bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of fractal dimension and lacunarity in the characterization of mast cell degranulation in rainbow trout (Onchorhynchus mykiss)
Authors: MANERA M. , DEZFULI B.S. , BORRECA C. , GIARI L. 
Published: August 2014

AbstractFractal analysis is a reliable method for describing, summarizing object complexity and heterogeneity and has been widely used in biology and medicine to deal with scale, size and shape management problems. The aim of present survey was to use fractal analysis as a complexity measure to characterize mast cells (MCs) degranulation in a rainbow trout ex vivo model (isolated organ bath). Compound 48/80, a condensation product of N‐methyl‐p‐methoxyphenethylamine with formaldehyde, was adopted as MCs degranulation agent in trout intestinal strips. Fractal dimension (D), as a measure of complexity, ‘roughness’ and lacunarity (λ), as a measure of rotational and translational invariance, heterogeneity, in other words, of the texture, were compared in MCs images taken from intestinal strips before and after compound 48/80 addition to evaluate if and how they were affected by degranulation. Such measures were also adopted to evaluate their discrimination efficacy between compound 48/80 degranulated group and not degranulated group and the results were compared with previously reported data obtained with conventional texture analysis (image histogram, run‐length matrix, co‐occurrence matrix, autoregressive model, wavelet transform) on the same experimental material. Outlines, skeletons and original greyscale images were fractal analysed to evaluate possible significant differences in the measures values according to the analysed feature. In particular, and considering outline and skeleton as analysed features, fractal dimensions from compound 48/80 treated intestinal strips were significantly higher than the corresponding untreated ones (paired t and Wilcoxon test, p < 0.05), whereas corresponding lacunarity values were significantly lower (paired Wilcoxon test, p < 0.05) but only for outline as analysed feature. Outlines roughness increase is consistent with an increased granular mediators interface, favourable for their biological action; while lacunarity (image heterogeneity) reduction is consistent with the biological informative content decrease, due to granule content depletion. In spite of the significant differences in fractal dimension and lacunarity values registered according to the analysed feature (greyscale obtained values were, on average, lower than those obtained from outlines and skeletons; General Linear Model, p < 0.01), the discrimination power between not degranulated and degranulated MCs was, on average, the same and fully comparable with previously performed texture analysis on the same experimental material (outline and skeleton misclassification error, 20% [two false negative cases]; greyscale misclassification error, 30% [two false negative cases and one false positive case]). Fractal analysis proved to be a reliable and objective method for the characterization of MCs degranulation.
Modelling broilers’ abdominal fat in response to dietary treatments
Authors: Salarpour A. , Rahmatnejad E. , Khotanlou H. 
Published: August 2014

SummaryNeural networks are capable of modelling any complex function and can be used in poultry production. Dietary crude fibre (CF) and exogenous enzymes (exEn) extensively affected abdominal fat (AF) of broilers. Current methods to studyAFand its correlation with dietaryCFlevels and exEn supplements are costly, laborious and time‐consuming. The purpose of this study was to develop an artificial neural network–genetic algorithm (ANN‐GA) to model data on the response of broiler chickens (AF) toCFand exEn from 0 to 42 days of age. A data set containing eight treatments was divided to the train, validation, and test data set of theANNmodels. The information about feeding eight diets at two periods [starter (0–21 days of age) and grower (22–42 days of age)] were used to estimateAFof broilers byANN‐GA. A multilayer feed‐forward neural network with different structures was developed usingmatlabsoftware, and optimal values for theANNweights were obtained using the genetic algorithm (GA). Crude fibre, and exEn were used as input variables andAFof broilers was output variable. The best model ofANN‐GAwas determined based on the train root mean square error (RMSE). The best selectedANN‐GAshowed desirable results,RMSE, 0.1286% andR2coefficient, 0.876 for test data.
A four‐country comparison of healthcare systems, implementation of diagnostic criteria, and treatment availability for functional gastrointestinal disorders
Authors: Schmulson M. , Corazziari E. , Ghoshal U. C. , Myung S.‐J. , Gerson C. D. , Quigley E. M. M. , Gwee K.‐A. , Sperber A. D. 
Published: August 2014

AbstractBackgroundVariations in healthcare provision around the world may impact how patients with functional gastrointestinal disorder (FGIDs) are investigated, diagnosed, and treated. However, these differences have not been reviewed.PurposesThe Multinational Working Team of the Rome Foundation, established to make recommendations on the conduct of multinational, cross‐cultural research in FGIDs, identified seven key issues that are analyzed herein: (i) coverage afforded by different healthcare systems/providers; (ii) level of the healthcare system where patients with FGIDs are treated; (iii) extent/types of diagnostic procedures typically undertaken to diagnose FGIDs; (iv) physicians’ familiarity with and implementation of the Rome diagnostic criteria in clinical practice; (v) range of medications approved for FGIDs and approval process for new agents; (vi) costs involved in treating FGIDs; and (vii) prevalence and role of complementary/alternative medicine (CAM) for FGIDs. Because it was not feasible to survey all countries around the world, we compared a selected number of countries based on their geographical and ethno‐cultural diversity. Thus, we included Italy and South Korea as representative of nations with broad‐based coverage of healthcare in the population and India and Mexico as newly industrialized countries where there may be limited provision of healthcare for substantial segments of the population. In light of the paucity of formal publications on these issues, we included additional sources from the medical literature as well as perspectives provided by local experts and the media. Finally, we provide future directions on healthcare issues that should be taken into account and implemented when conducting cross‐cultural and multinational research in FGIDs.
The Effect of Poverty and Income Disparity on the Psychological Well‐Being of Hong Kong Children
Authors: Ho Ka Yan , Li William H. C. , Chan Sophia S. C. 
Published: August 2014

AbstractObjectiveThis study explored the impact of poverty and income disparity on the psychological well‐being of Hong Kong Chinese children.Design and SampleA cross‐sectional study was conducted in 12 elementary schools from the three highest and three lowest median household income districts. A total of 1,725 pupils were recruited with 898 pupils came from low‐income and 827 from high‐income families.MeasuresParticipants were asked to respond to the Chinese version of the Center for Epidemiologic Studies Depression Scale for Children, the Rosenberg self‐esteem scale, and the Pediatric Quality of Life Inventory. The data were collected from 2012 to 2013.ResultsChildren from low‐income families reported statistically significant lower scores in self‐esteem and quality of life, but higher scores in depressive symptoms than those from high‐income families. Income disparity had their greatest impact on children's self‐esteem.ConclusionThis study has addressed a gap in the literature by comparing the self‐esteem, depressive symptoms, and quality of life among children living in low‐ and high‐income families. The results add further evidence to the literature that poverty and income disparity may have a negative impact on the psychological well‐being of children.
Pros and Cons of Body Mass Index as a Nutritional and Risk Assessment Tool in Dialysis Patients
Authors: Carrero Juan Jesús , Avesani Carla Maria 
Published: August 2014

AbstractObesity is a problem of serious concern among chronic kidney disease (CKD) patients; it is a risk factor for progression to end‐stage renal disease and its incidence and prevalence in dialysis patients exceeds those of the general population. Obesity, typically assessed with the simple metric of body mass index (BMI), is considered a mainstay for nutritional assessment in guidelines on nutrition in CKD. While regular BMI assessment in connection with the dialysis session is a simple and easy‐to‐use monitoring tool, such ease of access can lead to excess‐of‐use, as the value of this metric to health care professionals is overestimated. This review examines BMI as a clinical monitoring tool in CKD practice and offers a critical appraisal as to what a high or a low BMI may signify in this patient population. Topics discussed include the utility of BMI as a reflection of body size, body composition and body fat distribution, diagnostic versus prognostic performance, and consideration of temporal trends over single assessments.
Biophysical properties of striae distensae evaluated in vivo using non‐invasive assays
Authors: Stamatas G. N. , Lopes‐DaCunha A. , Nkengne A. , Bertin C. 
Published: August 2014

BackgroundStriae Distensae (SD) or stretch marks are manifestations of epidermal atrophy that occurs after tissue tearing due to rapid growth or over‐stretching and are characterized by distinct microstructural features. The objective of this in vivo study was to investigate the biophysical properties of SD lesions, including skin barrier function, skin surface hydration, mechanical properties, and chromophore concentrations, compared to normal adjacent skin.MethodsNon‐invasive methods were used on 29 volunteers with SD to characterize: (i) visual appearance (visual assessment and clinical imaging), (ii) skin barrier function by measuring transepidermal water loss, (iii) skin surface hydration using corneometry (skin capacitance), (iv) mechanical properties measuring skin elasticity under vacuum and surface propagation of a sonic wave, (v) the presence of erythema and pigmentation using diffuse reflectance spectroscopy, and (vi) the levels of interleukin‐1α on the skin surface.ResultsNo difference was observed in skin barrier function and a slight difference in skin hydration between the striae and adjacent uninvolved skin. Viscoelasticity measurements showed that SD lesions were significantly less firm, less elastic, and less deformable than normal skin (P < 0.05). Mechanical anisotropy was increased in SD compared to normal skin, reflecting the skin surface anisotropy reported previously. Diffuse reflectance spectroscopy showed no differences in the apparent hemoglobin concentrations between SD and control. Skin pigmentation and light scattering values were significantly lower in SD (P < 0.001) compared to adjacent skin and there was no correlation between them indicating independent causes: lower melanin production for pigmentation and altered collagen fiber structure in the dermis for light scattering.ConclusionsBased on these results, the distinct microstructural features characterizing SD lesions are accompanied by changes in the mechanical and optical properties. These changes however do not seem to affect the skin barrier and moisturization properties.
Development and Validation of a Risk Score Predicting Risk of Colorectal Cancer
Authors: Steffen Annika , MacInnis Robert J. , Joshy Grace , Giles Graham G. , Banks Emily , Roder David 
Published: August 2014

Abstract
Background: Quantifying the risk of colorectal cancer for individuals is likely to be useful for health service provision. Our aim was to develop and externally validate a prediction model to predict 5-year colorectal cancer risk.
Methods: We used proportional hazards regression to develop the model based on established personal and lifestyle colorectal cancer risk factors using data from 197,874 individuals from the 45 and Up Study, Australia. We subsequently validated the model using 24,233 participants from the Melbourne Collaborative Cohort Study (MCCS).
Results: A total of 1,103 and 224 cases of colorectal cancer were diagnosed in the development and validation sample, respectively. Our model, which includes age, sex, BMI, prevalent diabetes, ever having undergone colorectal cancer screening, smoking, and alcohol intake, exhibited a discriminatory accuracy of 0.73 [95% confidence interval (CI), 0.72–0.75] and 0.70 (95% CI, 0.66–0.73) using the development and validation sample, respectively. Calibration was good for both study samples. Stratified models according to colorectal cancer screening history, that additionally included family history, showed discriminatory accuracies of 0.75 (0.73–0.76) and 0.70 (0.67–0.72) for unscreened and screened individuals of the development sample, respectively. In the validation sample, discrimination was 0.68 (0.64–0.73) and 0.72 (0.67–0.76), respectively.
Conclusion: Our model exhibited adequate predictive performance that was maintained in the external population.
Impact: The model may be useful to design more powerful cancer prevention trials. In the group of unscreened individuals, the model may be useful as a preselection tool for population-based screening programs. Cancer Epidemiol Biomarkers Prev; 23(11); 2543–52. ©2014 AACR.
Dietary Manipulation of Oncogenic MicroRNA Expression in Human Rectal Mucosa: A Randomized Trial
Authors: Humphreys Karen J. , Conlon Michael A. , Young Graeme P. , Topping David L. , Hu Ying , Winter Jean M. , Bird Anthony R. , Cobiac Lynne , Kennedy Nicholas A. , Michael Michael Z. , Le Leu Richard K. 
Published: August 2014

Abstract
High red meat (HRM) intake is associated with increased colorectal cancer risk, while resistant starch is probably protective. Resistant starch fermentation produces butyrate, which can alter microRNA (miRNA) levels in colorectal cancer cells in vitro; effects of red meat and resistant starch on miRNA expression in vivo were unknown. This study examined whether a HRM diet altered miRNA expression in rectal mucosa tissue of healthy volunteers, and if supplementation with butyrylated resistant starch (HRM+HAMSB) modified this response. In a randomized cross-over design, 23 volunteers undertook four 4-week dietary interventions; an HRM diet (300 g/day lean red meat) and an HRM+HAMSB diet (HRM with 40 g/day butyrylated high amylose maize starch), preceded by an entry diet and separated by a washout. Fecal butyrate increased with the HRM+HAMSB diet. Levels of oncogenic mature miRNAs, including miR17–92 cluster miRNAs and miR21, increased in the rectal mucosa with the HRM diet, whereas the HRM+HAMSB diet restored miR17–92 miRNAs, but not miR21, to baseline levels. Elevated miR17–92 and miR21 in the HRM diet corresponded with increased cell proliferation, and a decrease in miR17–92 target gene transcript levels, including CDKN1A. The oncogenic miR17–92 cluster is differentially regulated by dietary factors that increase or decrease risk for colorectal cancer, and this may explain, at least in part, the respective risk profiles of HRM and resistant starch. These findings support increased resistant starch consumption as a means of reducing risk associated with an HRM diet. Cancer Prev Res; 7(8); 786–95. ©2014 AACR.
Greater Than the Sum of Its Parts: Single-Nucleus Sequencing Identifies Convergent Evolution of Independent EGFR Mutants in GBM
Authors: Gini Beatrice , Mischel Paul S. 
Published: August 2014

Abstract
Summary: Single-cell sequencing approaches are needed to characterize the genomic diversity of complex tumors, shedding light on their evolutionary paths and potentially suggesting more effective therapies. In this issue of Cancer Discovery, Francis and colleagues develop a novel integrative approach to identify distinct tumor subpopulations based on joint detection of clonal and subclonal events from bulk tumor and single-nucleus whole-genome sequencing, allowing them to infer a subclonal architecture. Surprisingly, the authors identify convergent evolution of multiple, mutually exclusive, independent EGFR gain-of-function variants in a single tumor. This study demonstrates the value of integrative single-cell genomics and highlights the biologic primacy of EGFR as an actionable target in glioblastoma. Cancer Discov; 4(8); 876–8. ©2014 AACR.
See related article by Francis et al., p. 956
Grammoplites vittatus (Valenciennes), (Scorpaeniformes, Platycephalidae), removed from synonymy with Grammoplites scaber (Linnaeus)
Authors: KNAPP LESLIE W. , IMAMURA HISASHI 
Published: August 2014

Grammoplites vittatus (Valenciennes), often previously overlooked by authors or regarded as a junior synonym of G. scaber (Linnaeus), is shown here to be a valid species. It has more gill rakers (7–8) then G. scaber and G. knappi (usually 6) and a narrower interorbital width than G. scaber. A key to the species of Grammoplites Fowler is given.
Analysis of qPCR reference gene stability determination methods and a practical approach for efficiency calculation on a turbot (Scophthalmus maximus) gonad dataset
Authors: Robledo Diego , Hernández-Urcera Jorge , Cal Rosa M , Pardo Belén G , Sánchez Laura , Martínez Paulino , Viñas Ana 
Published: August 2014

Abstract

Background
Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal reference genes for normalization and efficiency determination. There is no agreement on which method is the best to detect the most stable genes neither on how to perform efficiency determination. In this study we offer a comprehensive evaluation of the characteristics of reference gene selection methods and how to decide which one is more reliable when they show discordant outcomes. Also, we analyze the current efficiency calculation controversy. Our dataset is composed by gonad samples of turbot at different development times reared at different temperatures. Turbot (Scophthalmus maximus) is a relevant marine aquaculture European species with increasing production in the incoming years. Since females largely outgrow males, identification of genes related to sex determination, gonad development and reproductive behavior, and analysis of their expression profiles are of primary importance for turbot industry.

Results
We analyzed gene stability of six reference genes: RPS4, RPL17, GAPDH, ACTB, UBQ and B2M using the comparative delta-CT method, Bestkeeper, NormFinder and GeNorm approaches in gonad samples of turbot. Supported by descriptive statistics, we found NormFinder to be the best method, while on the other side, GeNorm results proved to be unreliable. According to our analysis, UBQ and RPS4 were the most stable genes, while B2M was the least stable gene. We also analyzed the efficiency calculation softwares LinRegPCR, LREanalyzer, DART and PCR-Miner and we recommend LinRegPCR for research purposes since it does not systematically overestimate efficiency.

Conclusion
Our results indicate that NormFinder and LinRegPCR are the best approaches for reference gene selection and efficiency determination, respectively. We also recommend the use of UBQ and RPS4 for normalization of gonad development samples in turbot.
Exosomes from IL-1β stimulated synovial fibroblasts induce osteoarthritic changes in articular chondrocytes
Authors: Kato Tomohiro , Miyaki Shigeru , Ishitobi Hiroyuki , Nakamura Yoshihiro , Nakasa Tomoyuki , Lotz Martin K , Ochi Mitsuo 
Published: August 2014

Abstract
Introduction
Osteoarthritis (OA) is a whole joint disease, and characterized by progressive degradation of articular cartilage, synovial hyperplasia, bone remodeling and angiogenesis in various joint tissues. Exosomes are a type of microvesicles (MVs) that may play a role in tissue-tissue and cell-cell communication in homeostasis and diseases. We hypothesized that exosomes function in a novel regulatory network that contributes to OA pathogenesis and examined the function of exosomes in communication among joint tissue cells.

Methods
Human synovial fibroblasts (SFB) and articular chondrocytes were obtained from normal knee joints. Exosomes isolated from conditioned medium of SFB were analyzed for size, numbers, markers and function. Normal articular chondrocytes were treated with exosomes from SFB, and Interleukin-1β (IL-1β) stimulated SFB. OA-related genes expression was quantified using real-time PCR. To analyze exosome effects on cartilage tissue, we performed glycosaminoglycan release assay. Angiogenic activity of these exosomes was tested in migration and tube formation assays. Cytokines and miRNAs in exosomes were analyzed by Bio-Plex multiplex assay and NanoString analysis.

Results
Exosomes from IL-1β stimulated SFB significantly up-regulated MMP-13 and ADAMTS-5 expression in articular chondrocytes, and down-regulated COL2A1 and ACAN compared with SFB derived exosomes. Migration and tube formation activity were significantly higher in human umbilical vein endothelial cells (HUVECs) treated with the exosomes from IL-1β stimulated SFB, which also induced significantly more proteoglycan release from cartilage explants. Inflammatory cytokines, IL-6, MMP-3 and VEGF in exosomes were only detectable at low level. IL-1β, TNFα MMP-9 and MMP-13 were not detectable in exosomes. NanoString analysis showed that levels of 50 miRNAs were differentially expressed in exosomes from IL-1β stimulated SFB compared to non-stimulated SFB.

Conclusions
Exosomes from IL-1β stimulated SFB induce OA-like changes both in vitro and in ex vivo models. Exosomes represent a novel mechanism by which pathogenic signals are communicated among different cell types in OA-affected joints.