bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment
Authors: Singh Dadabhai T , Trehan Rahul , Schmidt Bertil , Bretschneider Timo 
Published: February 2008

AbstractBackgroundPreparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any new emerging subtypes. Comparative phyloinformatics can be used to monitor, analyze, and possibly predict the evolution of viruses. However, in order to utilize the full functionality of available analysis packages for large-scale phyloinformatics studies, a team of computer scientists, biostatisticians and virologists is needed – a requirement which cannot be fulfilled in many cases. Furthermore, the time complexities of many algorithms involved leads to prohibitive runtimes on sequential computer platforms. This has so far hindered the use of comparative phyloinformatics as a commonly applied tool in this area.ResultsIn this paper the graphical-oriented workflow design system calledQuascadeand its efficient usage for comparative phyloinformatics are presented. In particular, we focus on how this task can be effectively performed in a distributed computing environment. As a proof of concept, the designed workflows are used for the phylogenetic analysis of neuraminidase of H5N1 isolates (micro level) and influenza viruses (macro level). The results of this paper are hence twofold. Firstly, this paper demonstrates the usefulness of a graphical user interface system to design and execute complex distributed workflows for large-scale phyloinformatics studies of virus genes. Secondly, the analysis of neuraminidase on different levels of complexity provides valuable insights of this virus's tendency for geographical based clustering in the phylogenetic tree and also shows the importance of glycan sites in its molecular evolution.ConclusionThe current study demonstrates the efficiency and utility of workflow systems providing a biologist friendly approach to complex biological dataset analysis using high performance computing. In particular, the utility of the platform Quascade for deploying distributed and parallelized versions of a variety of computationally intensive phylogenetic algorithms has been shown. Secondly, the analysis of the utilized H5N1 neuraminidase datasets at macro and micro levels has clearly indicated a pattern of spatial clustering of the H5N1 viral isolates based on geographical distribution rather than temporal or host range based clustering.
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations
Authors: Xu Qingwei , Shi Yixiang , Lu Qiang , Zhang Guoqing , Luo Qingming , Li Yixue 
Published: February 2008

Abstract

Background
The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to provide complex semantic queries and inference services based on it. 2) The term-centric view of GO annotation data and the fact that all information is stored in a single file. This makes attempts to retrieve GO annotations based on big volume datasets unmanageable. 3) No support of GOSlim.

Results
We propose a RDF model, GORouter, which encodes heterogeneous original data in a uniform RDF format, creates additional ontology mappings between GO terms, and introduces a set of inference rulebases. Furthermore, we use the Oracle Network Data Model (NDM) as the native RDF data repository and the table function RDF_MATCH to seamlessly combine the result of RDF queries with traditional relational data. As a result, the scale of GORouter is minimized; information not directly involved in semantic inference is put into relational tables.

Conclusion
Our work demonstrates how to use multiple semantic web tools and techniques to provide a mixture of semantic query and inference solutions of GO and its associations. GORouter is licensed under Apache License Version 2.0, and is accessible via the website: http://www.scbit.org/gorouter/.
Effects of GSK3 inhibitors on in vitro expansion and differentiation of human adipose-derived stem cells into adipocytes
Authors: Zaragosi Laure-Emmanuelle , Wdziekonski Brigitte , Fontaine Coralie , Villageois Phi , Peraldi Pascal , Dani Christian 
Published: February 2008

Abstract

Background
Multipotent stem cells exist within adipose tissue throughout life. An abnormal recruitment of these adipose precursor cells could participate to hyperplasia of adipose tissue observed in severe obesity or to hypoplasia of adipose tissue observed in lipodystrophy. Therefore, pharmacological molecules that control the pool of stem cells in adipose tissue are of great interest. Glycogen Synthase Kinase (GSK) 3 has been previously described as involved in differentiation of preadipose cells and might be a potential therapeutic target to modulate proliferation and differentiation of adipocyte precursors. However, the impact of GSK3 inhibition on human adipose-derived stem cells remained to be investigated. The aim of this study was to investigate GSK3 as a possible target for pharmacological inhibition of stem cell adipogenesis. To reach this goal, we studied the effects of pharmacological inhibitors of GSK3, i.e. lithium chloride (LiCl) and BIO on proliferation and adipocyte differentiation of multipotent stem cells derived from human adipose tissue.

Results
Our results showed that GSK3 inhibitors inhibited proliferation and clonogenicity of human stem cells, strongly suggesting that GSK3 inhibitors could be potent regulators of the pool of adipocyte precursors in adipose tissue. The impact of GSK3 inhibition on differentiation of hMADS cells was also investigated. Adipogenic and osteogenic differentiations were inhibited upon hMADS treatment with BIO. Whereas a chronic treatment was required to inhibit osteogenesis, a treatment that was strictly restricted to the early step of differentiation was sufficient to inhibit adipogenesis.

Conclusion
These results demonstrated the feasibility of a pharmacological approach to regulate adipose-derived stem cell function and that GSK3 could represent a potential target for controlling adipocyte precursor pool under conditions where fat tissue formation is impaired.
The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates
Authors: Porcelli Damiano , Barsanti Paolo , Pesole Graziano , Caggese Corrado 
Published: February 2008

Abstract

Background
When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, although the functional constraints involved may vary in different genes and lineages.

Results
We identified and annotated in the MitoComp2 dataset the orthologs of 68 nuclear genes controlling oxidative phosphorylation in 11 Drosophilidae species and in five non-Drosophilidae insects, and compared them with each other and with their counterparts in three vertebrates (Fugu rubripes, Danio rerio and Homo sapiens) and in the cnidarian Nematostella vectensis, taking into account conservation of gene structure and regulatory motifs, and preservation of gene paralogs in the genome. Comparative analysis indicates that the ancestral insect OXPHOS genes were intron rich and that extensive intron loss and lineage-specific intron gain occurred during evolution. Comparison with vertebrates and cnidarians also shows that many OXPHOS gene introns predate the cnidarian/Bilateria evolutionary split. The nuclear respiratory gene element (NRG) has played a key role in the evolution of the insect OXPHOS genes; it is constantly conserved in the OXPHOS orthologs of all the insect species examined, while their duplicates either completely lack the element or possess only relics of the motif.

Conclusion
Our observations reinforce the notion that the common ancestor of most animal phyla had intron-rich gene, and suggest that changes in the pattern of expression of the gene facilitate the fixation of duplications in the genome and the development of novel genetic functions.
Mitochondrial DNA structure in the Arabian Peninsula
Authors: Abu-Amero Khaled K , Larruga José M , Cabrera Vicente M , González Ana M 
Published: February 2008

Abstract

Background
Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.

Results
To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source.

Conclusion
Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.
Identification of a contemporary human parechovirus type 1 by VIDISCA and characterisation of its full genome
Authors: de Souza Luna Luciano Kleber , Baumgarte Sigrid , Grywna Klaus , Panning Marcus , Drexler Jan Felix , Drosten Christian 
Published: February 2008

Abstract

Background
Enteritis is caused by a spectrum of viruses that is most likely not fully characterised. When testing stool samples by cell culture, virus isolates are sometimes obtained which cannot be typed by current methods. In this study we used VIDISCA, a virus identification method which has not yet been widely applied, on such an untyped virus isolate.

Results
We found a human parechovirus (HPeV) type 1 (strain designation: BNI-788st). Because genomes of contemporary HPeV1 were not available, we determined its complete genome sequence. We found that the novel strain was likely the result of recombination between structural protein genes of an ancestor of contemporary HPeV1 strains and nonstructural protein genes from an unknown ancestor, most closely related to HPeV3. In contrast to the non-structural protein genes of other HPeV prototype strains, the non-structural protein genes of BNI-788st and HPeV3 prototype strains did not co-segregate in bootscan analysis with that of other prototype strains.

Conclusion
HPeV3 nonstructural protein genes may form a distinct element in a pool of circulating HPeV non-structural protein genes. More research into the complex HPeV evolution is required to connect virus ecology with disease patterns in humans.
Gene expression analyses in breast cancer epidemiology: the Norwegian Women and Cancer postgenome cohort study
Authors: Dumeaux Vanessa , Børresen-Dale Anne-Lise , Frantzen Jan-Ole , Kumle Merethe , Kristensen Vessela N , Lund Eiliv 
Published: February 2008

Abstract
Introduction
The introduction of high-throughput technologies, also called -omics technologies, into epidemiology has raised the need for high-quality observational studies to reduce several sources of error and bias.

Methods
The Norwegian Women and Cancer (NOWAC) postgenome cohort study consists of approximately 50,000 women born between 1943 and 1957 who gave blood samples between 2003 and 2006 and filled out a two-page questionnaire. Blood was collected in such a way that RNA is preserved and can be used for gene expression analyses. The women are part of the NOWAC study consisting of 172,471 women 30 to 70 years of age at recruitment from 1991 to 2006 who answered one to three questionnaires on diet, medication use, and lifestyle. In collaboration with the Norwegian Breast Cancer Group, every NOWAC participant born between 1943 and 1957 who is admitted to a collaborating hospital for a diagnostic biopsy or for surgery of breast cancer will be asked to donate a tumor biopsy and two blood samples. In parallel, at least three controls are approached for each breast cancer case in order to obtain blood samples from at least two controls per case. The controls are drawn at random from NOWAC matched by time of follow-up and age. In addition, 400 normal breast tissues as well as blood samples will be collected among healthy women participating at the Norwegian Mammography Screening program at the Breast Imaging Center at the University Hospital of North-Norway, Tromsø.

Results
The NOWAC postgenome cohort offers a unique opportunity (a) to study blood-derived gene expression profiles as a diagnostic test for breast cancer in a nested case-control design with adjustment for confounding factors related to different exposures, (b) to improve the reliability and accuracy of this approach by adjusting for an individual's genotype (for example, variants in genes coding for hormone and drug-metabolizing and detoxifying enzymes), (c) to study gene expression profiles from peripheral blood as surrogate tissue to biomonitor defined exposure (for example, hormone) and its association with disease risk (that is, breast cancer), and (d) to study gene variants (single nucleotide polymorphisms and copy number variations) and environmental exposure (endogenous and exogenous hormones) and their influence on the incidence of different molecular subtypes of breast cancer.

Conclusion
The NOWAC postgenome cohort combining a valid epidemiological approach with richness of biological samples should make an important contribution to the study of the etiology and system biology of breast cancer.
Craniotabes in Normal Newborns: The Earliest Sign of Subclinical Vitamin D Deficiency
Authors: Yorifuji Junko , Yorifuji Tohru , Tachibana Kenji , Nagai Shizuyo , Kawai Masahiko , Momoi Toru , Nagasaka Hironori , Hatayama Hiroshi , Nakahata Tatsutoshi 
Published: February 2008

Abstract
Context: Craniotabes in otherwise normal neonates has been regarded as physiological and left untreated.
Objective: Our objective was to investigate the role of vitamin D deficiency in the development of craniotabes in normal neonates.
Design and Setting: Newborn screening of craniotabes was conducted at the single largest obstetrical facility in Kyoto, Japan. Follow-up study at 1 month was conducted at Kyoto University Hospital.
Subjects: A total of 1120 consecutive normal Japanese neonates born in May, 2006, through April, 2007, were included in the study.
Main Outcome Measures: The incidence of craniotabes was scored each month. Neonates with craniotabes were followed up at 1 month with measurements of serum calcium, phosphorus, alkaline phosphatase (ALP), intact PTH, 25-OH vitamin D (25-OHD), urinary calcium, phosphorus, creatinine, and hand x-rays.
Results: Craniotabes was present in 246 (22.0%) neonates, and the incidence had obvious seasonal variations, highest in April-May and lowest in November. At 1 month, infants with craniotabes had significantly higher serum ALP compared with normal neonates; 6.9% of them had elevated intact PTH over 60 pg/ml, and 37.3% had 25-OHD less than 10 ng/ml. When separately analyzed according to the method of feeding, 56.9% of breast-fed infants showed 25-OHD less than 10 ng/ml, whereas none of formula/mixed-fed infants did, and breast-fed infants had significantly higher serum PTH and ALP compared with formula/mixed-fed infants.
Summary: These results suggest that craniotabes in normal neonates is associated with vitamin D deficiency in utero, and the deficiency persists at 1 month in many of them, especially when breast-fed.
Use of a toxicity factor to explain differences in nephrotoxicity and myelosuppression among the platinum antitumour derivatives cisplatin, carboplatin and nedaplatin in rats
Authors: Hanada Kazuhiko , Asano Kunihito , Nishimura Takako , Chimata Tomomi , Matsuo Yusuke , Tsuchiya Maki , Ogata Hiroyasu 
Published: February 2008

Abstract
The platinum antitumour drugs cisplatin, carboplatin and nedaplatin differ in their toxicity. The relationships between the pharmacokinetics of these drugs and developed parameters for predicting their nephrotoxicity and myelosuppression were investigated. The drugs were administered to male Wistar rats by intravenous bolus or infusion, and linearity of pharmacokinetics, total clearance and the apparent ratio of tissue concentrations of unchanged drug to plasma concentration (Kpapp) at steady state were determined. Apparent hydrolysis rates of each drug were determined in-vitro. Nephrotoxicity and myelosuppression were estimated by blood urea nitrogen (BUN) and platelet count, respectively. Tissue exposure to platinum was estimated as the product of the area under the plasma concentration-time curve for unchanged drug (AUCp), Kpapp and the apparent hydrolysis rate constant (khydrolysis), and toxicity factor was defined as the product of Kpapp × khydrolysis as an intrinsic drug parameter. The relationship between AUCp × toxicity factor and BUN fitted well to an Emax model. In bone marrow, this function was also correlated with platelet count. In summary, the product of AUCp × toxicity factor is a factor determining the pharmacokinetics of platinum drug-induced nephrotoxicity and myelosuppression in rats, and this toxicity factor may be a useful parameter for predicting the degree of toxicity of platinum antitumour compounds.
Antidiabetic activity of Croton klozchianus in rats and direct stimulation of insulin secretion in-vitro
Authors: Govindarajan R , Vijayakumar M , Rao Ch V , Pushpangadan P , Asare-Anane Henry , Persaud Shanta , Jones Peter , Houghton Peter J 
Published: February 2008

Abstract
Croton klozchianus is a relatively uninvestigated species with no pharmacological or phytochemical reports available, although it has been used clinically by Ayurvedic physicians to treat diabetes. We have investigated this use by studying the insulin secretion and antidiabetic activity of C. klozchianus. Treatment of diabetic rats with aerial parts of C. klozchianus extract (CK, 100 and 300 mg kg−1 body weight) for three weeks showed significant reduction in blood glucose (45.8% after 14 days for 300 mg kg−1). C. klozchianus extract caused a significant concentration-dependent increase in insulin secretion (8-fold at 2 mg mL−1 for cells challenged with 20 mm glucose) from MIN6 cells grown as monolayers and as pseudoislets, indicating that the antidiabetic activity may have been as a result of increased insulin secretion. It also had a role on the lipid profile of the rats by causing reduction in cholesterol and triglycerides and increasing high density lipoprotein significantly. The results obtained gave some scientific support to the traditional use of the plant as a treatment for diabetes.
Gastroprotective effect of a flavone from Lonchocarpus araripensis Benth. (Leguminosae) and the possible mechanism
Authors: Campos Deive A , de Lima Almi F , Ribeiro Saulo Rodrigo L , Silveira Edilberto R , Pessoa Otilia Deusdênia L , Rao Vietla S , Santos Flávia A 
Published: February 2008

Abstract
The gastroprotective effect of DDF (3,6-dimethoxy-6“, 6”-dimethyl-[2“, 3”: 7,8]-chromeneflavone) from Lonchocarpus araripensis Benth. (Leguminosae) on gastric damage induced by absolute ethanol (96%, 0.2 mL/mouse) and indometacin (30 mg kg−1, p.o.) in mice was investigated. Intraperitoneally administered DDF at dose levels of 50, 100 and 200 mg kg−1 markedly reduced the gastric lesions in the ethanol model by 62, 72 and 96%, and in the indometacin model by 34, 70 and 75%, respectively, as compared with misoprostol (50 μg kg−1, p.o.), the reference compound that caused lesion suppression by 67% in ethanol model and by 72% against indometacin-induced ulceration. The ED50 of DDF in reducing gastric lesions induced by ethanol and indometacin (dose of the DDF that reduced the gastric lesion area by 50% in relation to the control value) was 50.87 and 61.56 mg kg−1, respectively. Mechanistic studies were carried out at 100 mg kg−1 DDF using the ethanol model. Compared with N-acetylcysteine (750 mg kg−1, p.o.), a donor of sulfhydryls, DDF only partially replenished the ethanol-induced depletion of gastric mucosal NP-SH. Pretreatment with TRPV1 antagonist capsazepine (5 mg kg−1, i.p.) or the non-selective cyclooxygenase inhibitor indometacin (10 mg kg−1, p.o.) effectively blocked the gastroprotective effect of DDF (100 mg kg−1) against ethanol damage. Furthermore, the effect of DDF was significantly reduced in mice pretreated with L-NAME, or glibenclamide, the respective inhibitors of nitric oxide synthase and K+ATP channel activation. These data provide evidence to show that DDF affords gastroprotection against gastric damage induced by ethanol and indometacin by different and complementary mechanisms, which include involvement of endogenous prostaglandins, nitric oxide release, the activation of TRPV1 receptor or K+ATP channels, besides a sparing effect on NP-SH reserve.
Numbers of Achiral and Chiral Monosubstituted Alkanes Having a Given Carbon Content and Given Numbers of Asymmetric and Pseudoasymmetric Centers
Authors: Fujita Shinsaku 
Published: February 2008

Abstract
Monosubstituted alkanes as stereoisomers have been counted combinatorially by regarding them as nested planted promolecules, where the resulting numbers have been itemized with respect to carbon content (k), to the number of asymmetric carbons (l), as well as to the number of pseudoasymmetric carbons (m). To accomplish such itemization, the definitions of RS-stereogenic centers, asymmetric centers, and pseudoasymmetric centers have been discussed in detail. Each itemized number has been obtained as the coefficient of the term xkylzm appearing in a respective generating function, which has been derived by following Fujita’s proligand method (S. Fujita, Theor. Chem. Acc.2005, 113, 73; 2005, 113, 80; S. Fujita, Theor. Chem. Acc.2006, 115, 37). The itemized values up to carbon content 30 have been listed in tabular forms, which are distinctively concerned with achiral stereoisomers, chiral stereoisomers, and constitutional isomers (graphs).
Rhodium-catalyzed Addition of Organo[2-(hydroxymethyl)phenyl]dimethylsilanes to Arenesulfonylimines
Authors: Nakao Yoshiaki , Takeda Masahide , Chen Jinshui , Hiyama Tamejiro , Ichikawa Yoshitaka , Shintani Ryo , Hayashi Tamio 
Published: February 2008

Abstract
The title reaction is found to proceed in the presence of a rhodium/diene catalyst. Variously substituted diarylmethylamines and allylamines having an N-arenesulfonyl protection are obtained in good yields, which are important building blocks in organic synthesis.