bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winner of the 2008 Systematic Review Competition: Knee Osteoarthritis after Anterior Cruciate Ligament Injury
Authors: Øiestad Britt Elin , Engebretsen Lars , Storheim Kjersti , Risberg May Arna 
Published: June 2009

Background This is a systematic review of studies on the prevalence of osteoarthritis in the tibiofemoral joint more than 10 years after an anterior cruciate ligament injury, the radiologic classification methods used, and risk factors for development of knee osteoarthritis. Methods A systematic search was performed in PubMed, EMBASE, and AMED. Inclusion criteria were studies involving patients with anterior cruciate ligament injury, either isolated or combined with medial collateral ligament or meniscal injury and either surgically or nonsurgically treated, and a minimum 10-year follow-up with radiologic assessment. Methodological quality was evaluated using a modified version of the Coleman methodology score. Results Seven prospective and 24 retrospective studies were included. The mean modified Coleman methodology score was 52 of 90. Reported prevalence of knee osteoarthritis for subjects with isolated anterior cruciate ligament injury was between 0% and 13%. For subjects with anterior cruciate ligament and additional meniscal injury, the prevalence varied between 21% and 48%. Seven different radiologic classification systems were used in the studies. Only 3 studies reported reliability results for the radiologic assessments. The most frequently reported risk factor for development of knee osteoarthritis was meniscal injury. Conclusion This systematic review suggests that the prevalence rates of knee osteoarthritis after anterior cruciate ligament reconstruction reported by previous reviews have been too high. The highest rated studies reported low prevalence of knee osteoarthritis for individuals with isolated anterior cruciate ligament injury (0%-13%) and a higher prevalence of knee osteoarthritis for subjects with combined injuries (21%-48%). Overall, the modified Coleman methodology score was low for the included studies. No universal methodological radiologic classification method exists, making comparisons of the studies and stating firm conclusions on the prevalence of knee osteoarthritis more than 10 years after anterior cruciate ligament injury difficult.
Double-Bundle Anterior Cruciate Ligament Reconstruction
Authors: Ferretti Andrea , Monaco Edoardo , Labianca Luca , De Carli Angelo , Maestri Barbara , Conteduca Fabio 
Published: June 2009

Background Single-bundle anterior cruciate ligament reconstruction seems to be insufficient to control a combined rotatory load of internal and valgus torque, whereas anatomical double-bundle reconstruction might produce a better biomechanical outcome, especially during rotatory loads. Hypothesis The addition of the posterolateral bundle to the anteromedial bundle, in an in vivo double-bundle computer-assisted anterior cruciate ligament reconstruction, is able to reduce the internal rotation of the tibia at different degrees of flexion. Study Design Controlled laboratory study. Methods Ten consecutive anterior cruciate ligament reconstruction procedures were performed in male patients using double-bundle gracilis and semitendinosus tendon graft with the 2.0 OrthoPilot anterior cruciate ligament navigation system. Anteroposterior displacement at 30°, 60°, and 90° as well as internal and external rotation at 0°, 15°, 30°, 45°, 60°, and 90° of knee flexion were evaluated before reconstruction, after fixation of the anteromedial bundle, and then after fixation of the posterolateral bundle. Results Fixation of the anteromedial bundle significantly (P <. 05) reduced the anteroposterior displacement at 30°, 60°, and 90° of knee flexion; the internal rotation at 15°, 30°, 45°, and 60°; and the external rotation at 0°, 30°, 60°, and 90°. The addition of the posterolateral bundle to the anteromedial bundle did not significantly reduce internal and external rotation of the tibia at degrees of flexion measured (P >. 05). Conclusion The hypothesis that the addition of the posterolateral bundle to the anteromedial bundle is able to reduce internal rotation of the tibia, minimizing the pivot-shift phenomenon, was not confirmed. Clinical Relevance The effective role of the anatomical double-bundle procedure in better restoring knee kinematics and allowing better clinical outcomes should be questioned in an in vivo model of anterior cruciate ligament reconstruction using doubled semitendinosus and gracilis graft.
Hyperglycemic Events in Non–Intensive Care Unit Patients Receiving Parenteral Nutrition
Authors: Pleva Melissa , Mirtallo Jay M. , Steinberg Steven M. 
Published: June 2009

Background:Evidence supports the benefits of tight glycemic control in many patient populations. There is no consensus on appropriate targets for blood glucose (BG) values in patients receiving parenteral nutrition (PN). Characterization of the frequency of BG abnormalities is necessary to identify effective strategies to improve glycemic control in this patient population.Methods:Data were retrospectively collected over a 2‐month period from 50 non–intensive care unit (ICU) patients who received PN. Frequencies of abnormal BG (defined as BG outside the range of 2 criteria: 80–200 mg/dL and 100–150 mg/dL) were determined. An event of hyperglycemia was defined as the 48‐hour period following a BG value outside of 80–200 mg/dL. Each event was evaluated for resolution within 48 hours of the triggering BG value.Results:Hyperglycemia (at least 1 BG value >200 mg/dL) occurred in 22 patients (44%). Of the 1738 BG values measured, 8.7% were >200 mg/dL, resulting in 1.4 events of hyperglycemia per patient. The average blood glucose value for the population was 140 mg/dL. The frequency of hyperglycemia and hypoglycemia increased substantially, with only 1 patient having a PN course with normoglycemia using the 100–150 mg/dL criterion.Conclusion:The frequency of hyperglycemia in non‐ICU PN patients is high according to either evaluation criterion. A method is described for using events to characterize hyperglycemia, which may be more useful than traditional methods in clinical decision making and identification of need for process improvements. These data suggest the need to develop better methods for BG control in non‐ICU PN patients.
Analysis of the Ten-Eleven Translocation 2 (TET2) gene in familial myeloproliferative neoplasms
Authors: Saint-Martin Cécile , Leroy Gwendoline , Delhommeau François , Panelatti Gérard , Dupont Sabrina , James Chloé , Plo Isabelle , Bordessoule Dominique , Chomienne Christine , Delannoy André , Devidas Alain , Gardembas-Pain Martine , Isnard Françoise , Plumelle Yves , Bernard Olivier , Vainchenker William , Najman Albert , Bellanné-Chantelot Christine ,   the French Group of Familial Myeloproliferative Disorders
Published: June 2009

Abstract
The JAK2V617F mutation does not elucidate the phenotypic variability observed in myeloproliferative neoplasm (MPN) families. A putative tumor suppressor gene, TET2, was recently implicated in MPN and myelodysplastic syndromes through the identification of acquired mutations affecting hematopoietic stem cells. The present study analyzed the TET2 gene in 61 MPN cases from 42 families. Fifteen distinct mutations were identified in 12 (20%) JAK2V617F-positive or -negative patients. In a patient with 2 TET2 mutations, the analysis of 5 blood samples at different phases of her disease showed the sequential occurrence of JAK2V617F and TET2 mutations concomitantly to the disease evolution. Analysis of familial segregation confirmed that TET2 mutations were not inherited but somatically acquired. TET2 mutations were mainly observed (10 of 12) in patients with primary myelofibrosis or patients with polycythemia vera or essential thrombocythemia who secondarily evolved toward myelofibrosis or acute myeloid leukemia.
Adjunctive resectional lung surgery for extensively drug-resistant tuberculosis: Table 1—
Authors: Dravniece G. , Cain K. P. , Holtz T. H. , Riekstina V. , Leimane V. , Zaleskis R. 
Published: June 2009

Extensively drug-resistant (XDR) tuberculosis (TB) poses significant management challenges as there are limited pharmacological treatment options for cure. Adjunctive resectional lung surgery decreases case-fatality rates for some patients with multidrug-resistant tuberculosis (MDR-TB), but its use has not been well documented for patients with XDR-TB.We describe 17 XDR-TB patients treated with surgery as part of their case management in Latvia during 1999–2005. One patient had no previous TB treatment history, 10 were previously treated for drug-susceptible TB and six were previously treated for MDR-TB.Mycobacterium tuberculosisisolates from the 17 patients were resistant to a mean of 9.2 drugs. Due to failure of pharmacological therapy, one due to a large cavity and one due to pulmonary haemorrhage, 15 patients were treated with surgery. Despite failure of pharmacological treatment in 15 out of 17 patients, eight (47%) were cured with adjunctive surgical treatment. Surgery should be explored as a possible treatment option for patients with XDR-TB.
End-points and clinical trial design in pulmonary arterial hypertension: have we made progress?
Authors: Peacock A. J. , Naeije R. , Galiè N. , Rubin L. 
Published: June 2009

There is enormous interest in the treatment of pulmonary arterial hypertension (PAH), so it is appropriate to consider the design of trials of new therapies and the end-points to be measured when trying to decide whether or not a therapy is effective.In May 2003, the first meeting devoted solely to the discussion of end-points and trial design in PAH was held in Gleneagles, UK. At that time, most of the randomised controlled trials in PAH had used 6-min walking distance and/or resting haemodynamics as their primary end-points.The present article considers the progress that has been made since 2003. It deals with aspects of clinical trial design (such as noninferiority, superiority and withdrawal trials), considers end-points used in previous and current studies (such as 6-min walking distance, time to clinical worsening, haemodynamics, imaging and plasma brain natriuretic peptide), and considers what end-points might be used in the future.The second end-points meeting was held in Turnberry, UK, in June 2007. It had a similar format to the first meeting. Much of what is presented here is a summary of the workshops from that meeting. An attempt has been made to both summarise the current state of end-points and trial design and suggest new ways in which they could be improved. The present article forms one of a series being published in theEuropean Respiratory Journalon pulmonary hypertension.
Sleep, sleep-disordered breathing and metabolic consequences
Authors: Lévy P. , Bonsignore M. R. , Eckel J. 
Published: June 2009

Sleep profoundly affects metabolic pathways. In healthy subjects, experimental sleep restriction caused insulin resistance (IR) and increased evening cortisol and sympathetic activation. Increased obesity in subjects reporting short sleep duration leads to speculation that, during recent decades, decreased sleeping time in the general population may have contributed to the increasing prevalence of obesity. Causal inference is difficult due to lack of control for confounders and inconsistent evidence of temporal sequence.In the general population, obstructive sleep apnoea (OSA) is associated with glucose intolerance. OSA severity is also associated with the degree of IR. However, OSA at baseline does not seem to significantly predict the development of diabetes. Prevalence of the metabolic syndrome is higher in patients with OSA than in obese subjects without OSA. Treatment with continuous positive airway pressure seems to improve glucose metabolism both in diabetic and nondiabetic OSA but mainly in nonobese subjects.The relative role of obesity and OSA in the pathogenesis of metabolic alterations is still unclear and is intensively studied in clinical and experimental models. In the intermittent hypoxia model in rodents, strong interactions are likely to occur between haemodynamic alterations, systemic inflammation and metabolic changes, modulated by genetic background. Molecular and cellular mechanisms are currently being investigated.
ERS/ESTS clinical guidelines on fitness for radical therapy in lung cancer patients (surgery and chemo-radiotherapy)
Authors: Brunelli A. , Charloux A. , Bolliger C. T. , Rocco G. , Sculier J-P. , Varela G. , Licker M. , Ferguson M. K. , Faivre-Finn C. , Huber R. M. , Clini E. M. , Win T. , De Ruysscher D. , Goldman L. 
Published: June 2009

A collaboration of multidisciplinary experts on the functional evaluation of lung cancer patients has been facilitated by the European Respiratory Society (ERS) and the European Society of Thoracic Surgery (ESTS), in order to draw up recommendations and provide clinicians with clear, up-to-date guidelines on fitness for surgery and chemo-radiotherapy.The subject was divided into different topics, which were then assigned to at least two experts. The authors searched the literature according to their own strategies, with no central literature review being performed. The draft reports written by the experts on each topic were reviewed, discussed and voted on by the entire expert panel. The evidence supporting each recommendation was summarised, and graded as described by the Scottish Intercollegiate Guidelines Network Grading Review Group. Clinical practice guidelines were generated and finalised in a functional algorithm for risk stratification of the lung resection candidates, emphasising cardiological evaluation, forced expiratory volume in 1 s, systematic carbon monoxide lung diffusion capacity and exercise testing.Contrary to lung resection, for which the scientific evidences are more robust, we were unable to recommend any specific test, cut-off value, or algorithm before chemo-radiotherapy due to the lack of data. We recommend that lung cancer patients should be managed in specialised settings by multidisciplinary teams.
Current status of research on osteoporosis in COPD: a systematic review
Authors: Graat-Verboom L. , Wouters E. F. M. , Smeenk F. W. J. M. , van den Borne B. E. E. M. , Lunde R. , Spruit M. A. 
Published: June 2009

Patients with chronic obstructive pulmonary disease (COPD) are at increased risk of osteoporosis. However, the prevalence, correlates and effectiveness of treatment of osteoporosis in COPD patients remain unclear.We performed a systematic review of the literature to answer three questions. 1) What is the prevalence of osteoporosis in COPD? 2) What are identified correlates of osteoporosis in COPD? 3) What are the effects of treatment of osteoporosis in COPD? A computerised literature search in MEDLINE/PubMed and the Cochrane database was carried out. In addition, reference lists were searched by hand and authors were contacted if necessary.The prevalence of osteoporosis and osteopenia varied 9–69% and 27–67%, respectively. Prevalence of osteoporosis was generally higher than in healthy subjects and some other chronic lung diseases. Correlates of osteoporosis in COPD are mainly measures of body composition, disease severity and the use of corticosteroids, although causality has not been proven. Effects of treatment of osteoporosis have not been investigated in samples consisting of COPD patients only.Longitudinal follow-up to assess determinants of osteoporosis in COPD and randomised placebo-controlled trials on the effects of treatment of osteoporosis in patients with COPD only are warranted.
ZAK negatively regulates RhoGDIβ-induced Rac1-mediated hypertrophic growth and cell migration
Authors: Huang Chih-Yang , Yang Li-Chiu , Liu Kuan-Yu , Chang I-Chang , Liao Pao-Hsin , Chou Janet Ing-Yuh , Chou Ming-Yung , Lin Wei-Wen , Yang Jaw-Ji 
Published: June 2009

Abstract
RhoGDIβ, a Rho GDP dissociation inhibitor, induced hypertrophic growth and cell migration in a cultured cardiomyoblast cell line, H9c2. We demonstrated that RhoGDIβ plays a previously undefined role in regulating Rac1 expression through transcription to induce hypertrophic growth and cell migration and that these functions are blocked by the expression of a dominant-negative form of Rac1. We also demonstrated that knockdown of RhoGDIβ expression by RNA interference blocked RhoGDIβ-induced Rac1 expression and cell migration. We demonstrated that the co-expression of ZAK and RhoGDIβ in cells resulted in an inhibition in the activity of ZAK to induce ANF expression. Knockdown of ZAK expression in ZAK-RhoGDIβ-expressing cells by ZAK-specific RNA interference restored the activities of RhoGDIβ.
geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research
Authors: Glez-Peña Daniel , Díaz Fernando , Hernández Jesús M , Corchado Juan M , Fdez-Riverola Florentino 
Published: June 2009

Abstract

Background
Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technological solutions to biomedical research, and contributing to the treatment and cure of diseases. Although different microarray techniques have been successfully used to investigate useful information for cancer diagnosis at the gene expression level, the true integration of existing methods into day-to-day clinical practice is still a long way off. Within this context, case-based reasoning emerges as a suitable paradigm specially intended for the development of biomedical informatics applications and decision support systems, given the support and collaboration involved in such a translational development. With the goals of removing barriers against multi-disciplinary collaboration and facilitating the dissemination and transfer of knowledge to real practice, case-based reasoning systems have the potential to be applied to translational research mainly because their computational reasoning paradigm is similar to the way clinicians gather, analyze and process information in their own practice of clinical medicine.

Results
In addressing the issue of bridging the existing gap between biomedical researchers and clinicians who work in the domain of cancer diagnosis, prognosis and treatment, we have developed and made accessible a common interactive framework. Our geneCBR system implements a freely available software tool that allows the use of combined techniques that can be applied to gene selection, clustering, knowledge extraction and prediction for aiding diagnosis in cancer research. For biomedical researches, geneCBR expert mode offers a core workbench for designing and testing new techniques and experiments. For pathologists or oncologists, geneCBR diagnostic mode implements an effective and reliable system that can diagnose cancer subtypes based on the analysis of microarray data using a CBR architecture. For programmers, geneCBR programming mode includes an advanced edition module for run-time modification of previous coded techniques.

Conclusion
geneCBR is a new translational tool that can effectively support the integrative work of programmers, biomedical researches and clinicians working together in a common framework. The code is freely available under the GPL license and can be obtained at http://www.genecbr.org.
DOTcvpSB, a software toolbox for dynamic optimization in systems biology
Authors: Hirmajer Tomáš , Balsa-Canto Eva , Banga Julio R 
Published: June 2009

Abstract

Background
Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations. Dynamic optimization addresses this class of systems, seeking the computation of the optimal time-varying conditions (control variables) to minimize or maximize a certain performance index. Dynamic optimization can solve many important problems in systems biology, including optimal control for obtaining a desired biological performance, the analysis of network designs and computer aided design of biological units.

Results
Here, we present a software toolbox, DOTcvpSB, which uses a rich ensemble of state-of-the-art numerical methods for solving continuous and mixed-integer dynamic optimization (MIDO) problems. The toolbox has been written in MATLAB and provides an easy and user friendly environment, including a graphical user interface, while ensuring a good numerical performance. Problems are easily stated thanks to the compact input definition. The toolbox also offers the possibility of importing SBML models, thus enabling it as a powerful optimization companion to modelling packages in systems biology. It serves as a means of handling generic black-box models as well.

Conclusion
Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use.
A-MADMAN: Annotation-based microarray data meta-analysis tool
Authors: Bisognin Andrea , Coppe Alessandro , Ferrari Francesco , Risso Davide , Romualdi Chiara , Bicciato Silvio , Bortoluzzi Stefania 
Published: June 2009

Abstract

Background
Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis.

Results
This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data.

Conclusion
A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/.