bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planet Mars: Story of Another World
Authors: Leatherland Alex 
Published: June 2009

Mars has captured the imagination of people throughout the ages, inspiring many stories. Remarkably, though, little was known about the red planet until recently. Through a great deal of exploration and theory, planetary scientists have striven to correct this situation.Over the course of the past half century, since the first flyby of Mars by NASA's Mariner 4 spacecraft in 1967, a multitude of probes have landed on, orbited, and flown past the planet. From these missions, a great deal has been learned about Mars. Its surface has now been studied to a respectable level of detail, revealing an astonishing amount of information about volcanoes such as Olympus Mons in Mars's Tharsis region; about the gigantic Valles Marineris (Valley of Wonder), the largest known canyon in the solar system; and about lava flows, outflow channels, and the Martian regolith, among many other aspects of the planet.
Dynamic Planet: Mercury in the Context of Its Environment
Authors: Wood Alan 
Published: June 2009

Mercury, the Sun's nearest neighbor, is tantalizingly close to the Earth yet is one of the least explored objects in our solar system. The planet's proximity to the Sun makes Earth‐based observations extremely difficult, and the harsh environment presents a significant challenge to spacecraft. Nevertheless, we are currently on the verge of a new era of exploration of this fascinating, mysterious, and largely uncharted world.Much of our knowledge about Mercury has come from just three flybys by NASA's Mariner 10 spacecraft in the mid‐1970s. This mission sent back stunning images of about 45% of the planet's surface and made the truly puzzling discovery of a magnetic field, the source of which is still unknown. Currently, NASA's Mercury Surface, Space Environment, Geochemistry, and Ranging (MESSENGER) mission is beginning to explore Mercury and aims to answer many unresolved questions about the structure, composition, magnetic field, and history of this incredible world. To date, MESSENGER has conducted two flybys and is expected to go into orbit around Mercury in March 2011. Later, in 2013, the European Space Agency's BepiColombo mission, which uses a twin spacecraft approach, will head for the planet to understand the detail of this dynamic system.
Integrated Tsunami Data for Better Hazard Assessments
Authors: Dunbar Paula 
Published: June 2009

With nearly 230,000 fatalities, the 26 December 2004 Indian Ocean tsunami was the deadliest tsunami in history, illustrating the importance of developing basin‐wide warning systems. Key to creating these systems is easy access to quality‐controlled, verified data on past tsunamis: Warning centers, emergency managers, and modelers need to know if and when similar events have occurred.Following the 2004 tsunami, the National Oceanic and Atmospheric Administration's (NOAA) National Geophysical Data Center (NGDC) began examining all aspects of the tsunami data archive to help answer questions regarding the frequency and severity of past tsunamis. Historical databases span insufficient time to reveal a region's full tsunami hazard, so a global database of citations to articles on tsunami deposits was added to the archive. NGDC further expanded the archive to include high‐resolution tide gauge data, deep‐ocean sensor data, and digital elevation models used for propagation and inundation. NGDC continuously reviews data for accuracy, making modifications as new information is obtained.
Evolving Views on a Dynamic Greenhouse Earth: Climatic and Biotic Events of the Paleogene (CBEP 2009) Conference; Wellington, New Zealand, 12–15 January 2009
Authors: Hollis Chris , Huber Matthew 
Published: June 2009

The Paleogene (65–24 million years ago) was a dynamic period in Earth's history in which major mammal groups became established and diversified, rapid and repeated extreme global warming events occurred, and climate began its stuttering progression from a greenhouse to an icehouse climate state. With atmospheric carbon dioxide concentrations in the range projected to occur over the next several centuries (>1000 parts per million), the Paleogene is also a window into our future (see J. C. Zachos et al., Nature, 451, 279–283, 2008).Long‐standing interest in understanding the causes and consequences of global change in the Paleogene and the current timeliness of greenhouse climate research explain why conferences are periodically devoted to the climatic and biotic events of the Paleogene. The 2009 conference, held in New Zealand, attracted 130 participants from 20 countries. Presentations demonstrated substantial progress in new climate proxy development, new multiproxy approaches, and closer integration of paleoclimate records with climate models, consolidating around three main issues.
Wnt5 is required for notochord cell intercalation in the ascidian Halocynthia roretzi
Authors: Niwano Tomoko , Takatori Naohito , Kumano Gaku , Nishida Hiroki 
Published: June 2009

Background information. In the embryos of various animals, the body elongates after gastrulation by morphogenetic movements involving convergent extension. The Wnt/PCP (planar cell polarity) pathway plays roles in this process, particularly mediolateral polarization and intercalation of the embryonic cells. In ascidians, several factors in this pathway, including Wnt5, have been identified and found to be involved in the intercalation process of notochord cells.Results. In the present study, the role of the Wnt5 genes, Hr‐Wnt5α (Halocynthia roretzi Wnt5α) and Hr‐Wnt5β, in convergent extension was investigated in the ascidian H. roretzi by injecting antisense oligonucleotides and mRNAs into single precursor blastomeres of various tissues, including notochord, at the 64‐cell stage. Hr‐Wnt5α is expressed in developing notochord and was essential for notochord morphogenesis. Precise quantitative control of its expression level was crucial for proper cell intercalation. Overexpression of Wnt5 proteins in notochord and other tissues that surround the notochord indicated that Wnt5α plays a role within the notochord, and is unlikely to be the source of polarizing cues arising outside the notochord. Detailed mosaic analysis of the behaviour of individual notochord cells overexpressing Wnt5α indicated that a Wnt5α‐manipulated cell does not affect the behaviour of neighbouring notochord cells, suggesting that Wnt5α works in a cell‐autonomous manner. This is further supported by comparison of the results of Wnt5α and Dsh (Dishevelled) knockdown experiments. In addition, our results suggest that the Wnt/PCP pathway is also involved in mediolateral intercalation of cells of the ventral row of the nerve cord (floor plate) and the endodermal strand.Conclusion. The present study highlights the role of the Wnt5α signal in notochord convergent extension movements in ascidian embryos. Our results raise the novel possibility that Wnt5α functions in a cell‐autonomous manner in activation of the Wnt/PCP pathway to polarize the protrusive activity that drives convergent extension.
Calcium-sensing beyond neurotransmitters: functions of synaptotagmins in neuroendocrine and endocrine secretion
Authors: Gustavsson Natalia , Han Weiping 
Published: June 2009

Neurotransmitters, neuropeptides and hormones are released through the regulated exocytosis of SVs (synaptic vesicles) and LDCVs (large dense-core vesicles), a process that is controlled by calcium. Synaptotagmins are a family of type 1 membrane proteins that share a common domain structure. Most synaptotagmins are located in brain and endocrine cells, and some of these synaptotagmins bind to phospholipids and calcium at levels that trigger regulated exocytosis of SVs and LDCVs. This led to the proposed synaptotagmin–calcium-sensor paradigm, that is, members of the synaptotagmin family function as calcium sensors for the regulated exocytosis of neurotransmitters, neuropeptides and hormones. Here, we provide an overview of the synaptotagmin family, and review the recent mouse genetic studies aimed at understanding the functions of synaptotagmins in neurotransmission and endocrine-hormone secretion. Also, we discuss potential roles of synaptotagmins in non-traditional endocrine systems.
Rationale for Strength and Skill Goals in Tongue Resistance Training: A Review
Authors: Steele Catriona M. , Bailey Gemma L. , Molfenter Sonja M. , Yeates Erin M. 
Published: June 2009

AbstractRecent evidence in the dysphagia literature shows that tongue resistance training can be used to improve tongue strength. In this review article, we summarize what is known about the tongue and its role in swallowing. We review the literature on tongue pressure generation capacity (strength) and response to tongue resistance exercises. Tongue skill is introduced as a possible alternate goal in tongue resistance training, based on consideration of related literature regarding neural adaptation and improvements in motor performance resulting from treatment approaches in which goal-oriented practice and performance-specific feedback are provided.
The Application of Tongue Endurance Measures to Functional Dining
Authors: Kays Stephanie , Robbins JoAnne 
Published: June 2009

Abstract
While tongue strength has been shown to be critical for safe swallowing, measures of tongue endurance may be more functional, given that dining requires multiple swallows performed over a period of time. Recent findings demonstrate that the act of eating a meal reduces tongue endurance in both young and older adults, but young adults tend to have higher baseline endurance measures, suggesting that older adults present with reduced reserve to safely complete a meal with minimal effort. Furthermore, observed changes in tongue endurance after dining vary with respect to anatomic tongue location, age, and gender. Evidence from studies of limb muscle endurance is utilized to discuss these findings.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Authors: Capella-Gutiérrez Salvador , Silla-Martínez José M. , Gabaldón Toni 
Published: June 2009

Abstract
Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.
Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications.
Contact: tgabaldon@crg.es
Adaptive intervention in probabilistic boolean networks
Authors: Layek Ritwik , Datta Aniruddha , Pal Ranadip , Dougherty Edward R. 
Published: June 2009

AbstractMotivation: A basic problem of translational systems biology is to utilize gene regulatory networks as a vehicle to design therapeutic intervention strategies to beneficially alter network and, therefore, cellular dynamics. One strain of research has this problem from the perspective of control theory via the design of optimal Markov chain decision processes, mainly in the framework of probabilistic Boolean networks (PBNs). Full optimization assumes that the network is accurately modeled and, to the extent that model inference is inaccurate, which can be expected for gene regulatory networks owing to the combination of model complexity and a paucity of time-course data, the designed intervention strategy may perform poorly. We desire intervention strategies that do not assume accurate full-model inference.Results: This article demonstrates the feasibility of applying on-line adaptive control to improve intervention performance in genetic regulatory networks modeled by PBNs. It shows via simulations that when the network is modeled by a member of a known family of PBNs, an adaptive design can yield improved performance in terms of the average cost. Two algorithms are presented, one better suited for instantaneously random PBNs and the other better suited for context-sensitive PBNs with low switching probability between the constituent BNs.Contact: edward@ece.tamu.edu
Identifying the topology of protein complexes from affinity purification assays
Authors: Friedel Caroline C. , Zimmer Ralf 
Published: June 2009

Abstract
Motivation: Recent advances in high-throughput technologies have made it possible to investigate not only individual protein interactions, but also the association of these proteins in complexes. So far the focus has been on the prediction of complexes as sets of proteins from the experimental results. The modular substructure and the physical interactions within the protein complexes have been mostly ignored.
Results: We present an approach for identifying the direct physical interactions and the subcomponent structure of protein complexes predicted from affinity purification assays. Our algorithm calculates the union of all maximum spanning trees from scoring networks for each protein complex to extract relevant interactions. In a subsequent step this network is extended to interactions which are not accounted for by alternative indirect paths. We show that the interactions identified with this approach are more accurate in predicting experimentally derived physical interactions than baseline approaches. Based on these networks, the subcomponent structure of the complexes can be resolved more satisfactorily and subcomplexes can be identified. The usefulness of our method is illustrated on the RNA polymerases for which the modular substructure can be successfully reconstructed.
Availability: A Java implementation of the prediction methods and supplementary material are available at http://www.bio.ifi.lmu.de/Complexes/Substructures/.
Contact: caroline.friedel@bio.ifi.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Importing ArrayExpress datasets into R/Bioconductor
Authors: Kauffmann Audrey , Rayner Tim F. , Parkinson Helen , Kapushesky Misha , Lukk Margus , Brazma Alvis , Huber Wolfgang 
Published: June 2009

Abstract
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software. However, easy ways for importing datasets from ArrayExpress into R/Bioconductor have been lacking. Here, we present such a tool that is suitable for both interactive and automated use.
Availability: The ArrayExpress package is available from the Bioconductor project at http://www.bioconductor.org. A users guide and examples are provided with the package.
Contact: audrey@ebi.ac.uk
Supplementary information: Supplementary data are available Bioinformatics online.
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
Authors: Raue A. , Kreutz C. , Maiwald T. , Bachmann J. , Schilling M. , Klingmüller U. , Timmer J. 
Published: June 2009

AbstractMotivation: Mathematical description of biological reaction networks by differential equations leads to large models whose parameters are calibrated in order to optimally explain experimental data. Often only parts of the model can be observed directly. Given a model that sufficiently describes the measured data, it is important to infer how well model parameters are determined by the amount and quality of experimental data. This knowledge is essential for further investigation of model predictions. For this reason a major topic in modeling is identifiability analysis.Results: We suggest an approach that exploits the profile likelihood. It enables to detect structural non-identifiabilities, which manifest in functionally related model parameters. Furthermore, practical non-identifiabilities are detected, that might arise due to limited amount and quality of experimental data. Last but not least confidence intervals can be derived. The results are easy to interpret and can be used for experimental planning and for model reduction.Availability: An implementation is freely available for MATLAB and the PottersWheel modeling toolbox at http://web.me.com/andreas.raue/profile/software.html.Contact: andreas.raue@me.comSupplementary information: Supplementary data are available at Bioinformatics online.
Surface electrocardiogram to predict outcome in candidates for cardiac resynchronization therapy: a sub‐analysis of the CARE‐HF trial
Authors: Gervais Renaud , Leclercq Christophe , Shankar Aparna , Jacobs Sandra , Eiskjær Hans , Johannessen Arne , Freemantle Nick , Cleland John G.F. , Tavazzi Luigi , Daubert Claude ,   on behalf of the CARE‐HF investigators
Published: June 2009

AimsIn CARE‐HF, cardiac resynchronization therapy (CRT) lowered morbidity and mortality in patients with moderate to severe heart failure. We examined whether baseline and follow‐up electrocardiographic characteristics might predict long‐term outcome.Methods and resultsCARE‐HF randomly assigned 409 patients to medical therapy (MT) plus CRT, and 404 patients to MT alone. Electrocardiographic measurements were made at baseline during sinus rhythm, and at 3 months during paced or spontaneous rhythm depending on treatment assignment. Favourable outcome was defined as freedom from death, urgent transplantation, or cardiovascular hospitalization. Among patients assigned to CRT, 39% had unfavourable outcomes including 55 deaths. By single variable analysis, (i) prolonged PR interval, left QRS axis (but not QRS duration), and left bundle branch block (BBB) at baseline, and (ii) heart rate, PR, and QRS duration at 3 months predicted unfavourable outcome. By multiple variable analysis, treatment assignment (P = 0.0001), PR (P = 0.0004), and right BBB (P < 0.00013) at baseline predicted outcome, whereas baseline JTc and QRS duration at 3 months predicted all‐cause mortality and heart failure hospitalization (P = 0.0071).ConclusionIn CARE‐HF, QRS duration at baseline did not predict outcome, but QRS at 3 months was a predictor by single variable analysis. Patients with prolonged PR interval and the 5% of patients with right BBB had a particularly high event rate.
Identification of genetic markers associated with fatness and leg weakness traits in the pig
Authors: Fan B. , Onteru S. K. , Nikkilä M. T. , Stalder K. J. , Rothschild M. F. 
Published: June 2009

SummaryPigs have undergone long‐term selection in commercial conditions for improved rate and efficiency of lean gain. Interestingly, it has been observed in both experimental and field conditions that leg weakness has increased over time, concurrent with the selection for improved rate of lean gain, while fatter animals tend to have better leg action, and foot and leg (FL) structure. The exact molecular mechanisms or individual genes responsible for this apparent genetic correlation between fatness and leg weakness and other physical adaptability traits have been less well reported. Based on our recent studies involving candidate genes and leg weakness traits, the present investigation has identified 30 SNPs from 26 genes that were found to be associated with 10th rib backfat in a sow population consisting of 2066 animals. The specific alleles associated with increased backfat tended to be associated with better overall leg action, as shown for the genes including MTHFR, WNT2, APOE, BMP8, GNRHR and OXTR, while inconsistent associations with the single FL structure trait and backfat were observed for other genes. This study suggests that in some cases there may be a common genetic mechanism or linked genes regulating fatness and leg weakness. Such relationships are clearly complex, and the utilization of genetic markers associated with both traits should be treated cautiously.
Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle
Authors: Rincon G. , Farber E. A. , Farber C. R. , Nkrumah J. D. , Medrano J. F. 
Published: June 2009

SummaryIdentification of the genes and polymorphisms underlying quantitative traits, and understanding how these genes and polymorphisms affect economic traits, are important for successful marker‐assisted selection and more efficient management strategies in commercial cattle populations. Signal transducer and activator of transcription 6 (STAT6) gene is tightly connected to IL‐4 and IL‐13 signalling and plays a key role in TH2 polarization of the immune system. In addition, STAT6 acts as a mediator of leptin signalling and has been associated with body weight regulation. The objective of this study was to determine if SNPs within the bovine STAT6 gene are associated with economically important traits in feedlot cattle. The approach consisted of resequencing STAT6 using a panel of DNA from unrelated animals of different beef breeds. Specifically, 16 kb of STAT6 was resequenced in 47 animals and the process revealed 39 SNPs. From the 39 SNPs, a panel of 15 tag SNPs was genotyped in 1500 beef cattle samples with phenotypes to perform a marker‐trait association analysis. Among the 15 tag SNPs, five and six were polymorphic in Bos taurus and Bos indicus respectively. An association analysis was performed between the 15 tag SNPs and 14 performance and production traits. SNP ss115492459:C > A, ss115492461:A > G and ss115492458:G > C were significantly associated with back fat, calculated yield grade, cutability, hot carcass weight, dry matter intake, days on feed, back fat rate and average daily gain. These three SNPs were present in all Bos taurus beef breeds examined. Our results provide evidence that polymorphisms in STAT6 are associated with carcass and growth efficiency traits, and may be used for marker‐assisted selection and management in feedlot cattle.