bluuebunny/crossref_metadata_2025_split huggingface dataset:
New autophotosensitive semiaromatic hyperbranched polyimides with excellent thermal stabilities and low birefringences
Authors: Liu Changwei , Zhao Xiaogang , Li Yan , Yang Dong , Wang Lina , Jin Lin , Chen Chunhai , Zhou Hongwei 
Published: October 2012

A series of autophotosensitive semiaromatic hyperbranched polyimides were prepared by (A2 + B3)-type method and endcapped with 3-aminophenylacetylene. The photosensitive-hyperbranched polyimides (PHBPIs) showed excellent solubility, excellent optical properties, and low birefringences in the range of 0.0010–0.0027, caused by their special hyperbranched structures and alicyclic chain segments reduced both intramolecular and intermolecular charge transfer complex effect. The cured films also showed high glass transition temperatures between 204°C and 220°C, excellent thermal stabilities with 10% thermal decomposing temperatures in the range of 476–495°C, and good mechanical properties. The PHBPIs had photosensitivities ( Dg) in the range of 80–162 mJ/cm2 and showed a clear negative image with a line width of 8 µm when exposed to an ultraviolet light of 365 nm ( i-line).
A literature-based approach to evaluate the predictive capacity of a marker using time-dependent summary receiver operating characteristics
Authors: Combescure C , Daures JP , Foucher Y 
Published: November 2012

Summary Meta-analyses are popular tools to summarize the results of publications. Prognostic performances of a marker are usually summarized by meta-analyses of survival curves or hazard ratios. These approaches may detect a difference in survival according to the marker but do not allow evaluation of its prognostic capacity. Time-dependent receiver operating characteristic curves evaluate the ability of a marker to predict time-to-event. In this article, we describe an adaptation of time-dependent summary receiver operating characteristic curves from published survival curves. To achieve this goal, we modeled the marker and the time-to-event distributions using non-linear mixed models. First, we applied this methodology to individual data in kidney transplantation presented as aggregated data, in order to validate the method. Second, we re-analyzed a published meta-analysis, which focused on the capacity of KI-67 to predict the overall survival of patients with breast cancer.
A hybrid projection method for solving a common solution of a system of equilibrium problems and fixed point problems for asymptotically strict pseudocontractions in the intermediate sense in Hilbert spaces
Authors: Watchararuangwit Chatchawan , Phuangphoo Pongrus , Kumam Poom 
Published: October 2012

Abstract
In this paper, we introduce a new iterative algorithm which is constructed by using the hybrid projection method for finding a common solution of a system of equilibrium problems of bifunctions satisfying certain conditions and a common solution of fixed point problems of a family of uniformly Lipschitz continuous and asymptotically

λ
i

-strict pseudocontractive mappings in the intermediate sense. We prove the strong convergence theorem for a new iterative algorithm under some mild conditions in Hilbert spaces. Finally, we also give a numerical example which supports our results.

MSC:47H05, 47H09, 47H10.
Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data
Authors: Iliadis Alexandros , Anastassiou Dimitris , Wang Xiaodong 
Published: October 2012

Abstract

Background
Typically, the first phase of a genome wide association study (GWAS) includes genotyping across hundreds of individuals and validation of the most significant SNPs. Allelotyping of pooled genomic DNA is a common approach to reduce the overall cost of the study. Knowledge of haplotype structure can provide additional information to single locus analyses. Several methods have been proposed for estimating haplotype frequencies in a population from pooled DNA data.

Results
We introduce a technique for haplotype frequency estimation in a population from pooled DNA samples focusing on datasets containing a small number of individuals per pool (2 or 3 individuals) and a large number of markers. We compare our method with the publicly available state-of-the-art algorithms HIPPO and HAPLOPOOL on datasets of varying number of pools and marker sizes. We demonstrate that our algorithm provides improvements in terms of accuracy and computational time over competing methods for large number of markers while demonstrating comparable performance for smaller marker sizes. Our method is implemented in the "Tree-Based Deterministic Sampling Pool" (TDSPool) package which is available for download at http://www.ee.columbia.edu/~anastas/tdspool.

Conclusions
Using a tree-based determinstic sampling technique we present an algorithm for haplotype frequency estimation from pooled data. Our method demonstrates superior performance in datasets with large number of markers and could be the method of choice for haplotype frequency estimation in such datasets.
The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.
Authors: Young Philip R , Lashbrooke Justin G , Alexandersson Erik , Jacobson Dan , Moser Claudio , Velasco Riccardo , Vivier Melané A 
Published: October 2012

AbstractBackgroundCarotenoids are a heterogeneous group of plant isoprenoids primarily involved in photosynthesis. In plants the cleavage of carotenoids leads to the formation of the phytohormones abscisic acid and strigolactone, and C13-norisoprenoids involved in the characteristic flavour and aroma compounds in flowers and fruits and are of specific importance in the varietal character of grapes and wine. This work extends the previous reports of carotenoid gene expression and photosynthetic pigment analysis by providing an up-to-date pathway analysis and an important framework for the analysis of carotenoid metabolic pathways in grapevine.ResultsComparative genomics was used to identify 42 genes putatively involved in carotenoid biosynthesis/catabolism in grapevine. The genes are distributed on 16 of the 19 chromosomes and have been localised to the physical map of the heterozygous ENTAV115 grapevine sequence. Nine of the genes occur as single copies whereas the rest of the carotenoid metabolic genes have more than one paralogue. The cDNA copies of eleven corresponding genes fromVitis viniferaL. cv. Pinotage were characterised, and four where shown to be functional. Microarrays provided expression profiles of 39 accessions in the metabolic pathway during three berry developmental stages in Sauvignon blanc, whereas an optimised HPLC analysis provided the concentrations of individual carotenoids. This provides evidence of the functioning of the lutein epoxide cycle and the respective genes in grapevine. Similarly, orthologues of genes leading to the formation of strigolactone involved in shoot branching inhibition were identified:CCD7,CCD8andMAX1. Moreover, the isoforms typically have different expression patterns, confirming the complex regulation of the pathway. Of particular interest is the expression pattern of the threeVvNCEDs: Our results support previous findings thatVvNCED3is likely the isoform linked to ABA content in berries.ConclusionsThe carotenoid metabolic pathway is well characterised, and the genes and enzymes have been studied in a number of plants. The study of the 42 carotenoid pathway genes of grapevine showed that they share a high degree of similarity with other eudicots. Expression and pigment profiling of developing berries provided insights into the most complete grapevine carotenoid pathway representation. This study represents an important reference study for further characterisation of carotenoid biosynthesis and catabolism in grapevine.
QTL mapping of the production of wine aroma compounds by yeast
Authors: Steyer Damien , Ambroset Chloe , Brion Christian , Claudel Patricia , Delobel Pierre , Sanchez Isabelle , Erny Claude , Blondin Bruno , Karst Francis , Legras Jean-Luc 
Published: October 2012

Abstract

Background
Wine aroma results from the combination of numerous volatile compounds, some produced by yeast and others produced in the grapes and further metabolized by yeast. However, little is known about the consequences of the genetic variation of yeast on the production of these volatile metabolites, or on the metabolic pathways involved in the metabolism of grape compounds. As a tool to decipher how wine aroma develops, we analyzed, under two experimental conditions, the production of 44 compounds by a population of 30 segregants from a cross between a laboratory strain and an industrial strain genotyped at high density.

Results
We detected eight genomic regions explaining the diversity concerning 15 compounds, some produced de novo by yeast, such as nerolidol, ethyl esters and phenyl ethanol, and others derived from grape compounds such as citronellol, and cis-rose oxide. In three of these eight regions, we identified genes involved in the phenotype. Hemizygote comparison allowed the attribution of differences in the production of nerolidol and 2-phenyl ethanol to the PDR8 and ABZ1 genes, respectively. Deletion of a PLB2 gene confirmed its involvement in the production of ethyl esters. A comparison of allelic variants of PDR8 and ABZ1 in a set of available sequences revealed that both genes present a higher than expected number of non-synonymous mutations indicating possible balancing selection.

Conclusions
This study illustrates the value of QTL analysis for the analysis of metabolic traits, and in particular the production of wine aromas. It also identifies the particular role of the PDR8 gene in the production of farnesyldiphosphate derivatives, of ABZ1 in the production of numerous compounds and of PLB2 in ethyl ester synthesis. This work also provides a basis for elucidating the metabolism of various grape compounds, such as citronellol and cis-rose oxide.
Detection of genetic association and functional polymorphisms of UGDH affecting milk production trait in Chinese Holstein cattle
Authors: Xu Qing , Mei Gui , Sun Dongxiao , Zhang Qin , Zhang Yuan , Yin Cengceng , Chen Huiyong , Ding Xiangdong , Liu Jianfeng 
Published: November 2012

Abstract

Background
We previously localized a quantitative trait locus (QTL) on bovine chromosome 6 affecting milk production traits to a 1.5-Mb region between BMS483 and MNB-209 via genome scanning followed by fine mapping.

Results
Totally 15 genes were mapped within such linkage region through bioinformatic analysis of the cattle-human comparative map and bovine genome assembly. Of them, the UDP-glucose dehydrogenase (UGDH) was suggested as a potential positional candidate gene for milk production traits based on its corresponding physiological and biochemical functions and genetic effects. By sequencing all the coding exons and the untranslated regions in UGDH with pooled DNA of 8 sires represented the separated families detected in our previous studies, a total of ten SNPs were identified and genotyped in 1417 Holstein cows of 8 separation families. Individual SNP-based association analysis revealed 4 significant associations of SNP Ex1-1, SNP Int3-1, SNP Int5-1, and SNP Ex12-3 with milk yield (P < 0.05), and 2 significant associations of SNP Ex1-1 and SNP Ex12-3 with protein yield (P < 0.05). Furthermore, our haplotype-based association analyses indicated that haplotypes G-C-C, formed by SNP Ex12-2-SNP Int11-1-SNP Ex11-1, T-G, formed by SNP Int9-3-SNP Int9-2, and C-C, formed by SNP Int5-1-SNP Int3-1, are significantly associated with protein percentage (F=4.15; P=0.0418) and fat percentage (F=5.18~7.25; P=0.0072~0.0231). Finally, by using an in vitro expression assay, we demonstrated that the A allele of SNP Ex1-1 and T allele of SNP Ex11-1of UGDH significantly decreases the expression of UGDH by 68.0% at the RNA, and 50.1% at the protein level, suggesting that SNP Ex1-1 and Ex11-1 represent two functional polymorphisms affecting expression of UGDH and may partly contributed to the observed association of the gene with milk production traits in our samples.

Conclusions
Taken together, our findings strongly indicate that UGDH gene could be involved in genetic variation underlying the QTL for milk production traits.
Escherichia coli RecG functionally suppresses human Bloom syndrome phenotypes
Authors: Killen Michael W , Stults Dawn M , Wilson William A , Pierce Andrew J 
Published: October 2012

Abstract
Defects in the human BLM gene cause Bloom syndrome, notable for early development of tumors in a broad variety of tissues. On the basis of sequence similarity, BLM has been identified as one of the five human homologs of RecQ from Escherichia coli. Nevertheless, biochemical characterization of the BLM protein indicates far greater functional similarity to the E. coli RecG protein and there is no known RecG homolog in human cells. To explore the possibility that the shared biochemistries of BLM and RecG may represent an example of convergent evolution of cellular function where in humans BLM has evolved to fulfill the genomic stabilization role of RecG, we determined whether expression of RecG in human BLM-deficient cells could suppress established functional cellular Bloom syndrome phenotypes. We found that RecG can indeed largely suppress both the definitive elevated sister chromatid exchange phenotype and the more recently demonstrated gene cluster instability phenotype of BLM-deficient cells. In contrast, expression of RecG has no impact on either of these phenotypes in human cells with functional BLM protein. These results suggest that the combination of biochemical activities shared by RecG and BLM fill the same evolutionary niche in preserving genomic integrity without requiring exactly identical molecular mechanisms.
Physical activity and environmental enrichment regulate the generation of neural precursors in the adult mouse substantia nigra in a dopamine-dependent manner
Authors: Klaissle Philipp , Lesemann Anne , Huehnchen Petra , Hermann Andreas , Storch Alexander , Steiner Barbara 
Published: October 2012

Abstract

Background
Parkinson’s disease is characterized by a continuous loss of neurons within the substantia nigra (SN) leading to a depletion of dopamine. Within the adult SN as a non-neurogenic region, cells with mainly oligodendrocytic precursor characteristics, expressing the neuro-glial antigen-2 (NG2) are continuously generated. Proliferation of these cells is altered in animal models of Parkinson’s disease (PD). Exercise and environmental enrichment re-increase proliferation of NG2+ cells in PD models, however, a possible mechanistic role of dopamine for this increase is not completely understood. NG2+ cells can differentiate into oligodendrocytes but also into microglia and neurons as observed in vitro suggesting a possible hint for endogenous regenerative capacity of the SN. We investigated the role of dopamine in NG2-generation and differentiation in the adult SN stimulated by physical activity and environmental enrichment.

Results
We used the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-model for dopamine depletion and analysed newborn cells in the SN at different maturation stages and time points depending on voluntary physical activity, enriched environment and levodopa-treatment. We describe an activity- induced increase of new NG2-positive cells and also mature oligodendrocytes in the SN of healthy mice. Running and enriched environment refused to stimulate NG2-generation and oligodendrogenesis in MPTP-mice, an effect which could be reversed by pharmacological levodopa-induced rescue.

Conclusion
We suggest dopamine being a key regulator for activity-induced generation of NG2-cells and oliogodendrocytes in the SN as a potentially relevant mechanism in endogenous nigral cellular plasticity.
Training dual-task walking in community-dwelling adults within 1 year of stroke: a protocol for a single-blind randomized controlled trial
Authors: Plummer-D’Amato Prudence , Kyvelidou Anastasia , Sternad Dagmar , Najafi Bijan , Villalobos Raymond M , Zurakowski David 
Published: October 2012

AbstractBackgroundCommunity ambulation is a highly complex skill requiring the ability to adapt to increased environmental complexity and perform multiple tasks simultaneously. After stroke, individuals demonstrate a diminished ability to perform dual-tasks. Current evidence suggests that conventional rehabilitation does not adequately address gait-related dual-task impairments after stroke, which may be contributing to low levels of participation and physical inactivity in community-dwelling stroke survivors. The objective of this study is to investigate the efficacy of dual-task gait training in community-dwelling adults within 1 year of stroke. Specifically, we will compare the effects of dual-task gait training and single-task gait training on cognitive-motor interference during walking at preferred speed and at fastest comfortable speed (Aim 1), locomotor control during obstacle negotiation (Aim 2), and spontaneous physical activity (Aim 3).Methods/DesignThis single-blind randomized controlled trial will involve 44 individuals within 12 months of stroke. Following baseline evaluation, participants will be randomly allocated to single- or dual-task gait training. Both groups will receive 12, 30-minute sessions provided one-on-one over 4–6 weeks in an outpatient therapy setting. Single-task gait training involves practice of gait activities incorporating motor relearning principles. Dual-task gait training involves an identical gait training protocol; the critical difference being that the dual-task gait training group will practice the gait activities while simultaneously performing a cognitive task for 75% of the repetitions. Blinded assessors will measure outcomes at baseline, post-intervention, and 6 months after completion of the intervention. The primary outcome measure will be dual-task effects on gait speed and cognition during unobstructed walking. Secondary outcomes include spatiotemporal and kinetic gait parameters during unobstructed single- and dual-task walking at preferred and fastest comfortable walking speeds, gait parameters during high and low obstacle crossing, spontaneous physical activity, executive function, lower extremity motor function, Timed Up and Go, balance self-efficacy, number of falls, and stroke-related disability. Hypotheses for each aim will be tested using an intention-to-treat analysis with repeated measures ANOVA design.DiscussionThis trial will provide evidence to help clinicians make decisions about the types of activities to include in rehabilitation to improve dual-task walking after stroke.Trial registrationClinicalTrials.gov NCT01568957
Expression of ERBB3 binding protein 1 (EBP1) in salivary adenoid cystic carcinoma and its clinicopathological relevance
Authors: Sun Jian , Luo Yixi , Tian Zhen , Gu Liang , Xia Shu Chi , Yu Youcheng 
Published: October 2012

AbstractBackgroundERBB3 binding protein 1 (EBP1) gene transfer into human salivary adenoid cystic carcinoma cells has been shown to significantly inhibit cell proliferation and reduce tumor metastasis in mouse models. In the current study, to evaluate if EBP1 is a novel biomarker capable of identifying patients at higher risk of disease progression and recurrence, we examined the EBP1 expression profile in adenoid cystic carcinoma (ACC) patients and analyzed its clinicopathological relevance. To understand the underlying anti-metastatic mechanism, we investigated if EBP1 regulates invasion-related molecules.MethodsWe performed immunohistochemical analysis on 132 primary adenoid cystic carcinoma and adjacent non-cancerous tissues using commercial EBP1, MMP9, E-cadherin and ICAM-1 antibodies. Results were correlated to clinicopathological parameters, long-term survival and invasion-related molecules by statistical analysis. Cell motility and invasiveness of vector or wild-typeEBP1-transfected ACC-M cell lines were evaluated using wound healing and Boyden chamber assays. MMP9, E-cadherin and ICAM-1 proteins in these cell lines were detected using western blot assay.ResultsThe expression of EBP1 was significantly higher in non-cancerous adjacent tissues compared with corresponding cancer tissues. The intensity and percentage of cells that reacted with EBP1 antibodies were significantly higher in cases with tubular pattern than those with solid pattern (P<0.0001). We also found adenoid cystic carcinoma with local lymphatic metastasis had significantly lower EBP1 expression than ACC with no local lymphatic node metastasis (P<0.0001). Similar findings were observed in ACC with lung metastasis compared with cases with no lung metastasis (P<0.0001), in particular, in cases with perineural invasion compared with cases with no perineural invasion (P<0.0001). Furthermore, a decrease in EBP1 expression was positively associated with a reduction in overall survival of ACC patients. Of note, EBP1 inhibits migration and invasiveness of ACC cells by upregulating E-cadherin but downregulating MMP9. In clinical adenoid cystic carcinoma patients, higher EBP1 expression was positively correlated with E-cadherin levels (P<0.001) but negatively correlated with MMP9 expression (P=0.0002).ConclusionsEBP1 expression is reduced in adenoid cystic carcinoma, indicating unfavorable prognosis of ACC patients. Its regulation of MMP9 and E-cadherin protein levels suggests a critical therapeutic potential.
Phenotype-dependent effects of EpCAM expression on growth and invasion of human breast cancer cell lines
Authors: Martowicz Agnieszka , Spizzo Gilbert , Gastl Guenther , Untergasser Gerold 
Published: October 2012

Abstract

Background
The epithelial cell adhesion molecule (EpCAM) has been shown to be overexpressed in breast cancer and stem cells and has emerged as an attractive target for immunotherapy of breast cancer patients. This study analyzes the effects of EpCAM on breast cancer cell lines with epithelial or mesenchymal phenotype.

Methods
For this purpose, shRNA-mediated knockdown of EpCAM gene expression was performed in EpCAMhigh breast cancer cell lines with epithelial phenotype (MCF-7, T47D and SkBR3). Moreover, EpCAMlow breast carcinoma cell lines with mesenchymal phenotype (MDA-MB-231, Hs578t) and inducible overexpression of EpCAM were used to study effects on proliferation, migration and in vivo growth.

Results
In comparison to non-specific silencing controls (n/s-crtl) knockdown of EpCAM (E#2) in EpCAMhigh cell lines resulted in reduced cell proliferation under serum-reduced culture conditions. Moreover, DNA synthesis under 3D culture conditions in collagen was significantly reduced. Xenografts of MCF-7 and T47D cells with knockdown of EpCAM formed smaller tumors that were less invasive. EpCAMlow cell lines with tetracycline-inducible overexpression of EpCAM showed no increased cell proliferation or migration under serum-reduced growth conditions. MDA-MB-231 xenografts with EpCAM overexpression showed reduced invasion into host tissue and more infiltrates of chicken granulocytes.

Conclusions
The role of EpCAM in breast cancer strongly depends on the epithelial or mesenchymal phenotype of tumor cells. Cancer cells with epithelial phenotype need EpCAM as a growth- and invasion-promoting factor, whereas tumor cells with a mesenchymal phenotype are independent of EpCAM in invasion processes and tumor progression. These findings might have clinical implications for EpCAM-based targeting strategies in patients with invasive breast cancer.