bluuebunny/crossref_metadata_2025_split huggingface dataset:
mTRAQ‐based quantification of potential endometrial carcinoma biomarkers from archived formalin‐fixed paraffin‐embedded tissues
Authors: DeSouza Leroi V. , Krakovska Olga , Darfler Marlene M. , Krizman David B. , Romaschin Alexander D. , Colgan Terence J. , Siu K. W. Michael 
Published: July 2010

AbstractFormalin‐fixed paraffin‐embedded (FFPE) tissues are the primary and preferred medium for archiving patients' samples. Here we demonstrate relative quantifications of protein biomarkers in extracts of laser microdissected epithelial cells from FFPE endometrial carcinoma tissues versus those from normal proliferative endometria by means of targeted proteomic analyses using LC–multiple reaction monitoring (MRM) MS with MRM Tags for Relative and Absolute Quantitation (mTRAQ) labeling. Comparable results of differential expressions for pyruvate kinase isoform M2 (PK‐M2) and polymeric Ig receptor were observed between analyses on laser microdissected epithelial cells from FFPE tissues and corresponding homogenates from frozen tissues of the same individuals that had previously been analyzed and reported. We also identified PK‐M2 in the normal proliferative phase of the endometrium. Other biomarkers in addition to PK‐M2 and polymeric Ig receptor were also observed but not consistently and/or were at levels below the threshold for quantification.
The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative
Authors: Gibson Frank , Hoogland Christine , Martinez‐Bartolomé Salvador , Medina‐Aunon J. Alberto , Albar Juan Pablo , Babnigg Gyorgy , Wipat Anil , Hermjakob Henning , Almeida Jonas S. , Stanislaus Romesh , Paton Norman W. , Jones Andrew R. 
Published: July 2010

AbstractThe Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel‐based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.
Discussion point: are web‐based eCRFs a compliance problem for industry?
Authors: Wilsher Colin 
Published: July 2010

AbstractPharmaceutical companies often rely upon web‐based electronic Case Report Forms (eCRFs) for clinical investigators to enter trial data at their site. Using web‐based technology means that the investigator directly enters data onto the sponsor company's server via the Internet. Does this cause a problem with complying with international standards regarding data integrity? Copyright © 2010 John Wiley & Sons, Ltd.
Body mass and growth of overwintering brown trout in relation to stream habitat complexity
Authors: Koljonen Saija , Huusko Ari , Mäki‐Petäys Aki , Mykrä Heikki , Muotka Timo 
Published: July 2010

AbstractIn winter, juvenile salmonids hide within the substrate during the day and emerge to feed on drifting invertebrates at night. In channelized streams, where the streambed heterogeneity has been artificially reduced, suitable microhabitats (low‐flow refugia) may be in short supply. Therefore, restoration of stream habitat by enhancement structures might improve the overwintering conditions of juvenile salmonids. We used a set of artificial streams to test whether individually‐marked juvenile brown trout of two age‐classes (age‐0 and age‐1 trout) loose mass during the winter differently in channelized and semi‐natural streams. Fish of both age‐classes lost mass early in the winter (November to January), but age‐0 fish in the channelized streams lost more of their initial mass than did the restored‐stream fish (ca. 10% vs. 2.5% on average, respectively). They then exhibited zero‐growth in both treatments in late winter (January to April), and by early spring (May), the channelized‐stream fish had completely caught up for their greater initial mass loss. In control tanks where the fish were fed continuously, age‐0 trout exhibited zero‐growth from November to January, then gaining mass constantly through the rest of the experiment. Significant time*treatment interaction was also detected for age‐1 trout, but all differences were caused by the faster growth of fish in the control tanks, whereas the two channel treatments did not differ significantly. The shortage of suitable sheltering sites in the channelized streams apparently intensified competition and caused greater initial mass loss in age‐0 trout. Furthermore, growth compensation exhibited by juvenile trout may have negative impacts on the long‐term fitness of individuals. Therefore, by increasing the amount of sheltering sites, in‐stream restoration may have potential to enhance the overwintering success of juvenile salmonids. Copyright © 2010 John Wiley & Sons, Ltd.
Hydrologic thresholds for riparian forest conservation in a regulated large Mediterranean river
Authors: González E. , González‐Sanchis M. , Comín F. A. , Muller E. 
Published: July 2010

AbstractMost riparian trees are phreatophytic, water table‐dependent plants which broadly differ in their tolerance to drought and permanent flooding. In semi‐arid settings, as water is limiting, inundations may be regarded as inputs rather than stresses for the survival of phreatophytes. In this study, the mortality rates and abundances of Populus alba, P. nigra, Salix alba and local Tamarix spp. were examined in 43 plots with different hydrologic conditions distributed across the floodplain of a large semi‐arid and Mediterranean river, the Ebro River (Spain). The objectives were to determine hydrologic thresholds for the maintenance of declining populations of those species, while providing novel information on their phreatophytic nature, and to examine shifts in the species composition along hydrologic gradients. All species exhibited significant relationships between mortality rates and hydrologic variables (deepest water table—WT, flood duration—FD and flood frequency—FF). S. alba was found to be the species with lowest tolerance to drier conditions (hydrologic thresholds for maintaining a mortality rate <50%: WT > −1.22 m; FD: out of observation range; FF > 5.4 events y−1), followed by P. nigra (WT > −2.18 m; FD > 11.1%; FF > 3.8 events y−1), Tamarix spp. (WT > −2.96 m; FD > 3.7%; FF > 2.5 events y−1) and P. alba (WT > −3.45 m; FD > 1.7%; FF > 2.0 events y−1). Only a significant reduction in S. alba relative abundance was observed as conditions got drier. The results provided quantitative information useful to guide management plans for the protection of Mediterranean phreatophytic tree species from further degradation and suggested that eventual natural or regulation‐induced droughts and groundwater declines would accelerate the loss of all phreatophytic species, especially S. alba. Copyright © 2010 John Wiley & Sons, Ltd.
How to link call rate and p‐values for Hardy–Weinberg equilibrium as measures of genome‐wide SNP data quality
Authors: Finner Helmut , Strassburger Klaus , Heid Iris M. , Herder Christian , Rathmann Wolfgang , Giani Guido , Dickhaus Thorsten , Lichtner Peter , Meitinger Thomas , Wichmann H.‐Erich , Illig Thomas , Gieger Christian 
Published: July 2010

AbstractWe study the link between two quality measures of SNP (single nucleotide polymorphism) data in genome‐wide association (GWA) studies, that is, per SNP call rates (CR) and p‐values for testing Hardy–Weinberg equilibrium (HWE). The aim is to improve these measures by applying methods based on realized randomized p‐values, the false discovery rate and estimates for the proportion of false hypotheses. While exact non‐randomized conditional p‐values for testing HWE cannot be recommended for estimating the proportion of false hypotheses, their realized randomized counterparts should be used. P‐values corresponding to the asymptotic unconditional chi‐square test lead to reasonable estimates only if SNPs with low minor allele frequency are excluded. We provide an algorithm to compute the probability that SNPs violate HWE given the observed CR, which yields an improved measure of data quality. The proposed methods are applied to SNP data from the KORA (Cooperative Health Research in the Region of Augsburg, Southern Germany) 500 K project, a GWA study in a population‐based sample genotyped by Affymetrix GeneChip 500 K arrays using the calling algorithm BRLMM 1.4.0. We show that all SNPs with CR = 100 per cent are nearly in perfect HWE which militates in favor of the population to meet the conditions required for HWE at least for these SNPs. Moreover, we show that the proportion of SNPs not being in HWE increases with decreasing CR. We conclude that using a single threshold for judging HWE p‐values without taking the CR into account is problematic. Instead we recommend a stratified analysis with respect to CR. Copyright © 2010 John Wiley & Sons, Ltd.
Beta‐mapping and beta‐regression for changes of ordinal‐rating measurements on Likert scales: A comparison of the change scores among multiple treatment groups
Authors: Zou Kelly H. , Carlsson Martin O. , Quinn Sheila A. 
Published: July 2010

AbstractPatient reported outcome and observer evaluative studies in clinical trials andpost‐hocanalyses often use instruments that measure responses on ordinal‐rating or Likert scales. We propose a flexible distributional approach by modeling the change scores from the baseline to the end of the study using independent beta distributions. The two shape parameters of the fitted beta distributions are estimated by matching‐moments. Covariates and the interaction terms are included in multivariate beta‐regression analyses under generalized linear mixed models. These methods are illustrated on the treatment satisfaction data in an overactive bladder drug study with four treatment arms. Monte‐Carlo simulations were conducted to compare the Type 1 errors and statistical powers using a beta likelihood ratio test of the proposed method against its fully nonparametric or parametric alternatives. Copyright © 2010 John Wiley & Sons, Ltd.
Effects of alkali and silane treatment on the mechanical properties of jute‐fiber‐reinforced recycled polypropylene composites
Authors: Wang Xinxin , Cui Yihua , Xu Qi , Xie Bo , Li Wei 
Published: July 2010

AbstractJute‐fibers‐reinforced thermoplastic composites are widely used in the automobile, packaging, and electronic industries because of their various advantages such as low cost, ease of recycling, and biodegradability. However, the applications of these kinds of composites are limited because of their unsatisfactory mechanical properties, which are caused by the poor interfacial compatibility between jute fibers and the thermoplastic matrix. In this work, four methods, including (i) alkali treatment, (ii) alkali and silane treatment, (iii) alkali and (maleic anhydride)‐polypropylene (MAPP) treatment, and (iv) alkali, silane, and MAPP treatment (ASMT) were used to treat jute fibers and improve the interfacial adhesion of jute‐fiber‐reinforced recycled polypropylene composites (JRPCS). The mechanical properties and impact fracture surfaces of the composites were observed, and their fracture mechanism was analyzed. The results showed that ASMT composites possessed the optimum comprehensive mechanical properties. When the weight fraction of jute fibers was 15%, the tensile strength and impact toughness were increased by 46 and 36%, respectively, compared to those of untreated composites. The strongest interfacial adhesion between jute fibers and recycled polypropylene was obtained for ASMT composites. The fracture styles of this kind of composite included fiber breakage, fiber pull‐out, and interfacial debonding. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers.
Correlation of morphology, rheology, and performance improvement in gasoline tubes based on PA‐6 nanocomposites
Authors: Moghri Mehdi , Garmabi Hamid , Molajavadi Vadoud 
Published: July 2010

AbstractPA‐6/organo‐modified layered silicate nanocompounds were prepared by the melt mixing of PA‐6 with different nanoclay loadings in a corotating twin‐screw extruder. Gasoline tubes based on these nanocompounds were produced at different silicate loadings. Thermal, mechanical, rheological, and barrier properties of the different samples were investigated and correlated to their morphology. Transmission electron microscopy, wide angle X‐ray scattering, and linear melt state viscoelastic measurements were used to characterize the different aspects of nanoclay dispersion in the nanocomposite samples. While tensile modulus, softening point, heat distortion temperature, and gasoline barrier properties of the prepared tubes were improved considerably by increasing the clay content, performance improvement with respect to clay content (after a certain value) decreased with increasing clay loading. It could be attributed to the re‐agglomeration of tactoids at higher concentrations. These findings were correlated with the rheological and morphological observations. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers
Child categorization
Authors: Gelman Susan A. , Meyer Meredith 
Published: July 2010

AbstractCategorization is a process that spans all of development, beginning in earliest infancy yet changing as children's knowledge and cognitive skills develop. In this review article, we address three core issues regarding childhood categorization. First, we discuss the extent to which early categories are rooted in perceptual similarity versus knowledge‐enriched theories. We argue for a composite perspective in which categories are steeped in commonsense theories from a young age but also are informed by low‐level similarity and associative learning cues. Second, we examine the role of language in early categorization. We review evidence to suggest that language is a powerful means of expressing, communicating, shaping, and supporting category knowledge. Finally, we consider categories in context. We discuss sources of variability and flexibility in children's categories, as well as the ways in which children's categories are used within larger knowledge systems (e.g., to form analogies, make inferences, or construct theories). Categorization is a process that is intrinsically tied to nearly all aspects of cognition, and its study provides insight into cognitive development, broadly construed.WIREs Cogn Sci2011 2 95–105 DOI: 10.1002/wcs.96This article is categorized under:Linguistics > Language AcquisitionPsychology > Development and AgingPsychology > Language
Short‐term variations in wind power: Some quantile‐type models for probabilistic forecasting
Authors: Pritchard Geoffrey 
Published: July 2010

AbstractWe discuss some ways of formulating quantile‐type models for forecasting variations in wind power in the short term (within a few hours). Such models predict quantiles of the conditional distribution of the wind power available at some future time using information presently available. A natural reference for models of this kind is a ‘probabilistic‐persistence’ quantile forecast whose only input is the present wind power. Using data from some New Zealand wind farms, we find that more complex quantile models can readily improve on probabilistic persistence in resolution but not in sharpness. The most valuable model inputs, apart from the present power, are found to be real‐time air pressure measurements and a power total‐variation indicator. Copyright © 2010 John Wiley & Sons, Ltd.
Risk Factors for Litigation Following Major Transectional Bile Duct Injury Sustained at Laparoscopic Cholecystectomy
Authors: Perera M. T. P. R. , Silva M. A. , Shah A. J. , Hardstaff R. , Bramhall S. R. , Issac J. , Buckels J. A. C. , Mirza D. F. 
Published: July 2010

AbstractBackgroundBile duct injuries after laparoscopic cholecystectomy often cause long‐term morbidity, with a number of patients resorting to litigation. The present study aimed to analyze risk factors for litigation and to quantify the subsequent medicolegal burden.MethodsA total of 67/106 patients (26 male) with major laparoscopic cholecystectomy bile duct injuries (LCBDI) and a minimum 2‐year follow‐up, replied to a questionnaire covering patient perception toward the complication, physical/psychological recovery, and subsequent litigation. These data were collated with prospectively collected data related to the LCBDI and subsequent management, and a multivariate regression model was designed to identify potential risk factors associated with litigation.ResultsMost patients felt they had been inadequately informed prior to surgery [47/67 (70%)] and after the LCBDI [50/67 (75%)], and a majority remained psychologically traumatized at the time of evaluation [50/67 (75%)]. Of these, 22 patients had started litigation by means of a “letter of demand” (LOD; n = 10) or prosecution (n = 12). Nineteen (19/22%) cases have been closed in favor of the plaintiff. There was no difference between the awards for LOD versus prosecution cases, and average compensation was £40,800 versus £89,875, respectively (p = n.s). On multivariate analysis, age < 52 years (p = 0.03), associated vascular injury (p = 0.014), immediate nonspecialist repair (p = 0.009), and perceived incomplete recovery following LCBDI (p = 0.017) were identified as independent predictors for possible litigation.ConclusionsOn the basis of the present study, nearly one third of patients with major transectional LCBDI are likely to resort to litigation. Younger patients and those in whom repair is attempted prior to specialist referral are likely to initiate litigation.
Diagnostic Value of Inflammation Markers in Predicting Perforation in Acute Sigmoid Diverticulitis
Authors: Käser S. A. , Fankhauser G. , Glauser P. M. , Toia D. , Maurer Christoph A. 
Published: July 2010

AbstractBackgroundThe importance of inflammation markers in predicting perforation in acute sigmoid diverticulitis is not well known. Predicting perforation by clinical examination alone may be hazardous. If perforation is suspected, then appropriate diagnostic tools such as computed tomography (CT) are indicated, and surgical intervention might be necessary.MethodsA cohort of consecutive patients with acute sigmoid diverticulitis diagnosed by CT and with complete laboratory findings (n = 247) were retrospectively divided into two groups, one with perforation (n = 86) and another without (n = 161). The latest values of C‐reactive protein (CRP), white blood cell count (WBC), and serum bilirubin, as well as the activity of the alkaline phosphatase (AP) measured during the 48 h period before the CT scan, were assessed.ResultsIn the Wilcoxon rank sum test CRP and WBC correlate significantly (p < 0.05) with perforation in acute sigmoid diverticulitis, whereas the logistic regression model shows only CRP to correlate significantly (p = 0.001) with perforation. The sensitivities/specificities for perforation are 98%/5% for elevated CRP (>5 mg/l), 86%/27% for a CRP higher than 50 mg/l, 44%/81% for a CRP higher than 150 mg/l, 28%/93% for a CRP higher than 200 mg/l, 88%/44% for elevated WBC (>10 × 109/l), 35%/90% for hyperbilirubinemia (>20 μmol/l), and 35%/91% for elevated AP (>110 U/l).ConclusionsA CRP below 50 mg/l suggests a perforation to be unlikely in acute sigmoid diverticulitis, whereas a CRP higher than 200 mg/l is a strong indicator of perforation.
Marjolin’s Ulcers in sub‐Saharan Africa
Authors: Nthumba Peter M. 
Published: July 2010

AbstractBackgroundCutaneous malignancies are considered rare among Africans. Trauma, its sequelae, and other chronic non‐healing wounds are known to predispose to malignant degeneration. Not much is known of the demographics of Marjolin’s ulcers in sub‐Saharan Africa.MethodsPathology records on patients suspected to have Marjolin’s ulcers submitted to the Pathology Department were extracted from a database of 75,124 specimens. A review of the English literature on Marjolin’s ulcers from Nigeria, a sub‐Saharan country, was also performed.ResultsOf 210 specimens from suspected Marjolin’s ulcers, 167 records had a histological diagnosis of malignancy, with a male to female ratio of 1:1.4, and a mean age of 48 years (range: 4–97 years). There were 163 (97.6%) squamous cell carcinomas, 3 (1.8%) sarcomas, and 1 (0.6%) malignant melanoma. Burn scars, chronic ulcers, osteomyelitis, and “other” ulcers constituted 82 (49%), 70 (42%), 9 (5.4%), and 6 (3.6%), respectively. Subjects in six sub‐Saharan Marjolin’s ulcer studies had a mean age between 36 and 42 years, with a mean latent period 16 years.ConclusionsMarjolin’s ulcers in sub‐Saharan African have a shorter latent period, and they occur in younger patients. Provision of early stable wound cover is essential for prevention of malignant degeneration of scars, while early appropriate intervention is crucial in the treatment of chronic ulcers.
Percutaneous Radiofrequency Ablation versus Partial Hepatectomy for Multicentric Small Hepatocellular Carcinomas: A Nonrandomized Comparative Study
Authors: Guo Wei‐Xing , Zhai Bo , Lai Eric C. H. , Li Nan , Shi Jie , Lau Wan‐Yee , Wu Meng‐Chao , Cheng Shu‐Qun 
Published: July 2010

AbstractBackgroundThe aim of this study was to compare the results of percutaneous radiofrequency ablation (RFA) with those of partial hepatectomy (PH) in the treatment of multicentric small hepatocellular carcinomas (HCCs). With advances in RFA, it is not known whether the minimally invasive approach with percutaneous RFA could attain comparable survival outcomes but with a lower morbidity in patients with multicentric HCCs.MethodsFrom January 2002 and December 2007, 159 patients who had two or three HCCs, with the largest tumor no more than 5 cm in diameter, had no major vascular invasion or extrahepatic metastases, and were treated with either PH (n = 73) or RFA (n = 86) were included in the study.ResultsThere was no procedure‐related mortality in both groups of patients. Major complications happened significantly more often after PH than after RFA (19.2 vs. 8.1%). The hospital stay was significantly longer after PH than after RFA (median = 9 vs. 3 days). The 1‐, 3‐, and 5‐year overall survival rates for the PH and RFA groups were 91.8, 68.7, 44.5% and 94.2, 64.4, 21.2%, respectively. The corresponding disease‐free survival rates for the two groups were 62.1, 33.6, 3.6% and 29.4, 2.7, 0%, respectively. The PH group had significantly longer overall survival and disease‐free survival than the RFA group.ConclusionsPH resulted in better survival outcomes than RFA for patients with multicentric small HCCs. However, RFA had the benefits of lower procedure‐related morbidity and shorter hospital stay.