bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of sensorimotor training on knee proprioception and function for patients with knee osteoarthritis: a preliminary report
Authors: Tsauo Jau-Yih , Cheng Pai-Fu , Yang Rong-Sen 
Published: April 2008

Objective: To investigate the effects of a sensorimotor training programme in osteoarthritic patients. Design: Randomized, single-blind, controlled trial. Setting: Kinesiology laboratory at School of Physical Therapy. Participants: A total of 60 patients were randomly assigned to the training group and the control group. Only 29 patients (training group, 15; control group, 14) completed the study. Intervention: The training group underwent a sensorimotor training programme using a sling suspension system complemented by a routine physical therapy. The control group underwent a routine physical therapy. Main measures: Active joint repositioning, functional testings, and self-reported function with the Western Ontario & McMaster Universities Arthritis Index before and after the eight-week intervention. Results: There were significant differences between the two groups with respect to the improvement in proprioception as measured by active joint repositioning (the changes in the absolute error were 1.9± 1.7°, training group versus 0.1 ± 2.8°, control group (P<0.05), and in self-reported functional difficulty (33.2 ±35.1, training group versus 8.0± 10.2, control group; P<0.05)). There was no significant difference between the two groups in other outcomes. Conclusion: A sensorimotor training using a sling suspension system improved the patients' proprioception in the knee joints and their self-reported function. Thus, these exercises may serve as an exercise programme for patients with knee osteoarthritis.
An exploratory randomized controlled trial of assisted practice for improving sit-to-stand in stroke patients in the hospital setting
Authors: Britton Elizabeth , Harris Nigel , Turton Ailie 
Published: April 2008

Objectives: To evaluate the amount of practice achieved and assess potential for effects on performance of 30 minutes of daily training in sit-to-stand. Design: Randomized controlled pilot study. Setting: Stroke rehabilitation unit, UK. Participants: Eighteen stroke patients needing `stand by' help to sit-to-stand. Interventions: In addition to usual rehabilitation the experimental group (n = 9) practised sit-to-stand and leg strengthening exercises for 30 minutes, on weekdays for two weeks, with a physiotherapy assistant. The control group received arm therapy. Main outcome measures: Frequency of sit-to-stands per day. Performance measures: rise time, weight taken through the affected foot at `thighs off', number of attempts needed to achieve three successful sit-to-stands and the number of sit-to-stands performed in 60 seconds. Outcome was measured one and two weeks after baseline assessment. Results: Sit-to-stand frequency averaged 18 per day. Thirty minutes of practice in sit-to-stand resulted in a mean of 50 (SD 17.2) extra stands per day. There was a significant mean difference of 10% body weight taken through the affected foot after one week of intervention: The control group had reduced weight through the affected leg while the training group increased weight (F1,16 = 11.1, P= 0.004, 95% confidence interval (CI) -16.61 to -3.72). No significant differences between groups were found on other measures. Results two weeks after baseline were inconclusive due to loss of five participants. Conclusions: Task-specific practice given for 30 minutes a day appears promising for patients learning to sit-to-stand.
The effect of the GENTLE/s robot-mediated therapy system on arm function after stroke
Authors: Coote Susan , Murphy Brendan , Harwin William , Stokes Emma 
Published: April 2008

Objective: To evaluate the effect of robot-mediated therapy on arm dysfunction post stroke. Design: A series of single-case studies using a randomized multiple baseline design with ABC or ACB order. Subjects (n = 20) had a baseline length of 8, 9 or 10 data points. They continued measurement during the B — robot-mediated therapy and C — sling suspension phases. Setting: Physiotherapy department, teaching hospital. Subjects: Twenty subjects with varying degrees of motor and sensory deficit completed the study. Subjects attended three times a week, with each phase lasting three weeks. Interventions: In the robot-mediated therapy phase they practised three functional exercises with haptic and visual feedback from the system. In the sling suspension phase they practised three single-plane exercises. Each treatment phase was three weeks long. Main measures: The range of active shoulder flexion, the Fugl-Meyer motor assessment and the Motor Assessment Scale were measured at each visit. Results: Each subject had a varied response to the measurement and intervention phases. The rate of recovery was greater during the robot-mediated therapy phase than in the baseline phase for the majority of subjects. The rate of recovery during the robot-mediated therapy phase was also greater than that during the sling suspension phase for most subjects. Conclusion: The positive treatment effect for both groups suggests that robot-mediated therapy can have a treatment effect greater than the same duration of non-functional exercises. Further studies investigating the optimal duration of treatment in the form of a randomized controlled trial are warranted.
How Tough are Better Business Bureau/Wise Giving Alliance Financial Standards?
Authors: Bhattacharya Rinku , Tinkelman Daniel 
Published: April 2008

The use of financial efficiency ratios to judge charities' performance is controversial. The authors investigate the stringency of one widely used set of standards by examining reported 2001 data for more than 111,000 organizations. The authors suggest the ability of many organizations to comply inhibits protests against the widespread use of these ratios. The Wise Giving Alliance adopted stricter standards in 2003, and the authors find that more organizations will be able to meet the new standards. As in the past, the great majority of organizations report compliance. The authors note marked differences in the rates of compliance with both the program spending and fund-raising efficiency standards by sector. Also, organizations with larger special events tend to incur relatively larger costs. The authors question the use of the same ratios for all organizations. The authors note no evidence of widespread expense allocation manipulation around the critical levels of ratios monitored by the Alliance.
Gender, economics and culture: diversity and the international evolution of smoking prevalence
Authors: Stevens Andy RA , Caan Woody 
Published: April 2008

Aims: To examine whether the observed diversity between national patterns of smoking prevalence could require modification of the World Health Organization (WHO) linear model for an international `smoking pandemic' (a worldwide epidemic) to address data from non-western countries. Method: We conducted secondary research using current measures in three publicly available databases: Globalink, the International Labour Organization and the World Bank (all internetaccessible). The measures we used are the separate percentage data for men and women on: smoking and employment and national income per capita (US$) and percentage growth per annum. Results: Regression analysis showed that women smokers were more frequent in countries with higher national income, but women were less likely to smoke in countries of rapid growth. Men were less likely to smoke in countries with higher national income, but more likely to smoke in countries of rapid growth. Two principle components together explained 62% of all the variance in the international data. The largest factor was positively correlated with the percentage of employed females, the percentage of female smokers and national income per capita, but negatively correlated with the percentage of male smokers and percentage annual growth. The effect of female employment was not continuous, but above a threshold of 51%, was associated with a higher prevalence of female smoking. The smaller, second factor was only weakly correlated with any smoking variables. Conclusions: In his 1994 model (subsequently adopted by the WHO) Lopez looked at historical trends in `stages' of smoking prevalence. These have been associated with `stages' of economic development. We extended this analysis to look at a dynamic change (% annual growth) and a social indicator (employment). Male and female smoking is affected differentially by economic change and by level of income. These are also strongly related to the percentage of women in employment. This has implications for workplace policies on smoking.
Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes
Authors: Margaria Tiziana , Kubczak Christian , Steffen Bernhard 
Published: April 2008

AbstractBackgroundWith Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout.MethodsBio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.ConclusionsAs a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.
AMMO-Prot: amine system project 3D-model finder
Authors: Navas-Delgado Ismael , Montañez Raúl , Pino-Ángeles Almudena , Moya-García Aurelio A , Urdiales José Luis , Sánchez-Jiménez Francisca , Aldana-Montes José F 
Published: April 2008

Abstract

Background
Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accumulated, which need to be integrated in order to be effective in the advance of biological knowledge in the field. For this purpose, a multidisciplinary group has started an ontology-based system named the Amine System Project (ASP) for which amine-related information is the validation bench.

Results
In this paper, we describe the Ontology-Based Mediator developed in the Amine System Project (http://asp.uma.es) using the infrastructure of Semantic Directories, and how this system has been used to solve a case related to amine metabolism-related protein structures.

Conclusions
This infrastructure is used to publish and manage not only ontologies and their relationships, but also metadata relating to the resources committed with the ontologies. The system developed is available at http://asp.uma.es/WebMediator.
Reconstructing networks of pathways via significance analysis of their intersections
Authors: Francesconi Mirko , Remondini Daniel , Neretti Nicola , Sedivy John M , Cooper Leon N , Verondini Ettore , Milanesi Luciano , Castellani Gastone 
Published: April 2008

Abstract

Background
Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically approached by applying post hoc corrections to control the false discovery rate, without taking into account prior biological knowledge. Pathway or gene ontology analysis can provide an alternative way to relax the significance threshold applied to single genes and may lead to a better biological interpretation.

Results
Here we propose a new analysis method based on the study of networks of pathways. These networks are reconstructed considering both the significance of single pathways (network nodes) and the intersection between them (links).
We apply this method for the reconstruction of networks of pathways to two gene expression datasets: the first one obtained from a c-Myc rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein; the second one obtained from the comparison of Acute Myeloid Leukemia and Acute Lymphoblastic Leukemia derived from bone marrow samples.

Conclusion
Our method extends statistical models that have been recently adopted for the significance analysis of functional groups of genes to infer links between these groups. We show that groups of genes at the interface between different pathways can be considered as relevant even if the pathways they belong to are not significant by themselves.
A yeast three-hybrid system that reconstitutes mammalian hypoxia inducible factor regulatory machinery
Authors: Alcaide-German Maria L , Vara-Vega Alicia , Garcia-Fernandez Luis F , Landazuri Manuel O , del Peso Luis 
Published: April 2008

Abstract

Background
Several human pathologies, including neoplasia and ischemic cardiovascular diseases, course with an unbalance between oxygen supply and demand (hypoxia). Cells within hypoxic regions respond with the induction of a specific genetic program, under the control of the Hypoxia Inducible Factor (HIF), that mediates their adaptation to the lack of oxygen. The activity of HIF is mainly regulated by the EGL-nine homolog (EGLN) enzymes that hydroxylate the alpha subunit of this transcription factor in an oxygen-dependent reaction. Hydroxylated HIF is then recognized and ubiquitinilated by the product of the tumor suppressor gene, pVHL, leading to its proteosomal degradation. Under hypoxia, the hydroxylation of HIF by the EGLNs is compromised due to the lack of oxygen, which is a reaction cosubstrate. Thus, HIF escapes degradation and drives the transcription of its target genes. Since the progression of the aforementioned pathologies might be influenced by activation of HIF-target genes, development of small molecules with the ability to interfere with the HIF-regulatory machinery is of great interest.

Results
Herein we describe a yeast three-hybrid system that reconstitutes mammalian HIF regulation by the EGLNs and VHL. In this system, yeast growth, under specific nutrient restrictions, is driven by the interaction between the β domain of VHL and a hydroxyproline-containing HIFα peptide. In turn, this interaction is strictly dependent on EGLN activity that hydroxylates the HIFα peptide. Importantly, this system accurately preserves the specificity of the hydroxylation reaction toward specific substrates. We propose that this system, in combination with a matched control, can be used as a simple and inexpensive assay to identify molecules that specifically modulate EGLN activity. As a proof of principle we show that two known EGLN inhibitors, dimethyloxaloylglycine (DMOG) and 6-chlor-3-hydroxychinolin-2-carbonic acid-N-carboxymethylamide (S956711), have a profound and specific effect on the yeast HIF/EGLN/VHL system.

Conclusion
The system described in this work accurately reconstitutes HIF regulation while preserving EGLN substrate specificity. Thus, it is a valuable tool to study HIF regulation, and particularly EGLN biochemistry, in a cellular context. In addition, we demonstrate that this system can be used to identify specific inhibitors of the EGLN enzymes.
Axon-bearing and axon-less horizontal cell subtypes are generated consecutively during chick retinal development from progenitors that are sensitive to follistatin
Authors: Edqvist Per-Henrik D , Lek Madelen , Boije Henrik , Lindbäck Sarah M , Hallböök Finn 
Published: April 2008

Abstract

Background
Horizontal cells are retinal interneurons that modulate the output from photoreceptors. A rich literature on the morphological classification and functional properties of HCs in different animals exists, however, the understanding of the events underlying their development is still limited. In most vertebrates including chicken, two main horizontal cell (HC) subtypes are identified based on the presence or absence of an axon.

Results
In this work we have molecularly characterized three HC subtypes based on Lim1, Isl1, GABA and TrkA, a classification that is consistent with three chick HC subtypes previously defined by morphology. The axon-bearing and axon-less HC subpopulations molecularly defined by Lim1 and Isl1, are born consecutively on embryonic day (E) 3–4 and E4–5, respectively, and exhibit temporally distinguishable periods of migration. Their relative numbers are not adjusted by apoptosis. A sharp decrease of high endogenous levels of the activin-inhibitor follistatin at E3 coincides with the appearance of the Lim1 positive cells. Extending the follistatin exposure of the HC retinal progenitor cells by injection of follistatin at E3 increased the number of both Lim1- and Isl1 positive HCs when analysed at E9.

Conclusion
The results imply that the axon-bearing and axon-less HC subgroups are defined early and are generated consecutively from a retinal progenitor cell population that is sensitive to the inhibitory action of follistatin. The results are consistent with a model wherein added follistatin causes HC-generating progenitors to proliferate beyond the normal period of HC generation, thus producing extra HCs of both types that migrate to the HC layer.
Expression patterns of protein kinase D 3 during mouse development
Authors: Ellwanger Kornelia , Pfizenmaier Klaus , Lutz Sylke , Hausser Angelika 
Published: April 2008

Abstract

Background
The PKD family of serine/threonine kinases comprises a single member in Drosophila (dPKD), two isoforms in C. elegans (DKF-1 and 2) and three members, PKD1, PKD2 and PKD3 in mammals. PKD1 and PKD2 have been the focus of most studies up to date, which implicate these enzymes in very diverse cellular functions, including Golgi organization and plasma membrane directed transport, immune responses, apoptosis and cell proliferation. Concerning PKD3, a role in the formation of vesicular transport carriers at the trans-Golgi network (TGN) and in basal glucose transport has been inferred from in vitro studies. So far, however, the physiological functions of the kinase during development remain unknown.

Results
We have examined the expression pattern of PKD3 during the development of mouse embryos by immunohistochemistry. Using a PKD3 specific antibody we demonstrate that the kinase is differentially expressed during organogenesis. In the developing heart a strong PKD3 expression is constantly detected from E10 to E16.5. From E12.5 on PKD3 is increasingly expressed in neuronal as well as in the supporting connective tissue and in skeletal muscles.

Conclusion
The data presented support an important role for PKD3 during development of these tissues.
Burkholderia pseudomallei genome plasticity associated with genomic island variation
Authors: Tumapa Sarinna , Holden Matthew TG , Vesaratchavest Mongkol , Wuthiekanun Vanaporn , Limmathurotsakul Direk , Chierakul Wirongrong , Feil Edward J , Currie Bart J , Day Nicholas PJ , Nierman William C , Peacock Sharon J 
Published: April 2008

Abstract

Background

Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival.

Results
Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis.

Conclusion
Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.
Identification of Tmem10/Opalin as a novel marker for oligodendrocytes using gene expression profiling
Authors: Kippert Angelika , Trajkovic Katarina , Fitzner Dirk , Opitz Lennart , Simons Mikael 
Published: April 2008

AbstractBackgroundDuring the development of the central nervous system, oligodendrocytes generate large amounts of myelin, a multilayered insulating membrane that ensheathes axons, thereby allowing the fast conduction of the action potential and maintaining axonal integrity. Differentiation of oligodendrocytes to myelin-forming cells requires the downregulation of RhoA GTPase activity.ResultsTo gain insights into the molecular mechanisms of oligodendrocyte differentiation, we performed microarray expression profiling of the oligodendroglial cell line, Oli-neu, treated with the Rho kinase (ROCK) inhibitor, Y-27632 or with conditioned neuronal medium. This resulted in the identification of the transmembrane protein 10 (Tmem10/Opalin), a novel type I transmembrane protein enriched in differentiating oligodendrocytes. In primary cultures, Tmem10 was abundantly expressed in O4-positive oligodendrocytes, but not in oligodendroglial precursor cells, astrocytes, microglia or neurons. In mature oligodendrocytes Tmem10 was enriched in the rims and processes of the cells and was only found to a lesser extent in the membrane sheets.ConclusionTogether, our results demonstrate that Tmem10 is a novel marker for in vitro generated oligodendrocytes.