bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ruffus: a lightweight Python library for computational pipelines
Authors: Goodstadt Leo 
Published: September 2010

Abstract
Summary: Computational pipelines are common place in scientific research. However, most of the resources for constructing pipelines are heavyweight systems with graphical user interfaces. Ruffus is a library for the creation of computational pipelines. Its lightweight and unobtrusive design recommends it for use even for the most trivial of analyses. At the same time, it is powerful enough to have been used for complex workflows involving more than 50 interdependent stages.
Availability and implementation: Ruffus is written in python. Source code, a short tutorial, examples and a comprehensive user manual are freely available at http://www.ruffus.org.uk. The example program is available at http://www.ruffus.org.uk/examples/bioinformatics
Contact: ruffus@llew.org.uk
Spatial quantification and classification of skin response following perturbation using organotypic skin cultures
Authors: Pommerencke Thora , Westphal Kathi , Ernst Claudia , Safferling Kai , Dickhaus Hartmut , Steinberg Thorsten , Tomakidi Pascal , Grabe Niels 
Published: September 2010

AbstractMotivation: For a mechanistic understanding of skin and its response to an induced perturbation, systems biology is gaining increasing attention. Unfortunately, quantitative and spatial expression data for skin, like for most other tissues, are almost not available.Results: Integrating organotypic skin cultures, whole-slide scanning and subsequent image processing provides bioinformatics with a novel source of spatial expression data. We here used this approach to quantitatively describe the effect of treating organotypic skin cultures with sodium dodecyl sulphate in a non-corrosive concentration. We first measured the differentiation-related spatial expression gradient of Heat-Shock-Protein 27 in a time series of up to 24 h. Secondly, a multi-dimensional tissue classifier for predicting skin irritation was developed based on abstract features of these profiles. We obtained a high specificity of 0.94 and a sensitivity of 0.92 compared with manual classification. Our results demonstrate that the integration of tissue cultures, whole-slide scanning and image processing is well suited for both the standardized data acquisition for systems biological tissue models and a highly robust classification of tissue responses.Contact: niels.grabe@bioquant.uni-heidelberg.deSupplementary information: Supplementary data are available at Bioinformatics online.
The comparative morphology of the wings and axillae of selected Heteroptera
Authors: Betts C. R. 
Published: September 2010

The wings of selected species are here treated as functional deformable aerofoils and their morphology described with this in mind. A novel type of non‐tubular vein structure in the forewing and hindwing membranes, a ‘channel vein’, is described. The presence of small, cuticular membrane thickenings in the hindwing is recorded and their possible functions are discussed.A comparative account of the structure and musculature of the axillae is presented with a view in particular to clarifying some of the associated terminology.A mechanism for wing folding is described and previously unrecorded adaptations for this purpose seen inNotonectaare described and discussed.
A taxonomic revision of cuscuses allied to Phalanger orientalis (Marsupialia: Phalangeridae)
Authors: MENZIES J. I. , PERNETTA J. C. 
Published: September 2010

A computer‐assisted discriminant analysis programme using a set of metric skull characters in a large number of specimens of cuscuses of the Phulnnger orientalis group was used to distinguish between species and subspecies. Non‐metric characters were used to support conclusions.Results indicated that several taxa which had customarily been included in the widespread species orientalis were not closely related to that species. The programme also identified the components of the long‐haired mountain cuscus group and we show that the holotype of one species, vestitus, appears to be unrelated to the widespread species with which it has been associated since Tate's revision of 1945. Finally we were able to demonstrate the presence of 10 distinct species in the orientalis group (of which one is described as new) and 12 subspecies (of which three are described as new).The same suite of metric and non‐metric characters allowed construction of dendrograms indicating possible relationships between the various sub‐groups and their component species. We speculate on the evolution of this group of cuscuses in New Guinea and their spread to other islands in the region.We recount what is known about cuscus biology and provide means for identification.
Clinicopathological significance of sentinel node biopsy in Japanese patients with cutaneous malignant melanoma
Authors: NORO Sachiko , YAMAZAKI Naoya , NAKANISHI Yukihiro , YAMAMOTO Akifumi , SASAJIMA Yuko , KAWANA Seiji 
Published: September 2010

AbstractSentinel node biopsy (SNB) for malignant melanoma began to be performed in our department in 1997. A total of 121 patients underwent SNB. Sentinel node (SN) were identified in 39 (83.0%) of the 47 cases in which the blue dye method alone was used, and in 71 (95.9%) of the 74 cases by combination of dye, radioisotope, and γ probe methods. The excised SN was cut through its longest meridian, and the cut surfaces were stained with hematoxylin and eosin (HE) and examined for the presence (SN+) or absence (SN−) of melanoma cells. If no melanoma cells were detected, serial sections were prepared and examined by sequential staining with HE, for S‐100 protein, with HE, for HMB‐45, with HE, and for Melan‐A. In this study minute metastasis (SNm+) was defined as tumor cells newly identified in the immunostained section. The thickness of tumors ranged 0–38.0 mm, and their mean thickness was 4.5 mm. There were 39 SN+ cases (39/110 [39 + 71]; 35.5%) and seven SNm+ cases (7/110 [39 + 71]; 6.4%). The 5‐year survival rate was significantly higher in the SN− group than in the SN+ group and SNm+ group combined (P = 0.0002). The survival rate of the SNm+ group was not significantly different from that of the SN+ group (P = 0.3848). The 5‐year survival rate of the SN+ group and SNm+ group combined was significantly higher than that of the group with clinically unequivocal metastatic nodes (P = 0.0001). Accurate SNB results will provide important prognostic information for Japanese patients with melanoma.
Electronic health records: which practices have them, and how are clinicians using them?
Authors: Simon Steven R. , McCarthy Madeline L. , Kaushal Rainu , Jenter Chelsea A. , Volk Lynn A. , Poon Eric G. , Yee Kevin C. , Orav E. John , Williams Deborah H. , Bates David W. 
Published: September 2010

AbstractBackground  Limited data exist to estimate the use of electronic health records (EHRs) in ambulatory care practices in the United States.Methods  We surveyed a stratified random sample of 1829 office practices in Massachusetts in 2005. The one‐page survey measured use of health information technology, plans for EHR adoption and perceived barriers to adoption.Results  A total of 847 surveys were returned, for a response rate of 46%. Overall, 18% of office practices reported having an EHR. Primary‐care‐only and mixed practices reported similar adoption rates (23% and 25%, respectively, P = 0.70). The adoption rate in specialty practices (14%) was lower compared with both primary‐care‐only (P < 0.01) and mixed (P < 0.05) practices. The number of clinicians in the practice strongly correlated with EHR adoption (P < 0.001), with fewer small practices adopting EHRs. Among practices that have EHRs with laboratory and radiology result retrieval capabilities, at least 87% of practices report that a majority of their clinicians actively use these functionalities, while 74% of practices with electronic decision support report that the majority of clinicians actively use it. Among the practices without an EHR, 13% plan to implement one within the next 12 months, 24% within the next 1–2 years, 11% within the next 3–5 years, and 52% reported having no plans to implement an EHR in the foreseeable future. The most frequently reported barrier to implementation was lack of adequate funding (42%).Conclusions  Overall, fewer than 1 in 5 medical practices in Massachusetts have an EHR. Even among adopters, though, doctor usage of EHR functions varied considerably by functionality and across practices. Many clinicians are not actively using functionalities that are necessary to improve health care quality and patient safety. Furthermore, among practices that do not have EHRs, more than half have no plan for adoption. Inadequate funding remains an important barrier to EHR adoption in ambulatory care practices in the United States.
Audit of health promotion practice within a UK hospital: results of a pilot study
Authors: Haynes Charlotte L. , Cook Gary A. 
Published: September 2010

AbstractIntroduction and aim  There is clear evidence that modifiable risk factors – smoking, alcohol misuse, poor diet, lack of exercise and obesity – are detrimental to health. UK public health policy now requires hospitals to have in‐place health promotion programmes to empower patients to swap risky for healthy behaviours. This audit aimed to determine a baseline level of health promotion practice for modifiable risk factors in a UK hospital.Method  Case notes from two hundred and fifty hospitalized adult patients (excluding all terminally ill patients), discharged alive between January and June 2004, were audited for evidence of screening for risk factors (smoking, alcohol, diet, exercise and obesity) and the provision of health promotion to change these risk behaviours.Results  The majority of inpatients were asked about smoking (88%) and alcohol consumption (74%), but few were screened for obesity (18%) or asked about their normal diet (5%) and physical activity (3%). Health promotion was delivered to a third of smokers and over half of inpatients reporting misuse of alcohol. Healthy diets, exercise and weight management were rarely discussed. Only three inpatients were screened for all risk factors.Conclusion  This study indicates that the majority of hospital inpatients were screened for smoking and alcohol use, but improvements need to be made in the delivery of health promotion for smoking cessation and sensible drinking. It is clear that inpatients’ are not routinely screened for diet, exercise and weight status, nor delivered health promotion for the management of these risk behaviours.
Accuracy assessment of prediction in patient outcomes
Authors: Bartfay Emma , Bartfay Wally J. 
Published: September 2010

AbstractIn order to provide effective health care to patients, clinicians must rely on their ability to accurately diagnose disease and to prognosticate the outcomes. Prognostic studies have received considerable attention in health science and medicine in relation to patient outcomes. However, little effort has been spent on evaluating prognostic accuracy. The purpose of this paper is to present a comprehensive review of the methods for assessing prognostic accuracy in patient outcome prediction. The strengths and limitations of these approaches are critically appraised. We argue that we need to consider incorporating accuracy assessment for predicting patient outcomes both in clinical practice and in research.
Measuring patient assessments of the quality of outpatient care: a systematic review
Authors: Säilä Tiina , Mattila Elina , Kaila Minna , Aalto Pirjo , Kaunonen Marja 
Published: September 2010

AbstractRationale, aims and objectives  The aim of the study was to answer three questions: first, what methods have been used to measure patient assessments of the quality of care? Second, how do outpatients rate their care? And third, what needs to be taken into account in measuring patient assessments of the quality of care?Methods  Systematic review of the literature. Electronic searches were conducted on Medline, CINAHL and the Cochrane Database of Systematic Reviews. To be included, articles were to deal with patients’ assessments of health care in ambulatory units for somatic adult patients. They were to have been published between January 2000 and May 2005, written in English, Swedish or Finnish with an English abstract, and the research was to have been conducted in Europe. The search terms used were: ambulatory care, ambulatory care facilities, outpatient, outpatients, patient satisfaction and quality of health care. The articles were screened by two independent reviewers in three phases.Results  Thirty‐five articles were included. The quality of care was measured using both quantitative and qualitative methods. Only a few studies relied on the single criterion of patient satisfaction for quality measurements. It is easy to identify common sources of dissatisfaction in different studies. Sources of satisfaction are more closely dependent on the target population, the context and research design.Conclusion  Patient satisfaction is widely used as one indicator among others in assessing the quality of outpatient care. However, there is no single, universally accepted method for measuring this.
The case‐mix of chronic illness hospitalization rates in a managed care population: implications for health management programmes
Authors: Linden Ariel , Goldberg Steven 
Published: September 2010

AbstractObjective  This paper reports on the case‐mix of hospitalized patients based on their health plan enrolment and utilization experience, absent a health management (HM) programme. The implications for achieving targeted reductions in admissions within the context of implementing a population HM programme are discussed.Study design  Descriptive.Methods  Members were identified with asthma, coronary artery disease, congestive heart failure and diabetes. These cohorts were then mapped to disease‐specific hospitalizations across a 2‐year period (2004–2005). Four distinct case‐mix categories were developed. Group 1 comprised members hospitalized for the specific condition in both years. Group 2 comprised all identified members of a disease cohort in 2004 that were not hospitalized in that year but were admitted for the condition in 2005. Members were assigned to Group 3 if they were hospitalized in 2005, did not appear in the 2004 identified cohort but were, in fact, enrolled in the health plan. Group 4 comprised new health plan enrollees in 2005 and were subsequently hospitalized during that year.Results  Of the total admissions in 2005, on average 6.4% came from Group 1, 62.4% came from group 2, 10% from group 3 and 21.2% from Group 4.Conclusions  If an HM programme was to be implemented in this population, the typical identification methods currently used by the industry would have resulted in most hospitalized patients either being initially classified as low risk or going undetected. Improving identification and stratification methods will allow HM programmes to better tailor interventions to impact hospitalization rates for the chronically ill.
Evidence‐based medicine beyond the bedside: keeping an eye on context
Authors: Tilburt Jon C. 
Published: September 2010

Abstract
Rationale  Evidence‐based medicine is being applied to decisions in a range of contexts beyond one‐to‐one patient care. Yet considerable disagreement persists regarding the defining components of evidence‐based decision‐making, particularly in institutional and public health contexts.
Aims and Objectives  This article reviews the key elements of evidence‐based decision‐making for clinical medicine, and adapts those key elements and argues for their broad applicability to a variety of decision‐making contexts including institutional, public health, and self‐care decision‐making contexts.
Methods  Conceptual Analysis.
Results  Evidence based decision‐making involves research evidence, “social and institutional circumstances”, and “values” of stakeholders. Furthermore, evidence‐based decision‐making includes “judgment” exercised by experts to appropriately weigh and integrate the various decision‐making elements.
Conclusion  Asking critical questions about the purposes and context of a specific decision, basic principles of evidence‐based reasoning can be appropriately applied beyond the bedside.
Translating psoriasis treatment guidelines into clinical practice – the need for educational interventions and strategies for broad dissemination
Authors: Nast Alexander , Erdmann Ricardo , Pathirana Delano , Rzany Berthold 
Published: September 2010

Abstract
Rationale  Evidence‐based guidelines can make a substantial contribution to improving medical care. However, it is important to ensure that guidelines are: (1) developed in areas in which they are needed the most; and (2) translated effectively into everyday clinical practice.
Objectives  To evaluate the need for guidelines in the treatment of psoriasis vulgaris, the success of the dissemination activities undertaken to date, and the potential benefits of educational interventions in encouraging guideline compliance.
Methods  All dermatologists working in the Berlin‐Brandenburg region of Germany were invited to attend a workshop on the psoriasis treatment guidelines. Participants could take part in a survey examining the general need for psoriasis guidelines and the success of previous dissemination activities.
Results  A total of 42% of survey participants had not received a copy of the guidelines prior to the workshop. Of those who had received a copy, only 15% had studied the guidelines in detail. In total, 76% of survey participants felt that physicians' low levels of confidence in administering systemic treatments had resulted in these treatment options being used less frequently than they should. Seventy‐nine per cent of survey participants believed that the guidelines would be helpful in improving physicians' confidence and ultimately lead to an increased use of systemic treatments.
Conclusion  The results of the present study indicate that there is a great need for guidelines on the treatment of psoriasis vulgaris in Germany, especially in light of dermatologists' low levels of confidence administering systemic treatments. Strategies for broad dissemination are essential for proper guideline implementation.
Interpretation of tests of heterogeneity and bias in meta‐analysis
Authors: Ioannidis John P. A. 
Published: September 2010

AbstractStatistical tests of heterogeneity and bias, in particular publication bias, are very popular in meta‐analyses. These tests use statistical approaches whose limitations are often not recognized. Moreover, it is often implied with inappropriate confidence that these tests can provide reliable answers to questions that in essence are not of statistical nature. Statistical heterogeneity is only a correlate of clinical and pragmatic heterogeneity and the correlation may sometimes be weak. Similarly, statistical signals may hint to bias, but seen in isolation they cannot fully prove or disprove bias in general, let alone specific causes of bias, such as publication bias in particular. Both false‐positive and false‐negative signals of heterogeneity and bias can be common and their prevalence may be anticipated based on some rational considerations. Here I discuss the major common challenges and flaws that emerge in using and interpreting statistical tests of heterogeneity and bias in meta‐analyses. I discuss misinterpretations that can occur at the level of statistical inference, clinical/pragmatic inference and specific cause attribution. Suggestions are made on how to avoid these flaws, use these tests properly and learn from them.
User‐driven health care: answering multidimensional information needs in individual patients utilizing post–EBM approaches: an operational model
Authors: Biswas Rakesh , Maniam Jayanthy , Lee Edwin Wen Huo , Gopal Premalatha , Umakanth Shashikiran , Dahiya Sumit , Ahmed Sayeed 
Published: September 2010

AbstractThe hypothesis in the conceptual model was that a user‐driven innovation in presently available information and communication technology infrastructure would be able to meet patient and health professional users information needs and help them attain better health outcomes. An operational model was created to plan a trial on a sample diabetic population utilizing a randomized control trial design, assigning one randomly selected group of diabetics to receive electronic information intervention and analyse if it would improve their health outcomes in comparison with a matched diabetic population who would only receive regular medical intervention. Diabetes was chosen for this particular trial, as it is a major chronic illness in Malaysia as elsewhere in the world.It is in essence a position paper for how the study concept should be organized to stimulate wider discussion prior to beginning the study.
Meta‐analysis of repeated measures study designs
Authors: Peters Jaime L. , Mengersen Kerrie L. 
Published: September 2010

Abstract
Rationale, aims and objectives  Repeated measures studies are found in many areas of research, particularly in areas of healthcare. There is currently little information available to inform the method of meta‐analysis of repeated measures studies so that the structural dependence of the data is appropriately accommodated and the findings are meaningful.
Method  Using a published meta‐analysis on the impact of diet advice on weight reduction of obese or overweight individuals, we demonstrate possible approaches for repeated measures meta‐analysis. These approaches differ in terms of the type of result obtained (e.g. effect at a particular time‐point, trend over time, change between time‐points) and the data needed for the analysis (e.g. means, regression slope estimates). Some approaches involve violating assumptions of independence in the data structure and so to investigate the impact of this violation a simulation study is carried out.
Results  The different approaches described for the meta‐analyses of repeated measures studies can all provide useful effect estimates depending on the question to be addressed by the meta‐analysis. However, violation of the independence assumption in some approaches can lead to biased estimates.
Conclusions  In practice, the methods available to carry out meta‐analyses of repeated measures studies will not only depend upon the question of interest, but also on the data available from the primary studies.
The effectiveness of clinical guideline implementation strategies – a synthesis of systematic review findings
Authors: Prior Mathew , Guerin Michelle , Grimmer‐Somers Karen 
Published: September 2010

Abstract
Objective  To establish the effectiveness of clinical guideline implementation strategies.
Data sources/study setting  Systematic reviews in full text, English language, 1987–2007, reporting any measure of clinical process change or cost–benefit analysis.
Study design  Overview of secondary evidence
Data collection/extraction methods  Independent critical appraisal using AMSTAR, primary author undertaking all data extraction using a purpose‐built form.
Principal findings  We identified 144 potential papers, from which 33 systematic reviews were included. These reflected 714 primary studies involving 22 512 clinicians, in a range of health care settings. Implementation strategies were varied, rarely comparable, with variable outcomes. Effective implementation strategies included multifaceted interventions, interactive education and clinical reminder systems. Didactic education and passive dissemination strategies were ineffective. Cost‐effectiveness studies were rare.
Conclusions  Successful guideline implementation strategies should be multifaceted, and actively engage clinicians throughout the process.