bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems Biology for Simulating Patient Physiology During the Postgenomic Era of Medicine
Authors: Schmidt BJ 
Published: March 2014

Systems pharmacology models capable of accurately recapitulating sophisticated patient phenotypes have enabled the investigation of mechanisms responsible for therapeutic efficacy. Although omics data sets are capable of characterizing the operation of subcellular networks, their utility in mechanistically predicting quantitative, clinically accessible outcome measures has been limited. Developing insights into clinical outcomes from omics data sets will benefit from modeling approaches that can integrate molecular networks mechanistically with simulations of patient pathophysiology across compartments and scales.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e106; doi: 10.1038/psp.2014.2; published online 19 March 2014
Higher Prevalence of Autoimmune Diseases and Longer Spells of Vertigo in Patients Affected With Familial Ménière's Disease: A Clinical Comparison of Familial and Sporadic Ménière's Disease
Authors: Hietikko Elina , Sorri Martti , Männikkö Minna , Kotimäki Jouko 
Published: March 2014

Purpose
This study compared clinical features, predisposing factors, and concomitant diseases between sporadic and familial Ménière's disease (MD).

Method

Retrospective chart review and postal questionnaire were used. Participants were 250 definite patients with MD (sporadic,
n
=149; familial,
n
= 101) who fulfilled the American Academy of Otorhinolaryngology–Head and Neck Surgery (1995) criteria.

Results

On average, familial patients were affected 5.6 years earlier than sporadic patients, and they suffered from significantly longer spells of vertigo (
p
= .007). The prevalence of rheumatoid arthritis (
p
= .002) and other autoimmune diseases (
p
= .046) was higher among the familial patients, who also had more migraine (
p
= .036) and hearing impairment (
p
= .002) in their families.

Conclusion
The clinical features of familial and sporadic MD are very similar in general, but some differences do exist. Familial MD patients are affected earlier and suffer from longer spells of vertigo.

Supplemental Material

https://doi.org/10.23641/asha.14963505
Vocal Interaction Between Children With Down Syndrome and Their Parents
Authors: Thiemann-Bourque Kathy S. , Warren Steven F. , Brady Nancy , Gilkerson Jill , Richards Jeffrey A. 
Published: March 2014

Purpose
The purpose of this study was to describe differences in parent input and child vocal behaviors of children with Down syndrome (DS) compared with typically developing (TD) children. The goals were to describe the language learning environments at distinctly different ages in early childhood.

Method
Nine children with DS and 9 age-matched TD children participated; 4 children in each group were ages 9–11 months, and 5 were between 25 and 54 months. Measures were derived from automated vocal analysis. A digital language processor measured the richness of the child's language environment, including number of adult words, conversational turns, and child vocalizations.

Results
Analyses indicated no significant differences in words spoken by parents of younger versus older children with DS and significantly more words spoken by parents of TD children than parents of children with DS. Differences between the DS and TD groups were observed in rates of all vocal behaviors, with no differences noted between the younger versus older children with DS, and the younger TD children did not vocalize significantly more than the younger DS children.

Conclusions
Parents of children with DS continue to provide consistent levels of input across the early language learning years; however, child vocal behaviors remain low after the age of 24 months, suggesting the need for additional and alternative intervention approaches.
Optimal metabolic route search based on atom mappings
Authors: Latendresse Mario , Krummenacker Markus , Karp Peter D. 
Published: March 2014

Abstract
Motivation: A key computational problem in metabolic engineering is finding efficient metabolic routes from a source to a target compound in genome-scale reaction networks, potentially considering the addition of new reactions. Efficiency can be based on many factors, such as route lengths, atoms conserved and the number of new reactions, and the new enzymes to catalyze them, added to the route. Fast algorithms are needed to systematically search these large genome-scale reaction networks.
Results: We present the algorithm used in the new RouteSearch tool within the Pathway Tools software. This algorithm is based on a general Branch-and-Bound search and involves constructing a network of atom mappings to facilitate efficient searching. As far as we know, it is the first published algorithm that finds guaranteed optimal routes where atom conservation is part of the optimality criteria. RouteSearch includes a graphical user interface that speeds user understanding of its search results. We evaluated the algorithm on five example metabolic-engineering problems from the literature; for one problem the published solution was equivalent to the optimal route found by RouteSearch; for the remaining four problems, RouteSearch found the published solution as one of its best-scored solutions. These problems were each solved in less than 5 s of computational time.
Availability and implementation: RouteSearch is accessible at BioCyc.org by using the menu command RouteSearch and by downloading Pathway Tools. Pathway Tools software is freely available to academic users, and for a fee to commercial users. Download from: http://biocyc.org/download.shtml .
Contact: mario.latendresse@sri.com
Supplementary information: Supplementary data are available at Bioinformatics online.
KAnalyze: a fast versatile pipelined K-mer toolkit
Authors: Audano Peter , Vannberg Fredrik 
Published: March 2014

Abstract
Motivation : Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language.
Results : As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes.
Availability and implementation : KAnalyze is available on SourceForge:
https://sourceforge.net/projects/kanalyze/
Contact: fredrik.vannberg@biology.gatech.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
Cardiac Arrest during Hospitalization for Delivery in the United States, 1998–2011
Authors: Mhyre Jill M. , Tsen Lawrence C. , Einav Sharon , Kuklina Elena V. , Leffert Lisa R. , Bateman Brian T. 
Published: March 2014

Abstract

Background:
The objective of this analysis was to evaluate the frequency, distribution of potential etiologies, and survival rates of maternal cardiopulmonary arrest during the hospitalization for delivery in the United States.

Methods:
By using data from the Nationwide Inpatient Sample during the years 1998 through 2011, the authors obtained weighted estimates of the number of U.S. hospitalizations for delivery complicated by maternal cardiac arrest. Clinical and demographic risk factors, potential etiologies, and outcomes were identified and compared in women with and without cardiac arrest. The authors tested for temporal trends in the occurrence and survival associated with maternal arrest.

Results:
Cardiac arrest complicated 1 in 12,000 or 8.5 per 100,000 hospitalizations for delivery (99% CI, 7.7 to 9.3 per 100,000). The most common potential etiologies of arrest included hemorrhage, heart failure, amniotic fluid embolism, and sepsis. Among patients with cardiac arrest, 58.9% of patients (99% CI, 54.8 to 63.0%) survived to hospital discharge.

Conclusions:
Approximately 1 in 12,000 hospitalizations for delivery is complicated by cardiac arrest, most frequently due to hemorrhage, heart failure, amniotic fluid embolism, or sepsis. Survival depends on the underlying etiology of arrest.
Role of Vitamin D in Children With Hepatosteatosis
Authors: Yildiz Ismail , Erol Oguz B. , Toprak Sadik , Cantez Mustafa S. , Omer Beyhan , Kilic Ayse , Oguz Fatma , Uysalol Metin , Yekeler Ensar , Unuvar Emin 
Published: March 2014

ABSTRACTBackground:The increasing incidence of obesity in children is a significant risk factor for nonalcoholic fatty liver disease and obesity‐associated morbidity. Vitamin D has a major role in bone mineral metabolism and has antimicrobial, antioxidant properties. In this study we aimed to investigate the role of vitamin D in children with obesity with hepatosteatosis.Methods:A total of 101 children with obesity were included in this study. Hepatosteatosis was diagnosed and graded using ultrasonography. Serum levels of 25‐hydroxyvitamin D (25‐(OH) vitamin D), calcium, phosphate, alkaline phosphatase, and parathormone were tested. Two‐sided t test and Pearson χ2 tests were used for the relation between vitamin D and hepatosteatosis.Results:In our study group, 45.5% were girls (n = 46) and the mean age was 11.5 ± 2.8 years (range 3–17 years). Hepatosteatosis was identified in 58 children (57.4%). The diagnosis of grade 1 and grade 2 hepatosteatosis was made in 41 (40.6%) and 17 (16.8%) children, respectively. Median serum 25‐(OH) vitamin D levels in children without hepatosteatosis was 16.4 ng/mL (interquartile range 12.4–24.8 ng/mL), whereas children with grade 1 and grade 2 hepatosteatosis had 25‐(OH) vitamin D levels of 14.2 ng/mL (interquartile range 9.5–21.2 ng/mL) and 11.5 ng/mL (interquartile range 7.5–16.7 ng/mL), respectively (P = 0.005). There was a positive correlation between insulin resistance and the grade of hepatosteatosis (P = 0.03).Conclusions:Serum vitamin D levels in children with obesity with hepatosteatosis are significantly lower than vitamin D levels in children with obesity without hepatosteatosis. In this observational study we only refer to the association of vitamin D deficiency/insufficiency with hepatosteatosis.
Prospective Assessment of Inpatient Boxed Warning Prescriber Adherence
Authors: Kloet Megan A. , Lohr Brian R. , Smithburger Pamela L. , Seybert Amy L. , Kane-Gill Sandra L. 
Published: March 2014

Objective
To evaluate medication boxed warning nonadherence in the inpatient setting.

Methods
This was a prospective cohort quality improvement project approved by our institution’s Total Quality Council. General medicine and ICU patients 18 years and older were included if they were cared for by a prescriber-led multidisciplinary team that included a pharmacist. Patients were evaluated for medication orders with an actionable boxed warning; if boxed warning nonadherence occurred, the physician’s reason was determined. Patients with boxed warning nonadherence were monitored for adverse drug reactions until discharge.

Results
A total of 393 patients (224 general medicine and 169 ICU) were evaluated for nonadherence to 149 actionable boxed warnings. There were 293 drugs (175 general medicine and 118 ICU) with boxed warnings prescribed, and more than 50% of these were medications restarted from home. A total of 23 boxed warning nonadherences occurred in general medicine patients, and NSAIDs accounted for 81% of these events. ICU patients experienced 11 boxed warning nonadherences, with nearly 54% from anti-infectives and immunosuppressants. Antipsychotics were the most commonly ordered boxed warning medication class in ICU patients. Reasons for nonadherence included knowledge deficit and an acceptable risk-to-benefit ratio. Two adverse drug reactions occurred from boxed warning nonadherences, both because of a drug-drug interaction.

Conclusions
Boxed warning nonadherence is a concern in the inpatient setting, specifically with NSAID use in general medicine patients and antipsychotic use in ICU patients. More than half of boxed warning nonadherence occurred in medications restarted from home, which emphasizes the need for medication evaluation during transitions of care.
Comparison of practitioners' views on managing equity investments
Authors: Prorokowski Lukasz , Roszkowska Paulina 
Published: March 2014

Purpose
– The purpose of this paper is to examine the extent to which Central European emerging stock markets (focusing on Poland) have been affected by the recent international financial crisis, and how the current investment climate (barriers, risks, challenges and opportunities) influences appetite for investments in Polish equities. In doing so, the study aims to report timely findings in relation to the determinants of the safety and profitability of international portfolio diversification to the Polish stock market.

Design/methodology/approach
– Based on qualitative empirical research, the authors analyse the differences between the foreign (UK) and domestic (Poland) investors' views on equity investments in Poland. The study builds on questionnaires and interviews with practitioners associated with the Polish stock market.

Findings
– The authors report that the global financial crisis influenced changes to domestic and international investors' appetite for risk related to equity investments in emerging stock markets: investors are more prudent about emerging markets but the Polish stock market has shown substantial growth potential and positively distinguished itself from other Central European stock exchanges; particular types of investment risks associated with equity investments in the Polish stock market have abated. Polish equities are an attractive component of the international portfolio diversification, provided that trading strategies are adjusted to the contemporary investment environment.

Originality/value
– This paper addresses the absence of the academic literature devoted to the analysis of equity investments in the contemporary Central European emerging stock markets. The authors discuss the differences in appetite for risk between the UK and Polish investors and assumptions about investments in Poland. The authors also contribute to the international debate on investor protection and regulations that can improve investment processes.
The effect of an MBA on the development of women's management competencies
Authors: Lämsä Anna-Maija , Savela Terttu 
Published: March 2014

Purpose
– This article aims to report the findings of a study of the effect of a women's Master of Business Administration (MBA) programme in Finland called the femaleMBA on the development of women's management competencies. The gendered nature of the competency development was also analyzed.

Design/methodology/approach
– A qualitative interview study was conducted with 20 women who completed the programme. Content analysis was used to analyze the data.

Findings
– In addition to improving the women's business competencies and their mastery of management language, the programme contributed to the creation of a clearer managerial identity, greater assertiveness, and increased credibility in a managerial role. The development of management competencies was shown to be gendered in varying ways. An all-women learning environment was experienced as a safe and supportive social context for development.

Research limitations/implications
– Only a specifically women's MBA was studied. The topic should also be studied in a mixed MBA group.

Practical implications
– MBAs should pay systematic attention to the informal and social learning context. A combination of “masculinity” and “femininity” might be worth taking into consideration when all-women management development programmes are planned and conducted. This study suggests that an all-women group in an MBA has the potential to challenge and even transform participants' ideas and assumptions about the dominance of masculinity in management and to increase their understanding of the importance of femininity in management.

Originality/value
– A gender angle on research into management development and particularly MBAs is very rare. This study shed light on the topic by showing that competency development in MBAs is not, as is often assumed, gender neutral but gendered.
The role of dialogue between executives and ground-level employees mediated by MACS
Authors: Pärl Ülle 
Published: March 2014

Purpose– The purpose is to understand the manner in which companies use management accounting and control systems (MACS) for dialogical communication in assisting collaboration and the coordination of actions. The task of the research is to answer the following questions: why is it important to support dialogical communication by MACS in the organisation? Who are the salient stakeholder(s) in a company implementing collaboration and cooperation? How does one analyse and understand the role of MACS as a medium for supporting dialogical communication? Which aspects of dialogical communication are (not) fulfilled in the implementation of MACS and why?Design/methodology/approach– This study's philosophical assumptions are based on relational constructivism as a social science perspective. This study uses a participative action and observation case study as its methodology.Findings– Based on this case study, it can be concluded that most of the assumptions that dialogue could take place were fulfilled in departments in need of changes for competition and economic reasons. In the departments that did not need changes, assumptions of mutual openness, mutual confirmation and non-manipulation were not fulfilled – information from MACS was hidden and censored. The open dialogue by MACS between ground and senior groups was prevented resulting in a lack of information on different practices at the organisational level. One assumption that was problematic even in departments in need of changes was the assumption of non-evaluation. There is a paradox or contradiction between the contemporary business environment needing innovativeness and creativity, which means free and open communication without evaluation, and the coordination and control function which is a common part of MACS.Research limitations/implications– In this study, the data collection, documentation and analysis were carefully conducted and several methods applied to deal with possible bias. Nevertheless, the problem of the observer bias cannot be entirely eliminated since an individual researcher can never be separated from his or her background, philosophical views and experiences.Practical implications– The paper makes a strong practical contribution. Based on this case study, it has been demonstrated that MACS could be a medium to support dialogue between senior and ground levels if: senior management sees the need for dialogue between organisational members; management and other organisational members support and believe in dialogue which could be mediated by MACS.Originality/value– The conceptual novelty of the research lies in tying the concept of dialogue in the environment of stakeholder capitalism with the MACS framework. The contribution of this research is to shed more light on the role of MACS as one option of mediums for supporting dialogue between top and ground-level managers.
A review of enabling factors in construction industry productivity in an Australian environment
Authors: Hughes Rami , Thorpe David 
Published: March 2014

Purpose
– The purpose of the research discussed in this paper is to ascertain the perception, from the project manager's viewpoint, of factors affecting construction productivity in the State of Queensland, Australia.

Design/methodology/approach
– The research was conducted by a structured questionnaire that was sent to 89 randomly selected construction project managers in Queensland, Australia. This questionnaire requested background information about the respondents and then sought a score, using a 0-4 Likert scale, from each of them with respect to the importance of 47 factors identified from the literature that were considered likely to affect construction productivity. The factors were stratified into primary factors and secondary factors contributing to three of the primary factors. There were 36 responses. These factors were rated by the respondents and then ranked using a relative importance index approach.

Findings
– The research evaluated the relative importance of the primary factors with respect to their effect on construction productivity. The 15 highest ranking factors are discussed. Three factors – rework, poor supervisor competency, and incomplete drawings – were ranked as having a strong effect on construction productivity. There was also an analysis of the secondary factors in relation to three of the primary factors.

Research limitations/implications
– The research focused on the State of Queensland in Australia. It had a response rate of 40 per cent. It provides insight into the factors affecting productivity on construction projects in Australia. Further research to investigate the identified factors in depth, using targeted interviews of expert project management professionals, is currently being undertaken.

Practical implications
– The construction industry can use the findings in this paper as a basis for improving the productivity of construction projects.

Originality/value
– This research is original research, which has highlighted a number of key areas of which construction productivity can be improved.
Aspects of project learning in construction: a socio-technical model
Authors: Mohammed Alashwal Ali , Abdul-Rahman Hamzah 
Published: March 2014

Purpose
– The purpose of this paper is to determine the measurement constructs of learning within construction projects' milieu. The literature indicated some mechanisms of learning in projects under four aspects, namely knowledge sharing, knowledge creation, team action to learn, and learning support. The empirical study attempts to verify whether intra-project learning can be measured through these aspects.

Design/methodology/approach
– The study used a survey method to collect the data from 36 mega-sized building projects in Malaysia. In total, 203 questionnaires were collected from professionals working in the sites of these projects. The data were analysed using principal component analysis (PCA) to determine the constructs of intra-project learning. Partial least squares-path modeling was used then to confirm the results of PCA and determine the contribution of each construct to intra-project learning.

Findings
– The results affirmed two constructs of intra-project learning, named, social and technical and each consisted of four indicators of learning.

Originality/value
– The paper emphasized the socio-technical perspective of learning and contributed to developing a hierarchical measurement model of learning in construction project. A project manager can propose new initiatives in response to the new perspective of learning for team building and continuous development. Lastly, the paper provides a comprehensive presentation of how to estimate the hierarchical measurement models of project learning as a latent variable.