bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical fitness in people with a spinal cord injury: the association with complications and duration of rehabilitation
Authors: Haisma J.A. , Bussmann J.B.J. , Stam H.J. , Sluis T.A.R. , Bergen M.P. , Post M.W.M. , Dallmeijer A.J. , van der Woude L.H.V. 
Published: November 2007

Objective: To assess the association between physical fitness and its recovery over time on the one hand, and complications and duration of phases of rehabilitation on the other. Design and setting: Prospective cohort study at eight rehabilitation centres. Subjects: People with a spinal cord injury were assessed four times: at the start of active rehabilitation (n = 110), three months later (n = 92), at discharge (n = 137) and a year after discharge from inpatient rehabilitation (n = 91). Main measures: Physical fitness was defined as aerobic capacity, determined at each occasion by the peak oxygen uptake (peak Vo2; L/min) and the peak power output (peak PO; W) during a maximal exercise test. On these occasions, spasticity, musculoskeletal and neurogenic pain were determined (1 = present; 0 = absent). During inpatient rehabilitation, complications (urinary tract infection, pulmonary infection or pressure sore) and bed rest were registered (1 = complication; 0 = no complications, and 1 = bed rest; 0 = no bed rest). Complications and bed rest occurring during the year after discharge were registered similarly. Results: Multilevel random coefficient analyses revealed associations in multivariate models (P ≤ 0.05). The peak oxygen uptake was negatively associated with complications after discharge. The recovery of peak power output over time was negatively associated with bed rest and spasticity. Both physical fitness and its recovery were negatively associated with the duration of active rehabilitation. Conclusion: Results suggest that limiting complications, spasticity or bed rest may improve fitness. A longer duration of active rehabilitation is not associated with an increase in physical fitness.
Does the use of a constraint mitten to encourage use of the hemiplegic upper limb improve arm function in adults with subacute stroke?
Authors: Burns Alison , Burridge Jane , Pickering Ruth 
Published: November 2007

Objective: To evaluate the effect of a constraint mitten, worn on the unaffected upper limb, on the arm and hand function of participants with hemiplegia. To estimate the sample size for a future trial. Design: An A-B-A design. Setting: Inpatient, outpatient and domiciliary setting. Subjects Ten participants with mild to moderate residual upper limb hemiparesis, between 1 and 12 months post stroke. Intervention: Following a two-week baseline period, 10 participants were advised to wear the constraint mitten on the unaffected upper limb for 9 waking hours/day for two weeks to encourage use of the hemiplegic arm. Existing levels of therapy continued during the whole study. Main measures: The primary outcome measure was the Action Research Arm Test. At the end of the intervention phase participants completed a questionnaire. Participants also recorded their daily use of the constraint mitten during the intervention phase. Results: A mean improvement in the Action Research Arm Test score of 4.0 points (95% confidence interval 1.7 to 6.2; P=00.016) was found during the intervention phase after correcting for background recovery. Mean compliance was 6.7 hours/day (74%), 90% of participants were positive about the intervention and would recommend the treatment to other stroke survivors, although 50% were relieved to stop the mitten-wearing phase. Conclusions: The use of a constraint mitten in upper limb stroke rehabilitation may be a useful adjunct to enhance functional recovery with minimal additional resources. The positive findings from this preliminary study warrant a larger randomized controlled trial of 200 participants in total.
Institutional Problems of the Emerging Scientific Community in Iran
Authors: Khosrokhavar Farhad , Ghaneirad Mohammad-Amin , Toloo Ghasem 
Published: November 2007

This article attempts to explore the concept of scientific community at the macro-national level in the context of Iran. Institutionalisation of science and its professional growth has been constrained by several factors. The article first conceptualises the notion of science community as found in the literature in the context of Iran, and attempts to map through some indicators. The main focus, however, lies in mapping some institutional problems through empirical research. This was undertaken in 2002–04 in order to analyse the structure of the scientific community in Iran in the ‘exact sciences’ (mathematics, physics, chemistry, biology and earth sciences). The empirical work was done in two complementary perspectives: through a questionnaire and statistical analysis of it, and through semi-structured interviews with the researchers. There are number of problems confronting scientists in Iran. Facilities provided by institutions is one of the major problems of research. Another is the tenuous cooperation among scientists. This is reported by most of the researchers, who deplore the lack of cooperation among their group. Relationships are mostly with the Ph.D. students and only marginally with colleagues. Our research shows that the more brilliant the scientists, the more frustrated they are from scientific institutions in Iran. Medium-range researchers seem to be much happier about the scientific institution to which they belong than the brighter scholars. The scientific institutions in Iran seem to be built for the needs of the former rather than the latter. These institutions seem not to play a positive role in the case of the best scientists. On the whole, many ingredients of the scientific community, at least at its inception, are present among Iranian scientists: the strong desire for scientific achievement in spite of personal, institutional and economic problems.
CREB is a critical regulator of normal hematopoiesis and leukemogenesis
Authors: Cheng Jerry C. , Kinjo Kentaro , Judelson Dejah R. , Chang Jenny , Wu Winston S. , Schmid Ingrid , Shankar Deepa B. , Kasahara Noriyuki , Stripecke Renata , Bhatia Ravi , Landaw Elliot M. , Sakamoto Kathleen M. 
Published: November 2007

AbstractThe cAMP-responsive element binding protein (CREB) is a 43-kDa nuclear transcription factor that regulates cell growth, memory, and glucose homeostasis. We showed previously that CREB is amplified in myeloid leukemia blasts and expressed at higher levels in leukemia stem cells from patients with myeloid leukemia. CREB transgenic mice develop myeloproliferative disease after 1 year, but not leukemia, suggesting that CREB contributes to but is not sufficient for leukemogenesis. Here, we show that CREB is most highly expressed in lineage negative hematopoietic stem cells (HSCs). To understand the role of CREB in hematopoietic progenitors and leukemia cells, we examined the effects of RNA interference (RNAi) to knock down CREB expression in vitro and in vivo. Transduction of primary HSCs or myeloid leukemia cells with lentiviral CREB shRNAs resulted in decreased proliferation of stem cells, cell- cycle abnormalities, and inhibition of CREB transcription. Mice that received transplants of bone marrow transduced with CREB shRNA had decreased committed progenitors compared with control mice. Mice injected with Ba/F3 cells expressing either Bcr-Abl wild-type or T315I mutation with CREB shRNA had delayed leukemic infiltration by bioluminescence imaging and prolonged median survival. Our results suggest that CREB is critical for normal myelopoiesis and leukemia cell proliferation.
N-linked glycosylation of VWF modulates its interaction with ADAMTS13
Authors: McKinnon Thomas A. J. , Chion Alain C. K. , Millington Alexander J. , Lane David A. , Laffan Mike A. 
Published: November 2007

AbstractWe examined the role of N-linked glycan structures of VWF on its interaction with ADAMTS13. PNGase F digestion followed by lectin analysis demonstrated that more than 90% of VWF N-linked glycan chains could be removed from the molecule (PNG-VWF) without disruption of its multimeric structure or its ability to bind to collagen. PNG-VWF had an approximately 4-fold increased affinity for ADAMTS13 compared with control VWF. PNG-VWF was cleaved by ADAMTS13 faster than control VWF and was also proteolysed in the absence of urea. Occupancy of the N-linked glycan sites at N1515 and N1574 and their presentation of ABO(H) blood group sugars were confirmed with an isolated tryptic fragment. Recombinant VWF was mutated to prevent glycosylation at these sites. Mutation of N1515 did not alter ADAMTS13 binding or increase rate of ADAMTS13 proteolysis. Mutation of N1574 increased the susceptibility of VWF to ADAMTS13 proteolysis and allowed cleavage in the absence of urea. Mutation of N1574 in the isolated recombinant VWF-A2 domain also increased binding and ADAMTS13 proteolysis. These data demonstrate that the N-linked glycans of VWF have a modulatory effect on the interaction with ADAMTS13. At least part of this effect is conformational, but steric hindrance may also be important.
Redistribution of accumulated cell iron: a modality of chelation with therapeutic implications
Authors: Sohn Yang-Sung , Breuer William , Munnich Arnold , Cabantchik Z. Ioav 
Published: November 2007

AbstractVarious pathologies are characterized by the accumulation of toxic iron in cell compartments. In anemia of chronic disease, iron is withheld by macrophages, leaving extracellular fluids iron-depleted. In Friedreich ataxia, iron levels rise in the mitochondria of excitable cells but decrease in the cytosol. We explored the possibility of using deferiprone, a membrane-permeant iron chelator in clinical use, to capture labile iron accumulated in specific organelles of cardiomyocytes and macrophages and convey it to other locations for physiologic reuse. Deferiprone's capacity for shuttling iron between cellular organelles was assessed with organelle-targeted fluorescent iron sensors in conjunction with time-lapse fluorescence microscopy imaging. Deferiprone facilitated transfer of iron from extracellular media into nuclei and mitochondria, from nuclei to mitochondria, from endosomes to nuclei, and from intracellular compartments to extracellular apotransferrin. Furthermore, it mobilized iron from iron-loaded cells and donated it to preerythroid cells for hemoglobin synthesis, both in the presence and in the absence of transferrin. These unique properties of deferiprone underlie mechanistically its capacity to alleviate iron accumulation in dentate nuclei of Friedreich ataxia patients and to donate tissue-chelated iron to plasma transferrin in thalassemia intermedia patients. Deferiprone's shuttling properties could be exploited clinically for treating diseases involving regional iron accumulation.
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
Authors: Sherman Brad T , Huang Da Wei , Tan Qina , Guo Yongjian , Bour Stephan , Liu David , Stephens Robert , Baseler Michael W , Lane H Clifford , Lempicki Richard A 
Published: November 2007

Abstract

Background
Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis.

Description
The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner.

Conclusion
The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.
Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes
Authors: Chou Jeff W , Zhou Tong , Kaufmann William K , Paules Richard S , Bushel Pierre R 
Published: November 2007

Abstract

Background
A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions.

Results
Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV) or ionizing radiation (IR)-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying biological processes affected by IR- and/or UV- induced DNA damage.

Conclusion
EPIG competed with CLICK and performed better than CAST in extracting patterns from simulated data. EPIG extracted more biological informative patterns and co-expressed genes from both C. elegans and IR/UV-treated human fibroblasts. Using Gene Ontology analysis of the genes in the patterns extracted by EPIG, several key biological categories related to p53-dependent cell cycle control were revealed from the IR/UV data. Among them were mitotic cell cycle, DNA replication, DNA repair, cell cycle checkpoint, and G0-like status transition. EPIG can be applied to data sets from a variety of experimental designs.
Adverse health effects of low levels of perceived control in Swedish and Russian community samples
Authors: Lundberg Johanna , Bobak Martin , Malyutina Sofia , Kristenson Margareta , Pikhart Hynek 
Published: November 2007

Abstract

Background
This cross-sectional study of two middle-aged community samples from Sweden and Russia examined the distribution of perceived control scores in the two populations, investigated differences in individual control items between the populations, and assessed the association between perceived control and self-rated health.

Methods
The samples consisted of men and women aged 45–69 years, randomly selected from national and local population registers in southeast Sweden (n = 1007) and in Novosibirsk, Russia (n = 9231). Data were collected by structured questionnaires and clinical measures at a visit to a clinic. The questionnaire covered socioeconomic and lifestyle factors, societal circumstances, and psychosocial measures. Self-rated health was assessed by standard single question with five possible answers, with a cut-off point at the top two alternatives.

Results
32.2 % of Swedish men and women reported good health, compared to 10.3 % of Russian men and women. Levels of perceived control were also significantly lower in Russia than in Sweden and varied by socio-demographic parameters in both populations. Sub-item analysis of the control questionnaire revealed substantial differences between the populations both in the perception of control over life and over health. Logistic regression analysis revealed that the odds ratios (OR) of poor self-rated health were significantly increased in men and women with low perceived control in both countries (OR between 2.61 and 4.26).

Conclusion
Although the cross-sectional design does not allow causal inference, these results support the view that perceived control influences health, and that it may mediate the link between socioeconomic hardship and health.
Effect of Fagonia Arabica (Dhamasa) on in vitro thrombolysis
Authors: Prasad Sweta , Kashyap Rajpal Singh , Deopujari Jayant Y , Purohit Hemant J , Taori Girdhar M , Daginawala Hatim F 
Published: November 2007

Abstract

Background
Atherothrombotic diseases such as myocardial or cerebral infarction are serious consequences of the thrombus formed in blood vessels. Thrombolytic agents are used to dissolve the already formed clots in the blood vessels; however, these drugs have certain limitations which cause serious and sometimes fatal consequences. Herbal preparations have been used since ancient times for the treatment of several diseases. Herbs and their components possessing antithrombotic activity have been reported before; however, herbs that could be used for thrombolysis has not been reported so far. This study's aim was to investigate whether herbal preparations (aqueous extract) possess thrombolytic activity or not.

Methods
An in vitro thrombolytic model was used to check the clot lysis effect of six aqueous herbal extracts viz., Tinospora cordifolia, Rubia cordifolia, Hemidesmus indicus, Glycyrrhiza glabra Linn, Fagonia Arabica and Bacopa monnieri Linn along with Streptokinase as a positive control and water as a negative control.

Results
Using an in vitro thrombolytic model, Tinospora cordifolia, Rubia cordifolia, Hemidesmus indicus, Glycyrrhiza glabra Linn, Fagonia Arabica and Bacopa monnieri Linn showed 19.3%, 14.5%, 20.3%, 17.8%, 75.6% and 41.8% clot lysis respectively . Among the herbs studied Fagonia arabica showed significant % of clot lysis (75.6%) with reference to Streptokinase (86.2%).

Conclusion
Through our study it was found that Dhamasa possesses thrombolytic properties that could lyse blood clots in vitro; however, in vivo clot dissolving properties and active component(s) of Dhamasa for clot lysis are yet to be discovered. Once found Dhamasa could be incorporated as a thrombolytic agent for the improvement of patients suffering from Atherothrombotic diseases.
The role of voltage-gated potassium channels in the regulation of mouse uterine contractility
Authors: Smith Ryan C , McClure Marisa C , Smith Margaret A , Abel Peter W , Bradley Michael E 
Published: November 2007

Abstract

Background
Uterine smooth muscle cells exhibit ionic currents that appear to be important in the control of uterine contractility, but how these currents might produce the changes in contractile activity seen in pregnant myometrium has not been established. There are conflicting reports concerning the role of voltage-gated potassium (Kv) channels and large-conductance, calcium-activated potassium (BK) channels in the regulation of uterine contractility. In this study we provide molecular and functional evidence for a role for Kv channels in the regulation of spontaneous contractile activity in mouse myometrium, and also demonstrate a change in Kv channel regulation of contractility in pregnant mouse myometrium.

Methods
Functional assays which evaluated the effects of channel blockers and various contractile agonists were accomplished by quantifying contractility of isolated uterine smooth muscle obtained from nonpregnant mice as well as mice at various stages of pregnancy. Expression of Kv channel proteins in isolated uterine smooth muscle was evaluated by Western blots.

Results
The Kv channel blocker 4-aminopyridine (4-AP) caused contractions in nonpregnant mouse myometrium (EC50 = 54 micromolar, maximal effect at 300 micromolar) but this effect disappeared in pregnant mice; similarly, the Kv4.2/Kv4.3 blocker phrixotoxin-2 caused contractions in nonpregnant, but not pregnant, myometrium. Contractile responses to 4-AP were not dependent upon nerves, as neither tetrodotoxin nor storage of tissues at room temperature significantly altered these responses, nor were responses dependent upon the presence of the endometrium. Spontaneous contractions and contractions in response to 4-AP did not appear to be mediated by BK, as the BK channel-selective blockers iberiotoxin, verruculogen, or tetraethylammonium failed to affect either spontaneous contractions or 4-AP-elicited responses. A number of different Kv channel alpha subunit proteins were found in isolated myometrium from both nonpregnant and term-pregnant mice, and one of these proteins – Kv4.3 – was found to disappear in term-pregnant tissues.

Conclusion
These findings suggest a role for Kv channels in the regulation of uterine contractility, and that changes in the expression and/or function of specific Kv channels may account for the functional changes seen in pregnant myometrium.
Evaluation of the IS6110 PCR assay for the rapid diagnosis of tuberculous meningitis
Authors: Deshpande Poonam S , Kashyap Rajpal S , Ramteke Sonali S , Nagdev Khushboo J , Purohit Hemant J , Taori Girdhar M , Daginawala Hatim F 
Published: November 2007

AbstractBackgroundTuberculous meningitis (TBM) is one of the common clinical manifestations of extra-pulmonary tuberculosis. It is difficult to diagnose due to a lack of rapid, sensitive, and specific tests. Newer methods, which are easy and reliable, are required to diagnose TBM at an early stage. Thus our aim was to evaluate the polymerase chain reaction (PCR) technique, using primers directed against the IS6110 gene, for the detection ofMycobacterium tuberculosisin the CSF, for the diagnosis of TBM patients.MethodsAn in-house IS6110PCR method using a specific pair of primers designed to amplify the insertion sequence, IS6110, in theM. tuberculosisgenome was used to analyze CSF. A total of 80 CSF samples from different groups of patients were studied (confirmed TBM n = 35, clinically suspected TBM n = 16, non-TBM infectious meningitis n = 12, non infectious neurological diseases n = 17).ResultsPCR gave a sensitivity of 91.4% and specificity of 75.9% for the diagnosis of TBM in patients with TBM confirmed by culture. In 16 clinically diagnosed, but unconfirmed, TBM cases PCR was positive in 10 (62.5%) cases. There were seven (24.1%) PCR-positive cases among the 29 patients with non-TBM and non-infectious neurological disease.ConclusionWe conclude that the performance of an in-house IS6110PCR assay is valuable in the rapid diagnosis of tuberculous meningitis.