bluuebunny/crossref_metadata_2025_split huggingface dataset:
A lifestyle intervention as supplement to a physical activity programme in rehabilitation after stroke: a randomized controlled trial
Authors: Lund A , Michelet M , Sandvik L , Wyller TB , Sveen U 
Published: December 2011

Objective: To evaluate the effectiveness of lifestyle group intervention on well-being, occupation and social participation. Design: A randomized controlled trial. Setting: Senior centres in the community. Subjects: Of 204 stroke survivors screened, 99 (49%) were randomized three months after stroke whereby 86 (87%) participants (mean (SD) age 77.0 (7.1) years) completed all assessments (39 in the intervention group and 47 in the control group). Intervention: A lifestyle course in combination with physical activity (intervention group) compared with physical activity alone (control group). Both programmes were held once a week for nine months. Main outcome measure: The Short Form Questionnaire (SF-36), addressing well-being and social participation. Assessments were performed at baseline and at nine months follow-up. Results: We found no statistically significant differences between the groups at the nine months follow-up in the SF-36. Adjusted mean differences in change scores in the eight subscales of SF-36 were; ‘mental health’ (+1.8, 95% confidence interval (CI) –4.0, +7.6), ‘vitality’ (−3.0, 95% CI −9.6, +3.6), ‘bodily pain’ (+3.3, 95% CI −7.8, +14.4), ‘general health’ (−1.6, 95% CI −8.4, +5.1), ‘social functioning’ (−2.5, 95% CI −12.8, +7.8), ‘physical functioning’ (+1.0, 95% CI −6.7, +8.6), ‘role physical’ (−7.1, 95% CI −22.7, +8.4), ‘role emotional’ (+11.8, 95% CI −4.4, +28.0). Conclusions: Improvements were seen in both groups, but no statistically significant differences were found in the intervention group compared to controls. An intervention comprising regular group-based activity with peers may be sufficient in the long-term rehabilitation after stroke.
Immune function and brain abnormalities in patients with systemic lupus erythematosus without overt neuropsychiatric manifestations
Authors: Kozora E , Filley CM , Zhang L , Brown MS , Miller DE , Arciniegas DB , Pelzman JL , West SG 
Published: December 2011

Objective: This study examined the relationship between immune, cognitive and neuroimaging assessments in subjects with systemic lupus erythematosus (SLE) without histories of overt neuropsychiatric (NP) disorders. Methods: In total, 84 subjects with nonNPSLE and 37 healthy controls completed neuropsychological testing from the American College of Rheumatology SLE battery. Serum autoantibody and cytokine measures, volumetric magnetic resonance imaging, and magnetic resonance spectroscopy data were collected on a subset of subjects. Results: NonNPSLE subjects had lower scores on measures of visual/complex attention, visuomotor speed and verbal memory compared with controls. No clinically significant differences between nonNPSLE patients and controls were found on serum measures of lupus anticoagulant, anticardiolipin antibodies, beta 2-glycoproteins, or pro-inflammatory cytokines (interleukin (IL)-1, IL-6, interferon alpha (IFN-alpha), and interferon gamma (IFN-gamma)). Higher scores on a global cognitive impairment index and a memory impairment index were correlated with lower IFN-alpha. Few associations between immune functions and neuroimaging parameters were found. Conclusions: Results indicated that nonNPSLE patients demonstrated cognitive impairment but not immune differences compared with controls. In these subjects, who were relatively young and with mild disease, no relationship between cognitive dysfunction, immune parameters, or previously documented neuroimaging abnormalities were noted. Immune measures acquired from cerebrospinal fluid instead of serum may yield stronger associations.
Perceptions des barrières à la stratégie de formation des médecins généralistes à la chirurgie essentielle pour l’offre de soins obstétricaux et chirurgicaux d’urgence au Burkina Faso
Authors: Traoré Abdoulaye , Bocoum Fadima , Sennen Hounton , Méda Nicolas , Diagbouga et Serge P. 
Published: December 2011

Résumé Réduire de 75% les ratios de la mortalité maternelle d’ici à 2015 est l’un des défis majeurs des pays pauvres dans le cadre des Objectifs du Millénaire pour le Développement. Au Burkina Faso, on estime que 60% des femmes accouchent toujours sans assistance médicale, et que 480 d’entre elles meurent pour 100 000 naissances vivantes. Pour relever ce défi le pays a initié depuis 1992 une stratégie dite des « médecins formés à la chirurgie essentielle », pour officier dans les hôpitaux de district. Douze ans après, l’Organisation Ouest Africaine de la Santé et le Centre Muraz ont promu une évaluation de cette stratégie, avec un volet qualitatif devant analyser les perceptions qu’ont les concernés de ses facteurs limitants. Plusieurs profils d’informateurs ont été interrogés à cet effet. La stratégie s’est avérée une option adaptée au contexte. Toutefois, sa viabilité est mise à épreuve du fait que la formation ne soit pas diplômante, avec des avantages incitatifs. Les médecins formés, qui sont aussi les « Chefs de District », s’investissaient plus dans les tâches managériales que dans les activités cliniques. Ainsi, bien qu’elle soit une réponse alternative efficace au déficit des spécialistes, la stratégie pourrait aussi être efficiente si la formation était labellisée. A défaut, un nouveau profil de chef de district pourrait être envisagé, en y excluant la condition d’être formé à la chirurgie essentielle. L’augmentation des effectifs des Attachés de Santé en Chirurgie, formés en 2 ans, et qui sont actuellement les principaux acteurs des interventions chirurgicales dans les hôpitaux de district, est déjà une alternative à portée de main. Le recyclage et le suivi des médecins formés, mais aussi le suivi du matériel (approvisionnement et maintenance) seraient également des dispositions de renforcement des acquis.
MST1 mutations in autosomal recessive primary immunodeficiency characterized by defective naive T-cell survival
Authors: Nehme Nadine T. , Schmid Jana Pachlopnik , Debeurme Franck , André-Schmutz Isabelle , Lim Annick , Nitschke Patrick , Rieux-Laucat Frédéric , Lutz Patrick , Picard Capucine , Mahlaoui Nizar , Fischer Alain , de Saint Basile Geneviève 
Published: December 2011

Abstract
The molecular mechanisms that underlie T-cell quiescence are poorly understood. In the present study, we report a primary immunodeficiency phenotype associated with MST1 deficiency and primarily characterized by a progressive loss of naive T cells. The in vivo consequences include recurrent bacterial and viral infections and autoimmune manifestations. MST1-deficient T cells poorly expressed the transcription factor FOXO1, the IL-7 receptor, and BCL2. Conversely, FAS expression and the FAS-mediating apoptotic pathway were up-regulated. These abnormalities suggest that increased cell death of naive and proliferating T cells is the main mechanism underlying this novel immunodeficiency. Our results characterize a new mechanism in primary T-cell immunodeficiencies and highlight a role of the MST1/FOXO1 pathway in controlling the death of human naive T cells.
Jetset: selecting the optimal microarray probe set to represent a gene
Authors: Li Qiyuan , Birkbak Nicolai J , Gyorffy Balazs , Szallasi Zoltan , Eklund Aron C 
Published: December 2011

Abstract

Background
Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task.

Results
We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes that were nominally detected by multiple probe sets, and we found that the probe set chosen by our method showed stronger concordance.

Conclusions
This method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest.
Phylogenetically informed logic relationships improve detection of biological network organization
Authors: Cui Jike , DeLuca Todd F , Jung Jae-Yoon , Wall Dennis P 
Published: December 2011

Abstract

Background
A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses.

Results
Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks.

Conclusion
Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction.
A potential role of the JNK pathway in hyperoxia-induced cell death, myofibroblast transdifferentiation and TGF-β1-mediated injury in the developing murine lung
Authors: Li Zhang , Choo-Wing Rayman , Sun Huanxing , Sureshbabu Angara , Sakurai Reiko , Rehan Virender K , Bhandari Vineet 
Published: December 2011

Abstract

Background
Transforming growth factor-beta 1 (TGF-β1) has been implicated in hyperoxia-induced cell death and impaired alveolarization in the developing lung. In addition, the c-JunNH2-terminal kinase (JNK) pathway has been shown to have a role for TGF-β1-mediated effects. We hypothesized that the JNK pathway is an important regulator of hyperoxia-induced pulmonary responses in the developing murine lung.

Results
We used cultured human lung epithelial cells, fetal rat lung fibroblasts and a neonatal TGF-β1 transgenic mouse model. We demonstrate that hyperoxia inhibits cell proliferation, activates cell death mediators and causes cell death, and promotes myofibroblast transdifferentiation, in a dose-dependent manner. Except for fibroblast proliferation, the effects were mediated via the JNK pathway. In addition, since we observed increased expression of TGF-β1 by epithelial cells on exposure to hyperoxia, we used a TGF-β1 transgenic mouse model to determine the role of JNK activation in TGF-β1 induced effects on lung development and on exposure to hyperoxia. We noted that, in this model, inhibition of JNK signaling significantly improved the spontaneously impaired alveolarization in room air and decreased mortality on exposure to hyperoxia.

Conclusions
When viewed in combination, these studies demonstrate that hyperoxia-induced cell death, myofibroblast transdifferentiation, TGF-β1- and hyperoxia-mediated pulmonary responses are mediated, at least in part, via signaling through the JNK pathway.
RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus
Authors: Villar Emilie , Klopp Christophe , Noirot Céline , Novaes Evandro , Kirst Matias , Plomion Christophe , Gion Jean-Marc 
Published: December 2011

Abstract

Background
In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit.

Results
Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed.

Conclusions
For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.
Functional characterization of TRICHOMELESS2, a new single-repeat R3 MYB transcription factor in the regulation of trichome patterning in Arabidopsis
Authors: Gan Lijun , Xia Kai , Chen Jin-Gui , Wang Shucai 
Published: December 2011

Abstract

Background
Single-repeat R3 MYB transcription factors (single-repeat MYBs) play important roles in controlling trichome patterning in Arabidopsis. It was proposed that single-repeat MYBs negatively regulate trichome formation by competing with GLABRA1 (GL1) for binding GLABRA3/ENHANCER OF GLABRA3 (GL3/EGL3), thus inhibiting the formation of activator complex TTG1(TRANSPARENT TESTA GLABRA1)-GL3/EGL3-GL1 that is required for the activation of GLABRA2 (GL2), whose product is a positive regulator of trichome formation. Previously we identified a novel single-repeat MYB transcription factor, TRICHOMELESS1 (TCL1), which negatively regulates trichome formation on the inflorescence stems and pedicels by directly suppressing the expression of GL1.

Results
We analyzed here the role of TRICHOMELESS2 (TCL2), a previously-uncharacterized single-repeat MYB transcription factor in trichome patterning in Arabidopsis. We showed that TCL2 is closely related to TCL1, and like TCL1 and other single-repeat MYBs, TCL2 interacts with GL3. Overexpression of TCL2 conferred glabrous phenotype while knockdown of TCL2 via RNAi induced ectopic trichome formation on the inflorescence stems and pedicels, a phenotype that was previously observed in tcl1 mutants. These results suggested that TCL2 may have overlapping function with TCL1 in controlling trichome formation on inflorescences. On the other hand, although the transcription of TCL2, like TCL1, is not controlled by the activator complex formed by GL1 and GL3, and TCL2 and TCL1 proteins are more than 80% identical at the amino acid level, the expression of TCL2 under the control of TCL1 promoter only partially recovered the mutant phenotype of tcl1, implying that TCL2 and TCL1 are not fully functional equivalent.

Conclusions
TCL2 function redundantly with TCL1 in controlling trichome formation on inflorescences, but they are not fully functional equivalent. Transcription of TCL2 is not controlled by activator complex formed by GL1 and GL3, but MIR156 controlled SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) transcription factors. However, SPLs might require co-activators to regulate the expression of their target genes, including TCL1, TRY and possibly, TCL2.
GmPHD5 acts as an important regulator for crosstalk between histone H3K4 di-methylation and H3K14 acetylation in response to salinity stress in soybean
Authors: Wu Tao , Pi Er-Xu , Tsai Sau-Na , Lam Hon-Ming , Sun Sai-Ming , Kwan Yiu Wa , Ngai Sai-Ming 
Published: December 2011

Abstract

Background
Accumulated evidence suggest that specific patterns of histone posttranslational modifications (PTMs) and their crosstalks may determine transcriptional outcomes. However, the regulatory mechanisms of these "histone codes" in plants remain largely unknown.

Results
In this study, we demonstrate for the first time that a salinity stress inducible PHD (plant homeodomain) finger domain containing protein GmPHD5 can read the "histone code" underlying the methylated H3K4. GmPHD5 interacts with other DNA binding proteins, including GmGNAT1 (an acetyl transferase), GmElongin A (a transcription elongation factor) and GmISWI (a chromatin remodeling protein). Our results suggest that GmPHD5 can recognize specific histone methylated H3K4, with preference to di-methylated H3K4. Here, we illustrate that the interaction between GmPHD5 and GmGNAT1 is regulated by the self-acetylation of GmGNAT1, which can also acetylate histone H3. GmGNAT1 exhibits a preference toward acetylated histone H3K14. These results suggest a histone crosstalk between methylated H3K4 and acetylated H3K14. Consistent to its putative roles in gene regulation under salinity stress, we showed that GmPHD5 can bind to the promoters of some confirmed salinity inducible genes in soybean.

Conclusion
Here, we propose a model suggesting that the nuclear protein GmPHD5 is capable of regulating the crosstalk between histone methylation and histone acetylation of different lysine residues. Nevertheless, GmPHD5 could also recruit chromatin remodeling factors and transcription factors of salt stress inducible genes to regulate their expression in response to salinity stress.
Population versus hospital controls for case-control studies on cancers in Chinese hospitals
Authors: Li Lin , Zhang Min , Holman D'Arcy 
Published: December 2011

Abstract

Background
Correct control selection is crucial to the internal validity of case-control studies. Little information exists on differences between population and hospital controls in case-control studies on cancers in Chinese hospital setting.

Methods
We conducted three parallel case-control studies on leukemia, breast and colorectal cancers in China between 2009 and 2010, using population and hospital controls to separately match 540 incident cases by age, gender and residency at a 1:1 ratio. Demographic and lifestyle factors were measured using a validated questionnaire in face-to-face interview. Odds ratios (ORs) and 95% confidence intervals (CIs) were obtained using conditional logistic regression analyses.

Results
The two control groups had closely similar exposure distributions of 15 out of 16 factors, with the only exception being that hospital controls were less likely to have a BMI ≥ 25 (OR = 0.71, 95% CI: 0.54, 0.93). For exposure of green tea drinking, the adjusted ORs (95% CIs) comparing green tealeaves intake ≥ 1000 grams annually with non-drinkers were 0.51 (0.31, 0.83) and 0.21 (0.27, 0.74) for three cancers combined, 0.06 (0.01, 0.61) and 0.07 (0.01, 0.47) for breast cancer, 0.52 (0.29, 0.94) and 0.45 (0.25, 0.82) for colorectal cancer, 0.65 (0.08, 5.63) and 0.57 (0.07, 4.79) for leukemia using hospital and population controls respectively.

Conclusions
The study found that hospital controls were comparable with population controls for most demographic characteristics and lifestyle factors measured, but there was a slight difference between the two control groups. Hospital outpatients provide a satisfactory control group in hospital-based case-control study in the Chinese hospital setting.
Disease management for co-morbid depression and anxiety in diabetes mellitus: design of a randomised controlled trial in primary care
Authors: Stoop Corinne H , Spek Viola RM , Pop Victor JM , Pouwer François 
Published: December 2011

Abstract

Background
Depression and anxiety are common co-morbid health problems in patients with type 2 diabetes. Both depression and anxiety are associated with poor glycaemic control and increased risk of poor vascular outcomes and higher mortality rates. Results of previous studies have shown that in clinical practice, treatment of depression and anxiety is far from optimal as these symptoms are frequently overlooked and undertreated.

Methods/Design
This randomised controlled trial will examine the effectiveness of a disease management programme treating symptoms of depression and anxiety in primary care patients with Type 2 diabetes. Patients will be randomized on patient level in 1:1 ratio. Random block sizes of 2 and 4 are used. The disease management programme consists of screening, stepped treatment and monitoring of symptoms (n = 80). This will be compared to care as usual (n = 80).

Discussion
The disease management model for co-morbid depression and anxiety in primary care patients with diabetes is expected to result in reduced symptoms of depression and anxiety, improved quality of life, reduced diabetes specific distress and improved glyceamic control, compared to care as usual.

Trial Registration
Dutch Trial Register NTR2626