bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Differences in Salivary Pathogen Load during Tick Transmission Underlie Strain-Specific Variation in Transmission Efficiency ofAnaplasma marginale
Authors: Ueti Massaro W. , Knowles Donald P. , Davitt Christine M. , Scoles Glen A. , Baszler Timothy V. , Palmer Guy H. 
Published: October 2008

ABSTRACTThe relative fitness of arthropod-borne pathogens within the vector can be a major determinant of pathogen prevalence within the mammalian host population. Strains of the tick-borne rickettsiaAnaplasma marginalediffer markedly in transmission efficiency, with a consequent impact on pathogen strain structure. We have identified twoA. marginalestrains with significant differences in the transmission phenotype that is effected following infection of the salivary gland. We have proposed competing hypotheses to explain the phenotypes: (i) both strains are secreted equally, but there is an intrinsic difference in infectivity for the mammalian host, or (ii) one strain is secreted at a significantly higher level and thus represents delivery of a greater pathogen dose. Quantitative analysis of pathogen replication and secretion revealed that the high-efficiency St. Maries strain replicated to a 10-fold-higher titer and that a significantly greater percentage of infected ticks secretedA. marginaleinto the saliva and did so at a significantly higher level than for the low-efficiency Israel vaccine strain. Furthermore, the transmission phenotype of the vaccine strain could be restored to that of the St. Maries strain simply by increasing the delivered pathogen dose, either by direct inoculation of salivary gland organisms or by increasing the number of ticks during transmission feeding. We identified morphological differences in the colonization of each strain within the salivary glands and propose that these reflect strain-specific differences in replication and secretion pathways linked to the vector-pathogen interaction.
SF1
Authors: Feldman Michael B. 
Published: October 2008

Level - Beginner, but attendees should have some experience with a high-level programming language.
This tutorial is designed for those who have some familiarity with a programming language, but who are new to Ada. In the morning, we will discuss the basics of programming in Ada, including types, packages, syntax rules, and other Ada programming constructs. In the afternoon, we will cover Ada's object-oriented programming and concurrent-programming features. Many examples will be shown; freely downloadable Ada programming environments and tools will be demonstrated.
MA1
Authors: McCormick John W. 
Published: October 2008

Level - Intermediate. This tutorial assumes basic knowledge or experience with the Ada programming language.
This tutorial covers two of the major problems with parallel and real-time programming - time management and storage management. Parallel processing, whether on single-processor machines or multiple processors, has many pitfalls. We will examine these potential pitfalls, and discuss ways to avoid common problems, such as deadlocks and race conditions. We will also discuss how to write code that efficiently passes data with other parallel processes. The basics of parallel processing are covered, leading to a discussion and examples using Ada tasking. In addition, the Ada Real-Time Systems Annex is also covered.
Raindrop Size Distribution Modeling from a Statistical Rain Parameter Relation and Its Application to the TRMM Precipitation Radar Rain Retrieval Algorithm
Authors: Kozu Toshiaki , Iguchi Toshio , Shimomai Toyoshi , Kashiwagi Nobuhisa 
Published: October 2008

AbstractA generalized method is presented to derive a “two scale” raindrop size distribution (DSD) model over a spatial or temporal domain in which a statistical rain parameter relation exists. The two-scale model is generally defined as a model in which one DSD parameter is allowed to vary rapidly and the other is constant over a certain space or time domain. The existence of a rain parameter relation such as the radar reflectivity–rainfall rate (Z–R) relation over a spatial or temporal domain is an example of such a two-scale DSD model. A procedure is described that employs a statistical rain parameter relation with an assumption of the gamma DSD model. An example using Z–R relations obtained at Kototabang, West Sumatra, is presented. The result shows that the resulting two-scale DSD model expressed by conventional DSD parameters depends on the assumed value of parameter μ while rain parameter relations such as k–Ze relations from those models using different μ values are very close to each other, indicating the stability of the model against the variation of μ and the validity of this method. The result is applied to the DSD model for the Tropical Rainfall Measuring Mission (TRMM) precipitation radar 2A25 (versions 5 and 6) algorithm. The derivation procedure of the 2A25 DSD model is described. Through the application of this model, it has become possible to make a logically well-organized rain profiling algorithm and reasonable rain attenuation correction and rainfall estimates, as described in an earlier paper by Iguchi et al.
A Balanced Approximation of the One-Layer Shallow-Water Equations on a Sphere
Authors: Verkley W. T. M. 
Published: October 2008

AbstractA global version of the equivalent barotropic vorticity equation is derived for the one-layer shallow-water equations on a sphere. The equation has the same form as the corresponding beta plane version, but with one important difference: the stretching (Cressman) term in the expression of the potential vorticity retains its full dependence on f 2, where f is the Coriolis parameter. As a check of the resulting system, the dynamics of linear Rossby waves are considered. It is shown that these waves are rather accurate approximations of the westward-propagating waves of the second class of the original shallow-water equations. It is also concluded that for Rossby waves with short meridional wavelengths the factor f 2 in the stretching term can be replaced by the constant value f02, where f0 is the Coriolis parameter at ±45° latitude.
A Revised Hydrology for the ECMWF Model: Verification from Field Site to Terrestrial Water Storage and Impact in the Integrated Forecast System
Authors: Balsamo Gianpaolo , Beljaars Anton , Scipal Klaus , Viterbo Pedro , van den Hurk Bart , Hirschi Martin , Betts Alan K. 
Published: October 2008

Abstract
The Tiled ECMWF Scheme for Surface Exchanges over Land (TESSEL) is used operationally in the Integrated Forecast System (IFS) for describing the evolution of soil, vegetation, and snow over the continents at diverse spatial resolutions. A revised land surface hydrology (H-TESSEL) is introduced in the ECMWF operational model to address shortcomings of the land surface scheme, specifically the lack of surface runoff and the choice of a global uniform soil texture. New infiltration and runoff schemes are introduced with a dependency on the soil texture and standard deviation of orography. A set of experiments in stand-alone mode is used to assess the improved prediction of soil moisture at the local scale against field site observations. Comparison with basin-scale water balance (BSWB) and Global Runoff Data Centre (GRDC) datasets indicates a consistently larger dynamical range of land water mass over large continental areas and an improved prediction of river runoff, while the effect on atmospheric fluxes is fairly small. Finally, the ECMWF data assimilation and prediction systems are used to verify the effect on surface and near-surface quantities in the atmospheric-coupled mode. A midlatitude error reduction is seen both in soil moisture and in 2-m temperature.
Comparison of Human to Macaque Uterosacral–Cardinal Ligament Complex and Its Relationship to Pelvic Organ Prolapse
Authors: Shahryarinejad Azin , Vardy Michael David 
Published: October 2008

The uterosacral–cardinal ligament complex is thought to be the critical structure responsible for uterine and apical vaginal support. It is ill defined and can be difficult to dissect in the cadaver lab and in the operating room. Even less information is available on the analogous structures in the monkey model. We present this report to bring together what little is known to aid in studying this model and pelvic organ prolapse (POP), and to point out the need for critical assessment of this hormone-responsive tissue in the process of drug development. Competing Interests: This article was sponsored by Covance Inc. and Schering-Plough. The authors did not declare any other competing interests.
High-dose therapy followed by autologous purged stem cell transplantation and doxorubicin-based chemotherapy in patients with advanced follicular lymphoma: a randomized multicenter study by the GOELAMS with final results after a median follow-up of 9 years
Authors: Gyan Emmanuel , Foussard Charles , Bertrand Philippe , Michenet Patrick , Le Gouill Steven , Berthou Christian , Maisonneuve Hervé , Delwail Vincent , Gressin Rémi , Quittet Philippe , Vilque Jean-Pierre , Desablens Bernard , Jaubert Jérôme , Ramée Jean-François , Arakelyan Nina , Thyss Antoine , Moluçon-Chabrot Cécile , Delépine Roselyne , Milpied Noël , Colombat Philippe , Deconinck Eric 
Published: October 2008

Abstract
Autologous stem cell transplantation (ASCT) as first-line therapy for follicular lymphoma (FL) remains controversial. The multicenter study randomized 172 patients with untreated FL for either immunochemotherapy or high-dose therapy (HDT) followed by purged ASCT. Conditioning was performed with total body irradiation (TBI) and cyclophosphamide. The 9-year overall survival (OS) was similar in the HDT and conventional chemotherapy groups (76% and 80%, respectively). The 9-year progression-free survival (PFS) was higher in the ASCT than the chemotherapy group (64% vs 39%; P = .004). A PFS plateau was observed in the HDT group after 7 years. On multivariate analysis, OS and PFS were independently affected by the per-formance status score, the number of nodal areas involved, and the treatment group. Secondary malignancies were more frequent in the HDT than in the chemotherapy group (6 secondary myelodysplastic syndrome/acute myeloid leukemia and 6 second solid tumor cancers vs 1 acute myeloid leukemia, P = .01). The occurrence of a PFS plateau suggests that a subgroup of patients might have their FL cured by ASCT. However, the increased rate of secondary malignancies may discourage the use of purged ASCT in combination with TBI as first-line treatment for FL. This trial has been registered with ClinicalTrials.gov under identifier NCT00696735.
FUNYBASE: a FUNgal phYlogenomic dataBASE
Authors: Marthey Sylvain , Aguileta Gabriela , Rodolphe François , Gendrault Annie , Giraud Tatiana , Fournier Elisabeth , Lopez-Villavicencio Manuela , Gautier Angélique , Lebrun Marc-Henri , Chiapello Hélène 
Published: October 2008

Abstract

Background
The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi.

Description
FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented.

Conclusion
FUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
Authors: DiMaggio Peter A , McAllister Scott R , Floudas Christodoulos A , Feng Xiao-Jiang , Rabinowitz Joshua D , Rabitz Herschel A 
Published: October 2008

Abstract

Background
The analysis of large-scale data sets via clustering techniques is utilized in a number of applications. Biclustering in particular has emerged as an important problem in the analysis of gene expression data since genes may only jointly respond over a subset of conditions. Biclustering algorithms also have important applications in sample classification where, for instance, tissue samples can be classified as cancerous or normal. Many of the methods for biclustering, and clustering algorithms in general, utilize simplified models or heuristic strategies for identifying the "best" grouping of elements according to some metric and cluster definition and thus result in suboptimal clusters.

Results
In this article, we present a rigorous approach to biclustering, OREO, which is based on the Optimal RE-Ordering of the rows and columns of a data matrix so as to globally minimize the dissimilarity metric. The physical permutations of the rows and columns of the data matrix can be modeled as either a network flow problem or a traveling salesman problem. Cluster boundaries in one dimension are used to partition and re-order the other dimensions of the corresponding submatrices to generate biclusters. The performance of OREO is tested on (a) metabolite concentration data, (b) an image reconstruction matrix, (c) synthetic data with implanted biclusters, and gene expression data for (d) colon cancer data, (e) breast cancer data, as well as (f) yeast segregant data to validate the ability of the proposed method and compare it to existing biclustering and clustering methods.

Conclusion
We demonstrate that this rigorous global optimization method for biclustering produces clusters with more insightful groupings of similar entities, such as genes or metabolites sharing common functions, than other clustering and biclustering algorithms and can reconstruct underlying fundamental patterns in the data for several distinct sets of data matrices arising in important biological applications.
Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing
Authors: Floris Matteo , Orsini Massimiliano , Thanaraj Thangavel Alphonse 
Published: October 2008

Abstract

Background
It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function.

Results
(i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences.

Conclusion
(i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms – since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) Data: The reported resource (at http://www.bioinformatica.crs4.org/tools/dbs/splivap/) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
Authors: Alves Gelio , Ogurtsov Aleksey Y , Yu Yi-Kuo 
Published: October 2008

Abstract

Background
Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies.

Description
We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist) into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users.

Conclusion
We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.
Cloning of the cytochrome p450 reductase (crtR) gene and its involvement in the astaxanthin biosynthesis of Xanthophyllomyces dendrorhous
Authors: Alcaíno Jennifer , Barahona Salvador , Carmona Marisela , Lozano Carla , Marcoleta Andrés , Niklitschek Mauricio , Sepúlveda Dionisia , Baeza Marcelo , Cifuentes Víctor 
Published: October 2008

Abstract

Background
The yeast Xanthophyllomyces dendrorhous synthesizes astaxanthin, a carotenoid with high commercial interest. The proposed biosynthetic route in this organism is isopentenyl-pyrophosphate (IPP) → geranyleranyl pyrophosphate (GGPP) → phytoene → lycopene → β-carotene → astaxanthin. Recently, it has been published that the conversion of β-carotene into astaxanthin requires only one enzyme, astaxanthin synthase or CrtS, encoded by crtS gene. This enzyme belongs to the cytochrome P450 protein family.

Results
In this work, a crtR gene was isolated from X. dendrorhous yeast, which encodes a cytochrome P450 reductase (CPR) that provides CrtS with the necessary electrons for substrate oxygenation. We determined the structural organization of the crtR gene and its location in the yeast electrophoretic karyotype. Two transformants, CBSTr and T13, were obtained by deleting the crtR gene and inserting a hygromycin B resistance cassette. The carotenoid composition of the transformants was altered in relation to the wild type strain. CBSTr forms yellow colonies because it is unable to produce astaxanthin, hence accumulating β-carotene. T13 forms pale colonies because its astaxanthin content is reduced and its β-carotene content is increased.

Conclusion
In addition to the crtS gene, X. dendrorhous requires a novel gene, crtR, for the conversion of β-carotene to astaxanthin.