bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Assimilating AMMA Soundings on ECMWF Analyses and Forecasts
Authors: Agustí-Panareda Anna , Beljaars Anton , Cardinali Carla , Genkova Iliana , Thorncroft Chris 
Published: February 2010

Abstract
The field experiment of the African Monsoon Multidisciplinary Analysis (AMMA) project during the 2006 wet monsoon season provided an unprecedented amount of radiosonde/dropsonde data over the West African region. This paper explores the usage and impacts of this invaluable dataset in the European Centre for Medium-Range Weather Forecasts analyses and forecasts. These soundings are the only source of data that can provide 3D information on the thermodynamic and dynamic structures of the lower troposphere over continental West Africa. They are particularly important for the Sahel region located between 12° and 20°N, which is characterized by large gradients in temperature and moisture in the lower troposphere. An assimilation experiment comparison between the pre-AMMA and AMMA radiosonde networks shows that the extra AMMA soundings have a significant analysis impact on the low-level temperature over the Sahel and on the structure of the African easterly jet. However, the impacts of the extra AMMA data on the forecast disappear after 24 h. The soundings reveal large model biases in boundary layer temperature over the northern and eastern Sahel, which are consistent with the well-known model biases in cloud, rainfall, and radiation. Large analysis increments in temperature lead to increments in divergence and subsidence, which act to suppress convection. Thus, the analysis increments appear to have an undesirable feedback on the cloud and temperature model biases. The impact of the AMMA soundings on the African easterly jet is to enhance and extend the jet streak to 15°E, that is, toward the eastern part of the Sahel. No observations are assimilated east of 15°E at the level of the African easterly jet to support the jet enhancement farther east. Comparisons with independent atmospheric cloud motion vectors indicate that the African easterly jet in the analysis is too weak over this data-sparse region. This could have implications for the development of African easterly waves in the model forecast. Further experimentation by assimilating atmospheric motion vectors—currently not used—could address this problem.
A Qualitative Study On the Needs of Caregivers of Inpatients With Schizophrenia in India
Authors: Jagannathan A. , Thirthalli J. , Hamza A. , Hariprasad V.R. , Nagendra H.R. , Gangadhar B.N. 
Published: February 2010

Aim: To explore the needs of caregivers of inpatients with schizophrenia in India. Material: Thirty caregivers of inpatients with schizophrenia participated in five focus group discussions (FGD), where the needs of the caregivers were discussed. The FGDs were recorded, transcribed and similar needs were grouped and ranked according to their order of importance. Discussion: The main needs that emerged were regarding: managing the behaviour of patients; managing social-vocational problems of patients; health issues of caregivers; education about schizophrenia; rehabilitation; and managing sexual and marital problems of patients. Conclusion: This study has identified additional needs of caregivers from those found in other studies.
The Culture and Identity Schedule a Measure of Cultural Affiliation: Acculturation, Marginalization and Schizophrenia
Authors: Bhugra Dinesh , Leff Julian , Mallett Rosemarie , Morgan Craig , Zhao Jing-Hua 
Published: February 2010

Background: Previous epidemiological studies have shown a high incidence of schizophrenia in African-Caribbeans in the UK, but not in Asians. Aims: We investigated the hypothesis that cultural adherence might protect the Asians against the stress of living in a majority white culture. Methods: The Culture and Identity Schedule (CANDID) was given to patients with a diagnosis of schizophrenia making their first contact with psychiatric services, and to a matched group of controls randomly selected from the general population. Results: While the Asian patients displayed no drift away from the traditional values as espoused by their controls, the African-Caribbean patients were less traditional than their controls. Conclusions: The fact that a movement away from their traditional culture distinguishes African-Caribbean patients with a severe psychiatric illness, schizophrenia, from their mentally healthy controls strongly favours marginalization over biculturalism as an interpretation of this shift.
Operating Characteristics of a Partial‐Block Randomized Crossover Bioequivalence Study for Dutasteride, a Drug with a Long Half‐Life: Investigation Through Simulation and Comparison with Final Results
Authors: Cai Gengqian , Thiessen Jake J. , Baidoo Charlotte A. , Fossler Michael J. 
Published: February 2010

Studies to establish bioequivalence (BE) of a drug are important elements in support of drug applications. A typical BE study is conducted as a single dose, randomized, 2‐period crossover design. For drugs with long half lives (≥ 48 hours) and evaluation of multiple BE objectives in 1 trial, this design may not be adequate. A parallel design may then be a more appropriate choice. However, parallel designs require increased sample size, which can become substantial.One option that is a compromise between the complete randomized block design and the parallel design is a partial‐block crossover design. This approach came about during the development of a combination of dutasteride and tamsulosin. Previous experience with performing single‐dose dutasteride studies suggested that 28 days of washout is needed between treatments because of its half‐life of 7–9 days.Simulations were performed to assess the operating characteristics of this design using a previously developed PK model. Four scenarios were developed, and each scenario was simulated 500 times. The results showed that this design demonstrated acceptable consumer and producer risk. Partial‐block crossover designs should be considered for studies when the half‐life of the drug is long and there are more than 2 periods.
Simple surface sulfonation retards plasticiser migration and impacts upon blood/material contact activation processes
Authors: Gourlay Terence , Shedden Laurie , Horne David , Stefanou Demetrios M. 
Published: February 2010

Background. The use of Di-2-ethylhexyl phthalate (DEHP) plasticised polyvinyl chloride (DEHPPPVC) in medical devices persists despite evidence suggesting that DEHP migration can be harmful. Researchers have shown that a simple surface sulfonation process can retard the migration of DEHP, which may reduce the associated inflammatory response. The present study is designed to investigate the effects of surface sulfonation on DEHP migration and blood contact activation using in vitro and rodent models. Methods. The study was carried out in two phases: phase 1, in which the migration rate of DEHP from DEHPPPVC and sulfonated DEHP plasticised PVC (SDEHPPPVC) was measured; phase 2 of the study, in which the materials were incorporated into a rat recirculation biomaterial test model and blood samples taken to assess CD11b expression on neutrophils, IL-6 and Factor XIIa. Results. The initial DEHP concentration washed from the surface after storage was 37.19 ± 1.17 mg/l in the PPVC group and 5.89 ± 0.81 mg/l in the SPPVC group (p<0.0001). The post-wash migration rate was 3.07 ± 0.32 mg/l/hour in the PPVC group compared to 0.46 ± 0.038 mg/l/hour in the SPPVC group (p<0.0001). In phase 2 of the study, CD11b expression increased by 228.9% ± 37% over the test period in the PPVC group compared to 118.3% ± 46% in the SPPVC group (p<0.01). IL-6 levels rose from 3.1 ± 1.4 pg/ml to 263 ± 26 pg/ml in the PPVC group and 2.2 ± 1.6 pg/ml to 161 ± 29 pg/ml in the SPPVC group (p<0.01). Factor XIIa levels rose from 0.22 ± 0.13 g/ml to 3.7 ± 0.32 µg/ml and 0.28 ± 0.09 to 2.71 ± 0.21 µg/ml in the PPVC and SPPVC groups, respectively (p<0.05 at 90 minutes). Conclusions. The simple sulfonation process significantly retards the migration of DEHP and is associated with the moderation of contact activation processes.
Predicting MHC class I epitopes in large datasets
Authors: Roomp Kirsten , Antes Iris , Lengauer Thomas 
Published: February 2010

Abstract

Background
Experimental screening of large sets of peptides with respect to their MHC binding capabilities is still very demanding due to the large number of possible peptide sequences and the extensive polymorphism of the MHC proteins. Therefore, there is significant interest in the development of computational methods for predicting the binding capability of peptides to MHC molecules, as a first step towards selecting peptides for actual screening.

Results
We have examined the performance of four diverse MHC Class I prediction methods on comparatively large HLA-A and HLA-B allele peptide binding datasets extracted from the Immune Epitope Database and Analysis resource (IEDB). The chosen methods span a representative cross-section of available methodology for MHC binding predictions. Until the development of IEDB, such an analysis was not possible, as the available peptide sequence datasets were small and spread out over many separate efforts. We tested three datasets which differ in the IC50 cutoff criteria used to select the binders and non-binders. The best performance was achieved when predictions were performed on the dataset consisting only of strong binders (IC50 less than 10 nM) and clear non-binders (IC50 greater than 10,000 nM). In addition, robustness of the predictions was only achieved for alleles that were represented with a sufficiently large (greater than 200), balanced set of binders and non-binders.

Conclusions
All four methods show good to excellent performance on the comprehensive datasets, with the artificial neural networks based method outperforming the other methods. However, all methods show pronounced difficulties in correctly categorizing intermediate binders.
Evolutionary dynamics of U12-type spliceosomal introns
Authors: Lin Chiao-Feng , Mount Stephen M , Jarmołowski Artur , Makałowski Wojciech 
Published: February 2010

Abstract

Background
Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.

Results
We have investigated the evolution of U12-type introns among eighteen metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates. Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type. Although there are only nineteen U12-type introns in Drosophila melanogaster, we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage. Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype. We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported.

Conclusions
Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria. Loss of U12 introns or the genes containing them is more common than conversion to the U2-type. The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.
SoyTEdb: a comprehensive database of transposable elements in the soybean genome
Authors: Du Jianchang , Grant David , Tian Zhixi , Nelson Rex T , Zhu Liucun , Shoemaker Randy C , Ma Jianxin 
Published: February 2010

Abstract

Background
Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop.

Description
Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study.

Conclusion
SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.
Broad spectrum microarray for fingerprint-based bacterial species identification
Authors: Pasquer Frédérique , Pelludat Cosima , Duffy Brion , Frey Jürg E 
Published: February 2010

Abstract

Background
Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database.

Results
A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system.

Conclusions
These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.
High-level expression and purification of soluble recombinant FGF21 protein by SUMO fusion in Escherichia coli
Authors: Wang Huiyan , Xiao Yechen , Fu Lianjun , Zhao Hongxin , Zhang Yaofang , Wan Xiaoshan , Qin Yuxia , Huang Yadong , Gao Hongchang , Li Xiaokun 
Published: February 2010

Abstract

Background
Fibroblast growth factor 21 (FGF21) is a promising drug candidate to combat metabolic diseases. However, high-level expression and purification of recombinant FGF21 (rFGF21) in Escherichia coli (E. coli) is difficult because rFGF21 forms inclusion bodies in the bacteria making it difficult to purify and obtain high concentrations of bioactive rFGF21. To overcome this problem, we fused the FGF21 with SUMO (Small ubiquitin-related modifier) by polymerase chain reaction (PCR), and expressed the fused gene in E. coli BL21(DE3).

Results
By inducing with IPTG, SUMO-FGF21 was expressed at a high level. Its concentration reached 30% of total protein, and exceeded 95% of all soluble proteins. The fused protein was purified by DEAE sepharose FF and Ni-NTA affinity chromatography. Once cleaved by the SUMO protease, the purity of rFGF21 by high performance liquid chromatography (HPLC) was shown to be higher than 96% with low endotoxin level (<1.0 EU/ml). The results of in vivo animal experiments showed that rFGF21 produced by using this method, could decrease the concentration of plasma glucose in diabetic rats by streptozotocin (STZ) injection.

Conclusions
This study demonstrated that SUMO, when fused with FGF21, was able to promote its soluble expression of the latter in E. coli, making it more convenient to purify rFGF21 than previously. This may be a better method to produce rFGF21 for pharmaceutical research and development.
Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India
Authors: Ghosh Abhrajyoti , Dey Nirmalya , Bera Amit , Tiwari Amit , Sathyaniranjan KB , Chakrabarti Kalyan , Chattopadhyay Dhrubajyoti 
Published: February 2010

Abstract

Background
Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach.

Results
Two 16 S rRNA gene libraries were constructed and partial sequencing of the selected clones was carried out to identify bacterial strains present in the sediment. Phylogenetic analysis of partially sequenced 16 S rRNA gene sequences revealed the diversity of bacterial strains in the Sundarban sediment. At least 8 different bacterial phyla were detected. The major divisions of detected bacterial phyla were Proteobacteria (alpha, beta, gamma, and delta), Flexibacteria (CFB group), Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes and Gammatimonadates.

Conclusion
The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment. Many clones showed similarity with previously reported bacterial lineages recovered from various marine sediments. The present study indicates a probable hydrocarbon and oil contamination in this sediment. In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.
Phase I Clinical Trial of the CYP17 Inhibitor Abiraterone Acetate Demonstrating Clinical Activity in Patients With Castration-Resistant Prostate Cancer Who Received Prior Ketoconazole Therapy
Authors: Ryan Charles J. , Smith Matthew R. , Fong Lawrence , Rosenberg Jonathan E. , Kantoff Philip , Raynaud Florence , Martins Vanessa , Lee Gloria , Kheoh Thian , Kim Jennifer , Molina Arturo , Small Eric J. 
Published: February 2010

Purpose Abiraterone acetate is a prodrug of abiraterone, a selective inhibitor of CYP17, the enzyme catalyst for two essential steps in androgen biosynthesis. In castration-resistant prostate cancers (CRPCs), extragonadal androgen sources may sustain tumor growth despite a castrate environment. This phase I dose-escalation study of abiraterone acetate evaluated safety, pharmacokinetics, and effects on steroidogenesis and prostate-specific antigen (PSA) levels in men with CPRC with or without prior ketoconazole therapy. Patients and Methods Thirty-three men with chemotherapy-naïve progressive CRPC were enrolled. Nineteen patients (58%) had previously received ketoconazole for CRPC. Bone metastases were present in 70% of patients, and visceral involvement was present in 18%. Three patients (9%) had locally advanced disease without distant metastases. Fasted or fed cohorts received abiraterone acetate doses of 250, 500, 750, or 1,000 mg daily. Single-dose pharmacokinetic analyses were performed before continuous daily dosing. Results Adverse events were predominantly grade 1 or 2. No dose-limiting toxicities were observed. Hypertension (grade 3, 12%) and hypokalemia (grade 3, 6%; grade 4, 3%) were the most frequent serious toxicities and responded to medical management. Confirmed ≥ 50% PSA declines at week 12 were seen in 18 (55%) of 33 patients, including nine (47%) of 19 patients with prior ketoconazole therapy and nine (64%) of 14 patients without prior ketoconazole therapy. Substantial declines in circulating androgens and increases in mineralocorticoids were seen with all doses. Conclusion Abiraterone acetate was well tolerated and demonstrated activity in CRPC, including in patients previously treated with ketoconazole. Continued clinical study is warranted.