bluuebunny/crossref_metadata_2025_split huggingface dataset:
New intravascular contrast agent applied to dynamic contrast enhanced MR imaging of human breast cancer
Authors: Rydland J. , Bjørnerud A. , Haugen O. , Torheim G. , Torres C. , Kvistad K. A. , Haraldseth O. 
Published: December 2009

Purpose: To evaluate the feasibility of using dynamic contrast-enhanced MR imaging with a new intravascular contrast agent in grading human breast cancer. Material and Methods: 23 patients with 27 breast tumors (21 carcinomas and 6 fibroadenomas) were examined with dynamic MR imaging after administration of Clariscan, an iron oxide nanoparticle with large T1 relaxivity and a long plasma half life. A 3D T1-weighted gradient echo sequence with an acquisition time of 60 s was repeated at regular intervals of 3–5 min before and up to 1 h after injection of 2 mg/kg b.w. of Clariscan. The endothelial transfer constant, Kps, which reflects overall vascular permeability, and the fractional plasma volume, fPV, were estimated from time-intensity curves acquired from three separate regions of interest (ROIs): whole tumor, a permeability hot spot, and a blood volume hot spot. Kps and fPV were compared to the results of histologic tumor grading (Scarff-Bloom-Richardson, SBR) and microvascular density, MVD. Results: A statistically significant correlation between the MR-derived Kps parameters and the SBR score was obtained for the whole tumor ROI ( R = 0.70), and for the permeability hot spot ROIs ( R = 0.67). A correlation between fPV and SBR was detected for the blood volume hot spot ROIs ( R = 0.48). There was no statistically significant correlation between Kps or fPV with MVD. Conclusion: The results support the hypothesis that dynamic MR with the intravascular contrast agent Clariscan may be used for non-invasive tumor grading.
Model studies on acetabular component migration in total hip arthroplasty using CT and a semiautomated program for volume merging
Authors: Olivecrona L. , Olivecrona H. , Weidenhielm L. , Noz M. E. , Maguire G. Q. , Zeleznik M. P. 
Published: December 2009

Purpose: Validation of a non-invasive CT method for detection of acetabular cup migration after total hip arthroplasty in a phantom study. Material and Methods: 26 CT examinations were obtained of a pelvic model while altering the position of the acetabular cup. Using a previously described program for volume merging, the pelvi in different examinations were fused and the 3D alterations of the position of the acetabular cup were evaluated visually and numerically and correlated to direct measurements on the model. Results: Visually, two independent examiners differentiated between 0, 1 and 2 to 3 mm migration with 100% specificity and sensitivity. Numerically, the mean error over all cases between model and CT measurements was 0.04 mm (SD ± 0.33). The mean absolute error between model and CT data was 0.26 mm (SD ± 0.19). Intra- and interobserver 95% accuracy and repeatability limits were below 0.5/0.7 mm, respectively. No significant interobserver difference occurred. The data were normally distributed and not dependent on observer. Conclusion: The accuracy of this non-invasive method out-performs routine plain radiography. The method gives both visual and numerical correlates to migration and can be used in clinical practice.
Value of air trapping in detection of small airways disease in smokers
Authors: Vikgren J. , Bake B. , Ekberg-Jansson A. , Larsson S. , Tylén U. 
Published: December 2009

Purpose: To test the hypothesis that diffuse and/or focal air trapping are sensitive indicators of airflow obstruction in smoker's small airways disease, when age, gender and presence of emphysematous lesions were allowed for. Material and Methods: Fifty-eight smokers and 34 never smokers, recruited from a randomized population study of men born in 1933, were investigated by HRCT and by extended pulmonary function tests, including a sensitive test for small airways disease (N2 slope). Diffuse air trapping was evaluated by calculating a quotient of mean lung density at expiration and inspiration. Focal air trapping was scored visually by consensus. Results: Diffuse air trapping did not differ between non-emphysematous smokers and never smokers. Furthermore, diffuse air trapping correlated well to the quotient between the residual volume and total lung capacity (RV/TLC, p = 0.01) and was consequently higher in emphysematous smokers than in never smokers. Focal air trapping was found as frequently in smokers without emphysema as in never smokers. Smokers with emphysema showed significantly less focal air trapping. Neither the N2 slope nor any of the other lung function variables differed between those with and without focal air trapping among non-emphysematous smokers. Conclusion: Neither diffuse nor focal air trapping are sensitive indicators of smoker's small airways disease.
Diffusion-weighted imaging in hyperacute stroke – gold standard?
Authors: Wong Y.-Y. , Lam W. W.-M. 
Published: December 2009

Diffusion-weighted imaging (DWI) is more sensitive than CT and conventional T2-weighted MR imaging in the detection of early cerebral ischemia and infarction. In this case report, we present a case of a 79-year-old woman with symptoms of acute stroke, clinically and radiologically documented progression to complete stroke with an initial negative diffusion-weighted scan.
Clinical diagnostic and intervention studies of children with semantic—pragmatic language disorder
Authors: Adams Catherine 
Published: December 2009

AbstractThe diagnosis of semantic—pragmatic language disorder (SPLD) has been the subject of a number of research studies over the last two decades. Classification and diagnostic debates, while illuminating, have done little to develop tools to improve services to these children. In this paper, two children whose communication difficulties are suggestive of an SPLD diagnosis but who have differing profiles are studied. Using existing models of psycholinguistics and pragmatics to guide assessment and intervention, the diversity of language and social communicative behaviours that are covered by the label SPLD are exemplified. Consideration is given to whether the term SPLD is appropriate for both children or whether Bishop's revision of the diagnosis to ‘pragmatic language impairment’ might be more useful. Methods of intervention and evaluation for semantic and pragmatic deficits in these two cases are described. It is argued that existing tools can enable accurate explanation and modelling of the communication of children with SPLD and that there is a role for intervention studies in helping to refine those tools, to improve therapies and to understand the nature of the condition more fully.
ChiBE: interactive visualization and manipulation of BioPAX pathway models
Authors: Babur Ozgun , Dogrusoz Ugur , Demir Emek , Sander Chris 
Published: December 2009

Abstract
Summary: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large pathway datasets requires software that can combine data mapping, querying and visualization as well as providing access to diverse data resources on the Internet. ChiBE is an open source software application that features user-friendly multi-view display, navigation and manipulation of pathway models in BioPAX format. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context.
Availability: http://www.bilkent.edu.tr/%7Ebcbi/chibe.html
Contact: ugur@cs.bilkent.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Validation of double digest selective label database for sequenced prokaryotic genomes
Authors: Terletskiy Valery , Tyshchenko Valentina , Martinez-Ballesteros Ilargi , Garaizar Javier , Bikandi Joseba 
Published: December 2009

Abstract
Summary: A database for simulation of double digest selective label (DDSL) typing technique has been created and validated against a sequenced strain (Salmonella enterica serovar Typhimurium strain LT2). In silico bands were in agreement with experimental, and the technique was able to discriminate among strains belonging to the same species. When compared with other strain discrimination techniques, DDSL showed a higher discriminatory power. The database contains precomputed data which may be searched to retrieve experimental conditions for typing all up-to-dated sequenced prokaryotic microorganisms.
Availability: This is a new resource for molecular biology freely available on the Internet at http://insilico.ehu.es/DDSL
Contact: joseba.bikandi@ehu.es
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
Authors: Le Thanh , Altman Tom , Gardiner Katheleen 
Published: December 2009

Abstract
Motivation: Identification of motifs in biological sequences is a challenging problem because such motifs are often short, degenerate, and may contain gaps. Most algorithms that have been developed for motif-finding use the expectation-maximization (EM) algorithm iteratively. Although EM algorithms can converge quickly, they depend strongly on initialization parameters and can converge to local sub-optimal solutions. In addition, they cannot generate gapped motifs. The effectiveness of EM algorithms in motif finding can be improved by incorporating methods that choose different sets of initial parameters to enable escape from local optima, and that allow gapped alignments within motif models.
Results: We have developed HIGEDA, an algorithm that uses the hierarchical gene-set genetic algorithm (HGA) with EM to initiate and search for the best parameters for the motif model. In addition, HIGEDA can identify gapped motifs using a position weight matrix and dynamic programming to generate an optimal gapped alignment of the motif model with sequences from the dataset. We show that HIGEDA outperforms MEME and other motif-finding algorithms on both DNA and protein sequences.
Availability and implementation: Source code and test datasets are available for download at http://ouray.cudenver.edu/∼tnle/, implemented in C++ and supported on Linux and MS Windows.
Contact: katheleen.gardiner@ucdenver.edu
VirtualPlant: A Software Platform to Support Systems Biology Research
Authors: Katari Manpreet S. , Nowicki Steve D. , Aceituno Felipe F. , Nero Damion , Kelfer Jonathan , Thompson Lee Parnell , Cabello Juan M. , Davidson Rebecca S. , Goldberg Arthur P. , Shasha Dennis E. , Coruzzi Gloria M. , Gutieݩrrez Rodrigo A. 
Published: December 2009

Abstract
Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org.
Acute hypotension associated with leucocyte depletion filters during cell salvaged blood transfusion
Authors: Sreelakshmi T. R. , Eldridge J. 
Published: December 2009

SummaryIntra‐operative cell salvage is used in more than 75% of NHS hospitals in the United Kingdom and is a safe and cost effective alternative to allogenic blood transfusion. We report a case of acute hypotension during reinfusion of cell salvaged blood through a leucocyte depletion filter that occurred during a caesarean section. We review the literature of hypotension associated with the use of bedside leucocyte depletion filters.
Continuity of care and monitoring pain after discharge: patient perspective
Authors: Soler Rosa Suñer , Juvinyà Canal Dolors , Noguer Carmen Bertran , Poch Carme Graboleda , Brugada Motge Neus , del Mar Garcia Gil Maria 
Published: December 2009

suñer r.s., juvinyà d.c., Bertran c.n., Graboleda c.p., brugada n.m. & garcia m.m.g. (2010) Continuity of care and monitoring pain after discharge: patient perspective. Journal of Advanced Nursing66(1), 40–48.AbstractTitle.  Continuity of care and monitoring pain after discharge: patient perspective.Aim.  This paper is a report of a study conducted to evaluate, from the patients’ perspective, a Liaison and Continuity of Care Programme coordinating care provision between a hospital and primary care centres.Background.  Promoting continuity of care between hospitals and primary care improves quality of care, patient satisfaction and decreases further hospitalizations. However, inadequate pain management is common after discharge.Method.  A sample of patients from the Liaison and Continuity of Care Programme were included in a longitudinal study in 2007. We conducted standardized telephone interviews at 24 hours, 7 days, 1 and 3 months after discharge. Outcome measures included readmission, time between hospital discharge and readmission, information level at discharge, patient satisfaction, queries about care and information related to perceived state of health and pain.Results.  Eighty‐three adult patients (average age 69·3, 50·6% males) who needed continued care at discharge were followed. Ten participants died during follow‐up, and seven required readmission. A total of 49·4% of patients stated that they had understood the information given at discharge very well or perfectly. At 24 hours after discharge, 30% already had doubts about their state of health and the management of their condition. In relation to perceived health, only 25·3% stated that this was good or very good. Prevalence of pain 24‐hours after discharge was 58·3% in surgical patients and 17·1% in other patients.Conclusion.  The preparation and education of patients and family members should be improved before discharge, and appropriate written information must be given, especially if a patient has pain or requires complex care.
Redefining relationships and identity in young adults with type 1 diabetes
Authors: Sparud‐Lundin Carina , Öhrn Ingbritt , Danielson Ella 
Published: December 2009

sparud‐lundin c., öhrn i. & danielson e. (2010) Redefining relationships and identity in young adults with type 1 diabetes. Journal of Advanced Nursing66(1), 128–138.AbstractTitle.  Redefining relationships and identity in young adults with type 1 diabetes.Aim.  This paper is a report of a study exploring the meaning of interactions with and supports of self‐management from parents and other significant others for young adults with type 1 diabetes.Background.  Adolescence and young adulthood is known to be a critical period for people living with diabetes in terms of diabetes control, which is why support from significant others is of utmost importance during the transition to adult life.Method.  A grounded theory approach was used. Interviews with 13 young adults with type 1 diabetes and 13 parents 2 years after transfer to adult diabetes care were conducted during 2006–2007. Internet communication between young people on a diabetes website was also included in the constant comparative analysis.Findings.  Transition to adult life for young adults with diabetes was characterized by a relational and reflexive process leading to ongoing redefinition of relationships and identity. Parents were perceived as the most reliable supporters, compared to partners, siblings and other significant others. Chat friends can also become important through emotional, social and diabetes‐related support in internet communication. The young adults showed growing awareness of their own capacities, shortcomings and emotional reactions, reflections which contribute to a redefinition of self.Conclusion.  Further research is needed to explore how contemporary interactions contribute to development of the self. By focusing on supporting relationships, nurses are in a strategic position to develop knowledge and modify clinical programmes that promote diabetes management and care by taking supporting interactions into account from a contemporary point of view.
Determinants of hospital nurse intention to remain employed: broadening our understanding
Authors: Tourangeau Ann E. , Cummings Greta , Cranley Lisa A. , Ferron Era Mae , Harvey Sarah 
Published: December 2009

tourangeau a.e., cummings g., cranley l.a., ferron e.m. & harvey s. (2010) Determinants of hospital nurse intention to remain employed: broadening our understanding. Journal of Advanced Nursing66(1), 22–32.AbstractTitle.  Determinants of hospital nurse intention to remain employed: broadening ourunderstanding.Aim.  This paper is a report of a study to identify nurse reported determinants of intention to remain employed and to develop a model explaining determinants of hospital nurse intention to remain employed.Background.  A worsening shortage of nurses globally suggests that efforts must be made to promote retention of nurses. However, effective retention promotion strategies depend on understanding the factors influencing nurse retention.Methods.  A descriptive study using focus group methodology was implemented. Thirteen focus groups including 78 nurses were carried out in two Canadian provinces in 2007. Thematic analysis strategies were incorporated to analyse the data.Findings.  Eight thematic categories reflecting factors nurses described as influencing their intentions to remain employed emerged from focus groups: (1) relationships with co‐workers, (2) condition of the work environment, (3) relationship with and support from one’s manager, (4) work rewards, (5) organizational support and practices, (6) physical and psychological responses to work, (7) patient relationships and other job content, and (8) external factors. A model of determinants of hospital nurse intention to remain employed is hypothesized.Conclusion.  Findings were both similar to and different from previous research. The overriding concept of job satisfaction was not found. Rather, nurse assessments of satisfaction within eight thematic categories were found to influence intentions to remain employed. Further testing of the hypothesized model is required to determine its global utility. Understanding determinants of intention to remain employed can lead to development of strategies that strengthen nurse retention. Incorporation of this knowledge in nurse education programmes is essential.
Evidence for drought and forest declines during the recent megafaunal extinctions in Madagascar
Authors: Virah‐Sawmy Malika , Willis Katherine J. , Gillson Lindsey 
Published: December 2009

AbstractAim  There remains some uncertainty concerning the causes of extinctions of Madagascar’s megafauna. One hypothesis is that they were caused by over‐hunting by humans. A second hypothesis is that their extinction was caused by both environmental change and hunting. This paper systematically addresses the second hypothesis through examination of two new pollen records from south‐eastern Madagascar alongside other published records across the island.Location  South‐eastern Madagascar.Methods  We reconstructed past vegetation and fire dynamics over the past 6000 years at two sites in south‐eastern Madagascar (Ste‐Luce) using fossil pollen and charcoal contained in sedimentary sequences. We investigated drivers of vegetation changes and how these, in turn, influenced faunal species in the south‐east, using published climatic, archaeological and faunal records. Further, we also used published records to provide a synthesis of environmental changes on the whole island.Results  Vegetation reconstructions indicate that the mosaic vegetation in the region of Ste‐Luce was highly dynamic in response to climatic changes. The open woodland, surrounding the littoral forest, transformed into an ericoid grassland between c. 5800 and 5200 cal. yr bp, possibly in response to a moderate drought recorded during this period. The littoral forest was more stable between c. 5100 and 1000 cal. yr bp, with only some minor compositional changes c. 2800 cal. yr bp and between c. 1900 and 1000 cal. yr bp. Significant forest decline, however, is observed at c. 950 cal. yr bp, coinciding with a drought and a marine surge. A comparison of these results with a synthesis of published vegetation records across the island shows asynchronous vegetation changes in response to various droughts during the Holocene, except for the 950 cal. yr bp drought event, with evidence of widespread vegetation transformations and fires across the island.Main conclusions  Pronounced climatic desiccation between 1200 and 700 cal. yr bp may have been the slow driver framing and triggering vegetation transformations and decline in megafaunal populations. In addition, hunting by drought‐impacted human inhabitants and competition with newly introduced cattle would have amplified the impacts on megafaunal populations, leading to numerous extinctions in this period.
Transplantation tourism: high risk for the recipients
Authors: Yakupoglu Yarkın K. , Ozden Ender , Dilek Melda , Demirbas Alper , Adibelli Zelal , Sarikaya Saban , Akpolat Tekin 
Published: December 2009

Yakupoglu YK, Ozden E, Dilek M, Demirbas A, Adibelli Z, Sarikaya S, Akpolat T. Transplantation tourism: high risk for the recipients.  Clin Transplant 2010: 24: 835–838. © 2009 John Wiley & Sons A/S.Abstract:  Background:  The shortage of donor organ supply is forcing patients with end‐stage renal disease to alternative searches. The aim of this study is to present the clinical and laboratory data of five patients who were transplanted in Egypt from paid living‐unrelated donors and followed at our institution.Methods:  Five patients (four male, one female, mean age 51 yr) were included in this retrospective study.Results:  All allografts still have good function with a mean serum creatinine level of 0.9 mg/dL. Surgical and medical problems were common such as wound infection (n = 3), evisceration (n = 2), deep vein thrombosis (n = 2), unexplained abdominal incision requiring removal of an abdominal surgical compress left in situ during previous surgery, placement of allograft on the side of an unrepaired indirect inguinal hernia and transplant pyelonephritis.Conclusion:  Although recent developments increased success in renal transplantation, receiving a kidney from a paid living donor at a commercial transplant center still carries great risks for the recipient.