bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of volume vascularization index and flow index: a phantom study
Authors: Schulten‐Wijman M. J. N. C. , Struijk P. C. , Brezinka C. , De Jong N. , Steegers E. A. P. 
Published: August 2008

AbstractObjectivesThree‐dimensional (3D) power Doppler ultrasonography provides indices to quantify moving blood within a volume of interest (e.g. ovary, endometrium, tumor or placenta). The purpose of this study was to determine the influence of ultrasound instrument settings on vascularization index (VI) and flow index (FI) at different flow velocities, using a specially built flow phantom with a small tube diameter.MethodsBlood‐mimicking fluid was pumped at 10–100 mL/h through a plastic tube with a diameter of 0.65 mm within a virtual spherical volume (content 137.12 cm3) of a Voluson 730 Expert 3D power Doppler ultrasound instrument. VI and FI were determined at different pulse repetition frequency (PRF) settings, with minimal and maximal wall motion filter (WMF) settings. The measured VI was compared with the actual VI.ResultsThe ability to measure VI and FI at different flow velocities was highly dependent on the PRF and WMF settings. In our experimental set‐up, using a PRF of 0.3 kHz, flow velocities of about 2 cm/s and higher could be registered. Measured VI was overestimated up to 44 times relative to actual VI.ConclusionsOur main finding in a laboratory set‐up was a considerable overestimation of moving blood volume using 3D power Doppler ultrasound in a single small tube. The degree of overestimation depends on the spatial resolution and on the settings of the ultrasound instrument. When small vessels are involved in a clinical setting, interpretation of VI should take this overestimation of moving blood volume into account. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
Pattern recognition using transabdominal ultrasound to diagnose ovarian mature cystic teratoma
Authors: Tongsong Theera , Luewan Suchaya , Phadungkiatwattana Podjanee , Neeyalavira Vithida , Wanapirak Chanane , Khunamornpong Surapan , Sukpan Kornkanok 
Published: August 2008

AbstractObjectiveTo determine the validity of sonographic pattern recognition in the diagnosis of mature cystic teratoma.MethodsConsecutive patients scheduled for elective surgery for adnexal masses were included in the study. All patients underwent transabdominal ultrasound with color extended‐flow mapping within 24 hours prior to surgery. Examinations were performed by the same sonographer to identify benign cystic teratoma. The final diagnoses were based on histopathologic findings.ResultsA total of 329 consecutive patients were recruited; 23 were excluded because the masses were not adnexal masses. Of the remaining 306 patients, 36 masses were found to be mature cystic teratomas and 270 were nonteratomas. Sonographic pattern recognition showed a sensitivity of 94.4% and a specificity of 98.2%.ConclusionSonographic pattern recognition using transabdominal ultrasound with color extended‐flow mapping can accurately diagnose mature cystic teratoma.
Histopathology‐based combined surgical approach to rectovaginal endometriosis
Authors: Mangler Mandy , Loddenkemper Christoph , Lanowska Malgorzata , Bartley Julia , Schneider Achim , Köhler Christhardt 
Published: August 2008

AbstractObjectiveTo describe a new surgical approach to rectovaginal endometriosis. Rectovaginal endometriosis can be infiltrative or superficial involving the bowel. Only infiltrative disease should be treated by intestinal resection. However, infiltration of endometriosis cannot be confirmed by preoperative imaging techniques.MethodsA total of 48 women with infiltrative rectovaginal endometriosis were included in this prospective study. Surgery was performed using a newly developed technique. All bowel resections were indicated according to operative findings and not on the basis of preoperative imaging technique results.ResultsThe decision for rectosigmoidal resection was based on the results of the intraoperative dissection of the rectovaginal septum. Histologically, infiltration of the ventral bowel wall was confirmed in all cases.ConclusionThis new surgical technique for the treatment of rectovaginal endometriosis allows precise diagnosis and treatment with low morbidity. A resection of the mesorectum is not necessary because the endometriotic nodules are always located on the antimesenteric surface of the bowel.
Tephrostratigraphy of the late glacial and Holocene sediments of Puyehue Lake (Southern Volcanic Zone, Chile, 40°S)
Authors: Bertrand Sébastien , Castiaux Julie , Juvigné Etienne 
Published: August 2008

AbstractWe document the mineralogical and geochemical composition of tephra layers identified in the late Quaternary sediments of Puyehue Lake (Southern Volcanic Zone of the Andes, Chile, 40°S) to identify the source volcanoes and to present the first tephrostratigraphic model for the region. For the last millennium, we propose a multi-criteria correlation model based on five tephra layers identified at seven coring sites. The two upper tephras are thin fine-grained green layers composed of more than 80% rhyodacitic glass shards, and associated to the AD 1960 and AD 1921–22 eruptions of the Puyehue-Cordon de Caulle volcanic complex. The third tephra is a sandy layer dominated by orthopyroxene, and related to the AD 1907 eruption of Rininahue maar. An olivine-rich tephra was deposited at the end of the 16th century, and a tephra characterized by a two-pyroxene association marks the second half of the first millennium AD. In addition, we detail the tephra succession of an 11.22-m-long sediment core covering the last 18,000 yr. The results demonstrate that the central province of the Southern Volcanic Zone has been active throughout the last deglaciation and the Holocene, with no increase in volcanic activity during glacial unloading.
Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies
Authors: Dessailly Benoit , Redfern Oliver , Orengo Christine 
Published: August 2008

AbstractThe structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of functions, both in terms of molecular activities and biological processes. Some of these superfamilies, such as the Rossmann-fold P-loop nucleotide hydrolases or the TIM-barrel glycosidases, have been the subject of extensive structural studies which in turn have shed light on how evolution of the sequence and structure properties produce functional diversity amongst homologues. Recently, the Structure-Function Linkage Database (SFLD) has been setup with the aim of helping the study of structure-function correlations in such superfamilies. Since the evolutionary success of these large superfamilies suggests biological importance, several Structural Genomics Centers have focused on providing full structural coverage for representatives of all sequence families in these superfamilies.In this work we evaluate structure/function diversity in a set of these large superfamilies and attempt to assess the quality and quantity of biological information gained from Structural Genomics.
Towards realising Darwin’s dream: setting the trees free
Authors: Page Roderic 
Published: August 2008

AbstractThe fact that all living organisms are related by common descent is one of the central principles of modern biology. Since the early 1990's the amount of data available to evolutionary biologists has exploded, and Elsevier’s journal Molecular Phylogenetics and Evolution, has become the largest single publisher of evolutionary trees (phylogenies). These trees and their supporting data potentially form a tremendous resource for biologists, with applications in genomics, evolutionary biology, biodiversity, and public health. However, most published trees are not available in any public database, but instead languish as images, "locked up" in the pages of journals. A long term solution to this problem is to invert the relationship between journal and database, such that the database is the primary repository, and the journal article becomes effectively a "report" on that data, albeit a report that is citable, and thus has the same status as a scientific article. This vision is some way off being achieved. However, publishers could greatly enhance the scientific value of their digital content by expanding article metadata to include taxonomic names, shared digital identifiers, geographical coordinates, and data structures such as evolutionary trees. This metadata doesn’t require making the full text available, but could substantially improve the findability of that text.
GabiPD: GABI primary database - a plant integrative 'omics' database
Authors: Riaño-Pachón Diego Mauricio , Nagel Axel , Wagner Robert , Neigenfind Jost , Weber Elke , Diehl Svenja , Kersten Birgit 
Published: August 2008

AbstractThe GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different 'omics' fronts are incorporated in GabiPD (i.e., genomics, transcriptomics, metabolomics, proteomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant plant lines, markers). All data types are pointing to the central Gene’s GreenCard, where gene information is integrated from genome annotation projects. Within the Gene’s GreenCards links to all GabiPD data related to the corresponding genes as well as cross references to large UniGene sets from NCBI and to useful gene-based external data bases are displayed. A collection of ~400000 ESTs from different species, generated in different GABI projects, is made publicly available though GabiPD. These ESTs have been cross referenced to UniGene sets from NCBI and to sequences from different plant genome projects, in an effort to ease the transfer of functional information. The centralized Gene's GreenCard also allows visualizing ESTs aligned to annotated transcripts as well as identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from Solanum tuberosum (potato) and Hordeum vulgare (barley). Gene expression data in GabiPD can be visualized through MapManWeb, the web interface of MapMan. Access to the data in GabiPD is provided via either the web interface (http://www.gabipd.org) or webservices that are currently available for Arabidopsis-related information. GabiPD was accessed by more than 30000 unique visitors last year from around the world.
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
Authors: Bogojeska Jasmina , Alexa Adrian , Altmann André , Lengauer Thomas , Rahnenführer Jörg 
Published: August 2008

Abstract
Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.
Availability: Rtreemix is an R package that is freely available from the Bioconductor project at http://www.bioconductor.org and runs on Linux and Windows.
Contact: jasmina@mpi-inf.mpg.de
Eigen-R2 for dissecting variation in high-dimensional studies
Authors: Chen Lin S. , Storey John D. 
Published: August 2008

Abstract
Summary: We provide a new statistical algorithm and software package called ‘eigen-R2’ for dissecting the variation of a high-dimensional biological dataset with respect to other measured variables of interest. We apply eigen-R2 to two real-life examples and compare it with simply averaging R2 over many features.
Availability: An R-package eigenR2 is available at http://www.genomine.org/eigenr2/ and will be made publicly available via Bioconductor.
Contact: jstorey@princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Empirical profile mixture models for phylogenetic reconstruction
Authors: Si Quang Le , Gascuel Olivier , Lartillot Nicolas 
Published: August 2008

AbstractMotivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a maximum likelihood (ML) framework. In addition, these mixture models only perform well on large alignments, from which they can reliably learn the shapes of profiles, and their associated weights.Results: In this work, we introduce an expectation–maximization algorithm for estimating amino acid profile mixtures from alignment databases. We apply it, learning on the HSSP database, and observe that a set of 20 profiles is enough to provide a better statistical fit than currently available empirical matrices (WAG, JTT), in particular on saturated data.Availability: We have implemented these models into two currently available Bayesian and ML phylogenetic reconstruction programs. The two implementations, PhyloBayes, and PhyML, are freely available on our web site (http://atgc.lirmm.fr/cat). They run under Linux and MaxOSX operating systems.Contact: nicolas.lartillot@lirmm.frSupplementary information: Supplementary data are available at Bioinformatics online.
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule
Authors: Wieghaus Kristen A. , Gianchandani Erwin P. , Paige Mikell A. , Brown Milton L. , Botchwey Edward A. , Papin Jason A. 
Published: August 2008

Abstract
Motivation: Computational techniques have been applied to experimental datasets to identify drug mode-of-action. A shortcoming of existing approaches is the requirement of large reference databases of compound expression profiles. Here, we developed a new pathway-based compendium analysis that couples multi-timepoint, controlled microarray data for a single compound with systems-based network analysis to elucidate drug mechanism more efficiently.
Results: We applied this approach to a transcriptional regulatory footprint of phthalimide neovascular factor 1 (PNF1)—a novel synthetic small molecule that exhibits significant in vitro endothelial potency—spanning 1–48 h post-supplementation in human micro-vascular endothelial cells (HMVEC) to comprehensively interrogate PNF1 effects. We concluded that PNF1 first induces tumor necrosis factor-alpha (TNF-α) signaling pathway function which in turn affects transforming growth factor-beta (TGF-β) signaling. These results are consistent with our previous observations of PNF1-directed TGF-β signaling at 24 h, including differential regulation of TGF-β-induced matrix metalloproteinase 14 (MMP14/MT1-MMP) which is implicated in angiogenesis. Ultimately, we illustrate how our pathway-based compendium analysis more efficiently generates hypotheses for compound mechanism than existing techniques.
Availability: The microarray data generated as part of this study are available in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/).
Contact: botchwey@virginia.edu; papin@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes
Authors: Feng‐Yi Su Kathy , Narayanan Kutty Sujatha , Meier Rudolf 
Published: August 2008

AbstractThe Sepsidae is, with approximately 300 described species, a relatively small family of cyclorrhaphan flies whose behaviour, morphology, and development have been extensively studied. However, currently the only available tree for Sepsidae is more than 10 years old and was based entirely on morphological characters. Here, we present the results of parsimony and Bayesian analyses based on 75 species, ten genes, and morphology. Parsimony and Bayesian analyses produce largely congruent and well‐supported topologies regardless of whether indels are coded as 5th character states, as missing values, or all sites with indels are removed. The tree confirms the monophyly of Sepsidae and identifies the Ropalomeridae as its sister group. With regard to higher‐level relationships, we identify widespread conflict between the morphological and the DNA sequence data. The proposed hypothesis based on both partitions largely reflects the signal in the molecular data. Particularly surprising is the rejection of two relationship hypotheses with strong morphological support, namely the sister group relationship between Orygma and the remaining Sepsidae and the monophyly of the Sepsis species group. Our partitioned Bremer support (PBS) analyses imply that indel coding has a stronger effect on the relative performance of individual gene partitions than the exclusion of alignment‐ambiguous sequences or the location of a gene on the mitochondrial or nuclear genome. However, these analyses also reveal unexpectedly strong fluctuations in PBS values given that indel treatment has only a minor effect on tree topology and jacknife support. These unexpected fluctuations highlight the need for a comparative study across multiple data sets that investigates the influence of conflict and indel treatment on PBS values.© The Willi Hennig Society 2008.
Visiting America: notes from an alcohol‐focused study tour made in 1961
Authors: Edwards Griffith 
Published: August 2008

ABSTRACTAims  This paper has as its focus a study tour made by the author in 1961. Diary notes are used to capture a historical moment in the evolution of alcohol studies. The paper will argue for the continuing value today of such experiences in support of career development and the building of ‘the field’.Data sources  Diary notes and personal recollection.Findings  The United States was at the time more active than the United Kingdom in its response to alcohol problems. There was, however, a disjunction between the elite American research world and the world of action, which was not informed greatly by research. For the most part, treatment services and prevention strategies seemed driven by opinion rather than by evidence. But at the level of serious scientific endeavour there was opportunity to meet influential figures including Seldon Bacon, Morris Chafetz, Milton Gross, Ebbe Curtis Hoff, Harris Isbell, E. M. Jellinek, Mark Keller, Benjamin Kissen, Robert Strauss, Wolf Schmidt and Abraham Wikler, who generously made their time available.Conclusions  These diary notes provide a snapshot of a field of endeavour at a critical stage of transition from uninformed assumptions towards establishment of a research base which can inform public action. The visit was of tangible value to the visitor in several different identified ways. Such an experience is inevitably time‐bound and personal, but there are general conclusions to be drawn as to the benefits which will be derived from early travel opportunities in a field such as alcohol studies, which is all too easily culture‐bound in its horizons and assumptions. Alcohol science needs to be more reflective on its history and the mechanisms that help to make it happen.
Association between wind speed and the occurrence of sickle cell acute painful episodes: results of a case‐crossover study
Authors: Nolan Vikki G. , Zhang Yuqing , Lash Timothy , Sebastiani Paola , Steinberg Martin H. 
Published: August 2008

SummaryThe role of the weather as a trigger of sickle cell acute painful episodes has long been debated. To more accurately describe the role of the weather as a trigger of painful events, we conducted a case‐crossover study of the association between local weather conditions and the occurrence of painful episodes. From the Cooperative Study of Sickle Cell Disease, we identified 813 patients with sickle cell anaemia who had 3570 acute painful episodes. We found an association between wind speed and the onset of pain, specifically wind speed during the 24‐h period preceding the onset of pain. Analysing wind speed as a categorical trait, showed a 13% increase (95% confidence interval: 3%, 24%) in odds of pain, when comparing the high wind speed to lower wind speed (P = 0·007). In addition, the association between wind speed and painful episodes was found to be stronger among men, particularly those in the warmer climate regions of the United States. These results are in agreement with another study that found an association between wind speed and hospital visits for pain in the United Kingdom, and lends support to physiological and clinical studies that have suggested that skin cooling is associated with sickle vasoocclusion and perhaps pain.