bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collaborative research between clinicians and researchers: a multiple case study of implementation
Authors: Blevins Dean , Farmer Mary S , Edlund Carrie , Sullivan Greer , Kirchner JoAnn E 
Published: October 2010

Abstract

Background
Bottom-up, clinician-conceived and directed clinical intervention research, coupled with collaboration from researcher experts, is conceptually endorsed by the participatory research movement. This report presents the findings of an evaluation of a program in the Veterans Health Administration meant to encourage clinician-driven research by providing resources believed to be critical. The evaluation focused on the extent to which funded projects: maintained integrity to their original proposals; were methodologically rigorous; were characterized by collaboration between partners; and resulted in sustained clinical impact.

Methods
Researchers used quantitative (survey and archival) and qualitative (focus group) data to evaluate the implementation, evaluation, and sustainability of four clinical demonstration projects at four sites. Fourteen research center mentors and seventeen clinician researchers evaluated the level of collaboration using a six-dimensional model of participatory research.

Results
Results yielded mixed findings. Qualitative and quantitative data suggested that although the process was collaborative, clinicians' prior research experience was critical to the quality of the projects. Several challenges were common across sites, including subject recruitment, administrative support and logistics, and subsequent dissemination. Only one intervention achieved lasting clinical effect beyond the active project period. Qualitative analyses identified barriers and facilitators and suggested areas to improve sustainability.

Conclusions
Evaluation results suggest that this participatory research venture was successful in achieving clinician-directed collaboration, but did not produce sustainable interventions due to such implementation problems as lack of resources and administrative support.
Progranulin modulates zebrafish motoneuron development in vivoand rescues truncation defects associated with knockdown of Survival motor neuron 1
Authors: Chitramuthu Babykumari P , Baranowski David C , Kay Denis G , Bateman Andrew , Bennett Hugh PJ 
Published: October 2010

Abstract

Background
Progranulin (PGRN) encoded by the GRN gene, is a secreted glycoprotein growth factor that has been implicated in many physiological and pathophysiological processes. PGRN haploinsufficiency caused by autosomal dominant mutations within the GRN gene leads to progressive neuronal atrophy in the form of frontotemporal lobar degeneration (FTLD). This form of the disease is associated with neuronal inclusions that bear the ubiquitinated TAR DNA Binding Protein-43 (TDP-43) molecular signature (FTLD-U). The neurotrophic properties of PGRN in vitro have recently been reported but the role of PGRN in neurons is not well understood. Here we document the neuronal expression and functions of PGRN in spinal cord motoneuron (MN) maturation and branching in vivo using zebrafish, a well established model of vertebrate embryonic development.

Results
Whole-mount in situ hybridization and immunohistochemical analyses of zebrafish embryos revealed that zfPGRN-A is expressed within the peripheral and central nervous systems including the caudal primary (CaP) MNs within the spinal cord. Knockdown of zfPGRN-A mRNA translation mediated by antisense morpholino oligonucleotides disrupted normal CaP MN development resulting in both truncated MNs and inappropriate early branching. Ectopic over-expression of zfPGRN-A mRNA resulted in increased MN branching and rescued the truncation defects brought about by knockdown of zfPGRN-A expression. The ability of PGRN to interact with established MN developmental pathways was tested. PGRN over-expression was found to reverse the truncation defect resulting from knockdown of Survival of motor neuron 1 (smn1). This is involved in small ribonucleoprotein biogenesis RNA processing, mutations of which cause Spinal Muscular Atrophy (SMA) in humans. It did not reverse the MN defects caused by interfering with the neuronal guidance pathway by knockdown of expression of NRP-1, a semaphorin co-receptor.

Conclusions
Expression of PGRN within MNs and the observed phenotypes resulting from mRNA knockdown and over-expression are consistent with a role in the regulation of spinal cord MN development and branching. This study presents the first in vivo demonstration of the neurotrophic properties of PGRN and suggests possible future therapeutic applications in the treatment of neurodegenerative diseases.
Statistical inference of the time-varying structure of gene-regulation networks
Authors: Lèbre Sophie , Becq Jennifer , Devaux Frédéric , Stumpf Michael PH , Lelandais Gaëlle 
Published: October 2010

AbstractBackgroundBiological networks are highly dynamic in response to environmental and physiological cues. This variability is in contrast to conventional analyses of biological networks, which have overwhelmingly employed static graph models which stay constant over time to describe biological systems and their underlying molecular interactions.MethodsTo overcome these limitations, we propose here a new statistical modelling framework, the ARTIVA formalism (Auto Regressive TIme VArying models), and an associated inferential procedure that allows us to learn temporally varying gene-regulation networks from biological time-course expression data. ARTIVA simultaneously infers the topology of a regulatory network and how it changes over time. It allows us to recover the chronology of regulatory associations for individual genes involved in a specific biological process (development, stress response, etc.).ResultsWe demonstrate that the ARTIVA approach generates detailed insights into the function and dynamics of complex biological systems and exploits efficiently time-course data in systems biology. In particular, two biological scenarios are analyzed: the developmental stages ofDrosophila melanogasterand the response ofSaccharomyces cerevisiaeto benomyl poisoning.ConclusionsARTIVA does recover essential temporal dependencies in biological systems from transcriptional data, and provide a natural starting point to learn and investigate their dynamics in greater detail.
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy
Authors: Lin Chen-Ching , Hsiang Jen-Tsung , Wu Chia-Yi , Oyang Yen-Jen , Juan Hsueh-Fen , Huang Hsuan-Cheng 
Published: October 2010

Abstract

Background
Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear.

Results
We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy.

Conclusions
We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.
Elevated expression of Dickkopf-1 increases the sensitivity of human glioma cell line SHG44 to BCNU
Authors: Zhou Youxin , Li Wenshuai , Xu Qinian , Huang Yulun 
Published: October 2010

Abstract

Background
Studies have shown that Dickkopf-1 (DKK-1) is involved in tumorigenesis. Recently, we found that 9 out of 12 human glioma cell lines had high level of DKK-1 protein while the other 3 had very low or non-detectable level of DKK-1. The aim of this study is to further examine the function of DKK-1 in glioma cells.

Materials and methods
The glioma cell line SHG44 was obtained from a patient with grade II-III astrocytoma. SHG44 cells were transfected with a human DKK-1 gene. Transfection of the empty vector pcDNA3.1 was used as negative control. Sensitivity to BCNU was measured by Annexin-V staining. Expression of bax, bcl-2 and caspase-3 of three groups was determined by immunohistochemistry.

Results
The tranfection was confirmed by PCR, RT-PCR and Western blot. More apoptotic cell death was observed in the DKK-1 transfected cells, comparing to the non-transfected cells, or cells with empty vector. The expression of bax and caspase-3 of the SHG44 -DDK-1 increased, whereas the expression of bcl-2 decreased

Conclusion
Our results indicated that DKK-1 has a pro-apoptotic function of in glioma.
An embryo-specific expressing TGF-β family protein, growth-differentiation factor 3 (GDF3), augments progression of B16 melanoma
Authors: Ehira Nobuyuki , Oshiumi Hiroyuki , Matsumoto Misako , Kondo Takeshi , Asaka Masahiro , Seya Tsukasa 
Published: October 2010

Abstract
Malignant tumor cells often express embryonic antigens which share the expression with embryonic stem (ES) cells. The embryonic antigens are usually encoded by ES cell-specific genes, a number of which are associated with tumorigenesis and/or tumor progression. We examined the expression of ES cell-specific genes in the mouse B16 melanoma cell line to identify the factors promoting tumorigenesis. We found that endogenous growth-differentiation factor 3 (GDF3) expression was induced in implant B16 tumor during tumor progression in syngenic C57BL/6 mice. B16 F10, a subline with a high metastatic potential, continuously expressed GDF3 while low metastatic B16 F1 expressed comparatively decreased levels of GDF3. Overexpression of GDF3 promoted growth of implanted melanoma B16 F1 and F10 in syngenic mice. Ectopic expression of GDF3 was accompanied by an increased level of production of CD24/CD44. Such a profile was reported to be characteristic of melanoma stem cell-like cells. GDF3 expression was observed in embryonal carcinomas, primary testicular germ cell tumors, seminomas and breast carcinomas. However, the role of GDF3 in these cancers remains undetermined. Overexpression of GDF3 did not affect the growth of mouse hepatoma high or low metastatic sublines G5 or G1, both of which do not express GDF3. Since GDF3-driven CD24 acts as a receptor for endogenous innate immune ligands that modulate cell proliferation, CD24 is an effective determinant of tumorigenesis in malignant cell transformation. Finally, our results support the view that GDF3 has the ability to induce progression of CD24-inducible melanoma in mice.
Intensity modulated radiotherapy (IMRT) in the management of locally advanced oropharyngeal squamous cell carcinomata (SCC): disease control and functional outcome using the therapy outcome measure (TOM) score - report from a single U.K. institution
Authors: Ingle Charlotte J , Yip Kent , Caskie Valerie , Dyson Catherine , Ford Amanda , Scrase Christopher D 
Published: October 2010

Abstract

Introduction
This paper evaluates tumour control and toxicity especially in relation to swallowing dysfunction in those patients with locally advanced oropharyngeal squamous cell carcinoma who have undergone either primary chemo-radiation or post-operative parotid sparing IMRT. The TOM scoring system was used to assess dysphagia.

Methods
All patients with locally advanced (stage 3/4) squamous cell oropharyngeal cancer and who required either primary or post-operative RT were identified. Toxicity was recorded prospectively. The TOM score (0-5 where 5 indicates that the patient is able to eat a normal diet and 0-2 varying degrees of enteral feeding dependency), weights and trismus was recorded immediately prior to and following radiotherapy.

Results
24 patients were identified between 1/2003 and 11/2007. Median weight loss during radiotherapy was 9 kg. All but one patient had a gastrostomy (RIG) tube inserted prophylactically. With a mean follow-up of 37.1 months, 62.5% of pts had a TOM score of 5, 12.5% scored 3, 8% scored and 17% scored 0-2.. For those patients whose swallowing function did recover, it took on average 8.7 months. 15% patients experienced trismus secondary to radiotherapy. 2 year overall survival was 92% and disease specific survival 96%.

Conclusion
Excellent disease control with intensified schedules of radiotherapy with IMRT has been achieved in this patient population. Intermediate toxicity is significant but with longer follow-up, dysphagia continues to improve with 75% of patients not requiring any form of enteral or oral supplementation.
Conservative management of post-appendicectomy intra-abdominal abscesses
Authors: Dhaou Mahdi Ben , Ghorbel Sofiene , Chouikh Taieb , Charieg Awatef , Nouira Faouzi , Khalifa Sonia Ben , Khemakhem Rachid , Jlidi Said , Chaouachi Béji 
Published: October 2010

Abstract

Purpose
Appendicitis is the most common abdominal inflammatory process in children which were sometimes followed by complications including intra-abdominal abscess. This later needs classically a surgical drainage. We evaluated the efficacy of antibiotic treatment and surgical drainage.

Methods
Hospital records of children treated in our unit for intra-abdominal post appendectomy abscesses over a 6 years period were reviewed retrospectively.

Results
This study investigates a series of 14 children from 2 to 13 years of age with one or many abscesses after appendectomy, treated between 2002 and 2007. Seven underwent surgery and the others were treated with triple antibiotherapy. The two groups were comparable.
For the 7 patients who receive medical treatment alone, it was considered efficient in 6 cases (85%) with clinical, biological and radiological recovery of the abscess. There was one failure (14%). The duration of hospitalization from the day of diagnosis of intra-abdominal abscess was approximately 10.28 days (range 7 to 14 days). In the other group, the efficacy of treatment was considered satisfactory in all cases. The duration of hospitalization was about 13 days (range: 9 to 20).

Conclusion
Compared to surgical drainage, antibiotic management of intra-abdominal abscesses was a no invasive treatment with shorter hospitalization.
Disease-specific definitions of vitamin D deficiency need to be established in autoimmune and non-autoimmune chronic diseases: a retrospective comparison of three chronic diseases
Authors: Broder Anna R , Tobin Jonathan N , Putterman Chaim 
Published: October 2010

Abstract
Introduction
We compared the odds of vitamin D deficiency in three chronic diseases: systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 2 diabetes (T2DM), adjusting for medications, demographics, and laboratory parameters, common to all three diseases. We also designed multivariate models to determine whether different factors are associated with vitamin D deficiency in different racial/ethnic groups.

Methods
We identified all patients with non-overlapping diagnoses of SLE, RA, and T2DM, with 25-hydroxyvitamin D (25OHD) levels measured between 2000 and 2009. Vitamin D deficiency was defined as 25OHD levels <20 ng/ml, based on previously established definitions. Race/ethnicity was analyzed as African-American non-Hispanic (African-American), Hispanic non-African-American (Hispanic), and Other based on self report.

Results
We included 3,914 patients in the final analysis: 123 SLE, 100 RA, and 3,691 T2DM. Among African-Americans the frequency of vitamin D deficiency was 59% in SLE, 47% in RA, and 67% in T2DM. Among Hispanics the frequency of vitamin D deficiency was 67% in SLE, 50% in RA, and 59% in T2DM. Compared with the SLE group, the adjusted odds ratio of vitamin D deficiency was 1.1, 95% CI (0.62, 2.1) in the RA group, and 2.0, 95% CI (1.3, 3.1) in the T2DM group. In the multivariate analysis, older age, higher serum calcium and bisphosphonate therapy were associated with a lower odds of vitamin D deficiency in all three racial/ethnic groups: 1,330 African-American, 1,257 Hispanic, and 1,100 Other. T2DM, serum creatinine, and vitamin D supplementation were associated with vitamin D deficiency in some, but not all, racial/ethnic groups.

Conclusions
Vitamin D deficiency is highly prevalent in our patients with SLE, RA, and T2DM. While the odds of vitamin D deficiency are similar in RA and SLE patients in a multivariate analysis, T2DM patients have much higher odds of being vitamin D deficient. Different demographic and laboratory factors may be associated with vitamin D deficiency within different racial/ethnic groups. Therefore, disease-specific and race/ethnicity-specific definitions of vitamin D deficiency need to be established in future studies in order to define goals of vitamin D replacement in patients with autoimmune and non-autoimmune chronic diseases.
Treatment of euvolemic hyponatremia in the intensive care unit by urea
Authors: Decaux Guy , Andres Caroline , Gankam Kengne Fabrice , Soupart Alain 
Published: October 2010

Abstract
Introduction
Hyponatremia in the intensive care unit (ICU) is most commonly related to inappropriate secretion of antidiuretic hormone (SIADH). Fluid restriction is difficult to apply in these patients. We wanted to report the treatment of hyponatremia with urea in these patients.

Methods
Two groups of patients are reported. The first one is represented by a retrospective study of 50 consecutive patients with mild hyponatremia treated with urea. The second group is presented by a series of 35 consecutive patients with severe hyponatremia acquired outside the hospital (≤ 115 mEq/L) who where treated by isotonic saline and urea (0.5 to 1 g/kg/day), administered usually by gastric tube.

Results
In the first group with mild hyponatremia (128 ± 4 mEq/L) the serum sodium (SNa) increased to a mean value of 135 ± 4 mEq/L (P < 0.001) after two days of urea therapy (46 ± 25 g/day), despite a large fluid intake (> 2 L/day). The mean duration of urea therapy was six days (from 2 to 42 days). Six patients developed hyponatremia again once the urea was stopped, which necessitated its reintroduction. Six patients developed hypernatremia (maximum value 155 mEq/L). In the second group, SNa increased from 111 ± 3 mEq/L to 122 ± 4 mEq/L in one day (P < 0.001). All the patients with neurological symptoms made a rapid recovery. No side effects were observed.

Conclusions
These data show that urea is a simple and inexpensive therapy to treat euvolemic hyponatremia in the ICU.
Cost and mortality prediction using polymerase chain reaction pathogen detection in sepsis: evidence from three observational trials
Authors: Lehmann Lutz E , Herpichboehm Bernd , Kost Gerald J , Kollef Marin H , Stüber Frank 
Published: October 2010

Abstract
Introduction
Delays in adequate antimicrobial treatment contribute to high cost and mortality in sepsis. Polymerase chain reaction (PCR) assays are used alongside conventional cultures to accelerate the identification of microorganisms. We analyze the impact on medical outcomes and healthcare costs if improved adequacy of antimicrobial therapy is achieved by providing immediate coverage after positive PCR reports.

Methods
A mathematical prediction model describes the impact of PCR-based rapid adjustment of antimicrobial treatment. The model is applied to predict cost and medical outcomes for 221 sepsis episodes of 189 post-surgical and intensive care unit (ICU) sepsis patients with available PCR data from a prospective, observational trial of a multiplex PCR assay in five hospitals. While this trial demonstrated reduction of inadequate treatment days, data on outcomes associated with reduced inadequate initial antimicrobial treatment had to be obtained from two other, bigger, studies which involved 1,147 (thereof 316 inadequately treated) medical or surgical ICU patients. Our results are reported with the (5% to 95%) percentile ranges from Monte Carlo simulation in which the input parameters were randomly and independently varied according to their statistical characterization in the three underlying studies. The model allows predictions also for different patient groups or PCR assays.

Results
A total of 13.1% of PCR tests enabled earlier adequate treatment. We predict that cost for PCR testing (300 €/test) can be fully recovered for patients above 717 € (605 € to 1,710 €) daily treatment cost. A 2.6% (2.0 to 3.2%) absolute reduction of mortality is expected. Cost per incremental survivor calculates to 11,477 € (9,321 € to 14,977 €) and incremental cost-effectiveness ratio to 3,107 € (2,523 € to 4,055 €) per quality-adjusted life-year. Generally, for ICU patients with >25% incidence of inadequate empiric antimicrobial treatment, and at least 15% with a positive blood culture, PCR represents a cost-neutral adjunct method.

Conclusions
Rapid PCR identification of microorganisms has the potential to become a cost-effective component for managing sepsis. The prediction model tested with data from three observational trials should be utilized as a framework to deepen insights when integrating more complementary data associated with utilization of molecular assays in the management of sepsis.
Inhibition of monocyte chemoattractant protein-1 prevents diaphragmatic inflammation and maintains contractile function during endotoxemia
Authors: Labbe Katherine , Danialou Gawiyou , Gvozdic Dusanka , Demoule Alexandre , Divangahi Maziar , Boyd John H , Petrof Basil J 
Published: October 2010

Abstract
Introduction
Respiratory muscle weakness is common in sepsis patients. Proinflammatory mediators produced during sepsis have been implicated in diaphragmatic contractile dysfunction, but the role of chemokines has not been explored. This study addressed the role of monocyte chemoattractant protein-1 (MCP-1, also known as CCL2), in the pathogenesis of diaphragmatic inflammation and weakness during endotoxemia.

Methods
Mice were treated as follows (n = 6 per group): (a) saline, (b) endotoxin (25 μg/g IP), (c) endotoxin + anti-MCP-1 antibody, and (d) endotoxin + isotype control antibody. Muscles were also exposed to recombinant MCP-1 invivo and in vitro. Measurements were made of diaphragmatic force generation, leukocyte infiltration, and proinflammatory mediator (MCP-1, IL-1α, IL-1β, IL-6, NF-κB) expression/activity.

Results
Invivo, endotoxin-treated mice showed a large decrease in diaphragmatic force, together with upregulation of MCP-1 and other cytokines, but without an increase in intramuscular leukocytes. Antibody neutralization of MCP-1 prevented the endotoxin-induced force loss and reduced expression of MCP-1, IL-1α, IL-1β, and IL-6 in the diaphragm. MCP-1 treatment of nonseptic muscles also led to contractile weakness, and MCP-1 stimulated its own transcription independent of NF-κB activation in vitro.

Conclusions
These results suggest that MCP-1 plays an important role in the pathogenesis of diaphragmatic weakness during sepsis by both direct and indirect mechanisms. We speculate that its immunomodulatory properties and ability to modify skeletal muscle function make MCP-1 a potential therapeutic target in critically ill patients with sepsis and associated respiratory muscle weakness.