bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Features of Interleukin 10 Receptor Gene Mutations in Children With Very Early–Onset Inflammatory Bowel Disease
Authors: Beser Omer F. , Conde Cecilia Dominguez , Serwas Nina K. , Cokugras Fügen Cullu , Kutlu Tufan , Boztug Kaan , Erkan Tulay 
Published: November 2014

ABSTRACTObjectives:In the present study, we studied a cohort of patients with very early onset inflammatory bowel disease (IBD) to determine the frequency of mutations in the interleukin 10 (IL10) receptor genes as a cause of early‐onset IBD.Methods:Sanger sequencing was performed to determine the presence of IL10 and/or IL10 receptor mutations in 17 patients with a diagnosis of very early onset IBD (disease onset <2 years of age in 15 patients, between 3 and 4 years in the other 2). Mutation screening was performed including all of the coding regions of the IL10, IL10RA, and IL10RB genes. We then compared the follow‐up findings of the patients with IL10 receptor mutations in terms of demographic, clinical, laboratory, and treatment response properties with those of patients diagnosed as having very early onset IBD with no mutation.Results:We identified 3 patients bearing mutations in the IL10 or IL10 receptor genes, including 1 mutation in IL10RB that has been described recently (c.G477A, p.Trp159*) and 2 novel mutations affecting the IL10RA gene (c.T192G, p.Tyr64* and c.T133G, p.Trp45Gly). Collectively, these mutations thus provided genetic etiology for 17.6% of the cohort under investigation. The presence of a family history of IBD and the clinical course of Crohn disease differed between patients with mutations in the IL‐10 pathway and those without such mutations. Although perianal fistulas were found in all of the patients with IL10 receptor mutations, they were found in only 14.3% of those without such mutations. The lower values of weight‐for‐age and height‐for‐age z scores, necessity for more intensive therapy, achievement of longer periods until remission, and frequent relapses in the patients bearing mutations in the IL10 receptor genes all underlined the severity of the disease and its relatively poor response to treatment.Conclusions:In spite of the small number of patients with mutations affecting the IL‐10 signaling pathway in our study, in all of the patients with IL10 receptor mutations, the disease onset occurs at an early age, the prognosis is poor, and the response to treatment is insufficient.
Computerized Dose Range Checking Using Hard and Soft Stop Alerts Reduces Prescribing Errors in a Pediatric Intensive Care Unit
Authors: Balasuriya Lilanthi , Vyles David , Bakerman Paul , Holton Vanessa , Vaidya Vinay , Garcia-Filion Pamela , Westdorp Joan , Sanchez Christine , Kurz Rhonda 
Published: November 2014

Objective
An enhanced dose range checking (DRC) system was developed to evaluate prescription error rates in the pediatric intensive care unit and the pediatric cardiovascular intensive care unit.

Methods
An enhanced DRC system incorporating “soft” and “hard” alerts was designed and implemented. Practitioner responses to alerts for patients admitted to the pediatric intensive care unit and the pediatric cardiovascular intensive care unit were retrospectively reviewed.

Results
Alert rates increased from 0.3% to 3.4% after “go-live” (P < 0.001). Before go-live, all alerts were soft alerts. In the period after go-live, 68% of alerts were soft alerts and 32% were hard alerts. Before go-live, providers reduced doses only 1 time for every 10 dose alerts. After implementation of the enhanced computerized physician order entry system, the practitioners responded to soft alerts by reducing doses to more appropriate levels in 24.7% of orders (70/283), compared with 10% (3/30) before go-live (P = 0.0701). The practitioners deleted orders in 9.5% of cases (27/283) after implementation of the enhanced DRC system, as compared with no cancelled orders before go-live (P = 0.0774). Medication orders that triggered a soft alert were submitted unmodified in 65.7% (186/283) as compared with 90% (27/30) of orders before go-live (P = 0.0067). After go-live, 28.7% of hard alerts resulted in a reduced dose, 64% resulted in a cancelled order, and 7.4% were submitted as written.

Conclusions
Before go-live, alerts were often clinically irrelevant. After go-live, there was a statistically significant decrease in orders that were submitted unmodified and an increase in the number of orders that were reduced or cancelled.
GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands
Authors: Lassalle Florent , Périan Séverine , Bataillon Thomas , Nesme Xavier , Duret Laurent , Daubin Vincent 
Published: November 2014

AbstractThe characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes.
A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in Matlab
Authors: Sinha Shriprakash 
Published: November 2014

AbstractA tutorial introduction to computational modeling of Wnt signaling pathway in a human colorectal cancer dataset using static Bayesian network models is provided. The walkthrough might aid bio-logists/informaticians in understanding the design of computational experiments that is interleaved with exposition of the Matlab code and causal models from Bayesian Network toolbox. This is done in order to ease the understanding of beginner students and researchers in transition to computational signaling biology, who intend to work in the field of modeling of signaling pathways. The manuscript expounds the computational flow of the contents in advance article1via code development and takes the reader in a step by step process of how • the collection and the transformation of the available biological information from literature is done, • the integration of the heterogeneous data and prior biological knowledge in the network is achieved, • conditional probability tables for nodes in biologically inspired tables are estimated, • the simulation study is designed, • the hypothesis regarding a biological phenomena is transformed into computational framework, and • results and inferences drawn usingd-connectivity/separability are reported. The manuscript finally ends with a programming assignment to help the readers get hands on experience of a perturbation project. Matlab code with dataset is made available under GNU GPL v3 license at google code project onhttps://code.google.com/p/static-bn-for-wnt-signaling-pathwayInsight, Innovation and IntegrationSimulation study involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of beginner students and researchers in transition who intend to work on modeling of the pathway. This paucity might happen due to restrictive policies which enforce an unwanted embargo on the sharing of important scientific knowledge. The manuscript elucidates embedding of prior biological knowledge, integration of heterogeneous information, transformation of biological hypothesis into computational framework and design of experiments in a simple manner interleaved with aspects of Bayesian Network toolbox and Matlab code so as to help readers get a feel of a project related to modeling of the pathway.
Malate Synthesis and Secretion Mediated by a Manganese-Enhanced Malate Dehydrogenase Confers Superior Manganese Tolerance in Stylosanthes guianensis
Authors: Chen Zhijian , Sun Lili , Liu Pandao , Liu Guodao , Tian Jiang , Liao Hong 
Published: November 2014

Abstract
Manganese (Mn) toxicity is a major constraint limiting plant growth on acidic soils. Superior Mn tolerance in Stylosanthes spp. has been well documented, but its molecular mechanisms remain largely unknown. In this study, superior Mn tolerance in Stylosanthes guianensis was confirmed, as reflected by a high Mn toxicity threshold. Furthermore, genetic variation of Mn tolerance was evaluated using two S. guianensis genotypes, which revealed that the Fine-stem genotype had higher Mn tolerance than the TPRC2001-1 genotype, as exhibited through less reduction in dry weight under excess Mn, and accompanied by lower internal Mn concentrations. Interestingly, Mn-stimulated increases in malate concentrations and exudation rates were observed only in the Fine-stem genotype. Proteomic analysis of Fine-stem roots revealed that S. guianensis Malate Dehydrogenase1 (SgMDH1) accumulated in response to Mn toxicity. Western-blot and quantitative PCR analyses showed that Mn toxicity resulted in increased SgMDH1 accumulation only in Fine-stem roots, but not in TPRC2001-1. The function of SgMDH1-mediated malate synthesis was verified through in vitro biochemical analysis of SgMDH1 activities against oxaloacetate, as well as in vivo increased malate concentrations in yeast (Saccharomyces cerevisiae), soybean (Glycine max) hairy roots, and Arabidopsis (Arabidopsis thaliana) with SgMDH1 overexpression. Furthermore, SgMDH1 overexpression conferred Mn tolerance in Arabidopsis, which was accompanied by increased malate exudation and reduced plant Mn concentrations, suggesting that secreted malate could alleviate Mn toxicity in plants. Taken together, we conclude that the superior Mn tolerance of S. guianensis is achieved by coordination of internal and external Mn detoxification through malate synthesis and exudation, which is regulated by SgMDH1 at both transcription and protein levels.
7-Cyclopropyl-2′-deoxytubercidin: a carbocyclic side-chain derivative of 7-deaza-2′-deoxyadenosine
Authors: Yang Haozhe , Budow-Busse Simone , Eickmeier Henning , Reuter Hans , Seela Frank 
Published: November 2014

The title compound {systematic name: 4-amino-5-cyclopropyl-7-(2-deoxy-β-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine}, C14H18N4O3, exhibits anantiglycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′-exosugar pucker (S-type), withP= 120.0 (2)° and τm= 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is -ap(trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (antiorientation). Within the three-dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′-hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.
Emirati pre-service teachers’ experiences of teaching science during college internships
Authors: Kadbey Hanadi , Dickson Martina 
Published: November 2014

Purpose
– The purpose of this research is to explore the effect of internship experience on final-year pre-service teachers (PSTs) studying for a Bachelor of Education in Abu Dhabi. The UAE is undergoing a period of rapid education reform with a strong emphasis on use of student-centered learning strategies in the classroom. Teacher-training colleges, such as the one in which this research took place, have had to customize their programs to prepare and train teachers who can effectively implement this new approach.

Design/methodology/approach
– Semi-structured interviews were conducted with ten PSTs to explore the usefulness of the college science courses during their internship experience, and the challenges they faced during their internship. We also looked at how these experiences have influenced their confidence levels and the type of science teachers they want to be in the future.

Findings
– Results have shown that PSTs have variable opinions on the usefulness of the college courses. A perceived lack of emphasis placed by mentor teachers upon science may have long-term effects on the PSTs’ eventual use of teaching strategies. It was also shown that some of the PSTs still lacked confidence in science teaching.

Practical implications
– This research may provide national guidelines for teacher-training colleges in the UAE or in countries undergoing educational reform and moving towards student-centered approaches to learning.

Originality/value
– Research studies on the effect of internship on PSTs have been conducted in different countries but such studies have great novelty in the UAE.
Towards more employable Egyptian HE graduates – a case study
Authors: Abou-Setta Amal 
Published: November 2014

Purpose
– The unemployment rate in Egypt has reached 24.8 per cent of the labor force and is significantly higher among university graduates. Therefore, the purpose of this paper is to examine the relationship between Higher Education (HE) and employability in Egypt and to ask these pressing questions: How do students perceive the relationship? What are its main problems? What are the changes required to help improve the relationship from their own perspective?

Design/methodology/approach
– Offering an in-depth analysis of a case study of an Egyptian public university by interviewing four Egyptian HE students either in their final or their second-to-last year of study, this paper attempts to decipher the Egyptian HE students’ attitudes towards quality education and employability as an ultimate purpose. It also offers a macroscopic view of the necessary changes to make HE graduates more employable.

Findings
– The paper argues that, for effective HE reform to take place in Egypt, radical, comprehensive changes pertaining to programme design, curricula, assessment, pedagogy and admissions are called for, taking into account the contextual political, economic and cultural conditions.

Originality/value
– Although there is a considerable amount of research literature examining the significant discrepancy between university graduates’ educational gains and the functional requirements of the job market (Allen and De Weert 2007), not much of that research has examined the way graduates understand and manage their employability in light of the recent changes in both HE and the job market and the few studies focusing on this were mainly conducted in the Western world (Al-Harthi 2011).
The nature of parental involvement in the city of Abu Dhabi in a context of change
Authors: S. Baker Fiona , Blaik Hourani Rida 
Published: November 2014

Purpose– The purpose of this exploratory study is to explore parent and school administrator perspectives on the value and nature of parent involvement in the city of Abu Dhabi through their perceptions of roles and responsibilities.Design/methodology/approach– The study is conducted in a random purposive sample of Public–Private Partnership schools during Abu Dhabi Education Council’s school reform.Findings– Findings show that while both administrators and parents agree on the value of parental involvement, the perceptions of their own and each others’ roles and responsibilities means that parent involvement is characterized by unfulfilled expectations.Practical implications– Recommendations are made to arrive at realistic roles and responsibilities for parent involvement and recommendations for a model of mutually responsive practice to evolve within a policy framework, with the support of ADEC, and informed by international and locally based research.Originality/value– The paper sheds light on a new educational dimension beyond curricula and instruction.
A new integrated knowledge model in supplier selection
Authors: Akhavan Peyman , Elahi Behin , Jafari Mostafa 
Published: November 2014

Purpose– This paper aims to empirically explore the effects of intellectual capital (IC) on supplier selection (SS) and, consequently, investigates the consecutive impacts on an Asian automotive supply chain performance (SCP).Design/methodology/approach– A questionnaire-oriented survey obtained from top managers and expert employees from three different Asian automotive industries, all of which exist in the same supply chain, was utilized for factor analysis and structural equation modeling (SEM).Findings– The findings indicate that some dimensions of IC containing human capital, relational capital and structural capital sufficiently influence evaluation and selection of optimal suppliers which lead to more efficient performance of the supply chain.Research limitations/implications– First, as the research analyzes the findings extracted from three important Asian automotive companies which exist in the same supply chain, the results may not be applicable to other industries in different countries. Second, gathering data from other elements of the supply chain like wholesalers and retailers could enrich the research conducted. Besides, more advanced statistical methods could be utilized to evaluate the regression equations and SEM.Practical implications– With a comprehensive view on IC that takes into account its creation, protection and utilization, IC plays an essential role in selecting and assessing optimal suppliers which enhance competitive advantage, especially in knowledge-based organizations. IC will also increase the SCP efficiently and effectively.Originality/value– This study develops an integrated knowledge model for a SS issue based on IC, and focuses on the effects of its various elements. It offers assistance to managers who tend to select optimal suppliers effectively.
The effect of perceived price fairness through satisfaction and loyalty on international tourists’ price acceptance of Islamic-Iranian art products
Authors: Asadi Ali , Khazaei Pool Javad , Reza Jalilvand Mohammad 
Published: November 2014

Purpose– The purpose of this paper is to investigate the effect of perceived price fairness through satisfaction and loyalty on price acceptance. The antecedents of price fairness, including price perception and tourist vulnerability, will also be examined.Design/methodology/approach– The authors collected 674 questionnaires from international tourists who purchased Islamic-Iranian art products and analyzed simultaneous relations with a structural equation modeling.Findings– The results indicate that perceived price awareness and perceived vulnerability positively and significantly affect perceived price fairness. Additionally, perceived price fairness has a significant influence on customer satisfaction and loyalty. Moreover, customer satisfaction and loyalty were found to have a positive impact on price acceptance.Practical implications– Based on the findings, the results are expected to create a useful perspective for the researchers so they can present a broader model in future studies. The results of this research can help managers develop better pricing strategies and effective pricing mechanism design and, through recognition of factors influencing customer perception of the price, instigate better pricing.Originality/value– Although prior research focused on the relationships among the variables of perception of price, perceived vulnerability, perceived price fairness, satisfaction and loyalty and price acceptance, the current study considers the effect of these variables as a general compound model and in the context of Islamic-Iranian art tourism products.
Analyzing the results of buildings energy audit by using grey incidence analysis
Authors: Karimi Tooraj , Forrest Jeffrey 
Published: November 2014

Purpose
– The purpose of this paper is to analyse the results of energy audit reports and defines most favourable characteristics of system, which is energy consumption of buildings, and most favourable factors affecting these characteristics in order to modify and improve them.

Design/methodology/approach
– Grey set theory has the advantage of using fewer data to analyse many factors, and it is therefore more appropriate for system study rather than traditional statistical regression which requires massive data, normal distribution in the data and few variant factors. So, in this paper grey clustering and entropy of coefficient vector of grey evaluations are used to analyse energy consumption in buildings of the Oil Ministry in Tehran. Grey clustering in this study has been used for two purposes: First, all the variables of building relate to energy audit cluster in two main groups of indicators and the number of variables is reduced. Second, grey clustering with variable weights has been used to classify all buildings in three categories named “no standard deviation”, “low standard deviation” and “non-standard”. Entropy of coefficient vector of grey evaluations is calculated to investigate greyness of results.

Findings
– According to the results of the model, “the real building load coefficient” has been selected as the most important system characteristic and “uncontrolled area of the building” has been diagnosed as the most favourable factor which has the greatest effect on energy consumption of building.

Research limitations/implications
– Clustering greyness of 13 buildings is less than 0.5 and average uncertainly of clustering results is 66 per cent.

Practical implications
– It shows that among the 38 buildings surveyed in terms of energy consumption, three cases are in standard group, 24 cases are in “low standard deviation” group and 11 buildings are completely non-standard.

Originality/value
– In this research, a comprehensive analysis of the audit reports is proposed. This analysis helps the improvement of future audits, and assists in making energy conservation policies by studying the behaviour of system characteristic and related factors.