bluuebunny/crossref_metadata_2025_split huggingface dataset:
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties
Authors: Pugalenthi Ganesan , Tang Ke , Suganthan PN , Archunan G , Sowdhamini R 
Published: September 2007

Abstract

Background
Odorant binding proteins (OBPs) are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Although several sequence based search methods have been exploited for protein family prediction, less effort has been devoted to the prediction of OBPs from sequence data and this area is more challenging due to poor sequence identity between these proteins.

Results
In this paper, we propose a new algorithm that uses Regularized Least Squares Classifier (RLSC) in conjunction with multiple physicochemical properties of amino acids to predict odorant-binding proteins. The algorithm was applied to the dataset derived from Pfam and GenDiS database and we obtained overall prediction accuracy of 97.7% (94.5% and 98.4% for positive and negative classes respectively).

Conclusion
Our study suggests that RLSC is potentially useful for predicting the odorant binding proteins from sequence-derived properties irrespective of sequence similarity. Our method predicts 92.8% of 56 odorant binding proteins non-homologous to any protein in the swissprot database and 97.1% of the 414 independent dataset proteins, suggesting the usefulness of RLSC method for facilitating the prediction of odorant binding proteins from sequence information.
Apposition of iroquois expressing and non-expressing cells leads to cell sorting and fold formation in the Drosophilaimaginal wing disc
Authors: Villa-Cuesta Eugenia , González-Pérez Esther , Modolell Juan 
Published: September 2007

Abstract

Background
The organization of the different tissues of an animal requires mechanisms that regulate cell-cell adhesion to promote and maintain the physical separation of adjacent cell populations. In the Drosophila imaginal wing disc the iroquois homeobox genes are expressed in the notum anlage and contribute to the specification of notum identity. These genes are not expressed in the adjacent wing hinge territory. These territories are separated by an approximately straight boundary that in the mature disc is associated with an epithelial fold. The mechanism by which these two cell populations are kept separate is unclear.

Results
Here we show that the Iro-C genes participate in keeping the notum and wing cell populations separate. Indeed, within the notum anlage, cells not expressing Iro-C tend to join together and sort out from their Iro-C expressing neighbours. We also show that apposition of Iro-C expressing and non-expressing cells induces invagination and apico-basal shortening of the Iro-C- cells. This effect probably underlies formation of the fold that separates the notum and wing hinge territories. In addition, cells overexpressing a member of the Iro-C contact one another and become organized in a network of thin strings that surrounds and isolates large groups of non-overexpressing cells. The strings appear to exert a pulling force along their longitudinal axis.

Conclusion
Apposition of cells expressing and non-expressing the Iro-C, as it occurs in the notum-wing hinge border of the Drosophila wing disc, influences cell behaviour. It leads to cell sorting, and cellular invagination and apical-basal shortening. These effects probably account for keeping the prospective notum and wing hinge cell populations separate and underlie epithelial fold formation. Cells that overexpress a member of the Iro-C and that confront non-expressing cells establish contacts between themselves and become organized in a network of thin strings. This is a complex and unique phenotype that might be important for the generation of a straight notum-wing hinge border.
Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study
Authors: Yang Qiong , Kathiresan Sekar , Lin Jing-Ping , Tofler Geoffrey H , O'Donnell Christopher J 
Published: September 2007

Abstract

Background
Increased circulating levels of hemostatic factors as well as anemia have been associated with increased risk of cardiovascular disease (CVD). Known associations between hemostatic factors and sequence variants at genes encoding these factors explain only a small proportion of total phenotypic variation. We sought to confirm known putative loci and identify novel loci that may influence either trait in genome-wide association and linkage analyses using the Affymetrix GeneChip 100K single nucleotide polymorphism (SNP) set.

Methods
Plasma levels of circulating hemostatic factors (fibrinogen, factor VII, plasminogen activator inhibitor-1, von Willebrand factor, tissue plasminogen activator, D-dimer) and hematological phenotypes (platelet aggregation, viscosity, hemoglobin, red blood cell count, mean corpuscular volume, mean corpuscular hemoglobin concentration) were obtained in approximately 1000 Framingham Heart Study (FHS) participants from 310 families. Population-based association analyses using the generalized estimating equations (GEE), family-based association test (FBAT), and multipoint variance components linkage analyses were performed on the multivariable adjusted residuals of hemostatic and hematological phenotypes.

Results
In association analysis, the lowest GEE p-value for hemostatic factors was p = 4.5*10-16 for factor VII at SNP rs561241, a variant located near the F7 gene and in complete linkage disequilibrium (LD) (r2 = 1) with the Arg353Gln F7 SNP previously shown to account for 9% of total phenotypic variance. The lowest GEE p-value for hematological phenotypes was 7*10-8 at SNP rs2412522 on chromosome 4 for mean corpuscular hemoglobin concentration. We presented top 25 most significant GEE results with p-values in the range of 10-6 to 10-5 for hemostatic or hematological phenotypes. In relating 100K SNPs to known candidate genes, we identified two SNPs (rs1582055, rs4897475) in erythrocyte membrane protein band 4.1-like 2 (EPB41L2) associated with hematological phenotypes (GEE p < 10-3). In linkage analyses, the highest linkage LOD score for hemostatic factors was 3.3 for factor VII on chromosome 10 around 15 Mb, and for hematological phenotypes, LOD 3.4 for hemoglobin on chromosome 4 around 55 Mb. All GEE and FBAT association and variance components linkage results can be found at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007

Conclusion
Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.
Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study
Authors: Lunetta Kathryn L , D'Agostino Ralph B , Karasik David , Benjamin Emelia J , Guo Chao-Yu , Govindaraju Raju , Kiel Douglas P , Kelly-Hayes Margaret , Massaro Joseph M , Pencina Michael J , Seshadri Sudha , Murabito Joanne M 
Published: September 2007

Abstract

Background
Family studies and heritability estimates provide evidence for a genetic contribution to variation in the human life span.

Methods
We conducted a genome wide association study (Affymetrix 100K SNP GeneChip) for longevity-related traits in a community-based sample. We report on 5 longevity and aging traits in up to 1345 Framingham Study participants from 330 families. Multivariable-adjusted residuals were computed using appropriate models (Cox proportional hazards, logistic, or linear regression) and the residuals from these models were used to test for association with qualifying SNPs (70, 987 autosomal SNPs with genotypic call rate ≥80%, minor allele frequency ≥10%, Hardy-Weinberg test p ≥ 0.001).

Results
In family-based association test (FBAT) models, 8 SNPs in two regions approximately 500 kb apart on chromosome 1 (physical positions 73,091,610 and 73, 527,652) were associated with age at death (p-value < 10-5). The two sets of SNPs were in high linkage disequilibrium (minimum r2 = 0.58). The top 30 SNPs for generalized estimating equation (GEE) tests of association with age at death included rs10507486 (p = 0.0001) and rs4943794 (p = 0.0002), SNPs intronic to FOXO1A, a gene implicated in lifespan extension in animal models. FBAT models identified 7 SNPs and GEE models identified 9 SNPs associated with both age at death and morbidity-free survival at age 65 including rs2374983 near PON1. In the analysis of selected candidate genes, SNP associations (FBAT or GEE p-value < 0.01) were identified for age at death in or near the following genes: FOXO1A, GAPDH, KL, LEPR, PON1, PSEN1, SOD2, and WRN. Top ranked SNP associations in the GEE model for age at natural menopause included rs6910534 (p = 0.00003) near FOXO3a and rs3751591 (p = 0.00006) in CYP19A1. Results of all longevity phenotype-genotype associations for all autosomal SNPs are web posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007.

Conclusion
Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
Potential drug-drug and drug-disease interactions in prescriptions for ambulatory patients over 50 years of age in family medicine clinics in Mexico City
Authors: Doubova Svetlana Vladislavovna , Reyes-Morales Hortensia , Torres-Arreola Laura del Pilar , Suárez-Ortega Magdalena 
Published: September 2007

Abstract
Background
In Mexico, inappropriate prescription of drugs with potential interactions causing serious risks to patient health has been little studied. Work in this area has focused mainly on hospitalized patients, with only specific drug combinations analyzed; moreover, the studies have not produced conclusive results. In the present study, we determined the frequency of potential drug-drug and drug-disease interactions in prescriptions for ambulatory patients over 50 years of age, who used Mexican Institute of Social Security (IMSS) family medicine clinics. In addition, we aimed to identify the associated factors for these interactions.

Methods
We collected information on general patient characteristics, medical histories, and medication (complete data). The study included 624 ambulatory patients over 50 years of age, with non-malignant pain syndrome, who made ambulatory visits to two IMSS family medicine clinics in Mexico City. The patients received 7-day prescriptions for non-opioid analgesics. The potential interactions were identified by using the Thompson Micromedex program. Data were analyzed using descriptive, bivariate and multiple logistic regression analyses.

Results
The average number of prescribed drugs was 5.9 ± 2.5. About 80.0% of patients had prescriptions implying one or more potential drug-drug interactions and 3.8% of patients were prescribed drug combinations with interactions that should be avoided. Also, 64.0% of patients had prescriptions implying one or more potential drug disease interactions. The factors significantly associated with having one or more potential interactions included: taking 5 or more medicines (adjusted Odds Ratio (OR): 4.34, 95%CI: 2.76–6.83), patient age 60 years or older (adjusted OR: 1.66, 95% CI: 1.01–2.74) and suffering from cardiovascular diseases (adjusted OR: 7.26, 95% CI: 4.61–11.44).

Conclusion
The high frequency of prescription of drugs with potential drug interactions showed in this study suggests that it is common practice in primary care level. To lower the frequency of potential interactions it could be necessary to make a careful selection of therapeutic alternatives, and in cases without other options, patients should be continuously monitored to identify adverse events.
Selective repression of retinoic acid target genes by RIP140 during induced tumor cell differentiation of pluripotent human embryonal carcinoma cells
Authors: Heim Kelly C , White Kristina A , Deng Dexin , Tomlinson Craig R , Moore Jason H , Freemantle Sarah J , Spinella Michael J 
Published: September 2007

Abstract

Background
The use of retinoids as anti-cancer agents has been limited due to resistance and low efficacy. The dynamics of nuclear receptor coregulation are incompletely understood. Cell-and context-specific activities of nuclear receptors may be in part due to distinct coregulator complexes recruited to distinct subsets of target genes. RIP140 (also called NRIP1) is a ligand-dependent corepressor that is inducible with retinoic acid (RA). We had previously shown that RIP140 limits RA induced tumor cell differentiation of embryonal carcinoma; the pluriopotent stem cells of testicular germ cell tumors. This implies that RIP140 represses key genes required for RA-mediated tumor cell differentiation. Identification of these genes would be of considerable interest.

Results
To begin to address this issue, microarray technology was employed to elucidate in a de novo fashion the global role of RIP140 in RA target gene regulation of embryonal carcinoma. Subclasses of genes were affected by RIP140 in distinct manners.
Interestingly, approximately half of the RA-dependent genes were unaffected by RIP140. Hence, RIP140 appears to discriminate between different classes of RA target genes. In general, RIP140-dependent gene expression was consistent with RIP140 functioning to limit RA signaling and tumor cell differentiation. Few if any genes were regulated in a manner to support a role for RIP140 in "active repression". We also demonstrated that RIP140 silencing sensitizes embryonal carcinoma cells to low doses of RA.

Conclusion
Together the data demonstrates that RIP140 has profound effects on RA-mediated gene expression in this cancer stem cell model. The RIP140-dependent RA target genes identified here may be particularly important in mediating RA-induced tumor cell differentiation and the findings suggest that RIP140 may be an attractive target to sensitize tumor cells to retinoid-based differentiation therapy. We discuss these data in the context of proposed models of RIP140-mediated repression.
Mediterranean diet and insulin sensitivity, lipid profile and blood pressure levels, in overweight and obese people; The Attica study
Authors: Tzima Natalia , Pitsavos Christos , Panagiotakos Demosthenes B. , Skoumas John , Zampelas Antonis , Chrysohoou Christina , Stefanadis Christodoulos 
Published: September 2007

AbstractBackgroundWe aimed to investigate if overweight and obese adults "close" to Mediterranean diet present better insulin, lipids profile and better pressure levels, compared to individuals close to a more Westernized diet.MethodsThe ATTICA study is a population-based cohort that has randomly enrolled 3042 adult men and women, stratified by age – gender, from the greater area of Athens, during 2001–2002. Of them, in this work were have studied 1762 participants with excess body weight, meaning overweight (BMI: 25–29.9 kg/m2) and obese (BMI>30 kg/m2). 1064 were men and 698 women (20–89 years old). Adherence to Mediterranean diet was assessed through a diet-score that was based on a validated food-frequency questionnaire. Blood pressure was measured and also fasting glucose, insulin and blood lipids. Insulin sensitivity was also assessed by the homeostasis model assessment (HOMA) approach (glucose × insulin/22.5).ResultsIndividuals with excess bodyweight in the highest tertile of diet score, were more insulin sensitive than those in the lowest tertile (11.4% lower HOMA, p = 0.06), had 13% lower levels of total cholesterol (p = 0.001) and 3 mmHg decrease of systolic blood pressure levels (p < 0.001), when adjusted for age, sex and BMI. Multivariate analysis after taking into account several confounders demonstrated that insulin sensitivity, total cholesterol and systolic blood pressure were independently but only modestly correlated with Mediterranean diet in people with excess bodyweight.ConclusionAdherence to Mediterranean diet is modeslty associated with a better insulin sensitivity, lower levels of total cholesterol and lower levels of systolic blood pressure in overweight and obese subjects. This may suggest that compared to general population, the beneficial effect of this diet in cardiovascular system of excess body weight people is limited.
Spontaneous regression of metastatic renal cell carcinoma: case report
Authors: Lekanidi Katerina , Vlachou Paraskevi A. , Morgan Bruno , Vasanthan Subramaniam 
Published: September 2007

Abstract
Spontaneous regression of metastatic renal cell carcinoma is rarely observed. A case of suspected spontaneous regression of pulmonary metastases following nephrectomy for histologically proven renal cell carcinoma without systemic treatment is presented along with a brief review of the literature.
Whole body bone scintigraphy in osseous hydatosis: a case report
Authors: Ebrahimi Abdolali , Assadi Majid , Saghari Mohsen , Eftekhari Mohammad , Gholami Amir , Ghasemikhah Reza , Assadi Sakineh 
Published: September 2007

Abstract
Hydatid disease is common in many parts of the world, and causes considerable health and economic loss. This disease may develop in almost any part of the body.
Bone involvement is often asymptomatic, and its diagnosis is primarily based on radiographic findings. A whole body bone scan is able to show the extent and distribution of lesions.
We describe an unusual case of multifocal skeletal hydatosis and also explain the clinical and diagnostic points. We hope to stimulate a high index of suspicion among clinicians to facilitate early diagnosis and to consider this disease as a differential diagnosis in cases of multiple abnormal activity in bone scintigraphy especially among people in endemic areas.
A global analysis of genetic interactions in Caenorhabditis elegans
Authors: Byrne Alexandra B , Weirauch Matthew T , Wong Victoria , Koeva Martina , Dixon Scott J , Stuart Joshua M , Roy Peter J 
Published: September 2007

Abstract
Background
Understanding gene function and genetic relationships is fundamental to our efforts to better understand biological systems. Previous studies systematically describing genetic interactions on a global scale have either focused on core biological processes in protozoans or surveyed catastrophic interactions in metazoans. Here, we describe a reliable high-throughput approach capable of revealing both weak and strong genetic interactions in the nematode Caenorhabditis elegans.

Results
We investigated interactions between 11 'query' mutants in conserved signal transduction pathways and hundreds of 'target' genes compromised by RNA interference (RNAi). Mutant-RNAi combinations that grew more slowly than controls were identified, and genetic interactions inferred through an unbiased global analysis of the interaction matrix. A network of 1,246 interactions was uncovered, establishing the largest metazoan genetic-interaction network to date. We refer to this approach as systematic genetic interaction analysis (SGI). To investigate how genetic interactions connect genes on a global scale, we superimposed the SGI network on existing networks of physical, genetic, phenotypic and coexpression interactions. We identified 56 putative functional modules within the superimposed network, one of which regulates fat accumulation and is coordinated by interactions with bar-1(ga80), which encodes a homolog of β-catenin. We also discovered that SGI interactions link distinct subnetworks on a global scale. Finally, we showed that the properties of genetic networks are conserved between C. elegans and Saccharomyces cerevisiae, but that the connectivity of interactions within the current networks is not.

Conclusions
Synthetic genetic interactions may reveal redundancy among functional modules on a global scale, which is a previously unappreciated level of organization within metazoan systems. Although the buffering between functional modules may differ between species, studying these differences may provide insight into the evolution of divergent form and function.
Oxidation of Alcohols with Hydrogen Peroxide Catalyzed by Molybdenum(VI)–Peroxo Complex under Solvent-free Conditions
Authors: Luan Yi , Wang Ge , Luck Rudy L , Yang Mu , Han Xiao 
Published: September 2007

Abstract
The oxidation of primary, secondary, allylic, and aromatic alcohols to the corresponding carbonyl compounds proceeds in high yield catalyzed by molybdenum(VI)–peroxo complex with H2O2 under solvent-free conditions. Secondary –OH group are selectively oxidized even in the presence of a primary –OH group. Products/catalyst separation can be easily carried out by simple extraction and the catalytic system can be reused without much loss of activity.
Capillary-assembled Microchip for the Electrochemical Determination of Glucose
Authors: Inadumi Shingo , Hisamoto Hideaki , Mizutani Fumio 
Published: September 2007

Abstract
An electrochemical glucose-sensing chip is developed based on a capillary-assembled microchip (CAs-CHIP) technique, which involves the simple assemblage of square capillaries possessing anti-interferential, glucose-sensing and electrochemical-detecting functions in poly(dimethylsiloxane) micro-channels.
Diastereoselective Cyanomethylation of Chiral N-(tert-Butylsulfinyl)imines Promoted by Lewis Bases
Authors: Mukaiyama Teruaki , Michida Makoto 
Published: September 2007

Abstract
Cyanomethylation of chiral N-(tert-butylsulfinyl)imines with 2-trimethylsilylacetonitrile (TMSCH2CN) in the presence of a Lewis base such as tetrabutylammonium phenoxide (PhONn-Bu4) proceeds smoothly to afford the corresponding β-amino nitriles in good to high yields with excellent diastereoselectivities.
Porphyrin/MgCl2/Silica Gel Composite as a Cobalt-free Humidity Indicator
Authors: Fueda Yoshiyuki , Matsumoto Jin , Shiragami Tsutomu , Nobuhara Kazunori , Yasuda Masahide 
Published: September 2007

Abstract
In order to develop cobalt-free humidity indicator, the composite consisted of porphyrin, MgCl2, and silica gel was prepared. The composite exhibited a reversible color change from green to purple under dry and humid conditions, respectively.
Large Scale Fabrication of NiS Hollow Spheres with Controllable Diameter Sizes
Authors: Yin Xing , Wu Changzheng , Wang Chengle , Xie Yi 
Published: September 2007

Abstract
NiS hollow spheres with controllable diameter sizes have been prepared in large scale by a simple method, where cyclohexylamine, as both solvent and reductant, successfully controlled the rate of releasing S2−. NiS nanoparticles were self-aggregated into hollow spheres around the in situ formed poly(N-vinyl-2-pyrrolidone) (PVP, Mw=30,000) spherical micelles in the cyclohexylamine media. The as-obtained high-quality NiS hollow spheres with loosely packed nanoparticles would show interesting applications in optical device and lithium-ion battery.