bluuebunny/crossref_metadata_2025_split huggingface dataset:
PI3K/Akt/FoxO: a novel participant in signal transduction in bone cells under mechanical stimulation
Authors: Ma Yuanyuan , Wang Hang 
Published: June 2012

AbstractFoxO (forkhead box O) transcription factors, one of the main downstream mediators of PI3K (phosphatidylinositol‐3 kinase)/Akt [also known as PKB (protein kinase B)] signal transduction pathway, play an important role in modulating cellular homoeostasis. Recent studies have revealed the significance of FoxO in bone, the interaction of FoxO with β‐catenin, along with mechanical stress‐induced inactivation of FoxO via PI3K/Akt. We hypothesize that FoxO is a novel participant in mechanotransduction of bone cells in a PI3K/Akt‐dependent way. After describing downstream targets of FoxO, we speculate that FoxO would be involved in the positive effects of mechanical stimulation on bone cells directly through its target genes. We have also concisely represented the cross‐talk between ROS (reactive oxygen species) and Wnt/β‐catenin pathway, which leads us to hypothesize that the inhibition of FoxO caused by mechanical stress acts at the cross‐roads between ROS and Wnt/β‐catenin to regulate indirectly bone metabolism.
Relevance and formation mechanisms of negative ions upon ablation of Al2O3
Authors: Peláez R J , Afonso C N , Chen J , Esposito M , Lippert Th , Stender D , Wokaun A 
Published: June 2012

Abstract
The aim of this work is to study the significance of negative ions in the plasma produced by ablation of a simple oxide ceramic target (Al2O3) at distances and fluences typically used in pulsed-laser deposition processes. The results show that negative ions are indeed produced, the majority of which (>82%) being O− that are predominantly produced by neutralization of O+ followed by electron attachment. They represent one third of the O+ population at low fluences for a distance of 4 cm from the target at which most deposition experiments are performed. AlO− represents up to 15% of the negative ions and their amount increases at the expense of O− as fluence is increased. The most abundant as well as the fastest species in the plasma is by far Al+ that represent >80% of ions having kinetic energy <100 eV at low fluences. This result is consistent with earlier discussion on the possible existence of direct photoionization processes due to the high (6.4 eV) photon energy. Saturation effects, the formation mechanism for AlO− and Al2+, and expansion dynamics for negative ions are finally discussed.
RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Authors: Sahraeian Sayed Mohammad Ebrahim , Yoon Byung-Jun 
Published: June 2012

Abstract
Motivation: Recent technological advances in measuring molecular interactions have resulted in an increasing number of large-scale biological networks. Translation of these enormous network data into meaningful biological insights requires efficient computational techniques that can unearth the biological information that is encoded in the networks. One such example is network querying, which aims to identify similar subnetwork regions in a large target network that are similar to a given query network. Network querying tools can be used to identify novel biological pathways that are homologous to known pathways, thereby enabling knowledge transfer across different organisms.
Results: In this article, we introduce an efficient algorithm for querying large-scale biological networks, called RESQUE. The proposed algorithm adopts a semi-Markov random walk (SMRW) model to probabilistically estimate the correspondence scores between nodes that belong to different networks. The target network is iteratively reduced based on the estimated correspondence scores, which are also iteratively re-estimated to improve accuracy until the best matching subnetwork emerges. We demonstrate that the proposed network querying scheme is computationally efficient, can handle any network query with an arbitrary topology and yields accurate querying results.
Availability: The source code of RESQUE is freely available at http://www.ece.tamu.edu/~bjyoon/RESQUE/
Contact: bjyoon@ece.tamu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Identification of feedback loops in neural networks based on multi-step Granger causality
Authors: Dong Chao-Yi , Shin Dongkwan , Joo Sunghoon , Nam YoonKey , Cho Kwang-Hyun 
Published: June 2012

AbstractMotivation: Feedback circuits are crucial network motifs, ubiquitously found in many intra- and inter-cellular regulatory networks, and also act as basic building blocks for inducing synchronized bursting behaviors in neural network dynamics. Therefore, the system-level identification of feedback circuits using time-series measurements is critical to understand the underlying regulatory mechanism of synchronized bursting behaviors.Results: Multi-Step Granger Causality Method (MSGCM) was developed to identify feedback loops embedded in biological networks using time-series experimental measurements. Based on multivariate time-series analysis, MSGCM used a modified Wald test to infer the existence of multi-step Granger causality between a pair of network nodes. A significant bi-directional multi-step Granger causality between two nodes indicated the existence of a feedback loop. This new identification method resolved the drawback of the previous non-causal impulse response component method which was only applicable to networks containing no co-regulatory forward path. MSGCM also significantly improved the ratio of correct identification of feedback loops. In this study, the MSGCM was testified using synthetic pulsed neural network models and also in vitro cultured rat neural networks using multi-electrode array. As a result, we found a large number of feedback loops in the in vitro cultured neural networks with apparent synchronized oscillation, indicating a close relationship between synchronized oscillatory bursting behavior and underlying feedback loops. The MSGCM is an efficient method to investigate feedback loops embedded in in vitro cultured neural networks. The identified feedback loop motifs are considered as an important design principle responsible for the synchronized bursting behavior in neural networks.Contact: ckh@kaist.ac.krAvailability: The software implementing MSGCM is available at Supplementary Information.Supplementary Information: Supplementary material are available at Bioinformatics online.
DySC: software for greedy clustering of 16S rRNA reads
Authors: Zheng Zejun , Kramer Stefan , Schmidt Bertil 
Published: June 2012

Abstract
Summary: Pyrosequencing technologies are frequently used for sequencing the 16S ribosomal RNA marker gene for profiling microbial communities. Clustering of the produced reads is an important but time-consuming task. We present Dynamic Seed-based Clustering (DySC), a new tool based on the greedy clustering approach that uses a dynamic seeding strategy. Evaluations based on the normalized mutual information (NMI) criterion show that DySC produces higher quality clusters than UCLUST and CD-HIT at a comparable runtime.
Availability and implementation: DySC, implemented in C, is available at http://code.google.com/p/dysc/ under GNU GPL license.
Contact: bertil.schmidt@uni-mainz.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Bendix: intuitive helix geometry analysis and abstraction
Authors: Dahl Anna Caroline E. , Chavent Matthieu , Sansom Mark S. P. 
Published: June 2012

Abstract
Summary: The flexibility of α-helices is important for membrane protein function and calls for better visualization and analysis. Software is presented that quantifies and projects the helix axis evolution over time, with the choice of uniform or analytic heatmap graphics according to the local geometry. Bendix supports static, molecular dynamics, atomistic and coarse-grained input.
Availability and implementation: Bendix source code and documentation, including installation instructions, are freely available at http://sbcb.bioch.ox.ac.uk/Bendix. Bendix is written in Tcl as an extension to VMD and is supported by all major operating systems.
Contact: mark.sansom@bioch.ox.ac.uk
gSearch: a fast and flexible general search tool for whole-genome sequencing
Authors: Song Taemin , Hwang Kyu-Baek , Hsing Michael , Lee Kyungjoon , Bohn Justin , Kong Sek Won 
Published: June 2012

Abstract
Background: Various processes such as annotation and filtering of variants or comparison of variants in different genomes are required in whole-genome or exome analysis pipelines. However, processing different databases and searching among millions of genomic loci is not trivial.
Results: gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner. The proposed method is not a stand-alone annotation tool with its own reference databases. Rather, it is a search utility that readily accepts public or user-prepared reference files in various formats including GVF, Generic Feature Format version 3 (GFF3), Gene Transfer Format (GTF), VCF and Browser Extensible Data (BED) format. Compared to existing tools such as ANNOVAR, gSearch runs more than 10 times faster. For example, it is capable of annotating 52.8 million variants with allele frequencies in 6 min.
Availability: gSearch is available at http://ml.ssu.ac.kr/gSearch. It can be used as an independent search tool or can easily be integrated to existing pipelines through various programming environments such as Perl, Ruby and Python.
Contacts:
BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network
Authors: Otegui Javier , Ariño Arturo H. 
Published: June 2012

Abstract
Summary: In any data quality workflow, data publishers must become aware of issues in their data so these can be corrected. User feedback mechanisms provide one avenue, while global assessments of datasets provide another. To date, there is no publicly available tool to allow both biodiversity data institutions sharing their data through the Global Biodiversity Information Facility network and its potential users to assess datasets as a whole. Contributing to bridge this gap both for publishers and users, we introduce BIoDiversity DataSets Assessment Tool, an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.
Availability and implementation: The online application is accessible at http://www.unav.es/unzyec/mzna/biddsat/ and is supported by all major browsers. The source code is licensed under the GNU GPLv3 license (http://www.gnu.org/licenses/gpl-3.0.txt) and is available at https://github.com/jotegui/BIDDSAT.
Contact: jotellechea@alumni.unav.es
Predicting drug–target interactions from chemical and genomic kernels using Bayesian matrix factorization
Authors: Gönen Mehmet 
Published: June 2012

Abstract
Motivation: Identifying interactions between drug compounds and target proteins has a great practical importance in the drug discovery process for known diseases. Existing databases contain very few experimentally validated drug–target interactions and formulating successful computational methods for predicting interactions remains challenging.
Results: In this study, we consider four different drug–target interaction networks from humans involving enzymes, ion channels, G-protein-coupled receptors and nuclear receptors. We then propose a novel Bayesian formulation that combines dimensionality reduction, matrix factorization and binary classification for predicting drug–target interaction networks using only chemical similarity between drug compounds and genomic similarity between target proteins. The novelty of our approach comes from the joint Bayesian formulation of projecting drug compounds and target proteins into a unified subspace using the similarities and estimating the interaction network in that subspace. We propose using a variational approximation in order to obtain an efficient inference scheme and give its detailed derivations. Finally, we demonstrate the performance of our proposed method in three different scenarios: (i) exploratory data analysis using low-dimensional projections, (ii) predicting interactions for the out-of-sample drug compounds and (iii) predicting unknown interactions of the given network.
Availability: Software and Supplementary Material are available at http://users.ics.aalto.fi/gonen/kbmf2k.
Contact: mehmet.gonen@aalto.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
Harmonising the bioassessment of large rivers in the absence of near‐natural reference conditions – a case study of the Danube River
Authors: BIRK SEBASTIAN , van KOUWEN LEON , WILLBY NIGEL 
Published: June 2012

Summary1. International river catchments pose challenges for effective water resource management. Catchment‐wide strategies are often complicated by differences in national bioassessment and quality classification. Intercalibration efforts aim to harmonise these differences, but rely on the consistent delineation of near‐natural reference sites that are almost unavailable in today’s landscape, especially for large rivers.2. We introduce the concept of alternative benchmarking that is based on the notion of aquatic communities at similar (low) levels of impairment associated with least‐disturbed conditions (LDC) as defined by abiotic criteria. Using data acquired during the second Joint Danube Survey, we defined LDC sites based on a multivariate gradient of anthropogenic pressures, mostly related to morphological deterioration, that spans the entire navigable Danube.3. The river was subdivided into four stretches, each featuring homogeneous biological assemblages. Indirect gradient analysis revealed relationships between the pressure gradient and selected features of the macroinvertebrate and macrophyte community but not for diatoms or phytoplankton.4. We identified biological metrics suitable for the quality classification of individual stretches or the entire river. Impoundment is the major hydromorphological alteration on the Danube but various metrics still responded significantly to differences in the morphological condition of sites not affected by impoundment.5. A comparison of macroinvertebrate sampling techniques (airlift versus kick‐and‐sweep) revealed differences in how the acquired data reflect the effects of anthropogenic pressure. Biological metrics based only on kick‐and‐sweep sample data were insensitive to habitat deterioration in the heavily modified Upper Danube.6. This study exemplifies the empirical approach of alternative benchmarking in intercalibration and offers practical solutions to some of the challenges of large river bioassessment.
Gene therapy for haemophilia B
Authors: TUDDENHAM E. 
Published: June 2012

Summary. AAV virus mediated transfer of factor IX to humans is safe and effective at three dose levels. Two subjects treated at highest dose level developed immune mediated transaminitis which resolved on a short course of Prednisolone. Beneficial effects in terms of continuous elevation of factor IX level above base line was seen in all subjects, continuing for over 18 months. Further study of this treatment method is warranted.
Invasion history of North American Canada thistle, Cirsium arvense
Authors: Guggisberg Alessia , Welk Erik , Sforza René , Horvath David P. , Anderson James V. , Foley Michael E. , Rieseberg Loren H. 
Published: June 2012

AbstractAim  Canada thistle (Cirsium arvense– Cardueae, Asteraceae) is one of the worst invasive plants world‐wide. Native to Eurasia, its unintentional introduction into North America now threatens the native flora and is responsible for enormous agricultural losses. The goals of this study are to: (1) reconstruct the evolutionary history of C. arvense and estimate how often it may have colonized North America, (2) compare the genetic diversity between European and North American populations to detect signs of demographic bottlenecks and/or patterns of population admixture, and (3) conduct bioclimatic comparisons to infer eventual niche shifts following this species’ introduction into North America.Location  Europe and North America.Methods  A total of 1522 individuals from 58 populations were investigated with six microsatellite markers. Estimates of heterozygosity (HE) and allelic richness (RS) were quantified for each population, and population structure was inferred via analyses of molecular variance (AMOVAs), principal components analyses (PCAs), Mantel tests and Bayesian clustering analyses. Climatic niche spaces were based on 19 bioclimatic variables extracted from approximately 32,000 locations covering the entire range, and compared using PCA and hierarchical cluster analysis.Results  Although there is evidence of multiple introductions from divergent European lineages, North American populations of C. arvense exhibited significantly lower levels of genetic diversity than their putative ancestors. Bioclimatic comparisons pointed to a high degree of niche conservatism during invasion, but indicated that genotypes from the former USSR and Central European mountain chains were probably best adapted to invade North America upon entry into the continent.Main conclusions  Genetic and historical data suggest that C. arvense first entered North America from Western Europe with the first European settlers, and was later introduced from Eastern Europe into the prairie states during the agricultural boom. The species went through a significant bottleneck following its introduction into the New World, but the level of genetic diversity remained high owing to admixture between genetically differentiated lineages and to a highly efficient outcrossing breeding system.
The effects of fasting duration on gastric emptying in man, an exploration of the role of the endocannabinoid system and inter‐individual responsiveness
Authors: Jones R. B. , Dockray G. J. , Thompson D. G. 
Published: June 2012

AbstractBackground  In animal studies, gut vagal afferent neurons express cannabinoid (CB1) receptors, whose expression is increased by fasting. We aimed to explore the possibility that similar effects might be relevant in man in controlling gastric emptying.Methods  Fourteen healthy volunteers underwent measurements of gastric emptying using the 13C acetate breath test, after either a nutrient (skimmed milk) or non‐nutrient (water) meal following both a 12 and 24 h fast. Further gastric emptying studies were performed with and without the CB1 receptor antagonist Rimonabant (20 mg or 80 mg). Because of the inter‐individual variations observed, two subjects underwent additional studies with and without Rimonabant to determine intra‐individual consistency. Gastric emptying was evaluated as cumulative C13 : C12 ratio values, measured at 5 min intervals for 30 min.Key Results  In the group as a whole, fasting duration slowed gastric emptying for both the nutrient [120 ± 30 (mean ± SD) vs 101 ± 34, P < 0.05] and non‐nutrient [226 ± 62 vs 177 ± 47, P < 0.05] meals, but there was no effect of Rimonabant. However, there was consistent inter individual variation; thus while 12 subjects showed a slowing, two (14%) exhibited accelerated gastric emptying for both the nutrient and the non‐nutrient meal after 24 h fasting and in one of whom, Rimonabant consistently reversed the fasting effect on the non‐nutrient meal.Conclusions & Inferences  Extended fasting alters the gastric emptying of liquid meals but there are consistent differences between individuals. Where there is an accelerated response to fasting, Rimonabant appears to reverse the effect.
Interventions with Vitamins B6, B12 and C in Pregnancy
Authors: Dror Daphna K. , Allen Lindsay H. 
Published: June 2012

AbstractThe water‐soluble vitamins B6, B12 and C play important roles in maternal health as well as fetal development and physiology during gestation. This systematic review evaluates the risks and benefits of interventions with vitamins B6, B12 and C during pregnancy on maternal, neonatal and child health and nutrition outcomes. Relevant publications were identified by searching PubMed, Popline and Web of Science databases. Meta‐analyses were conducted for outcomes where results from at least three controlled trials were available. Potential benefits of vitamin B6 supplementation were reduction in nausea and vomiting, improvement in dental health, and treatment of some cases of anaemia. In meta‐analysis based on three small studies, vitamin B6 supplementation had a significant positive effect on birthweight (d = 217 g [95% confidence interval (CI) 130, 304]). Interventions with vitamin C alone or combined with vitamin E did not systematically reduce the incidence of pre‐eclampsia, premature rupture of membranes, or other adverse pregnancy outcomes. In meta‐analyses, vitamins C and E increased the risk of pregnancy‐related hypertension (relative risk 1.10 [95% CI 1.02, 1.19]). Effects of vitamin B6 or C intervention on other neonatal outcomes, including preterm birth, low birthweight, and perinatal morbidity and mortality, were not significant. Data on child health outcomes were lacking. Despite the prevalence of vitamin B12 deficiency amongst populations with limited intake of animal source foods, no intervention trials have evaluated vitamin B12 supplementation before or during pregnancy. In conclusion, existing evidence does not justify vitamin C supplementation during pregnancy. Additional studies are needed to confirm positive effects of vitamin B6 supplementation on infant birthweight and other outcomes. While vitamin B12 supplementation may reduce the incidence of neural tube defects in the offspring based on theoretical considerations, research is needed to support this hypothesis.
Perceived hazards of transfusion: can a clinician tool help patients' understanding?
Authors: Khan M. H. , Watson H. G. , Dombrowski S. U. 
Published: June 2012

AbstractObjectiveTo evaluate the use of a tool prompting counselling behaviour for blood transfusion by assessing clinicians' self‐reported counselling behaviours, and changes in patients' beliefs about transfusion.Methods and materialsMixed quantitative and qualitative methodology undertaken in two phases. In phase 1, clinicians' responses (n = 12) to a semi‐structured questionnaire were analysed to identify the content of discussions with patients about different aspects of receiving a blood transfusion. The content of discussions was coded using illness representation concepts from the Common Sense Self‐Regulation Model. Phase 2 included patients (n = 14) scheduled for elective surgery who completed a questionnaire on their beliefs about transfusion before and after counselling.ResultsThe most frequently coded illness representations targeted by clinicians using the tool were ‘consequence of treatment’ (32%) and ‘cure/control’ (30·5%). Two patient beliefs showed significant change following counselling using the checklist. After counselling, patients were more likely to disagree/strongly disagree with the statement that doctors relied too much on transfusion (P = 0·034) and more likely to agree/strongly agree that blood transfusion can result in new health problems (P = 0·041).ConclusionThis pilot study provides insight into how clinicians use a tool for blood transfusion counselling and shows the potential to influence patients' beliefs about transfusion. Whilst the checklist has a role in standardising practice, this pilot study highlights the need for optimising its use before undertaking a fully randomised evaluation of the tool.