bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis of allene oxides in Physcomitrella patens
Authors: Scholz Julia , Brodhun Florian , Hornung Ellen , Herrfurth Cornelia , Stumpe Michael , Beike Anna K , Faltin Bernd , Frank Wolfgang , Reski Ralf , Feussner Ivo 
Published: November 2012

Abstract

Background
The moss Physcomitrella patens contains C18- as well as C20-polyunsaturated fatty acids that can be metabolized by different enzymes to form oxylipins such as the cyclopentenone cis(+)-12-oxo phytodienoic acid. Mutants defective in the biosynthesis of cyclopentenones showed reduced fertility, aberrant sporophyte morphology and interrupted sporogenesis. The initial step in this biosynthetic route is the conversion of a fatty acid hydroperoxide to an allene oxide. This reaction is catalyzed by allene oxide synthase (AOS) belonging as hydroperoxide lyase (HPL) to the cytochrome P450 family Cyp74. In this study we characterized two AOS from P. patens, PpAOS1 and PpAOS2.

Results
Our results show that PpAOS1 is highly active with both C18 and C20-hydroperoxy-fatty acid substrates, whereas PpAOS2 is fully active only with C20-substrates, exhibiting trace activity (~1000-fold lower kcat/KM) with C18 substrates. Analysis of products of PpAOS1 and PpHPL further demonstrated that both enzymes have an inherent side activity mirroring the close inter-connection of AOS and HPL catalysis. By employing site directed mutagenesis we provide evidence that single amino acid residues in the active site are also determining the catalytic activity of a 9-/13-AOS – a finding that previously has only been reported for substrate specific 13-AOS. However, PpHPL cannot be converted into an AOS by exchanging the same determinant. Localization studies using YFP-labeled AOS showed that PpAOS2 is localized in the plastid while PpAOS1 may be found in the cytosol. Analysis of the wound-induced cis(+)-12-oxo phytodienoic acid accumulation in PpAOS1 and PpAOS2 single knock-out mutants showed that disruption of PpAOS1, in contrast to PpAOS2, results in a significantly decreased cis(+)-12-oxo phytodienoic acid formation. However, the knock-out mutants of neither PpAOS1 nor PpAOS2 showed reduced fertility, aberrant sporophyte morphology or interrupted sporogenesis.

Conclusions
Our study highlights five findings regarding the oxylipin metabolism in P. patens: (i) Both AOS isoforms are capable of metabolizing C18- and C20-derived substrates with different specificities suggesting that both enzymes might have different functions. (ii) Site directed mutagenesis demonstrated that the catalytic trajectories of 9-/13-PpAOS1 and PpHPL are closely inter-connected and PpAOS1 can be inter-converted by a single amino acid exchange into a HPL. (iii) In contrast to PpAOS1, PpAOS2 is localized in the plastid where oxylipin metabolism takes place. (iv) PpAOS1 is essential for wound-induced accumulation of cis(+)-12-oxo phytodienoic acid while PpAOS2 appears not to be involved in the process. (v) Knock-out mutants of neither AOS showed a deviating morphological phenotype suggesting that there are overlapping functions with other Cyp74 enzymes.
Evaluation of the Propensity score methods for estimating marginal odds ratios in case of small sample size
Authors: Pirracchio Romain , Resche-Rigon Matthieu , Chevret Sylvie 
Published: November 2012

Abstract

Background
Propensity score (PS) methods are increasingly used, even when sample sizes are small or treatments are seldom used. However, the relative performance of the two mainly recommended PS methods, namely PS-matching or inverse probability of treatment weighting (IPTW), have not been studied in the context of small sample sizes.

Methods
We conducted a series of Monte Carlo simulations to evaluate the influence of sample size, prevalence of treatment exposure, and strength of the association between the variables and the outcome and/or the treatment exposure, on the performance of these two methods.

Results
Decreasing the sample size from 1,000 to 40 subjects did not substantially alter the Type I error rate, and led to relative biases below 10%. The IPTW method performed better than the PS-matching down to 60 subjects. When N was set at 40, the PS matching estimators were either similarly or even less biased than the IPTW estimators. Including variables unrelated to the exposure but related to the outcome in the PS model decreased the bias and the variance as compared to models omitting such variables. Excluding the true confounder from the PS model resulted, whatever the method used, in a significantly biased estimation of treatment effect. These results were illustrated in a real dataset.

Conclusion
Even in case of small study samples or low prevalence of treatment, PS-matching and IPTW can yield correct estimations of treatment effect unless the true confounders and the variables related only to the outcome are not included in the PS model.
Healthcare professional acceptance of telemonitoring for chronic care patients in primary care
Authors: Asua José , Orruño Estibalitz , Reviriego Eva , Gagnon Marie Pierre 
Published: November 2012

Abstract

Background
A pilot experimentation of a telemonitoring system for chronic care patients is conducted in the Bilbao Primary Care Health Region (Basque Country, Spain). It seems important to understand the factors related to healthcare professionals’ acceptance of this new technology in order to inform its extension to the whole healthcare system.
This study aims to examine the psychosocial factors related to telemonitoring acceptance among healthcare professionals and to apply a theory-based instrument.

Methods
A validated questionnaire, based on an extension of the Technology Acceptance Model (TAM), was distributed to a total of 605 nurses, general practitioners and paediatricians. Logistic regression analysis was performed to test the theoretical model. Adjusted odds ratios (OR) and their 95% confidence intervals (CI) were computed.

Results
A response rate of 44.3% was achieved. The original TAM model was good at predicting intention to use the telemonitoring system. However, the extended model, that included other theoretical variables, was more powerful. Perceived Usefulness, Compatibility, and Facilitators were the significant predictors of intention. A detailed analysis showed that intention to use telemonitoring was best predicted by healthcare professionals’ beliefs that they would obtain adequate training and technical support and that telemonitoring would require important changes in their practice.

Conclusion
The extended TAM explained a significant portion of the variance in healthcare professionals' intention to use a telemonitoring system for chronic care patients in primary care. The perception of facilitators in the organisational context is the most important variable to consider for increasing healthcare professionals’ intention to use the new technology.
Enhancement of mouse sperm motility by trophinin-binding peptide
Authors: Park Seong Kyu , Yoon Jiwon , Wang Ling , Shibata Toshiaki K , Motamedchaboki Khatereh , Shim Kyung Jun , Chang Mun Seog , Lee Seung Ho , Tamura Naoaki , Hatakeyama Shingo , Nadano Daita , Sugihara Kazuhiro , Fukuda Michiko N 
Published: November 2012

Abstract

Background
Trophinin is an intrinsic membrane protein that forms a complex in the cytoplasm with bystin and tastin, linking it microtubule-associated motor dynein (ATPase) in some cell types. Previously, we found that human sperm tails contain trophinin, bystin and tastin proteins, and that trophinin-binding GWRQ (glycine, tryptophan, arginine, glutamine) peptide enhanced motility of human sperm.

Methods
Immunohistochemistry was employed to determine trophinin protein in mouse spermatozoa from wild type mouse, by using spermatozoa from trophinin null mutant mice as a negative control. Multivalent 8-branched GWRQ (glycine, tryptophan, arginine, glutamine) peptide or GWRQ-MAPS, was chemically synthesized, purified by HPLC and its structure was confirmed by MALDI-TOF mass spectrometry. Effect of GWRQ-MAPS on mouse spermatozoa from wild type and trophinin null mutant was assessed by a computer-assisted semen analyzer (CASA).

Results
Anti-trophinin antibody stained the principal (central) piece of the tail of wild type mouse sperm, whereas the antibody showed no staining on trophinin null sperm. Phage particles displaying GWRQ bound to the principal piece of sperm tail from wild type but not trophinin null mice. GWRQ-MAPS enhanced motility of spermatozoa from wild type but not trophinin null mice. CASA showed that GWRQ-MAPS enhanced both progressive motility and rapid motility in wild type mouse sperm.

Conclusions
Present study established the expression of trophinin in the mouse sperm tail and trophinin-dependent effect of GWRQ-MAPS on sperm motility. GWRQ causes a significant increase in sperm motility.
MDP-based handover policy in wireless relay systems
Authors: Dang Xiaoyu , Wang Jin-Yuan , Cao Zhe 
Published: November 2012

Abstract
Wireless relay transmission has been considered as a supplementary technology for future wireless communication system, and handover is a key element in wireless relay transmissions to support users’ mobility. Handover failure will result in the forced termination of an ongoing call, and a good handover scheme will provide good system performance. This article focuses on the handover decision problem in wireless relay transmission systems. Initially, the architecture of a single-cell relay system is introduced. The handover decision problem is formulated as a Markov decision process (MDP). In the proposed model, a profit function is used to evaluate the quality-of-service of the chosen serving node, and a cost function is used to model processing load and signaling cost. Based on the profit and cost functions, the reward function is formulated. Moreover, the objective is to maximize the expected total reward per connection. The value iteration algorithm is employed to determine the optimal handover policy. Furthermore, the analysis is generalized to multi-cell relay systems. Numerical results show that the proposed MDP-based handover policy is well behaved in wireless relay systems.
Metabolic profiles characterizing different phenotypes of polycystic ovary syndrome: plasma metabolomics analysis
Authors: Zhao Yue , Fu Li , Li Rong , Wang Li-Na , Yang Yan , Liu Na-Na , Zhang Chun-Mei , Wang Ying , Liu Ping , Tu Bin-Bin , Zhang Xue , Qiao Jie 
Published: November 2012

Abstract

Background
Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder accompanied with an increased risk of developing type 2 diabetes mellitus and cardiovascular disease; despite being a common condition, the pathogenesis of PCOS remains unclear. Our aim was to investigate the potential metabolic profiles for different phenotypes of PCOS, as well as for the early prognosis of complications.

Methods
A total of 217 women with PCOS and 48 healthy women as normal controls were studied. Plasma samples of subjects were tested using two different analytical platforms of metabolomics: 1H nuclear magnetic resonance (NMR) and gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS).

Results
Our results showed that carbohydrate, lipid and amino acid metabolisms were influenced in PCOS. The levels of lactate, long-chain fatty acids, triglyceride and very low-density lipoprotein were elevated, while glucose, phosphatidylcholine and high-density lipoprotein (HDL) concentrations were reduced in PCOS patients as compared with controls. Additionally, the levels of alanine, valine, serine, threonine, ornithine, phenylalanine, tyrosine and tryptophan were generally increased, whereas the levels of glycine and proline were significantly reduced in PCOS samples compared to controls. Furthermore, the ratio of branched-chain amino acid to aromatic amino acid concentrations (BCAA/AAA) in PCOS plasma was significantly reduced in PCOS patients and was insusceptible to obesity and insulin sensitivity.

Conclusions
Our results suggested that the enhanced glycolysis and inhibited tricarboxylic acid cycle (TAC) in women with PCOS. Decrease of BCAA/AAA ratio was directly correlated with the development of PCOS. Ovulatory dysfunction of PCOS patients was associated with raised production of serine, threonine, phenylalanine, tyrosine and ornithine. Elevated levels of valine and leucine, and decreased concentrations of glycine in PCOS plasma could contribute to insulin sensitivity and could be considered as the potential biomarkers for long-term risk assessment of diabetes mellitus.
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli
Authors: Töpfer Nadine , Jozefczuk Szymon , Nikoloski Zoran 
Published: November 2012

Abstract

Background
Changes in environmental conditions require temporal effectuation of different metabolic pathways in order to maintain the organisms’ viability but also to enable the settling into newly arising conditions. While analyses of robustness in biological systems have resulted in the characterization of reactions that facilitate homeostasis, temporal adaptation-related processes and the role of cellular pathways in the metabolic response to changing conditions remain elusive.

Results
Here we develop a flux-based approach that allows the integration of time-resolved transcriptomics data with genome-scale metabolic networks. Our framework uses bilevel optimization to extract temporal minimal operating networks from a given large-scale metabolic model. The minimality of the extracted networks enables the computation of elementary flux modes for each time point, which are in turn used to characterize the transitional behavior of the network as well as of individual reactions. Application of the approach to the metabolic network of Escherichia coli in conjunction with time-series gene expression data from cold and heat stress results in two distinct time-resolved modes for reaction utilization—constantly active and temporally (de)activated reactions. These patterns contrast the processes for the maintenance of basic cellular functioning and those required for adaptation. They also allow the prediction of reactions involved in time- and stress-specific metabolic response and are verified with respect to existing experimental studies.

Conclusions
Altogether, our findings pinpoint the inherent relation between the systemic properties of robustness and adaptability arising from the interplay of metabolic network structure and changing environment.
K-NN query algorithm based on PB-tree with the parallel lines division
Authors: Tang Jine , Zhou ZhangBing , Wang Qun 
Published: November 2012

Abstract
Spatial index and query are enabling techniques for achieving the vision of the Internet of Things. K-NN is an algorithm which is used widely in spatial database. Traditional query algorithms use R-tree as the index structure and improve the query efficiency by using the measurement distance and pruning strategy. Based on the study of previous algorithms, this paper proposes a novel K-NN query algorithm based on PB-tree with the parallel lines division. PB-tree index is different from the traditional R-tree index, where PB-tree adopts parallel lines to divide the spatial region and uses parallel lines as the parent node. It is similar to the binary tree index structure and requires to query three small portions nearest to the queried object in each K-NN query. Therefore, the search range is narrowed and the query efficiency is enhanced. Experiments show that PB-tree is better than the traditional R-tree from the aspect of query performance. PB-tree can avoid the deficiency of a large number of overlap and coverage among odes in R-tree and multiple index paths when searching data objects, and hence PB-tree can find K-NN objects meeting the conditions quickly and efficiently in large data sets.
Visual motion speed determines a behavioral switch from forward flight to expansion avoidance inDrosophila
Authors: Reiser Michael B. , Dickinson Michael H. 
Published: November 2012

SummaryAs an animal translates through the world, its eyes will experience a radiating pattern of optic flow in which there is a focus of expansion directly in front and a focus of contraction behind. For flying fruit flies, recent experiments indicate that flies actively steer away from patterns of expansion. Whereas such a reflex makes sense for avoiding obstacles, it presents a paradox of sorts because an insect could not navigate stably through a visual scene unless it tolerated flight towards a focus of expansion during episodes of forward translation. One possible solution to this paradox is that a fly's behavior might change such that it steers away from strong expansion, but actively steers toward weak expansion. In this study, we use a tethered flight arena to investigate the influence of stimulus strength on the magnitude and direction of turning responses to visual expansion in flies. These experiments indicate that the expansion-avoidance behavior exhibits a speed-dependent inversion. At slower speeds of expansion, flies exhibit an attraction to the focus of expansion, whereas the behavior transforms to expansion avoidance at higher speeds. Open-loop experiments indicate that this inversion of the expansion-avoidance response depends on whether or not the head is fixed to the thorax. The inversion of the expansion-avoidance response with stimulus strength has a clear manifestation under closed-loop conditions. Flies will actively orient toward a focus of expansion at low temporal frequency but steer away from it at high temporal frequency. The change in the response with temporal frequency does not require motion stimuli directly in front or behind the fly. Animals in which the stimulus was presented within 120° sectors on each side consistently steered toward expansion at low temporal frequency and steered toward contraction at high temporal frequency. A simple model based on an array of Hassenstein-Reichardt type elementary movement detectors suggests that the inversion of the expansion-avoidance reflex can explain the spatial distribution of straight flight segments and collision-avoidance saccades when flies fly freely within an open circular arena.
Mortality from desiccation contributes to a genotype-by-temperature interaction for cold survival inDrosophila melanogaster
Authors: Kobey Robert L. , Montooth Kristi 
Published: November 2012

SummarySurvival at cold temperatures is a complex trait, primarily due to the fact that the physiological cause of injury may differ across degrees of cold exposure experienced within the lifetime of an ectothermic individual. In order to better understand how chill-sensitive insects experience and adapt to low temperatures, we investigated the physiological basis for cold survival across a range of temperature exposures from -4°C to 6°C in five genetic lines of the fruit fly, Drosophila melanogaster. Genetic effects on cold survival were temperature dependent and resulted in a significant genotype-by-temperature interaction for survival across cold temperature exposures that differ by as little as 2°C. We investigated desiccation as a potential mechanism of injury across these temperature exposures. Flies were dehydrated following exposures near 6°C, while flies were not dehydrated following exposures near -4°C. Furthermore, decreasing humidity during cold exposure decreased survival, and increasing humidity during cold exposure increased survival at 6°C, but not at -4°C. These results support the conclusion that in D. melanogaster there are multiple physiological mechanisms of cold-induced mortality across relatively small differences in temperature and that desiccation contributes to mortality for exposures near 6°C but not for subzero temperatures. Because D. melanogaster has recently expanded its range from tropical to temperate latitudes, the complex physiologies underlying cold tolerance are likely to be important traits in the recent evolutionary history of this fruit fly.
The role of glucocorticoids in naturally fasting grey seal (Halichoerus grypus) pups: dexamethasone stimulates mass loss and protein utilisation, but not departure from the colony
Authors: Bennett Kimberley A. , Fedak Mike A. , Moss Simon E. W. , Pomeroy Patrick P. , Speakman John R. , Hall Ailsa J. 
Published: November 2012

SummarySeals must manage their energy reserves carefully while they fast on land to ensure they go to sea with sufficient fuel to sustain them until they find food. Glucocorticoids (GC) have been implicated in the control of fuel metabolism and termination of fasting in pinnipeds. Here we tested the hypothesis that dexamethasone, an artificial GC, increases fat and protein catabolism, and induces departure from the breeding colony in wild, fasting grey seal pups. A single intramuscular dose of dexamethasone completely suppressed cortisol production for 24-72 hours, demonstrating activation of GC receptors. In experiment 1, we compared the effects of a single dose of dexamethasone or saline administered ten days after weaning on fasting mass and body composition changes, cortisol, blood urea nitrogen (BUN) and glucose levels, and timing of departure from the colony. In experiment 2, we investigated the effects of dexamethasone on short-term (5 days) changes in mass loss, body composition and BUN. In experiment 1, dexamethasone induced a short-lived increase in mass loss, but there was no difference in timing of departure between dexamethasone and saline treated pups (n = 10). In experiment 2, dexamethasone increased protein and water loss and prevented a decrease in BUN levels (n = 11). Our data suggest changes in cortisol contribute to regulation of protein catabolism in fasting seal pups, irrespective of the sex of the animal, but do not terminate fasting. By affecting the rate of protein depletion, lasting changes in cortisol levels could influence the amount of time seal pups have to find food, and thus may have important consequences for their survival.
Three cone opsin genes determine the properties of the visual spectra in the Japanese anchovy Engraulis japonicus (Engraulidae, Teleostei)
Authors: Kondrashev Sergei L. , Miyazaki Taeko , Lamash Nina E. , Tsuchiya Tohru 
Published: November 2012

Summary
A complement of cone visual pigments was identified in the Japanese anchovy Engraulis japonicus, one of the engraulid fish species that has a retina specialized for polarization and color vision. The nature of the chromophore bound to opsin proteins was investigated using high performance liquid chromatography (HPLC). The opsin genes were then cloned and sequenced, and the absorption spectra of different types of cones were obtained by microspectrophotometry (MSP). Two green (EJ-RH2-1, EJ-RH2-2) and one red (EJ-LWS) cone opsin genes were identified and are presumably related to the Vitamin A1-based visual pigments (i.e., rhodopsins) with λmax values of 492, 474 and 512 nm for EJ-RH2-1, EJ-RH2-2, and EJ-LWS, respectively. The long and short cones from the ventro-temporal retinal zone consisted of a pure population of RH2 class gene-based pigments (λmax value of 492 nm). The long and short cones from other retinal areas and the lateral components of the triple cones possessed a mixture of RH2 and LWS class gene-based pigments that exhibited a λmax value approximately 502 nm. The central component of the triple cones contained only RH2 class gene-based pigments (λmax value of 474 nm). Thus, E. japonicus possesses a middle-wave range of spectral sensitivity and acquires different color vision systems in distinct visual fields. .