bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertical Structures of Precipitation in Cyclones Crossing the Oregon Cascades
Authors: Medina Socorro , Sukovich Ellen , Houze Robert A. 
Published: October 2007

Abstract
The vertical structure of radar echoes in extratropical cyclones moving over the Oregon Cascade Mountains from the Pacific Ocean indicates characteristic precipitation processes in three basic storm sectors. In the early sector of a cyclone, a leading edge echo (LEE) appears aloft and descends toward the surface. Updraft cells inferred from the vertically pointing Doppler radial velocity are often absent or weak. In the middle sector the radar echo consists of a thick, vertically continuous layer extending from the mountainside up to a height of approximately 5–6 km that lasts for several hours. When the middle sector passes over the windward slope of the Cascades, the vertical structure of the precipitation exhibits a double maximum echo (DME). One maximum is associated with the radar reflectivity bright band. The second reflectivity maximum is located approximately 1–2.5 km above the bright band. The secondary reflectivity maximum aloft does not appear until the middle sector passes over the windward slope of the Cascades, suggesting that this feature results from or is enhanced by the interaction of the baroclinic system with the terrain. In the intervening region between the two reflectivity maxima there is a turbulent layer with updraft cells (&gt;0.5 m s−1), spaced 1–3 km apart. This turbulent layer is thought to be crucial for enhancing the growth of precipitation particles and thus speeding up their fallout over the windward slope of the Cascades. In the late sector of the storm, the precipitation consists of generally isolated shallow convection echoes (SCEs), with low echo tops and, in some cases, upward motion near the tops of the cells. The SCEs become broader upon interacting with the windward slope of the Cascade Range, suggesting that orographic uplift enhances the convective cells. In the SCE period the precipitation decreases very sharply on the lee slope of the Cascades.
An Efficient Solution Method for the Buoyancy Wave Equation at Variable Wind and Temperature
Authors: Rõõm Rein , Zirk Marko 
Published: October 2007

Abstract
To solve a horizontally spectral, vertically discrete buoyancy wave equation in conditions of arbitrary wind and temperature distribution with height, a novel method is applied, which consists of a presentation of the solution in the form of a cumulative product of complex decrease factors. For decrease factors, a nonlinear, inhomogeneous, two-member recurrence formula follows that is initiated, assuming the radiative condition at the top. Singularities of the wave equation, corresponding to a critical layer in the vicinity of evanescent wind, are eliminated by turbulent friction. The estimation of minimal vertical resolution is derived, enabling solution stability and accuracy. The areas of application of the developed numerical scheme are the high-precision modeling of orographic waves for arbitrary orography in general atmospheric stratification conditions and testing of adiabatic kernels of numerical weather prediction models.
Detection of Rainfall Events Using Underwater Passive Aquatic Sensors and Air–Sea Temperature Changes in the Tropical Pacific Ocean
Authors: Ma Barry B. , Nystuen Jeffrey A. 
Published: October 2007

Abstract
Several years of long-term high temporal resolution ocean ambient noise data from the tropical Pacific Ocean are analyzed to detect oceanic rainfall. Ocean ambient noise generated by rainfall and wind are identified through an acoustic discrimination process. Once the spectra are classified, wind speed and rainfall rates are quantified using the empirical algorithms. Rainfall-rate time series have temporal resolutions of 1 min. These data provide a unique opportunity to study the rainfall events and patterns in two different climate regions, the intertropical convergence zone (ITCZ) of the tropical eastern Pacific (10° and 12°N, 95°W) and the equatorial western Pacific (0°, 165°E). At both locations the rain events have a mean rainfall of 15 mm h−1, but the events are longer in the eastern Pacific. After the rain event is defined, the probability that a rain event can be detected using the change in air–sea temperature often associated with the rainfall is investigated. The result shows that the rain event accompanied by the decrease of air temperature is a general feature, but that using the temperature difference to detect the rainfall has a very high false alarm rate, which makes it unsuitable for rainfall detection.
Evaluation of Boundary Layer Similarity Theory for Stable Conditions in CASES-99
Authors: Ha Kyung-Ja , Hyun Yu-Kyung , Oh Hyun-Mi , Kim Kyung-Eak , Mahrt Larry 
Published: October 2007

Abstract
The Monin–Obukhov similarity theory and a generalized formulation of the mixing length for the stable boundary layer are evaluated using the Cooperative Atmosphere–Surface Exchange Study-1999 (CASES-99) data. The large-scale wind forcing is classified into weak, intermediate, and strong winds. Although the stability parameter, z/L, is inversely dependent on the mean wind speed, the speed of the large-scale flow includes independent influences on the flux–gradient relationship. The dimensionless mean wind shear is found to obey existing stability functions when z/L is less than unity, particularly for the strong and intermediate wind classes. For weak mean winds and/or strong stability (z/L &gt; 1), this similarity theory breaks down. Deviations from similarity theory are examined in terms of intermittency. A case study of a weak-wind night indicates important modulation of the turbulence flux by mesoscale motions of unknown origin.
Influence of Anterior Cruciate Ligament Bundles on Knee Kinematics
Authors: Robinson James , Carrat Lionel , Granchi Carinne , Colombet Philippe 
Published: October 2007

Background The synergistic functions of the anteromedial and posterolateral bundles of the anterior cruciate ligament in restraining anterior laxity are known. Cadaveric experiments have also suggested different functions of the 2 bundles in controlling a combined rotatory load simulating the pivot shift. Hypothesis The posterolateral bundle is important in controlling the coupled tibial axial rotation laxity occurring during clinical laxity tests performed in vivo, particularly the pivot-shift maneuver. Study Design Cohort study; Level of evidence, 2. Methods Twenty-one patients underwent navigated 2-bundle anterior cruciate ligament reconstruction. The navigation was additionally used to measure the knee kinematics in response to the anterior drawer test (performed at 90°), Lachman test (performed at 20° of flexion), and pivot-shift test. Two sequential reconstruction protocols were used to assess the contribution of the anteromedial and posterolateral bundles to restraining tibial translations and coupled axial rotation occurring with the manually performed clinical laxity tests. Results Anterior tibial translation during the anterior drawer test was better restrained by anteromedial bundle reconstruction than by posterolateral bundle reconstruction. Conversely, posterolateral bundle reconstruction better restrained anterior tibial translation during the Lachman test. Both bundles contributed to the control of anterior laxity during the pivot shift. However, the posterolateral bundle was more important than was the anteromedial bundle in controlling the tibial rotational component (posterolateral bundle reconstruction caused a 53% reduction in tibial rotation laxity compared with a 42% reduction with anteromedial bundle reconstruction, P < .0001). Conclusion This study provides objective, in vivo data about how the anteromedial and posterolateral bundles act differentially to stabilize the knee, particularly during the pivot shift. The posterolateral bundle was important in controlling not only anterior laxity toward knee extension but the rotational component of the pivot shift.
The longitudinal relationship between the patient-reported Multiple Sclerosis Impact Scale and the clinician-assessed Multiple Sclerosis Functional Composite
Authors: Costelloe L. , O'Rourke K. , McGuigan C. , Walsh C. , Tubridy N. , Hutchinson M. 
Published: October 2007

Background To examine the longitudinal relationship between the patient-rated Multiple Sclerosis Impact Scale (MSIS-29) and the doctor-reported Multiple Sclerosis Functional Composite (MSFC). Methods Two-hundred and four MS patients at baseline and 150 patients one to three years later had MSFC and MSIS-29 assessments. Cross-sectional correlations between these measures and correlations of change in scores were examined. Minimally important change (MIC) in the MSFC was defined at either 0.5 or 0.32 SD from baseline. Effect sizes (ES) were calculated. Results Validity: The MSIS-29 physical correlated moderately with the total MSFC score and the 25-foot timed walk and 9-hole peg test. Correlations of the MSIS-29 physical with the PASAT, and the MSFC with the MSIS-29 psychological were weak. Responsiveness: When MIC in the MSFC was defined as 0.5, mean MSIS-29 physical change was 11.26 (ES = 0.53). At MSFC change of 0.32, mean MSIS-29 physical change was 10.4 (ES = 0.52). Change in MSFC scores correlated weakly with change in the MSIS-29 scores. Stability: In patients with stable MSFC scores, the mean MSIS-29 physical scores improved minimally over time with negligible ES. Conclusions Although the MSIS-29 physical demonstrates moderate cross-sectional correlation with the MSFC, the weak correlations of change scores between the two instruments indicate that they measure different aspects of the effects of multiple sclerosis morbidity. Multiple Sclerosis 2008; 14: 255—258. http://msj.sagepub.com
Polymorphisms of the cannabinoid 1 receptor gene and cognitive impairment in multiple sclerosis
Authors: Woolmore JA , Stone MJ , Holley SL , Jenkinson PM , Ike A. , Jones PW , Fryer AA , Strange RC , Stephens R. , Langdon DW , Hawkins CP 
Published: October 2007

Cognitive impairment occurs in 45—65% of multiple sclerosis (MS) patients. The cannabinoid system may potentially be neuroprotective in MS. We examined the relationship between polymorphisms of the CNR1 gene and neuropsychological outcome in MS using a test and confirmatory sample of patients. One hundred and ninety-four MS patients were assessed over five key areas of neuropsychological function, which are most commonly impaired in MS. The first 97 patients formed the test sample. A further confirmatory sample of 97 patients was used to test association found in the test sample. The schedule included: Wisconsin card sorting test 64 version, Rey auditory verbal learning task immediate and delayed scores, controlled oral word association task, judgement of line orientation and symbol digit modalities task. Three single nucleotide polymorphisms (SNPs) were typed within the CNR1 gene. For the overall neuropsychological assessment score we used a multiple linear regression model with selected covariates to show that subjects with the AA genotype of the SNP RS1049353 were more impaired (mean -2.47, SD 5.75, P = 0.008, Bonferroni corrected P = 0.024) than the other subjects (mean 0.24, SD 4.24). This was not confirmed when the association was retested in the confirmatory sample. No associations were identified between these CNR1 variants and cognitive impairment in MS. Multiple Sclerosis 2008; 14: 177—182. http://msj.sagepub.com
Fibroblast growth factor controls the timing of Scl, Lmo2, and Runx1 expression during embryonic blood development
Authors: Walmsley Maggie , Cleaver David , Patient Roger 
Published: October 2007

AbstractTo program pluripotent cells into blood, a knowledge of the locations of precursors during their journey through the embryo and the signals they experience would be informative. The anterior (a) and posterior (p) ventral blood islands (VBIs) in Xenopus are derived from opposite sides of the pregastrula embryo. The aVBI goes through a “hemangioblast” state, characterized by coexpression of blood and endothelial genes at neurula stages, whereas the pVBI expresses these genes in a nonoverlapping fashion several hours later, after commitment to either a blood or an endothelial fate. We describe a novel role for fibroblast growth factor (FGF) in controlling the timing of Scl, Lmo2, and Runx1 expression in the 2 VBI compartments. Blocking FGF signaling during gastrulation expands expression at neurula stages into posterior regions. We show, by lineage labeling, explant analysis, and targeted blocking of FGF signaling, that this is due to the pVBI prematurely expressing these genes with the timing of the aVBI. In contrast, overexpression of FGF in aVBI precursors eliminates the anterior hemangioblast program. Using this information, we have recapitulated the anterior hemangioblast program in pluripotent cells in vitro by inhibiting FGF signaling in anterior mesoderm induced by activin and exposed to bone morphogenetic protein (BMP) signaling.
Repertoire and frequency of immune cells reactive to Epstein-Barr virus–derived autologous lymphoblastoid cell lines
Authors: Bhaduri-McIntosh Sumita , Rotenberg Marisa J. , Gardner Benjamin , Robert Marie , Miller George 
Published: October 2007

AbstractAnswers to questions about frequency and repertoire of immune cells, relative contributions made by different types of immune cells toward the total Epstein-Barr virus (EBV)–directed response and the variation of such responses in healthy persons have been elusive because of disparities in assays, antigen presenting cells, and antigenic sources used in previous experiments. In this study, we addressed these questions using an assay that allowed direct comparison of responses generated by different types of cells of the immune system. This short-term (20-hour) ex vivo assay measured interferon-γ production by blood cells in response to autologous EBV-transformed lymphoblastoid cell lines (LCLs). Our experiments defined the variation in responses among persons and clearly distinguished 10 healthy EBV-immune from 10 healthy EBV-naive persons. In EBV-immune persons, 33% of responding cells were CD4+, 43.3% were CD8+, and 12.9% were γ-δ T cells. LCL-reactive CD8+ T cells were only 1.7-fold more frequent than similarly reactive CD4+T cells. Responses by γ-δ T cells were 6-fold higher in seropositive than in seronegative persons. Our findings emphasize the importance of CD4+ and γ-δ T-cell responses and have implications for immunotherapy and for identifying defects in T-cell populations that might predispose to development of EBV-associated lymphomas.
Strainer: software for analysis of population variation in community genomic datasets
Authors: Eppley John M , Tyson Gene W , Getz Wayne M , Banfield Jillian F 
Published: October 2007

Abstract

Background
Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes.

Results
We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.

Conclusion
The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Authors: Sclep Gert , Allemeersch Joke , Liechti Robin , De Meyer Björn , Beynon Jim , Bhalerao Rishikesh , Moreau Yves , Nietfeld Wilfried , Renou Jean-Pierre , Reymond Philippe , Kuiper Martin TR , Hilson Pierre 
Published: October 2007

Abstract

Background
The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference.

Results
GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.

Conclusion
To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Authors: Côté Richard G , Jones Philip , Martens Lennart , Kerrien Samuel , Reisinger Florian , Lin Quan , Leinonen Rasko , Apweiler Rolf , Hermjakob Henning 
Published: October 2007

Abstract

Background
Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs.

Results
We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface.

Conclusion
We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
Authors: Dalevi Daniel , DeSantis Todd Z , Fredslund Jakob , Andersen Gary L , Markowitz Victor M , Hugenholtz Philip 
Published: October 2007

Abstract

Background
Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.

Results
We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa.

Conclusion
GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website [1].