bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunogenetic sequence annotation based on IMGT-ONTOLOGY
Authors: Jabado-Michaloud Joumana , Folch Géraldine , Bellahcene Fatena , Ehrenmann François , Duroux Patrice , Giudicelli Véronique , Lefranc Marie-Paule 
Published: April 2009

AbstractIMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).
Protein Ontology and Community Curation
Authors: Arighi Cecilia 
Published: April 2009

AbstractThe Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways, complexes, or in disease modeling. This is useful for proteomics studies where isoforms and modified forms must be differentiated and for biological pathway/network representation where the cascade of events often depends on a specific protein modification. The PRO framework is designed to allow the community to curate any protein entities of interest and will provide a stable unique identifier to any protein type. PRO is manually curated starting with content derived from various data sources coupling with scientific literature. Only annotation with experimental evidence is included, and is in the form of relationship to other ontologies (such as Gene Ontology, Sequence Ontology, and PSI-MOD). We have developed a web-based curation editor for PRO community annotation. In the tutorial, we will first give a brief introduction to the ontology and its relevance to the research communities - OBO ontologies, MOD, pathway and other databases, and any resources that need references/links to protein types. We will show the components of the PRO entry report, and how to search the ontology. Then, we will walk through an example where we will teach the basic curation steps: accessing the web editor, entering the protein to be defined with source attribution, and adding functional annotation. We will provide the necessary tools and documentation so that the user will be able to start curating the protein types of interest. PRO URL: "http://pir.georgetown.edu/pro/":http://pir.georgetown.edu/pro/
Language Modeling as an Efficacious Early Language Intervention Approach With Young Children Demonstrating Complex Communication Needs
Authors: Solomon-Rice Patti , Soto Gloria 
Published: April 2009

Abstract
This article highlights evidence supporting the efficacy of adult language modeling and child imitation, including use of aided AAC modeling, during language intervention with young children demonstrating complex communication needs. First, four evidence-based language intervention approaches that incorporate adult language modeling and child imitation with young children demonstrating language delays are described. Second, two additional evidence-based language intervention approaches that incorporate aided AAC modeling during communication partner training, and direct clinical intervention with young children using aided AAC are further discussed. The article concludes with suggestions for strategies to use during language intervention with young children who use aided AAC.
Internet Resources for Augmentative and Alternative Communication in Early Intervention and Early Childhood Services
Authors: Robinson Nancy B. 
Published: April 2009

Abstract
The development and implementation of augmentative and alternative communication (AAC) tools for children in the earliest stages of communication and language development may include a range of communication modalities that include gesture, vocalization, actual objects, photos, picture icons, Speech Generating Devices (SGDs), and higher-tech AAC devices. Internet resources for AAC in early intervention settings include assessment tools, communication aids, early literacy supports, educational tools for professionals and families and much more. Some of the key resources that have been reviewed by a team of professionals through the Supporting Early Education Development Systems (SEEDS) Project in the Sacramento County Office of Education, Sacramento, California, are described.
Response to Intervention: Applications for AAC in Preschool Settings
Authors: Grether Sandra M. 
Published: April 2009

Abstract
Educators were previously encouraged to use IQ-achievement discrepancy to identify children with learning disabilities. The Individuals with Disabilities Education Improvement Act (IDEA, 2004) promotes an alternative method, “Response to Intervention” or RTI, to identify and provide early intervention to all children at risk for school failure. Recognition and Response (R & R) is the RTI model for preschool-aged children. Children with complex communication needs, who use augmentative and alternative communication (AAC), are at risk for failing in the preschool classroom and can benefit from the educational supports provided through R & R. This article discusses the levels of support provided by RTI and strategies and supports for achieving academic success for preschool children who use AAC.
CROC: finding chromosomal clusters in eukaryotic genomes
Authors: Pignatelli Miguel , Serras Florenci , Moya Andrés , Guigó Roderic , Corominas Montserrat 
Published: April 2009

AbstractSummary: There is increasing evidence showing that co-expression of genes that cluster along the genome is a common characteristic of eukaryotic transcriptomes. Several algorithms have been used to date in the identification of these kinds of gene organization. Here, we present a web tool called CROC that aims to help in the identification and analysis of genomic gene clusters. This method has been successfully used before in the identification of chromosomal clusters in different eukaryotic species.Availability: The web server is freely available to non-commercial users at the following address: http://metagenomics.uv.es/CROC/Contact: miguel.pignatelli@uv.es
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution
Authors: Kumar Anoop , Cowen Lenore 
Published: April 2009

Abstract
Motivation: While profile hidden Markov models (HMMs) are successful and powerful methods to recognize homologous proteins, they can break down when homology becomes too distant due to lack of sufficient training data. We show that we can improve the performance of HMMs in this domain by using a simple simulated model of evolution to create an augmented training set.
Results: We show, in two different remote protein homolog tasks, that HMMs whose training is augmented with simulated evolution outperform HMMs trained only on real data. We find that a mutation rate between 15 and 20% performs best for recognizing G-protein coupled receptor proteins in different classes, and for recognizing SCOP super-family proteins from different families.
Contacts: anoop.kumar@tufts.edu;lenore.cowen@tufts.edu
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays
Authors: Khan Zia , Bloom Joshua S. , Kruglyak Leonid , Singh Mona 
Published: April 2009

Abstract
Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome–genome comparisons.
Results: We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences.
Availability: Source code for the algorithm is available under a BSD open source license at http://compbio.cs.princeton.edu/mems. The implementation can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3.
Contact: zkhan@cs.princeton.edu;mona@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Anthropogenic and natural effects on the coastal lagoons in the southwest of Spain (Doñana National Park)
Authors: Sousa Arturo , García-Murillo Pablo , Morales Julia , García-Barrón Leoncio 
Published: April 2009

AbstractSousa, A., García-Murillo, P., Morales, J., and García-Barrón, L. 2009. Anthropogenic and natural effects on the coastal lagoons in the southwest of Spain (Doñana National Park). – ICES Journal of Marine Science, 66: 1508–1514. The Doñana peridunal lagoons, located in the southwest of Spain, have been well studied, because their conservation is of great interest. Since 1965, they have also been affected by the extraction of underground water for local coastal tourist resorts. A reconstruction of the evolution of this series of coastal lagoons reveals that, along with the anthropogenic effect, there was a natural effect resulting from the reactivation of mobile dune fronts that have blocked and filled the original lagoon complex—in the period 1920–1987, the lagoons were reduced by 70.7%. These fronts might have been fed by deposits of marine sand during the climatically driest phases of the Little Ice Age in Andalusia, Spain. Therefore, if the frequency and duration of dry periods increase, as well as droughts as a whole, because of global warming, the desiccation and disappearance of the lagoons could become more widespread, not only at this site in southwestern Europe, but in other Mediterranean coastal ecosystems as well.
Molecular identification of European flounder (Platichthys flesus) and its hybrids with European plaice (Pleuronectes platessa)
Authors: Kijewska Agnieszka , Burzyński Artur , Wenne Roman 
Published: April 2009

AbstractKijewska, A., Burzyński, A., and Wenne, R. 2009. Molecular identification of European flounder (Platichthys flesus) and its hybrids with European plaice (Pleuronectes platessa). – ICES Journal of Marine Science, 66: 902–906. European flounder (Platichthys flesus) and plaice (Pleuronectes platessa) are commercially important marine fish species inhabiting the continental shelf waters of Europe. Morphological similarity between the two makes it difficult to identify their hybrids, so species misclassification can generate errors in defining stocks in terms of their conservation and management. Flounder and plaice populations from the North Sea and the Baltic Sea were studied. Mitochondrial DNA (mtDNA) was used to confirm the morphological species identification. The set of molecular markers, two mitochondrial (cytochrome b and D-loop) and two nuclear (the ribosomal marker ITS and parathyroid hormone-related protein gene), was constructed to identify the two flatfish species and their hybrids. “Pure” flounder (P. flesus) were observed in the Bay of Gdańsk, Baltic Sea, and off the coast of Denmark in the North Sea. The fishing area near Bornholm in the Baltic is rich in P. flesus × P. platessa hybrids. The length difference of the amplified D-loop fragment was used for species identification. The characteristics of heteroplasmy in the control region (D-loop) can be useful as a population marker in the European flounder. Our studies demonstrate the utility of mtDNA polymorphism combined with nuclear molecular markers for correct identification of the morphologically similar and hybridized European flounder and plaice.
Testing the effectiveness of an acoustic deterrent device for excluding seals from Atlantic salmon rivers in Scotland
Authors: Graham Isla M. , Harris Robert N. , Denny Becks , Fowden Dan , Pullan Dave 
Published: April 2009

Abstract
Graham, I. M., Harris, R. N., Denny, B., Fowden, D., and Pullan, D. 2009. Testing the effectiveness of an acoustic deterrent device for excluding seals from Atlantic salmon rivers in Scotland. – ICES Journal of Marine Science, 66: 860–864. In Scotland, there is frequent conflict between salmon rod fisheries and seals, which is often managed by the shooting of seals in rivers, with potential negative impacts on protected populations of seals. Non-lethal devices have not been tested extensively in rivers as an alternative to shooting. Trials were carried out between January and May 2006 on the River North Esk and between October 2007 and February 2008 on the River Conon in northeast Scotland to examine the effectiveness of an acoustic deterrent device (ADD) at deterring seals from a specific area of river and as a barrier to the upstream movement of seals. The ADD was switched on and off alternately for periods of several days, and surveys were carried out to estimate the number of seals present within each river. The ADD had no significant effect on the absolute abundance of seals in the survey area in either river, but it did reduce seal movement upstream significantly, by ∼50% in both rivers. This reduction was constant over the 4-month period of both trials. The results suggest that ADDs might be a useful conservation tool in the management of seal–salmon conflicts, particularly in estuaries and rivers where the potential for adversely impacting cetaceans is limited.
The efficacy of culling seals seen preying on seabirds as a means of reducing seabird mortality
Authors: Makhado Azwianewi B. , Meÿer Mike A. , Crawford Robert J. M. , Underhill Les G. , Wilke Chris 
Published: April 2009

AbstractIn the 2006/2007 breeding season of Cape gannets Morus capensis at Malgas Island, the removal of 61 Cape fur seals Arctocephalus pusillus pusillus that preyed on gannet fledglings when they left to sea significantly reduced the mortality rate of these fledglings. However, because seals learned to avoid the boat used for their removal, it was not possible to remove all the seals that killed gannet fledglings and some mortality continued. The seals inflicting the mortality were all sub‐adult males, with an average age of <5 years. Sustained removal of these animals may reduce this feeding behaviour, which is at present having an adverse impact on several threatened seabirds in the Benguela ecosystem.
Effects of core binding factor α1 or bone morphogenic protein‐2 overexpression on osteoblast/cementoblast‐related gene expressions in NIH3T3 mouse cells and dental follicle cells
Authors: Pan K. , Yan S. , Ge S. , Li S. , Zhao Y. , Yang P. 
Published: April 2009

AbstractObjectives:  Bone morphogenic protein‐2 (BMP‐2) has long been used to promote bone and periodontal regeneration, while core binding factor α1 (CBFA1) plays important roles in both osteogenic differentiation and tooth morphogenesis. The aim of this study was to evaluate the effects of CBFA1 or BMP‐2 overexpression on osteoblast/cementoblast‐related gene expressions in NIH3T3 cells and dental follicle cells (DFCs).Materials and methods:  CBFA1 or BMP‐2 overexpression in NIH3T3 and DFCs was achieved by infection with retroviral vectors containing CBFA1 or BMP‐2 cDNA. Cells stably integrated with CBFA1 or BMP‐2 cDNA were selected with G418 for 14 days. Western blotting, real‐time reverse transcriptase–polymerase chain reaction, and in vitro mineralization assay were performed to evaluate effects of CBFA1 or BMP‐2 overexpression in cells undergoing osteoblast/cementoblast differentiation.Results:  Our results demonstrated that osteoblast/cementoblast‐related gene expression levels in CBFA1‐overexpressing NIH3T3 cells were higher than those in BMP‐2‐overexpressing cells. More mineral nodules were observed in CBFA1‐overexpressing NIH3T3 cells than in BMP‐2‐overexpressing cells. CBFA1 overexpression in DFCs also increased osteoblast/cementoblast‐related gene expression and promoted mineral nodule formation. However, no significant changes in gene expression levels nor mineral nodule formation were found in BMP‐2‐overexpressing DFCs when compared with empty vector transduced DFCs.Conclusions:  CBFA1 overexpression up‐regulated expression levels of osteoblast/cementoblast‐related genes and enhanced in vitro osteogenic differentiation more efficiently than BMP‐2 in both NIH3T3 cells and DFCs.
Are mesenchymal stromal cells from children resistant to apoptosis?
Authors: Dimitriou H. , Perdikogianni Ch. , Martimianaki G. , Choumerianou D. M. , Pelagiadis J. , Kalmanti M. 
Published: April 2009

AbstractObjectives:  Mesenchymal stromal cells (MSC) represent a novel cellular candidate in the field of transplantation and tissue regeneration. Their clinical application requires their in vitro expansion. The aim of this study was to assess the effect of conditions that would favour apoptosis, and of long‐term expansion, on the characteristics of MSC from children.Materials and methods:  Bone marrow mononuclear cells were cultured for 10 passages (P1–P10). Expression of CD105, CD146, CD95 and apoptosis by 7‐amino‐actinomycin D staining were evaluated. CFU‐F and cell doubling time (DT) were assessed in every passage. Cell‐cycle study was performed at P2 and P6.Results:  CFU‐F decreased from 38 ± 3.7 at P2 to 9.6 ± 3.2 per 10 MSC/cm2 at P10 and DT increased from 1.93 ± 0.1 (P2) to 6.1 ± 2.45 days (P10). A low percentage of apoptotic (dead) cells was detected at P2 and this did not change until P10. Cells at P2 were at G0/G1 phase, but in advanced passages more cells were in an active state. Induction of apoptosis (addition of anti‐Fas agonist antibody) using standard culture conditions, showed a minor effect on MSC survival. Serum deprivation of MSC (up to 72 h) revealed no substantial apoptotic effect while cells retained their tri‐lineage differentiation capacity.Conclusions:  We conclude that MSC from children retain their functional characteristics throughout serial passages and remain stable under conditions that usually cause apoptosis. These features render MSC, especially those of early passages, optimal candidates for use in clinical applications.
Photoperiod and food restriction differentially affect reproductive and immune responses in Siberian hamsters Phodopus sungorus
Authors: Zysling Devin A. , Garst Andrew D. , Demas Gregory E. 
Published: April 2009

Summary 1. Organisms must contend with seasonal fluctuations in energy availability. To maintain a positive energy balance year‐round, a number of adaptations have evolved including seasonal changes in reproduction, energetics and immunity. Photoperiod is the primary environmental signal most animals use to predict seasonal events. Despite the established link between energetics and immune function, little is known regarding how changes in energy availability affect immunity. 2. The goal of the present study was to determine the effects of food restriction on photoperiodic changes in reproduction and immune function in the Siberian hamster (Phodopus sungorus). Adult hamsters were housed in long or short days and were food restricted or fed ad libitum. Immune responses were quantified by measuring specific antibody production and bacterial killing capacity. 3. Food restriction decreased body and relative reproductive masses in long‐day animals. Antibody responses, but not bacterial killing ability, were enhanced in food restricted short‐day animals as compared with ad libitum fed controls. We also found differential effects of body fat on immune responses depending on the immune measure. 4. The effects of food restriction on immune function appear to vary based on the restriction regimen, the response measured, and the physiological state of the organism including energy balance, metabolic rate and reproductive status. 5. In conclusion, these results suggest that a wide range of factors can differentially affect immune function. In addition, these effects may vary based on the specific response examined. Future studies should include a variety of measurements to provide a more integrative and accurate picture of reproductive, energetic, and photoperiodic effects on immune function.