bluuebunny/crossref_metadata_2025_split huggingface dataset:
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
Authors: Kato Yuki , Sato Kengo , Hamada Michiaki , Watanabe Yoshihide , Asai Kiyoshi , Akutsu Tatsuya 
Published: September 2010

Abstract
Motivation: Considerable attention has been focused on predicting RNA–RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In general, there is a trade-off between range of interaction type and efficiency of a prediction algorithm, and thus efficient computational methods for predicting comprehensive type of interaction are still awaited.
Results: We present RactIP, a fast and accurate prediction method for RNA–RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities. Experimental results on real interaction data show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA–RNA interaction prediction. Moreover, we demonstrate that RactIP can run incomparably faster than competitive methods for predicting joint secondary structures.
Availability: RactIP is implemented in C++, and the source code is available at http://www.ncrna.org/software/ractip/
Contact: ykato@kuicr.kyoto-u.ac.jp; satoken@k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Discovering graphical Granger causality using the truncating lasso penalty
Authors: Shojaie Ali , Michailidis George 
Published: September 2010

Abstract
Motivation: Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes.
Results: In this article, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large p, small n setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples.
Availability: The proposed truncating lasso method is implemented in the R-package ‘grangerTlasso’ and is freely available at http://www.stat.lsa.umich.edu/∼shojaie/
Contact: shojaie@umich.edu
How threshold behaviour affects the use of subgraphs for network comparison
Authors: Rito Tiago , Wang Zi , Deane Charlotte M. , Reinert Gesine 
Published: September 2010

Abstract
Motivation: A wealth of protein–protein interaction (PPI) data has recently become available. These data are organized as PPI networks and an efficient and biologically meaningful method to compare such PPI networks is needed. As a first step, we would like to compare observed networks to established network models, under the aspect of small subgraph counts, as these are conjectured to relate to functional modules in the PPI network. We employ the software tool GraphCrunch with the Graphlet Degree Distribution Agreement (GDDA) score to examine the use of such counts for network comparison.
Results: Our results show that the GDDA score has a pronounced dependency on the number of edges and vertices of the networks being considered. This should be taken into account when testing the fit of models. We provide a method for assessing the statistical significance of the fit between random graph models and biological networks based on non-parametric tests. Using this method we examine the fit of Erdös–Rényi (ER), ER with fixed degree distribution and geometric (3D) models to PPI networks. Under these rigorous tests none of these models fit to the PPI networks. The GDDA score is not stable in the region of graph density relevant to current PPI networks. We hypothesize that this score instability is due to the networks under consideration having a graph density in the threshold region for the appearance of small subgraphs. This is true for both geometric (3D) and ER random graph models. Such threshold behaviour may be linked to the robustness and efficiency properties of the PPI networks.
Contact: tiago@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian experts in exploring reaction kinetics of transcription circuits
Authors: Yoshida Ryo , Saito Masaya M. , Nagao Hiromichi , Higuchi Tomoyuki 
Published: September 2010

AbstractMotivation Biochemical reactions in cells are made of several types of biological circuits. In current systems biology, making differential equation (DE) models simulatable in silico has been an appealing, general approach to uncover a complex world of biochemical reaction dynamics. Despite of a need for simulation-aided studies, our research field has yet provided no clear answers: how to specify kinetic values in models that are difficult to measure from experimental/theoretical analyses on biochemical kinetics.Results: We present a novel non-parametric Bayesian approach to this problem. The key idea lies in the development of a Dirichlet process (DP) prior distribution, called Bayesian experts, which reflects substantive knowledge on reaction mechanisms inherent in given models and experimentally observable kinetic evidences to the subsequent parameter search. The DP prior identifies significant local regions of unknown parameter space before proceeding to the posterior analyses. This article reports that a Bayesian expert-inducing stochastic search can effectively explore unknown parameters of in silico transcription circuits such that solutions of DEs reproduce transcriptomic time course profiles.Availability: A sample source code is available at the URL http://daweb.ism.ac.jp/∼yoshidar/lisdas/Contact: yoshidar@ism.ac.jp
Cytokinin Regulation of Auxin Synthesis in Arabidopsis Involves a Homeostatic Feedback Loop Regulated via Auxin and Cytokinin Signal Transduction
Authors: Jones Brian , Gunnerås Sara Andersson , Petersson Sara V. , Tarkowski Petr , Graham Neil , May Sean , Dolezal Karel , Sandberg Göran , Ljung Karin 
Published: September 2010

Abstract
Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.
Elevated overdose mortality rates among First Nations individuals in a Canadian setting: a population‐based analysis
Authors: Milloy M‐J. , Wood Evan , Reading Charlotte , Kane Daniel , Montaner Julio , Kerr Thomas 
Published: September 2010

ABSTRACTAims  To determine the total burden of illicit drug overdose mortality over the study period in the province of British Columbia and investigate possible population‐level determinants by estimating rates among subgroups including First Nations individuals.Design  Review of coroner case files.Setting  The province of British Columbia, Canada.Participants  Individuals dying from an illicit drug overdose between 2001 and 2005.Measurements  Age‐adjusted mortality rates, standardized mortality ratios (SMR) and years of potential life lost (YPLL), stratified by major population groups.Findings  Over the study period, 909 individuals died from illicit drug overdoses, including 104 (11.4%) First Nations individuals. Compared to the general population, First Nations males and females suffered from substantially elevated SMR and YPLL. In a multivariate logistic regression analysis, First Nations deaths were significantly more likely to be among women, related to injection drug use and to have occurred in the Downtown Eastside area of Vancouver, the local epicentre of human immunodeficiency virus infection and open drug use (all P < 0.05).Conclusions  This report found highly elevated overdose death rates and levels of premature mortality among First Nations Canadians in British Columbia compared to the general population. While previously unidentified, these findings are consistent with the poorer population health profile of First Nations Canadians. Although further research is needed to identify the causes of the elevated death rates, our findings support increased availability of evidence‐based overdose prevention measures.
Endoscopy‐negative acid reflux disease
Authors: SMOUT A. J. P. M. 
Published: September 2010

SUMMARYRecent clinical trials have yielded important new information about endoscopy‐negative acid reflux disease. Patients with this disease tend to be younger than those with endoscopy‐positive disease and are more likely to be female, thin and without hiatal hernia. The trials have shown that, in patients with endoscopy‐negative reflux disease, symptoms (particularly heartburn) tend to be less severe and less frequent than in patients with endoscopy‐positive disease. The overlap between the groups is such, however, that the symptoms cannot be used to distinguish reflux patients with oesophagitis from those without. Approximately 50% of patients with endoscopy‐negative disease were found to have levels of oesophageal acid exposure that fell within the normal range. Oesophageal pH monitoring is therefore of limited value in patients with endoscopy‐negative reflux disease, unless the test focuses on analysis of the correlation between symptoms and episodes of reflux. New studies have also made clear, for the first time, that endoscopy‐negative acid reflux disease has a measurable and substantial impact on the patients' general well‐being and quality of life. Patients with endoscopy‐negative disease have quality‐of‐life scores that are similar to those found in patients with oesophagitis.
The effectiveness of the ultrasound bladder scanner in reducing urinary tract infections: a meta‐analysis
Authors: Palese Alvisa , Buchini Sara , Deroma Laura , Barbone Fabio 
Published: September 2010

Aim.  To synthesise the evidence available in the literature on the effectiveness of the ultrasound bladder scanner in reducing the risk of urinary tract infection.Background.  Acute urinary retention is the inability to empty the bladder notwithstanding it being full and is frequent in the postoperative period. Using the ultrasound bladder scanner for the measurement of urinary residue, nurses are able to evaluate the presence of urinary retention, monitor the volume and the excessive relaxation of the bladder and avoid unnecessary catheterisations. The association between urinary catheterisation and urinary tract infection is well documented in the literature.Design.  A meta‐analysis was conducted.Method.  An extensive review was carried out by two researchers using multiple databases, including all articles published from 1 January 1986–8 February 2008. No restrictions were adopted with regard to language. Studies on (1) documenting hospitalised patients with a need to evaluate bladder urinary volume, (2) comparing the use of the ultrasound bladder scanner vs. the clinical judgment of the nurses in the evaluation of acute urinary retention followed by a decision regarding whether or not to apply a bladder catheter and (3) those documenting the impact on urinary tract infection associated with catheterisation were included.Results.  A total of 61 articles were retrieved, of which 58 were excluded because they did not meet the inclusion criteria. The overall effectiveness of the bladder ultrasound scanner in the reduction of urinary tract infection associated with catheterisation was OR 0·27 (IC95% 0·16–0·47; p‐value 0·00000294, variance 0·08, weight 12·50).Discussion.  The ultrasound bladder scanner helps to define and monitor bladder urinary volume and therefore, to catheterise patients only when necessary. Although there were numerous factors affecting the clinical heterogeneity of the included studies, the reduction in risk of urinary tract infection associated with catheterisation was consistent.Conclusion.  The use of the ultrasound bladder scanner for evaluating and monitoring the residue volume in immediate postoperative patients, aged 18 or above, reduces unnecessary catheterisations and therefore the risk of urinary tract infection associated with catheterisation.Relevance to clinical practice.  The systematic use of the ultrasound bladder scanner in the peri‐operative period could increase the appropriateness of catheterisation and reduce patient discomfort, costs and days of hospitalisation associated with urinary tract infection associated with catheterisation.
Policy impacts on pedagogical practice and ICT use: an exploration of the results from SITES 2006
Authors: Law N. , Lee M.W. , Chan A. 
Published: September 2010

AbstractThe Second Information Technology in Education Study (SITES) 2006 results reveal that principals' perceived presence of lifelong learning‐related pedagogical activities in their schools had changed markedly since the same data was collected in 1998 in SITES‐M1. More intriguing was the fact that the directions of the changes were quite different depending on the education systems concerned – many of the Asian countries reported very high increases while some of the European countries reported large drops over the same 8‐year period. This paper reports statistical evidence that the observed ‘pendulum swing’ reflects actual changes in teaching practices in these countries. Exploratory multilevel analyses results consistently show that national means of principals' vision can be used as a system‐level indicator predicting national means of pedagogical orientations in schools several years later. These findings also indicate the possibility of the ‘pendulum effect’ being a consequence of system‐level policy differences in the countries participating in the two SITES studies.
Is endoscopic forceps biopsy enough for a definitive diagnosis of gastric epithelial neoplasia?
Authors: Lee Chang Kyun , Chung Il‐Kwun , Lee Suck‐Ho , Kim Sang Pil , Lee Sae Hwan , Lee Tae Hoon , Kim Hong‐Soo , Park Sang‐Heum , Kim Sun‐Joo , Lee Ji‐Hye , Cho Hyun Deuk , Oh Mee‐Hye 
Published: September 2010

AbstractBackground and Aim:  Endoscopic forceps biopsy (EFB) as the primary histological diagnosis of gastric epithelial neoplasia (GEN) is debated in the era of endoscopic resection (ER). Our aim was to investigate the diagnostic reliability of EFB in patients with GEN compared with ER specimens as the reference standard for the final diagnosis in a large consecutive series.Methods:  This was a cross‐sectional retrospective study at a tertiary‐referral center. A total of 354 consecutive patients with 397 GENs underwent ER (endoscopic mucosal resection or endoscopic submucosal dissection). Discrepancy rates between the histological results from EFB and ER specimens were assessed. Discrepancies that could affect patient outcome or clinical care were considered major.Results:  The overall histological discrepancy rate between EFB and ER specimens was 44.5% (95% confidence interval [CI], 39.7–49.5%) among the enrolled patients. The overall discrepancy rate was significantly higher in the intraepithelial neoplasia (IEN) group than in the carcinoma group (49.8% vs 25.6%, P < 0.001). The major discrepancy rate was also significantly higher in the IEN group than in the carcinoma group (36.6% vs 7.0%, P < 0.001). In subgroup analysis of the IEN group, a major histological discrepancy rate of 33.6% (70/208) for low‐grade and 42.7% (44/103) for high‐grade IEN was found, respectively.Conclusions:  Endoscopic forceps biopsy was insufficient for a definitive diagnosis and therapeutic planning in patients with GEN. ER should be considered as not only definitive treatment but also a procedure for a precise histological diagnosis for lesions initially assessed as GEN by forceps biopsy specimens.
Cellular & molecular Ca2+ microdomains in olfactory cilia support low signaling amplification of odor transduction
Authors: Castillo Karen , Restrepo Diego , Bacigalupo Juan 
Published: September 2010

AbstractSignal transduction depends critically on the spatial localization of protein constituents. A key question in odor transduction is whether chemotransduction proteins organize into discrete molecular complexes throughout olfactory cilia or distribute homogeneously along the ciliary membrane. Our recordings of Ca2+ changes in individual cilia with unprecedented spatial and temporal resolution, by the use of two‐photon microscopy, provide solid evidence for Ca2+ microdomains (transducisomes). Dissociated frog olfactory neurons were preloaded with caged‐cAMP and fluo‐4 acetoxymethyl ester probe Ca2+ indicator. Ca2+ influx through cyclic nucleotide‐gated (CNG) channels was evoked by uniformly photoreleasing cAMP, while ciliary Ca2+ was measured. Discrete fluorescence events were clearly resolved. Events were missing in the absence of external Ca2+, consistent with the absence of internal Ca2+ sources. Fluorescence events at individual microdomains resembled single‐CNG channel fluctuations in shape, mean duration and kinetics, indicating that transducisomes typically contain one to three CNG channels. Inhibiting the Na+/Ca2+ exchanger or the Ca2+‐ATPase prolonged the decay of evoked intraciliary Ca2+ transients, supporting the participation of both transporters in ciliary Ca2+ clearance, and suggesting that both molecules localize close to the CNG channel. Chemosensory transducisomes provide a physical basis for the low amplification and for the linearity of odor responses at low odor concentrations.
Wound fluid lactate concentration: a helpful marker for diagnosing soft‐tissue infection in diabetic foot ulcers? Preliminary findings
Authors: Löffler M. , Zieker D. , Weinreich J. , Löb S. , Königsrainer I. , Symons S. , Bühler S. , Königsrainer A. , Northoff H. , Beckert S. 
Published: September 2010

Diabet. Med. 28, 175–178 (2011)AbstractAims  To investigate the impact of wound fluid lactate concentration on diagnosing soft‐tissue infection in diabetic foot ulcers.Methods  Lactate concentration in wound fluid obtained from diabetic foot ulcers was determined using a lactate analyser and compared with clinical examination findings.Results  Overall median wound fluid lactate concentration was 21.03 mm (5.58–80.40 mm). Wound lactate levels were significantly higher in infected compared with non‐infected diabetic foot ulcers (P = 0.001). Non‐infected diabetic foot ulcers that healed within 6 months of treatment showed a significantly lower wound fluid lactate concentration at baseline as opposed to those that did not heal (P = 0.007).Conclusions  Non‐healing diabetic foot ulcers are characterized by high wound fluid lactate levels. Assessment of wound fluid lactate concentration might be helpful for confirming the suspicion of soft tissue infection, particularly when clinical signs are atypical.
An RCT of coping and support groups to reduce burnout among nurses
Authors: Günüşen N.P. , Üstün B. 
Published: September 2010

GÜNÜŞEN N.P. & ÜSTÜN B. (2010) An RCT of coping and support groups to reduce burnout among nurses. International Nursing ReviewBackground:  Burnout is a fundamental problem among nurses. Nurses need to be trained to reduce burnout.Aim:  The aim of this study was to evaluate the effects of coping and support group interventions to reduce burnout among nurses.Methods:  A randomized controlled trial (RCT) was conducted at a University Hospital in Izmir, Turkey. Level of burnout was measured with Maslach Burnout Inventory before and after the intervention as well as in the following 6 months. A total of 108 nurses met the selection criteria and agreed to participate. To determine the effectiveness of the intervention, two‐factor repeated‐measures analysis of variance and paired t‐test with Bonferroni correction were used when appropriate. All analyses were conducted on an intention‐to‐treat basis.Results:  Right after the intervention, there was an immediate reduction in emotional exhaustion dimension of burnout with respect to time. However, in 6 months, scores were increased again. No significant difference was noted between groups and from the point of group × time interaction. There was not any change in depersonalization and personal accomplishment dimensions of burnout after the intervention.Conclusion:  By means of person‐directed interventions, emotional exhaustion level can be decreased. The fact that burnout reduces after the intervention and an increase is observed in 6 months is an important result. Repetitive interventions can render the effect to be long lasting. It is recommended that the number of intervention studies to reduce burnout be increased and that long‐term outcomes be observed.
COGNITIVE MAPPING AND REPERTORY GRIDS FOR QUALITATIVE SURVEY RESEARCH: SOME COMPARATIVE OBSERVATIONS
Authors: Brown Sylvia M. 
Published: September 2010

ABSTRACTA study of business strategy was carried out in 86 organizations in the crop protection industry. A multi‐operational approach was used to enable validation of data by triangulation, including cognitive mapping used in an unusual way. This provided an unintended opportunity to conduct a comparative evaluation of interactive investigational methods in a relatively controlled, if unsophisticated manner. Results were interesting enough to suggest that further investigation is needed into the impact of various subject‐generated factors such as face validity on methodological effectivness, as well as more traditional criteria such as construct validity of particular methods. Accordingly, process issues affecting repertory grids, cognitive mapping and software for the analysis of cognitive maps (COPE) are described and discussed. Recommendations are made for improvements to mapping and software and further studies suggested.