redundancy in human sequences is not easy to exploit because of huge memory requirements from traditional compression algorithms.
Results: We show how to obtain several times higher compression ratio than of the best reported results, on two large genome collections (1092 human and 775 plant genomes). Our inputs are variant call format files restricted to their essential fields. More precisely, our novel Ziv-Lempel-style compression algorithm squeezes a single human genome to ∼400 KB. The key to high compression is to look for similarities across the whole collection, not just against one reference sequence, what is typical for existing solutions.
Availability: http://sun.aei.polsl.pl/tgc (also as Supplementary Material) under a free license.
Supplementary data: Supplementary data are available at Bioinformatics online.
Contact: sebastian.deorowicz@polsl.pl
Determinants of repayment performance of group lending in China
Authors: Qinlan Zhang , Izumida Yoichi 
Published: August 2013

PurposeThe purpose of this paper aims to explore how borrower and group‐level characteristics affect repayment decisions of group borrowers by highlighting the case of rural credit cooperatives (RCCs) in Guizhou province in Southwest China.Design/methodology/approachThe Logit model was applied to test the determinants of repayment performance of RCCs' group lending. The authors used the survey data of 245 farm households in Guizhou province, collected in 2008.FindingsThe empirical results indicate that there is a serious mismatch between joint liability mechanisms and the social and economic conditions in rural China. Mechanisms such as threatening to withhold defaulters' future loans from RCCs failed to work. In addition, higher household incomes also did not improve repayment performance. However, factors such as a higher degree of acquaintanceship in a group, migrant income, and employment in government agencies, positively improved the chances of repayment.Practical implicationsGroup lending is more suitable for poorer areas with few opportunities for migration and limited access to finance. In addition, constructing the trustworthy relationship between micro‐lenders and customers and designing diverse and flexible financial services to meet heterogeneous demands are equally important.Originality/valueThis paper is an attempt to empirically explore the determinants of repayment performance in group lending programs in China. The results provide meaningful policy implications for the government and rural financial institutions.
An analysis on China's agricultural bilateral trade costs? 1995‐2007
Authors: Wen Simei , Zheng Jing , Liu Xiaoli 
Published: August 2013

PurposeThe trade cost is a significant factor which restricts the trade potential between two nations. This paper aims to make a measurement of agricultural bilateral trade costs of China.Design/methodology/approachBased on Novy model, this paper makes a measurement of agricultural bilateral trade costs before and after China joining the WTO (1995‐2007).FindingsThis paper finds that China's agricultural trade costs with its five major trade partners have not got a pronounced downward trend during 1995‐2007. In ascending order, these are: Malaysia, the USA, Japan, Brazil and Argentina in 2007. Otherwise, there is an obvious corresponding relationship between the trade potential and costs of agricultural products, which is that high costs lead to inadequate trade. With a simple regression, distance and free trade agreement are found to be main factors influencing agricultural trade costs.Originality/valueBased on the revised gravity model, this paper especially calculates the agricultural bilateral trade costs before and after China joining the WTO, which expands the understanding of trade costs in an industrial perspective. It can prove the agricultural market opening extent, and also help us to learn more about how China participates in the division of the world farm produce market.