bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood tests in tired elite athletes: expectations of athletes, coaches and sport science/sports medicine staff
Authors: Fallon K E 
Published: October 2006

Background:The issue of the expectations of elite athletes, their coaches and non-medically qualified athlete support staff of consultations with sports physicians has not been previously dealt with in the sports medicine literature. As fulfilment of expectations of the content of a consultation may influence patient’s satisfaction and clinical outcome, it is important to assess the expectations of athletes and, most importantly, coaches.Objective:To assess the expectations and beliefs about fatigue, particularly in relation to blood tests, of athletes, their coaches and support staff in the specific context of tiredness of <7 days’ duration.Subjects:28 senior sports science or non-medically qualified sports medicine staff, 22 elite coaches and 62 elite athletes from the Australian Institute of Sport were included in this study.Methods:A single questionnaire.Results:The expectation for a blood test at the initial consultation for short-term fatigue was particularly high among athletes (81%) and coaches (91%). This expectation increased in athletes if their performance was worsening. All groups unanimously suggested that a blood test be performed in cases of more prolonged fatigue. Increase in total training load was perceived to be the most important cause of fatigue, but issues relating to sleep were also thought to be highly relevant. All groups suggested that blood tests provide some degree of reassurance, and all groups suggested that the most important blood tests that might be performed related to exclusion of iron deficiency, anaemia and infection.Conclusion:Athletes and their coaches generally expect that blood tests will be performed even when fatigue has been present for <1 week. This is at odds with currently available evidence of the diagnostic utility of these tests. Despite the current evidence base, individual factors in the athletes, coaches and doctors need to be considered when deciding on whether such testing has to be performed.
Effects of aquatic interventions in children with neuromotor impairments: a systematic review of the literature
Authors: Getz Miriam , Hutzler Yeshayahu , Vermeer Adri 
Published: October 2006

Objective: To determine the effectiveness of aquatic interventions in children with neuromotor impairments. Design: A search of electronic databases that included MEDLINE, PubMed, ERIC, PsychLit, PEDro, Sport Discus, CINAHL and Cochrane between 1966 and January 2005 was conducted using the following keywords: ‘hydrotherapy’, ‘aquatic therapy’, ‘water exercise’, ‘aquatics’, ‘adapted aquatics’, ‘aquatic exercise’ and ‘swimming’. An additional resource, the Aquatic Therapy Research Bibliography until 1999, was explored manually. Titles and abstracts were assessed manually according to the following inclusion criteria: (1) population (children with neuromotor or neuromuscular impairments), (2) intervention (aquatic programme). Articles were reviewed according to merit of design, population participants and outcome measures with respect to International Classification of Function and Disability terminology (changes in body function, activity level and participation). Results: Eleven of the 173 articles that were retrieved met the inclusion criteria: one randomized control trial, two quasi-experimental studies, one cohort study, two case control studies and five case reports. Seven articles reported improvement in body functions, and seven articles reported improvement in activity level. Two of the four articles that investigated outcome measures regarding participation described positive effects while the findings of the other two revealed no change. None of the articles reported negative effects due to aquatic interventions. Conclusion: According to this review, there is a substantial lack of evidence-based research evaluating the specific effects of aquatic interventions in this population.
Patient education to prevent falls in subacute care
Authors: Haines Terry P , Hill Keith D , Bennell Kim L , Osborne Richard H 
Published: October 2006

Objective: To evaluate the effectiveness of a patient education programme for preventing falls in the subacute hospital setting. Design: Randomized controlled trial, subgroup analysis. Participants: Patients of a metropolitan subacute/aged rehabilitation hospital who were recommended for a patient education intervention for the prevention of falls when enrolled in a larger randomized controlled trial of a falls prevention programme. Methods: Participants in both the control and intervention groups who were recommended for the education programme intervention were followed for the duration of their hospital stay to determine if falls occurred. Only participants in the intervention group who were recommended for this intervention actually received it. In addition, these participants completed an evaluation survey at the completion of their education programme. Results: Intervention group participants in this subgroup analysis had a significantly lower incidence of falls than their control group counterparts (control: 16.0 falls/1000 participant-days, intervention: 8.2 falls/1000 participant-days, log-rank test: P = 0.007). However the difference in the proportion of fallers was not significant (relative risk 1.21, 95% confidence interval 0.68 to 2.14). Conclusion: Patient education is an important part of a multiple intervention falls prevention approach for the subacute hospital setting.
Imatinib combined with induction or consolidation chemotherapy in patients with de novo Philadelphia chromosome–positive acute lymphoblastic leukemia: results of the GRAAPH-2003 study
Authors: de Labarthe Adrienne , Rousselot Philippe , Huguet-Rigal Françoise , Delabesse Eric , Witz Francis , Maury Sébastien , Réa Delphine , Cayuela Jean-Michel , Vekemans Marie-Christine , Reman Oumedaly , Buzyn Agnès , Pigneux Arnaud , Escoffre Martine , Chalandon Yves , MacIntyre Elizabeth , Lhéritier Véronique , Vernant Jean-Paul , Thomas Xavier , Ifrah Norbert , Dombret Hervé ,   for the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)
Published: October 2006

AbstractThe combination of imatinib with chemotherapy has been recently reported as very promising in patients with Philadelphia chromosome–positive (Ph+) acute lymphoblastic leukemia (ALL). During 2004 and 2005, 45 patients with newly diagnosed Ph+ ALL were treated in the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAAPH) 2003 study, in which imatinib was started with HAM (mitoxantrone with intermediate-dose cytarabine) consolidation in good early responders (corticosensitive and chemosensitive ALL) or earlier during the induction course in combination with dexamethasone and vincristine in poor early responders (corticoresistant and/or chemoresistant ALL). Imatinib was then continuously administered until stem cell transplantation (SCT). Overall, complete remission (CR) and BCR-ABL real-time quantitative polymerase chain reaction (RQ-PCR) negativity rates were 96% and 29%, respectively. All of the 22 CR patients (100%) with a donor actually received allogeneic SCT in first CR. At 18 months, the estimated cumulative incidence of relapse, disease-free survival, and overall survival were 30%, 51%, and 65%, respectively. These 3 end points compared very favorably with results obtained in the pre-imatinib LALA-94 trial. This study confirms the value of the combined approach and encourages prospective trials to define the optimal chemotherapy that has to be combined with imatinib and to carefully reevaluate the place of allogeneic SCT in this new context.
Altered activation of AKT is required for the suppressive function of human CD4+CD25+ T regulatory cells
Authors: Crellin Natasha K. , Garcia Rosa V. , Levings Megan K. 
Published: October 2006

Abstract
Suppression by T regulatory cells (Treg cells) is a major mechanism by which the immune system controls responses to self and nonharmful foreign proteins. Although there are many different types of Treg cells, the best characterized are those that constitutively express cell-surface IL-2Rα (CD25). We investigated whether altered T-cell–receptor (TCR)–mediated signaling in pure populations of ex vivo human CD4+CD25+ Treg cells might underlie their unique phenotype, including hyporesponsiveness to TCR–mediated activation and lack of cytokine production. CD4+CD25+ Treg cells displayed a consistent defect in phosphorylation of AKT at serine 473 and reduced phosphorylation of the AKT substrates FOXO and S6. Restoration of AKT activity via lentiviral-mediated expression of an inducibly active form of the kinase revealed that reduced activity of this pathway was necessary for the suppressive function of CD4+CD25+ Treg cells. These data represent the first demonstration of a causal association between altered signaling and the function of CD4+CD25+ Treg cells. Moreover, we have created the first system allowing inducible abrogation of suppression through manipulation of the suppressor cells. This system will be a powerful tool to further study the mechanism(s) of suppression by CD4+CD25+ Treg cells.
Differential effects of cigarette smoke on oxidative stress and proinflammatory cytokine release in primary human airway epithelial cells and in a variety of transformed alveolar epithelial cells
Authors: Kode Aruna , Yang Se-Ran , Rahman Irfan 
Published: October 2006

Abstract

Background
Cigarette smoke mediated oxidative stress and inflammatory events in the airway and alveolar epithelium are important processes in the pathogenesis of smoking related pulmonary diseases. Previously, individual cell lines were used to assess the oxidative and proinflammatory effects of cigarette smoke with confounding results. In this study, a panel of human and rodent transformed epithelial cell lines were used to determine the effects of cigarette smoke extract (CSE) on oxidative stress markers, cell toxicity and proinflammatory cytokine release and compared the effects with that of primary human small airway epithelial cells (SAEC).

Methods
Primary human SAEC, transformed human (A549, H1299, H441), and rodent (murine MLE-15, rat L2) alveolar epithelial cells were treated with different concentrations of CSE (0.2–10%) ranging from 20 min to 24 hr. Cytotoxicity was assessed by lactate dehydrogenase release assay, trypan blue exclusion method and double staining with acridine orange and ethidium bromide. Glutathione concentration was measured by enzymatic recycling assay and 4-hydroxy-2-nonenal levels by using lipid peroxidation assay kit. The levels of proinflammatory cytokines (e.g. IL-8 and IL-6) were measured by ELISA. Nuclear translocation of the transcription factor, NF-κB was assessed by immunocytochemistry and immunoblotting.

Results
Cigarette smoke extract dose-dependently depleted glutathione concentration, increased 4-hydroxy-2-nonenal (4-HNE) levels, and caused necrosis in the transformed cell lines as well as in SAEC. None of the transformed cell lines showed any significant release of cytokines in response to CSE. CSE, however, induced IL-8 and IL-6 release in primary cell lines in a dose-dependent manner, which was associated with the nuclear translocation of NF-κB in SAEC.

Conclusion
This study suggests that primary, but not transformed, lung epithelial cells are an appropriate model to study the inflammatory mechanisms in response to cigarette smoke.
The accuracy of several multiple sequence alignment programs for proteins
Authors: Nuin Paulo AS , Wang Zhouzhi , Tillier Elisabeth RM 
Published: October 2006

Abstract

Background
There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs.

Results
We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases.

Conclusion
Our results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i) and ProbCons were consistently the most accurate, with Mafft being the faster of the two.
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
Authors: Kohany Oleksiy , Gentles Andrew J , Hankus Lukasz , Jurka Jerzy 
Published: October 2006

Abstract

Background
Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases.

Results
We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments.

Conclusion
Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication
Authors: Li Guiyun , Chen Nanhai , Feng Zehua , Buller R Mark L , Osborne John , Harms Tiara , Damon Inger , Upton Chris , Esteban David J 
Published: October 2006

Abstract

Background
Vaccinia virus (VACV)-DUKE was isolated from a lesion on a 54 year old female who presented to a doctor at the Duke University Medical Center. She was diagnosed with progressive vaccinia and treated with vaccinia immune globulin. The availability of the VACV-DUKE genome sequence permits a first time genomic comparison of a VACV isolate associated with a smallpox vaccine complication with the sequence of culture-derived clonal isolates of the Dryvax vaccine.

Results
This study showed that VACV-DUKE is most similar to VACV-ACAM2000 and CLONE3, two VACV clones isolated from the Dryvax® vaccine stock confirming VACV-DUKE as an isolate from Dryvax®. However, VACV-DUKE is unique because it is, to date, the only Dryvax® clone isolated from a patient experiencing a vaccine-associated complication. The 199,960 bp VACV-DUKE genome encodes 225 open reading frames, including 178 intact genes and 47 gene fragments. Between VACV-DUKE and the other Dryvax® isolates, the major genomic differences are in fragmentation of the ankyrin-like, and kelch-like genes, presence of a full-length Interferon-α/β receptor gene, and the absence of a duplication of 12 ORFs in the inverted terminal repeat. Excluding this region, the DNA sequence of VACV-DUKE differs from the other two Dryvax® isolates by less than 0.4%. DNA sequencing also indicated that there was little heterogeneity in the sample, supporting the hypothesis that virus from an individual lesion is clonal in origin despite the fact that the vaccine is a mixed population.

Conclusion
Virus in lesions that result from progressive vaccinia following vaccination with Dryvax are likely clonal in origin. The genomic sequence of VACV-DUKE is overall very similar to that of Dryvax® cell culture-derived clonal isolates. Furthermore, with the sequences of multiple clones from Dryvax® we can begin to appreciate the diversity of the viral population in the smallpox vaccine.
The immune-body cytokine network defines a social architecture of cell interactions
Authors: Frankenstein Ziv , Alon Uri , Cohen Irun R 
Published: October 2006

Abstract

Background
Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body cells), and one involving interactions between immune and body cells (immune-body interface). These cytokine connections determine the inflammatory response to injury and subsequent healing as well as the biologic consequences of the adaptive immune response to antigens. We informatically probed the cytokine database to uncover the underlying network architecture of the three networks.

Results
We now report that the three cytokine networks are among the densest of complex networks yet studied, and each features a characteristic profile of specific three-cell motifs. Some legitimate cytokine connections are shunned (anti-motifs). Certain immune cells can be paired by their input-output positions in a cytokine architecture tree of five tiers: macrophages (MΦ) and B cells (BC) comprise the first tier; the second tier is formed by T helper 1 (Th1) and T helper 2 (Th2) cells; the third tier includes dendritic cells (DC), mast cells (MAST), Natural Killer T cells (NK-T) and others; the fourth tier is formed by neutrophils (NEUT) and Natural Killer cells (NK); and the Cytotoxic T cell (CTL) stand alone as a fifth tier. The three-cell cytokine motif architecture of immune system cells places the immune system in a super-family that includes social networks and the World Wide Web. Body cells are less clearly stratified, although cells involved in wound healing and angiogenesis are most highly interconnected with immune cells.

Conclusion
Cytokine network architecture creates an innate cell-communication platform that organizes the biologic outcome of antigen recognition and inflammation. Informatics sheds new light on immune-body systems organization.

Reviewers
This article was reviewed by Neil Greenspan, Matthias von Herrath and Anne Cooke.
An improved method for preparing Agrobacterium cells that simplifies the Arabidopsis transformation protocol
Authors: Logemann Elke , Birkenbihl Rainer P , Ülker Bekir , Somssich Imre E 
Published: October 2006

Abstract

Background
The Agrobacterium vacuum (Bechtold et al 1993) and floral-dip (Clough and Bent 1998) are very efficient methods for generating transgenic Arabidopsis plants. These methods allow plant transformation without the need for tissue culture. Large volumes of bacterial cultures grown in liquid media are necessary for both of these transformation methods. This limits the number of transformations that can be done at a given time due to the need for expensive large shakers and limited space on them. Additionally, the bacterial colonies derived from solid media necessary for starting these liquid cultures often fail to grow in such large volumes. Therefore the optimum stage of plant material for transformation is often missed and new plant material needs to be grown.

Results
To avoid problems associated with large bacterial liquid cultures, we investigated whether bacteria grown on plates are also suitable for plant transformation. We demonstrate here that bacteria grown on plates can be used with similar efficiency for transforming plants even after one week of storage at 4°C. This makes it much easier to synchronize Agrobacterium and plants for transformation. DNA gel blot analysis was carried out on the T1 plants surviving the herbicide selection and demonstrated that the surviving plants are indeed transgenic.

Conclusion
The simplified method works as efficiently as the previously reported protocols and significantly reduces the workload, cost and time. Additionally, the protocol reduces the risk of large scale contaminations involving GMOs. Most importantly, many more independent transformations per day can be performed using this modified protocol.
Presence of apoptotic and nonapoptotic disseminated tumor cells reflects the response to neoadjuvant systemic therapy in breast cancer
Authors: Fehm Tanja , Becker Sven , Becker-Pergola Graziella , Sotlar Karl , Gebauer Gerhard , Dürr-Störzer Silke , Neubauer Hans , Wallwiener Diethelm , Solomayer Erich-Franz 
Published: October 2006

Abstract
Introduction
Neoadjuvant systemic therapy (NST) is an established strategy to reduce tumor size in breast cancer patients prior to breast-conserving therapy. The effect of NST on tumor cell dissemination in these patients is not known. The aim of this study was to investigate the incidence of disseminated tumor cells (DTC), including apoptotic DTC, in breast cancer patients after NST, and to investigate the correlation of DTC status with therapy response.

Methods
Bone marrow aspiration was performed in 157 patients after NST. DTC were detected by immunocytochemistry using the A45–B/B3 anticytokeratin antibody. To detect apoptotic DTC the antibody M30 (Roche Diagnostics, Germany) was used, which detects a neo-epitope expressed only after caspase cleavage of cytokeratin 18 during early apoptosis.

Results
The incidence of DTC in breast cancer patients was 53% after completion of NST. Tumor dissemination was observed more frequently in patients with no change/progressive disease (69%) than in patients with partial remission or complete remission of the primary tumor (46%) (P < 0.05). Ten out of 24 patients with complete remission, however, were still bone marrow positive. Apoptotic DTC were present in 36 of 157 (23%) breast cancer patients. Apoptotic cells only were detected in 14% of the patients with partial remission or complete remission, but were detected in just 5% of the patients with stable disease. Apoptotic DTC were detectable in none of the patients with tumor progression.

Conclusion
The pathological therapy response in breast cancer patients is reflected by the presence of apoptotic DTC. Patients with complete remission, however, may still have nonapoptotic DTC. These patients may also benefit from secondary adjuvant therapy.