bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Evolution of Hardware Circuits via Reconfigurable Architectures
Authors: Cancare Fabio , Bartolini Davide B. , Carminati Matteo , Sciuto Donatella , Santambrogio Marco D. 
Published: December 2012

Traditionally, hardware circuits are realized according to techniques that follow the classical phases of design and testing. A completely new approach in the creation of hardware circuits has been proposed---the Evolvable Hardware (EHW) paradigm, which bases the circuit synthesis on a goal-oriented evolutionary process inspired by biological evolution in Nature.
FPGA-based approaches have emerged as the main architectural solution to implement EHW systems. Various EHW systems have been proposed by researchers but most of them, being based on outdated chips, do not take advantage of the interesting features introduced in newer FPGAs. This article describes a project named Hardware Evolution over Reconfigurable Architectures (HERA), which aims at creating a complete and performance-oriented framework for the evolution of digital circuits, leveraging the reconfiguration technology available in FPGAs. The project is described from its birth to its current state, presenting its evolutionary technique tailored for FPGA-based circuits and the most recent enhancements to improve the scalability with respect to problem size. The developed EHW system outperforms the state of the art, proving its effectiveness in evolving both standard benchmarks and more complex real-world applications.
The Phenotype of Hormone-Related Allergic and Autoimmune Diseases in the Skin: Annular Lesions That Lateralize
Authors: Kollipara Ramya , Arora Chetna , Reisz Colleen 
Published: December 2012

Introduction. Sexual dimorphism with an increased prevalence in women has long been observed in various autoimmune, allergic, and skin diseases. Recent research has attempted to correlate this female predilection to physiologic changes seen in the menstrual cycle in order to more effectively diagnose and treat these diseases. Cases. We present five cases of cutaneous diseases in women with annular morphology and distributive features that favor one side over the other. In all cases, skin disease improved with ovarian suppression. Conclusion. Sexual dimorphism in the innate and adaptive immune systems has long been observed, with females demonstrating a more vigorous immune response compared to males. Female sex hormones promote T and B lymphocyte autoreactivity and favor the humoral arm of adaptive immunity. In addition to ovarian steroidogenesis and immunity, intricate pathways coexist in order to engage a single oocyte in each cycle, while simultaneously sustaining the ovarian reserve. Vigorous proinflammatory, vasoactive, and pigment-related cytokines emerge during the demise of the corpus luteum, influencing peripherical sex hormone metabolism	of the level of the macrophage and fibroblast. We propose that annular and lateralizing lesions are important manifestations of hormone-related inflammation and recognition of this linkage can lead to improved immune and reproductive health.
Singular Initial Value Problem for a System of Integro‐Differential Equations
Authors: Šmarda Zdeněk , Khan Yasir 
Published: December 2012

Analytical properties like existence, uniqueness, and asymptotic behavior of solutions are studied for the following singular initial value problem: ,
yi(0+) = 0,
t ∈ (0, t0], where y = (y1, …, yn),
ai > 0,
i = 1, …, n are constants and t0 > 0. An approach which combines topological method of T. Ważewski and Schauder′s fixed point theorem is used. Particular attention is paid to construction of asymptotic expansions of solutions for certain classes of systems of integrodifferential equations in a right‐hand neighbourhood of a singular point.
Exploring the Impact of Land Cover and Topography on Rainfall Maxima in the Netherlands
Authors: ter Maat H. W. , Moors E. J. , Hutjes R. W. A. , Holtslag A. A. M. , Dolman A. J. 
Published: December 2012

AbstractThe relative contribution of topography and land use on precipitation is analyzed in this paper for a forested area in the Netherlands. This area has an average yearly precipitation sum that can be 75–100 mm higher than the rest of the country. To analyze this contribution, different configurations of land use and topography are fed into a mesoscale model. The authors use the Regional Atmospheric Modeling System (RAMS) coupled with a land surface scheme simulating water vapor, heat, and momentum fluxes [Soil–Water–Atmosphere Plant System–Carbon (SWAPS-C)]. The model simulations are executed for two periods that cover varying large-scale synoptic conditions of summer and winter periods. The output of the experiments leads to the conclusion that the precipitation maximum at the Veluwe is forced by topography and land use. The effect of the forested area on the processes that influence precipitation is smaller in summertime conditions when the precipitation has a convective character. In frontal conditions, the forest has a more pronounced effect on local precipitation through the convergence of moisture. The effect of topography on monthly domain-averaged precipitation around the Veluwe is a 17% increase in the winter and a 10% increase in the summer, which is quite remarkable for topography with a maximum elevation of just above 100 m and moderate steepness. From this study, it appears that the version of RAMS using Mellor–Yamada turbulence parameterization simulates precipitation better in wintertime, but the configuration with the medium-range forecast (MRF) turbulence parameterization improves the simulation of precipitation in convective circumstances.
Demographic and lifestyle characteristics associated with non-willingness to participate in health promotion programmes among adults of a lower socioeconomic status in Singapore
Authors: Ng Charis Wei Ling , Heng Bee Hoon , Molina Joseph Antonio , Wong Lai Yin , George Pradeep Paul , Cheah Jason 
Published: December 2012

Introduction/Objective Lower socioeconomic groups have been found to have poorer health outcomes and engage in fewer health promoting behaviours. Understanding the reasons behind adverse lifestyle habits and non-willingness to participate in health promotion programmes among lower socioeconomic groups will enable administrators to modify the programmes and increase participation in this population. This study aimed to determine reasons for non-exercise, smoking and non-willingness to participate, and characteristics associated with non-willingness to participate in health promotion programmes among residents in Singapore. Method A cross-sectional survey was conducted on a purposive sample of residents living in four housing developments of one- and two-room households in Singapore from June to October 2009. The patterns of exercise and smoking, receptiveness towards health promotion programmes and the reasons for non-willingness to participate were elicited. Chi-square tests and logistic regression analysis were performed to identify differences between groups. Results Seven hundred and seventy-eight responses were analysed. Only 36.1% of respondents were willing to participate in at least one health promotion programme (health screening, talk or workshop). Older respondents aged 45–64 years and more than 65 years were less likely to participate than their younger counterparts (18–44 years). Malays were more likely than Chinese to participate, and respondents who do not exercise were less likely to participate than respondents who exercise (regularly/occasionally). Reasons for non-willingness to participate were ‘not interested’ and ‘no time’. Conclusion Health promotion messages should adapt to the needs and situation of the disadvantaged, to increase participation.
Promouvoir la consommation de légumes et de fruits chez des collégiens : application du protocole d’intervention mapping
Authors: Boucher Danielle , Côté Françoise , Gagné Camille 
Published: December 2012

Résumé: L’objectif de cet article est de présenter le processus suivi lors du développement, de la mise en œuvre et de l’évaluation d’un programme de promotion de la consommation de légumes et de fruits destiné à des collégiens. Un total de 385 collégiens québécois du Canada âgés de 18 ans en moyenne ont accepté volontairement de participer à cette étude. Le modèle de planification en six étapes de Bartholomew et collaborateurs (2006) a été utilisé. Basée sur la théorie du comportement planifié (Ajzen,1991), l’évaluation des besoins a été effectuée avec un questionnaire auto-administré développé à partir d’une revue de la littérature et de groupes de discussion focalisée auprès de collégiens. Cette première étape a permis d’identifier les déterminants psychosociaux sur lesquels intervenir spécifiquement. Les résultats consistent en un programme d’une durée de quatre heures et demie, qui a été offert à 167 collégiens (groupe expérimental). Adaptées à cette clientèle, et sur des bases théoriques, les activités incluaient l’utilisation d’outils d’auto-évaluation de la consommation quotidienne de légumes et de fruits, le calcul de portions avec une nutritionniste, un quiz sur le web, la rédaction d’un plan pour implanter ses intentions, les démonstrations culinaires de recettes d’un pair avec dégustations et tests de goût. Le programme s’est avéré efficace pour augmenter l’intention comportementale ainsi que le nombre de participants à consommer au moins cinq portions de légumes et de fruits chaque jour, à la fin du programme. Ce protocole permet de structurer une intervention sur mesure visant un changement comportemental chez une clientèle ciblée. Le développement d’un partenariat milieu/université accroît les chances de succès, tant pour l’implantation du programme que pour son efficacité.
¿Profesionalizar la promoción de la salud? Algunas reflexiones desde el contexto europeo
Authors: Contu Paolo 
Published: December 2012

Resumen: El proceso de globalización ha tenido repercusiones no sólo en el área económico-financiera sino también en las esferas social, cultural y educativa. Uno de estos efectos es el desarrollo de procesos para lograr la acreditación de programas académicos y el tránsito regulado de profesionales certificados en diversos campos entre los que se incluyen la salud pública y la promoción de la salud (PS). En este trabajo, se reflexiona sobre los retos que enfrenta la formación en PS en el continente europeo. Se presentan datos sobre la capacitación a nivel pregrado de promotores de salud concebidos como profesionales autónomos y sobre la definición de competencias básicas referidas a PS que se incluirían en el curriculum de distintos tipos de personal en formación. Finalmente, se presenta el proyecto CompHP, que ha buscado contribuir a la consolidación de una identidad en los profesionales europeos que trabajan en PS y su reconocimiento en el mercado laboral.
Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study
Authors: Zhao Zhongming , Guo An-Yuan , van den Oord Edwin JCG , Aliev Fazil , Jia Peilin , Edenberg Howard J , Riley Brien P , Dick Danielle M , Bettinger Jill C , Davies Andrew G , Grotewiel Michael S , Schuckit Marc A , Agrawal Arpana , Kramer John , Nurnberger John I , Kendler Kenneth S , Webb Bradley T , Miles Michael F 
Published: December 2012

Abstract

Background
A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation.

Results
In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism.

Conclusions
These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.
CTF: a CRF-based transcription factor binding sites finding system
Authors: He Yupeng , Zhang Yizhe , Zheng Guangyong , Wei Chaochun 
Published: December 2012

Abstract

Background
Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is able to locate the transcription factor binding sites (TFBSs) accurately in high throughput and it has become the gold-standard method for TFBS finding experimentally. However, due to its high cost, it is impractical to apply the method in a very large scale. Considering the large number of transcription factors, numerous cell types and various conditions, computational methods are still very valuable to accurate TFBS identification.

Results

In this paper, we proposed a novel integrated TFBS prediction system, CTF, based on Conditional Random Fields (CRFs). Integrating information from different sources, CTF was able to capture patterns of TFBSs contained in different features (sequence, chromatin and etc) and predicted the TFBS locations with a high accuracy. We compared CTF with several existing tools as well as the PWM baseline method on a dataset generated by ChIP-seq experiments (TFBSs of 13 transcription factors in mouse genome). Results showed that CTF performed significantly better than existing methods tested.

Conclusions
CTF is a powerful tool to predict TFBSs by integrating high throughput data and different features. It can be a useful complement to ChIP-seq and other experimental methods for TFBS identification and thus improve our ability to investigate functional elements in post-genomic era.
Availability: CTF is freely available to academic users at: http://cbb.sjtu.edu.cn/~ccwei/pub/software/CTF/CTF.php
RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia
Authors: Xu Junzhe , Sun Jingchun , Chen Jingchun , Wang Lily , Li Anna , Helm Matthew , Dubovsky Steven L , Bacanu Silviu-Alin , Zhao Zhongming , Chen Xiangning 
Published: December 2012

AbstractBackgroundWhile genome-wide association studies identified some promising candidates for schizophrenia, the majority of risk genes remained unknown. We were interested in testing whether integration gene expression and other functional information could facilitate the identification of susceptibility genes and related biological pathways.ResultsWe conducted high throughput sequencing analyses to evaluate mRNA expression in blood samples isolated from 3 schizophrenia patients and 3 healthy controls. We also conducted pooled sequencing of 10 schizophrenic patients and matched controls. Differentially expressed genes were identified by t-test. In the individually sequenced dataset, we identified 198 genes differentially expressed between cases and controls, of them 19 had been verified by the pooled sequencing dataset and 21 reached nominal significance in gene-based association analyses of a genome wide association dataset. Pathway analysis of these differentially expressed genes revealed that they were highly enriched in the immune related pathways. Two genes,S100A8andTYROBP, had consistent changes in expression in both individual and pooled sequencing datasets and were nominally significant in gene-based association analysis.ConclusionsIntegration of gene expression and pathway analyses with genome-wide association may be an efficient approach to identify risk genes for schizophrenia.
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning
Authors: Wu Yonghui , Levy Mia A , Micheel Christine M , Yeh Paul , Tang Buzhou , Cantrell Michael J , Cooreman Stacy M , Xu Hua 
Published: December 2012

Abstract

Background
Many cancer clinical trials now specify the particular status of a genetic lesion in a patient's tumor in the inclusion or exclusion criteria for trial enrollment. To facilitate search and identification of gene-associated clinical trials by potential participants and clinicians, it is important to develop automated methods to identify genetic information from narrative trial documents.

Methods
We developed a two-stage classification method to identify genes and genetic lesion statuses in clinical trial documents extracted from the National Cancer Institute's (NCI's) Physician Data Query (PDQ) cancer clinical trial database. The method consists of two steps: 1) to distinguish gene entities from non-gene entities such as English words; and 2) to determine whether and which genetic lesion status is associated with an identified gene entity. We developed and evaluated the performance of the method using a manually annotated data set containing 1,143 instances of the eight most frequently mentioned genes in cancer clinical trials. In addition, we applied the classifier to a real-world task of cancer trial annotation and evaluated its performance using a larger sample size (4,013 instances from 249 distinct human gene symbols detected from 250 trials).

Results
Our evaluation using a manually annotated data set showed that the two-stage classifier outperformed the single-stage classifier and achieved the best average accuracy of 83.7% for the eight most frequently mentioned genes when optimized feature sets were used. It also showed better generalizability when we applied the two-stage classifier trained on one set of genes to another independent gene. When a gene-neutral, two-stage classifier was applied to the real-world task of cancer trial annotation, it achieved a highest accuracy of 89.8%, demonstrating the feasibility of developing a gene-neutral classifier for this task.

Conclusions
We presented a machine learning-based approach to detect gene entities and the genetic lesion statuses from clinical trial documents and demonstrated its use in cancer trial annotation. Such methods would be valuable for building information retrieval tools targeting gene-associated clinical trials.
Regulation of fruit ascorbic acid concentrations during ripening in high and low vitamin C tomato cultivars
Authors: Mellidou Ifigeneia , Keulemans Johan , Kanellis Angelos K , Davey Mark W 
Published: December 2012

Abstract

Background
To gain insight into the regulation of fruit ascorbic acid (AsA) pool in tomatoes, a combination of metabolite analyses, non-labelled and radiolabelled substrate feeding experiments, enzyme activity measurements and gene expression studies were carried out in fruits of the ‘low-’ and ‘high-AsA’ tomato cultivars ‘Ailsa Craig’ and ‘Santorini’ respectively.

Results
The two cultivars exhibited different profiles of total AsA (totAsA, AsA + dehydroascorbate) and AsA accumulation during ripening, but both displayed a characteristic peak in concentrations at the breaker stage. Substrate feeding experiments demonstrated that the L-galactose pathway is the main AsA biosynthetic route in tomato fruits, but that substrates from alternative pathways can increase the AsA pool at specific developmental stages. In addition, we show that young fruits display a higher AsA biosynthetic capacity than mature ones, but this does not lead to higher AsA concentrations due to either enhanced rates of AsA breakdown (‘Ailsa Craig’) or decreased rates of AsA recycling (‘Santorini’), depending on the cultivar. In the later stages of ripening, differences in fruit totAsA-AsA concentrations of the two cultivars can be explained by differences in the rate of AsA recycling activities. Analysis of the expression of AsA metabolic genes showed that only the expression of one orthologue of GDP-L-galactose phosphorylase (SlGGP1), and of two monodehydroascorbate reductases (SlMDHAR1 and SlMDHAR3) correlated with the changes in fruit totAsA-AsA concentrations during fruit ripening in ‘Ailsa Craig’, and that only the expression of SlGGP1 was linked to the high AsA concentrations found in red ripe ‘Santorini’ fruits.

Conclusions
Results indicate that ‘Ailsa Craig’ and ‘Santorini’ use complementary mechanisms to maintain the fruit AsA pool. In the low-AsA cultivar (‘Ailsa Craig’), alternative routes of AsA biosynthesis may supplement biosynthesis via L-galactose, while in the high-AsA cultivar (‘Santorini’), enhanced AsA recycling activities appear to be responsible for AsA accumulation in the later stages of ripening. Gene expression studies indicate that expression of SlGGP1 and two orthologues of SlMDHAR are closely correlated with totAsA-AsA concentrations during ripening and are potentially good candidates for marker development for breeding and selection.
Impact of heavy proteinuria on clinical outcomes in patients on incident peritoneal dialysis
Authors: Kang Seok Hui , Cho Kyu Hyang , Park Jong Won , Yoon Kyung Woo , Do Jun Young 
Published: December 2012

Abstract

Background
There are few reports on the nutritional status changes and residual renal function (RRF) according to proteinuria levels in patients on peritoneal dialysis (PD).

Methods
A total of 388 patients on PD were enrolled. The patients were divided into 3 groups with respect to initial proteinuria: the A (n = 119; <500 mg/day), B (n = 218; 500–3,500 mg/day), and C groups (n = 51; >3,500 mg/day).

Results
The patients with higher proteinuria levels had a higher incidence of male sex, diabetes mellitus, and icodextrin use than those with lower proteinuria levels. Although initial peritoneal albumin loss in C group was lower than that detected in the other groups, no significant difference was observed in peritoneal albumin loss among the 3 groups at the end of follow-up period. At the time of PD initiation, the Geriatric nutritional risk index (GNRI) was lower in the C group than in the other 2 groups. However, at the end of the follow-up period, there was no significant difference in GNRI between the 3 groups. The GNRI increased, and the proteinuria level or RRF decreased more in the C group than in the other 2 groups. There were no significant differences in lean mass index or fat mass index change from the time of PD initiation to the end of the follow-up period. However, fat mass index and nPNA showed greater increases in the C group. The multivariate analysis revealed that proteinuria was negatively correlated with GNRI at the time of PD initiation and at the end of the follow-up period. The initial RRF and proteinuria were negatively correlated with the RRF decline during the follow-up.

Conclusion
The attenuation of the nephrotic proteinuria, along with the RRF decline, was associated with the improvement of the malnutrition.