O Apolônio de Tiana da biografia escrita por Filóstrato e os sofistas

Directory of Open Access Journals (Sweden)

Semíramis Corsi Silva

2016-12-01

Full Text Available Flávio Filóstrato foi um sofista grego que desenvolveu sua produção escrita no Império Romano da dinastia dos Severos (193-235 d.C.. Suas obras mais conhecidas são os textos de natureza biográfica Vida de Apolônio de Tiana e Vidas dos sofistas. Percebemos nestas duas obras muitas semelhanças entre os sofistas e o filósofo e sábio pitagórico Apolônio de Tiana, que acreditamos ser uma espécie de projeção do autor e de seu grupo. Neste artigo buscaremos comparar o Apolônio filostratiano com alguns aspectos dos sofistas da obra Vidas dos sofistas e tecer algumas considerações sobre as práticas de Apolônio relatadas por Filóstrato, paralelamente à análise de práticas e características de alguns importantes escritores do Império Romano com tradição de sofistas: Apuleio, Dião de Prusa e Élio Aristides. Além das obras de Filóstrato, utilizaremos textos de Apuleio, Dião de Prusa e Élio Aristides, bem como trabalhos historiográficos sobre a temática.

Read-through transcript from NM23-H1 into the neighboring NM23-H2 gene encodes a novel protein, NM23-LV

NARCIS (Netherlands)

Valentijn, Linda J.; Koster, Jan; Versteeg, Rogier

2006-01-01

NM23-H1 and NM23-H2 are neighboring genes on chromosome 17q. They encode nucleoside diphosphate kinases that have additional roles in signal transduction, transcription, and apoptosis. NM23-H1 expression is a strong marker for prognosis and metastatic behavior in many tumor types. A new

Apolipoprotein L1 confers pH-switchable ion permeability to phospholipid vesicles.

Science.gov (United States)

Bruno, Jonathan; Pozzi, Nicola; Oliva, Jonathan; Edwards, John C

2017-11-03

Apolipoprotein L1 (ApoL1) is a human serum protein conferring resistance to African trypanosomes, and certain ApoL1 variants increase susceptibility to some progressive kidney diseases. ApoL1 has been hypothesized to function like a pore-forming colicin and has been reported to have permeability effects on both intracellular and plasma membranes. Here, to gain insight into how ApoL1 may function in vivo , we used vesicle-based ion permeability, direct membrane association, and intrinsic fluorescence to study the activities of purified recombinant ApoL1. We found that ApoL1 confers chloride-selective permeability to preformed phospholipid vesicles and that this selectivity is strongly pH-sensitive, with maximal activity at pH 5 and little activity above pH 7. When ApoL1 and lipid were allowed to interact at low pH and were then brought to neutral pH, chloride permeability was suppressed, and potassium permeability was activated. Both chloride and potassium permeability linearly correlated with the mass of ApoL1 in the reaction mixture, and both exhibited lipid selectivity, requiring the presence of negatively charged lipids for activity. Potassium, but not chloride, permease activity required the presence of calcium ions in both the association and activation steps. Direct assessment of ApoL1-lipid associations confirmed that ApoL1 stably associates with phospholipid vesicles, requiring low pH and the presence of negatively charged phospholipids for maximal binding. Intrinsic fluorescence of ApoL1 supported the presence of a significant structural transition when ApoL1 is mixed with lipids at low pH. This pH-switchable ion-selective permeability may explain the different effects of ApoL1 reported in intracellular and plasma membrane environments. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

Science.gov (United States)

Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

2017-11-15

The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

Haldane to Dimer Phase Transition in the Spin-1 Haldane System with Bond-Alternating Nearest-Neighbor and Uniform Next-Nearest-Neighbor Exchange Interactions

OpenAIRE

Takashi, Tonegawa; Makoto, Kaburagi; Takeshi, Nakao; Department of Physics, Faculty of Science, Kobe University; Faculty of Cross-Cultural Studies, Kobe University; Department of Physics, Faculty of Science, Kobe University

1995-01-01

The Haldane to dimer phase transition is studied in the spin-1 Haldane system with bond-alternating nearest-neighbor and uniform next-nearest-neighbor exchange interactions, where both interactions are antiferromagnetic and thus compete with each other. By using a method of exact diagonalization, the ground-state phase diagram on the ratio of the next-nearest-neighbor interaction constant to the nearest-neighbor one versus the bond-alternation parameter of the nearest-neighbor interactions is...

Systematic identification of novel, essential host genes affecting bromovirus RNA replication.

Directory of Open Access Journals (Sweden)

Brandi L Gancarz

Full Text Available Positive-strand RNA virus replication involves viral proteins and cellular proteins at nearly every replication step. Brome mosaic virus (BMV is a well-established model for dissecting virus-host interactions and is one of very few viruses whose RNA replication, gene expression and encapsidation have been reproduced in the yeast Saccharomyces cerevisiae. Previously, our laboratory identified ∼100 non-essential host genes whose loss inhibited or enhanced BMV replication at least 3-fold. However, our isolation of additional BMV-modulating host genes by classical genetics and other results underscore that genes essential for cell growth also contribute to BMV RNA replication at a frequency that may be greater than that of non-essential genes. To systematically identify novel, essential host genes affecting BMV RNA replication, we tested a collection of ∼900 yeast strains, each with a single essential gene promoter replaced by a doxycycline-repressible promoter, allowing repression of gene expression by adding doxycycline to the growth medium. Using this strain array of ∼81% of essential yeast genes, we identified 24 essential host genes whose depleted expression reproducibly inhibited or enhanced BMV RNA replication. Relevant host genes are involved in ribosome biosynthesis, cell cycle regulation and protein homeostasis, among other cellular processes. BMV 2a(Pol levels were significantly increased in strains depleted for a heat shock protein (HSF1 or proteasome components (PRE1 and RPT6, suggesting these genes may affect BMV RNA replication by directly or indirectly modulating 2a(Pol localization, post-translational modification or interacting partners. Investigating the diverse functions of these newly identified essential host genes should advance our understanding of BMV-host interactions and normal cellular pathways, and suggest new modes of virus control.

ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

Directory of Open Access Journals (Sweden)

Brett A McKinney

Full Text Available Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k for each gene to optimize the Relief-F test statistics (importance scores for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to

Hypertension-attributed nephropathy: what's in a name?

Science.gov (United States)

Freedman, Barry I; Cohen, Arthur H

2016-01-01

Unrelated disease processes commonly occur in non-diabetic individuals with mild-to-moderate hypertension and low level or absent proteinuria who present with chronic kidney disease: primary glomerulosclerosis in those with recent African ancestry, and arteriolar nephrosclerosis with resultant glomerular ischaemia potentially related to hypertension and vascular disease risk factors in other cases. Unfortunately, nephrologists often indiscriminately apply a diagnosis of 'hypertensive nephrosclerosis' to patients in either scenario, which implies that the hypertension is causative of their renal disease. Although nephropathies that are associated with variants in the apolipoprotein L1 gene (APOL1) often cause secondarily elevated blood pressure, they belong to the spectrum of focal segmental glomerulosclerosis and are not initiated by systemic hypertension. Because genetic testing for APOL1 variants and other glomerulosclerosis-associated gene variants is available and can provide a precise definition of disease pathogenesis, we believe that the term 'hypertensive nephrosclerosis' should now be abandoned and replaced with either gene-based (for example, APOL1-associated) glomerulosclerosis or arteriolar nephrosclerosis. Precision medicine will be key to improving diagnostic accuracy in this field. Discrimination of these disparate disorders has the potential to eradicate primary forms of glomerulosclerosis that are associated with APOL1 renal-risk variants.

A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data

Directory of Open Access Journals (Sweden)

Ruzzo Walter L

2006-03-01

Full Text Available Abstract Background As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources. Methods In this paper, we address this issue by proposing a general framework for gene function prediction based on the k-nearest-neighbor (KNN algorithm. The choice of KNN is motivated by its simplicity, flexibility to incorporate different data types and adaptability to irregular feature spaces. A weakness of traditional KNN methods, especially when handling heterogeneous data, is that performance is subject to the often ad hoc choice of similarity metric. To address this weakness, we apply regression methods to infer a similarity metric as a weighted combination of a set of base similarity measures, which helps to locate the neighbors that are most likely to be in the same class as the target gene. We also suggest a novel voting scheme to generate confidence scores that estimate the accuracy of predictions. The method gracefully extends to multi-way classification problems. Results We apply this technique to gene function prediction according to three well-known Escherichia coli classification schemes suggested by biologists, using information derived from microarray and genome sequencing data. We demonstrate that our algorithm dramatically outperforms the naive KNN methods and is competitive with support vector machine (SVM algorithms for integrating heterogenous data. We also show that by combining different data sources, prediction accuracy can improve significantly. Conclusion Our extension of KNN with automatic feature weighting, multi-class prediction, and probabilistic inference, enhance prediction accuracy significantly while remaining efficient, intuitive and flexible. This general framework can also be applied to similar classification problems involving heterogeneous datasets.

A Putative Role of Apolipoprotein L1 Polymorphism in Renal Parenchymal Scarring Following Febrile Urinary Tract Infection in Nigerian Under-Five Children: Proposal for a Case-Control Association Study.

Science.gov (United States)

Anigilaje, Emmanuel Ademola

2018-06-14

Although urinary tract infection (UTI) resolves with prompt treatment in a majority of children, some children, especially those aged less than 5 years, also develop renal parenchymal scarring (RPS). RPS causes high blood pressure that may lead to severe chronic kidney disease and end-stage renal disease (ESRD). Although the risk of UTI is higher in white children than in black children, it is unknown whether RPS is more common in white children than in black children as data are scarce in this regard. A common genetic predisposition to kidney disease in African Americans and the sub-Saharan African blacks is the possession of apolipoprotein L1 (APOL1). APOL1 risk variants regulate the production of APOL1. APOL1 circulates in the blood, and it is also found in the kidney tissue. While circulating, APOL1 kills the trypanosome parasites; an increased APOL1 in kidney tissues, under the right environmental conditions, can also result in the death of kidney tissue (vascular endothelium, the podocytes, proximal tubules, and arterial cells), which, ultimately, is replaced by fibrous tissue. APOL1 may influence the development of RPS, as evidence affirms that its expression is increased in kidney tissue following UTI caused by bacteria. Thus, UTI may be a putative environmental risk factor responsible for APOL1-induced kidney injury. The aim of this proposal was to outline a study that seeks to determine if the possession of two copies of either G1 or G2 APOL1 variant increases the risk of having RPS, 6 months following a febrile UTI among Nigerian under-five children. This case-control association study seeks to determine whether the risk of RPS from febrile UTI is conditional on having 2 APOL1 risk alleles (either G1 or G2). Cases will be children with a confirmed RPS following a febrile UTI. Controls will be age-, gender-, and ethnic-matched children with a febrile UTI but without RPS. Children with vesicoureteral reflux and other congenital anomalies of the urinary

Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Science.gov (United States)

2011-01-01

Single cell profiling was performed to assess differences in RNA accumulation in neighboring hyphae of the fungus Aspergillus niger. A protocol was developed to isolate and amplify RNA from single hyphae or parts thereof. Microarray analysis resulted in a present call for 4 to 7% of the A. niger genes, of which 12% showed heterogeneous RNA levels. These genes belonged to a wide range of gene categories. PMID:21816052

Norrie disease and MAO genes: nearest neighbors.

Science.gov (United States)

Chen, Z Y; Denney, R M; Breakefield, X O

1995-01-01

The Norrie disease and MAO genes are tandemly arranged in the p11.4-p11.3 region of the human X chromosome in the order tel-MAOA-MAOB-NDP-cent. This relationship is conserved in the mouse in the order tel-MAOB-MAOA-NDP-cent. The MAO genes appear to have arisen by tandem duplication of an ancestral MAO gene, but their positional relationship to NDP appears to be random. Distinctive X-linked syndromes have been described for mutations in the MAOA and NDP genes, and in addition, individuals have been identified with contiguous gene syndromes due to chromosomal deletions which encompass two or three of these genes. Loss of function of the NDP gene causes a syndrome of congenital blindness and progressive hearing loss, sometimes accompanied by signs of CNS dysfunction, including variable mental retardation and psychiatric symptoms. Other mutations in the NDP gene have been found to underlie another X-linked eye disease, exudative vitreo-retinopathy. An MAOA deficiency state has been described in one family to date, with features of altered amine and amine metabolite levels, low normal intelligence, apparent difficulty in impulse control and cardiovascular difficulty in affected males. A contiguous gene syndrome in which all three genes are lacking, as well as other as yet unidentified flanking genes, results in severe mental retardation, small stature, seizures and congenital blindness, as well as altered amine and amine metabolites. Issues that remain to be resolved are the function of the NDP gene product, the frequency and phenotype of the MAOA deficiency state, and the possible occurrence and phenotype of an MAOB deficiency state.

Characterization of a gene from the EDM1-PSACH region of human chromosome 19p

Energy Technology Data Exchange (ETDEWEB)

Lennon, G.G.; Giorgi, D.; Martin, J.R. [Lawrence Livermore National Lab., CA (United States)] [and others

1994-09-01

Genetic linkage mapping has indicated that both multiple epiphyseal dysplasia (EDM1), a dominantly inherited chondrodysplasia, and pseudoachondroplasia (PSACH), a skeletal disorder associated with dwarfism, map to a 2-3 Mb region of human chromosome 19p. We have isolated a partial cDNA from this region using hybrid selection, and report on progress towards the characterization of the genomic structure and transcription of the corresponding gene. Sequence analysis of the cDNA to date indicates that this gene is likely to be expressed within extracellular matrix tissues. Defects in this gene or neighboring gene family members may therefore lead to EDM1, PSACH, or other connective tissue and skeletal disorders.

Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences.

Science.gov (United States)

Klopfenstein, Ned B; Stewart, Jane E; Ota, Yuko; Hanna, John W; Richardson, Bryce A; Ross-Davis, Amy L; Elías-Román, Rubén D; Korhonen, Kari; Keča, Nenad; Iturritxa, Eugenia; Alvarado-Rosales, Dionicio; Solheim, Halvor; Brazee, Nicholas J; Łakomy, Piotr; Cleary, Michelle R; Hasegawa, Eri; Kikuchi, Taisei; Garza-Ocañas, Fortunato; Tsopelas, Panaghiotis; Rigling, Daniel; Prospero, Simone; Tsykun, Tetyana; Bérubé, Jean A; Stefani, Franck O P; Jafarpour, Saeideh; Antonín, Vladimír; Tomšovský, Michal; McDonald, Geral I; Woodward, Stephen; Kim, Mee-Sook

2017-01-01

Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis

Elliptic Painlevé equations from next-nearest-neighbor translations on the E_8^{(1)} lattice

Science.gov (United States)

Joshi, Nalini; Nakazono, Nobutaka

2017-07-01

The well known elliptic discrete Painlevé equation of Sakai is constructed by a standard translation on the E_8(1) lattice, given by nearest neighbor vectors. In this paper, we give a new elliptic discrete Painlevé equation obtained by translations along next-nearest-neighbor vectors. This equation is a generic (8-parameter) version of a 2-parameter elliptic difference equation found by reduction from Adler’s partial difference equation, the so-called Q4 equation. We also provide a projective reduction of the well known equation of Sakai.

Susceptibility of Mice to Trypanosoma evansi Treated with Human Plasma Containing Different Concentrations of Apolipoprotein L-1

Science.gov (United States)

Fanfa, Vinicius R.; Otto, Mateus A.; Gressler, Lucas T.; Tavares, Kaio C.S.; Lazzarotto, Cícera R.; Tonin, Alexandre A.; Miletti, Luiz C.; Duarte, Marta M.M.F.; Monteiro, Silvia G.

2011-01-01

The aim of this study was to test the susceptibility of mice to Trypanosoma evansi treated with human plasma containing different concentrations of apolipoprotein L-1 (APOL1). For this experiment, a strain of T. evansi and human plasma (plasmas 1, 2, and 3) from 3 adult males clinically healthy were used. In vivo test used 50 mice divided in 5 groups (A to E) with 10 animals in each group. Animals of groups B to E were infected, and then treated with 0.2 ml of human plasma in the following outline: negative control (A), positive control (B), treatment with plasma 1 (C), treatment with plasma 2 (D), and treatment with plasma 3 (E). Mice treated with human plasma showed an increase in longevity of 40.9±0.3 (C), 20±9.0 (D) and 35.6±9.3 (E) days compared to the control group (B) which was 4.3±0.5 days. The number of surviving mice and free of the parasite (blood smear and PCR negative) at the end of the experiment was 90%, 0%, and 60% for groups C, D, and E, respectively. The quantification of APOL1 was performed due to the large difference in the treatments that differed in the source plasma. In plasmas 1, 2, and 3 was detected the concentration of 194, 99, and 115 mg/dl of APOL1, respectively. However, we believe that this difference in the treatment efficiency is related to the level of APOL1 in plasmas. PMID:22355213

NeighborHood

OpenAIRE

Corominola Ocaña, Víctor

2015-01-01

NeighborHood és una aplicació basada en el núvol, adaptable a qualsevol dispositiu (mòbil, tablet, desktop). L'objectiu d'aquesta aplicació és poder permetre als usuaris introduir a les persones del seu entorn més immediat i que aquestes persones siguin visibles per a la resta d'usuaris. NeighborHood es una aplicación basada en la nube, adaptable a cualquier dispositivo (móvil, tablet, desktop). El objetivo de esta aplicación es poder permitir a los usuarios introducir a las personas de su...

Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.

Science.gov (United States)

Kohnen, Markus V; Schmid-Siegert, Emanuel; Trevisan, Martine; Petrolati, Laure Allenbach; Sénéchal, Fabien; Müller-Moulé, Patricia; Maloof, Julin; Xenarios, Ioannis; Fankhauser, Christian

2016-12-01

In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs. © 2016 American Society of Plant Biologists. All rights reserved.

Gene flow for Echinococcus granulosus metapopulations determined by mitochondrial sequences: A reliable approach for reflecting epidemiological drift of parasite among neighboring countries.

Science.gov (United States)

Mahami-Oskouei, Mahmoud; Kaseb-Yazdanparast, Azam; Spotin, Adel; Shahbazi, Abbas; Adibpour, Mohammad; Ahmadpour, Ehsan; Ghabouli-Mehrabani, Nader

2016-12-01

In genetic diversity and population structure of Echinococcus granulosus, the gene flow can illustrate how the Echinococcus isolates have epidemiologically drifted among endemic neighboring countries. 51 isolates of hydatid cysts were collected from human, dog, cattle and sheep in northwest Iran, where placed co-border with Turkey. DNA samples were extracted, amplified and subjected to sequence analysis of NADH dehydrogenase subunit 1 (nad1) and cytochrome oxidase subunit 1 (cox1) genes. As well, sequences of Echinococcus at east to the southeast regions of Turkey were retrieved from GenBank database for the cox1 gene. The confirmed isolates were grouped as G1 (n = 74) and G3 (n = 6) genotypes. 31 unique haplotypes were identified inferred by the analyzed sequences of cox1 among two distinct populations. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing TUR1, IR15 and IR22 as the most common haplotypes. According to AMOVA test, the high value of haplotype diversity (0.94758-0.98901) of E. granulosus was reflected the total genetic variability within populations while nucleotide diversity was low (0.00727-0.01046) in Iranian and Turkish metapopulations. Neutrality indices of the cox1 were shown negative values (-15.078 to -10.057) in Echinococcus populations which indicating a significant divergence from neutrality. A pairwise fixation index (Fst) as a degree of gene flow was partially high value for all populations (0.151). The statistically Fst value indicates that E. granulosus sensu stricto (G1-G3) are genetically moderate differentiated among Iranian and Turkish isolates. The occurrence of TUR1 and IR15 elucidate that there is possibly the dawn of domestication due to transfer of alleles between populations through the diffusion of stock raising or anthropogenic movements. To evaluate the hypothetical evolutionary scenario, further exploration is necessitated to analyze isolates from

Neighboring and Urbanism: Commonality versus Friendship.

Science.gov (United States)

Silverman, Carol J.

1986-01-01

Examines a dimension of neighboring that need not assume friendship as the role model. When the model assumes only a sense of connectedness as defining neighboring, then the residential correlation, shown in many studies between urbanism and neighboring, disappears. Theories of neighboring, study variables, methods, and analysis are discussed.…

A dumbed-down approach to unite Fermilab, its neighbors

CERN Multimedia

Constable, B

2004-01-01

"...Fermilab is reaching out to its suburban neighbors...With the nation on orange alert, Fermilab scientists no longer can sit on the front porch and invite neighbors in for coffee and quasars" (1 page).

Endogenous 5-methylcytosine protects neighboring guanines from N7 and O6-methylation and O6-pyridyloxobutylation by the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone.

Science.gov (United States)

Ziegel, Rebecca; Shallop, Anthony; Upadhyaya, Pramod; Jones, Roger; Tretyakova, Natalia

2004-01-20

All CG dinucleotides along exons 5-8 of the p53 tumor suppressor gene contain endogenous 5-methylcytosine (MeC). These same sites (e.g., codons 157, 158, 245, 248, and 273) are mutational hot spots in smoking-induced lung cancer. Several groups used the UvrABC endonuclease incision assay to demonstrate that methylated CG dinucleotides of the p53 gene are the preferred binding sites for the diol epoxides of bay region polycyclic aromatic hydrocarbons (PAH). In contrast, effects of endogenous cytosine methylation on the distribution of DNA lesions induced by tobacco-specific nitrosamines, e.g., 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), have not been elucidated. In the work presented here, a stable isotope labeling HPLC-ESI-MS/MS approach was employed to analyze the reactivity of the N7 and O6 positions of guanines within hemimethylated and fully methylated CG dinucleotides toward NNK-derived methylating and pyridyloxobutylating species. 15N3-labeled guanine bases were placed within synthetic DNA sequences representing endogenously methylated p53 codons 154, 157, and 248, followed by treatment with acetylated precursors to NNK diazohydroxides. HPLC-ESI-MS/MS analysis was used to determine the relative yields of N7- and O6-guanine adducts at the 15N3-labeled position. In all cases, the presence of MeC inhibited the formation of N7-methylguanine, O6-methylguanine, and O6-pyridyloxobutylguanine at a neighboring G, with the greatest decrease observed in fully methylated dinucleotides and at guanines preceded by MeC. Furthermore, the O6-Me-dG/N7-Me-G molar ratios were decreased in the presence of the 5'-neighboring MeC, suggesting that the observed decline in O6-alkylguanine adduct yields is, at least partially, a result of an altered reactivity pattern in methylated CG dinucleotides. These results indicate that, unlike N2-guanine adducts of PAH diol epoxides, NNK-induced N7- and O6-alkylguanine adducts are not preferentially formed at the endogenously

Identifying influential neighbors in animal flocking.

Directory of Open Access Journals (Sweden)

Li Jiang

2017-11-01

Full Text Available Schools of fish and flocks of birds can move together in synchrony and decide on new directions of movement in a seamless way. This is possible because group members constantly share directional information with their neighbors. Although detecting the directionality of other group members is known to be important to maintain cohesion, it is not clear how many neighbors each individual can simultaneously track and pay attention to, and what the spatial distribution of these influential neighbors is. Here, we address these questions on shoals of Hemigrammus rhodostomus, a species of fish exhibiting strong schooling behavior. We adopt a data-driven analysis technique based on the study of short-term directional correlations to identify which neighbors have the strongest influence over the participation of an individual in a collective U-turn event. We find that fish mainly react to one or two neighbors at a time. Moreover, we find no correlation between the distance rank of a neighbor and its likelihood to be influential. We interpret our results in terms of fish allocating sequential and selective attention to their neighbors.

Identifying influential neighbors in animal flocking.

Science.gov (United States)

Jiang, Li; Giuggioli, Luca; Perna, Andrea; Escobedo, Ramón; Lecheval, Valentin; Sire, Clément; Han, Zhangang; Theraulaz, Guy

2017-11-01

Schools of fish and flocks of birds can move together in synchrony and decide on new directions of movement in a seamless way. This is possible because group members constantly share directional information with their neighbors. Although detecting the directionality of other group members is known to be important to maintain cohesion, it is not clear how many neighbors each individual can simultaneously track and pay attention to, and what the spatial distribution of these influential neighbors is. Here, we address these questions on shoals of Hemigrammus rhodostomus, a species of fish exhibiting strong schooling behavior. We adopt a data-driven analysis technique based on the study of short-term directional correlations to identify which neighbors have the strongest influence over the participation of an individual in a collective U-turn event. We find that fish mainly react to one or two neighbors at a time. Moreover, we find no correlation between the distance rank of a neighbor and its likelihood to be influential. We interpret our results in terms of fish allocating sequential and selective attention to their neighbors.

Novel algorithms reveal streptococcal transcriptomes and clues about undefined genes.

Science.gov (United States)

Ryan, Patricia A; Kirk, Brian W; Euler, Chad W; Schuch, Raymond; Fischetti, Vincent A

2007-07-01

Bacteria-host interactions are dynamic processes, and understanding transcriptional responses that directly or indirectly regulate the expression of genes involved in initial infection stages would illuminate the molecular events that result in host colonization. We used oligonucleotide microarrays to monitor (in vitro) differential gene expression in group A streptococci during pharyngeal cell adherence, the first overt infection stage. We present neighbor clustering, a new computational method for further analyzing bacterial microarray data that combines two informative characteristics of bacterial genes that share common function or regulation: (1) similar gene expression profiles (i.e., co-expression); and (2) physical proximity of genes on the chromosome. This method identifies statistically significant clusters of co-expressed gene neighbors that potentially share common function or regulation by coupling statistically analyzed gene expression profiles with the chromosomal position of genes. We applied this method to our own data and to those of others, and we show that it identified a greater number of differentially expressed genes, facilitating the reconstruction of more multimeric proteins and complete metabolic pathways than would have been possible without its application. We assessed the biological significance of two identified genes by assaying deletion mutants for adherence in vitro and show that neighbor clustering indeed provides biologically relevant data. Neighbor clustering provides a more comprehensive view of the molecular responses of streptococci during pharyngeal cell adherence.

Exactly solvable spin-1 Ising–Heisenberg diamond chain with the second-neighbor interaction between nodal spins

International Nuclear Information System (INIS)

Hovhannisyan, V V; Ananikian, N S; Strečka, J

2016-01-01

The spin-1 Ising–Heisenberg diamond chain with the second-neighbor interaction between nodal spins is rigorously solved using the transfer-matrix method. In particular, exact results for the ground state, magnetization process and specific heat are presented and discussed. It is shown that further-neighbor interaction between nodal spins gives rise to three novel ground states with a translationally broken symmetry, but at the same time, does not increases the total number of intermediate plateaus in a zero-temperature magnetization curve compared with the simplified model without this interaction term. The zero-field specific heat displays interesting thermal dependencies with a single- or double-peak structure. (paper)

New Sliding Puzzle with Neighbors Swap Motion

OpenAIRE

Prihardono, Ariyanto; Kawagoe, Kenichi

2015-01-01

The sliding puzzles (15-puzzle, 8-puzzle, 5-puzzle) are known to have 2 kind of puz-zle: solvable puzzle and unsolvable puzzle. In this thesis, we make a new puzzle with only 1 kind of it, solvable puzzle. This new puzzle is made by adopting sliding puzzle with several additional rules from M13 puzzle; the puzzle that is formed form The Mathieu group M13. This puzzle has a movement that called a neighbors swap motion, a rule of movement that enables every neighboring points to swap. This extr...

Neighbor Rupture Degree of Some Middle Graphs

Directory of Open Access Journals (Sweden)

Gökşen BACAK-TURAN

2017-12-01

Full Text Available Networks have an important place in our daily lives. Internet networks, electricity networks, water networks, transportation networks, social networks and biological networks are some of the networks we run into every aspects of our lives. A network consists of centers connected by links. A network is represented when centers and connections modelled by vertices and edges, respectively. In consequence of the failure of some centers or connection lines, measurement of the resistance of the network until the communication interrupted is called vulnerability of the network. In this study, neighbor rupture degree which is a parameter that explores the vulnerability values of the resulting graphs due to the failure of some centers of a communication network and its neighboring centers becoming nonfunctional were applied to some middle graphs and neighbor rupture degree of the $M(C_{n},$ $M(P_{n},$ $M(K_{1,n},$ $M(W_{n},$ $M(P_{n}\\times K_{2}$ and $M(C_{n}\\times K_{2}$ have been found.

Recrafting the neighbor-joining method

Directory of Open Access Journals (Sweden)

Pedersen Christian NS

2006-01-01

Full Text Available Abstract Background The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3 algorithm upon which all existing implementations are based. Results In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2 but the worst-case remains O(n3. We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Θ(n2 on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method. Conclusion The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.

Adaptive behavior of neighboring neurons during adaptation-induced plasticity of orientation tuning in V1

Directory of Open Access Journals (Sweden)

Shumikhina Svetlana

2009-12-01

Full Text Available Abstract Background Sensory neurons display transient changes of their response properties following prolonged exposure to an appropriate stimulus (adaptation. In adult cat primary visual cortex, orientation-selective neurons shift their preferred orientation after being adapted to a non-preferred orientation. The direction of those shifts, towards (attractive or away (repulsive from the adapter depends mostly on adaptation duration. How the adaptive behavior of a neuron is related to that of its neighbors remains unclear. Results Here we show that in most cases (75%, cells shift their preferred orientation in the same direction as their neighbors. We also found that cells shifting preferred orientation differently from their neighbors (25% display three interesting properties: (i larger variance of absolute shift amplitude, (ii wider tuning bandwidth and (iii larger range of preferred orientations among the cluster of cells. Several response properties of V1 neurons depend on their location within the cortical orientation map. Our results suggest that recording sites with both attractive and repulsive shifts following adaptation may be located in close proximity to iso-orientation domain boundaries or pinwheel centers. Indeed, those regions have a more diverse orientation distribution of local inputs that could account for the three properties above. On the other hand, sites with all cells shifting their preferred orientation in the same direction could be located within iso-orientation domains. Conclusions Our results suggest that the direction and amplitude of orientation preference shifts in V1 depend on location within the orientation map. This anisotropy of adaptation-induced plasticity, comparable to that of the visual cortex itself, could have important implications for our understanding of visual adaptation at the psychophysical level.

Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress

Directory of Open Access Journals (Sweden)

Christoph eSchmid

2013-08-01

Full Text Available Root-root interactions are much more sophisticated than previously thought, yet the mechanisms of belowground neighbor perception remain largely obscure. Genome-wide transcriptome analyses allow detailed insight into plant reactions to environmental cues.A root interaction trial was set up to explore both morphological and whole genome transcriptional responses in roots of Arabidopsis thaliana in the presence or absence of an inferior competitor, Hieracium pilosella.Neighbor perception was indicated by Arabidopsis roots predominantly growing away from the neighbor (segregation, while solitary plants placed more roots towards the middle of the pot. Total biomass remained unaffected. Database comparisons in transcriptome analysis revealed considerable similarity between Arabidopsis root reactions to neighbors and reactions to pathogens. Detailed analyses of the functional category ‘biotic stress’ using MapMan tools found the sub-category ‘pathogenesis-related proteins’ highly significantly induced. A comparison to a study on intraspecific competition brought forward a core of genes consistently involved in reactions to neighbor roots.We conclude that beyond resource depletion roots perceive neighboring roots or their associated microorganisms by a relatively uniform mechanism that involves the strong induction of pathogenesis-related proteins. In an ecological context the findings reveal that belowground neighbor detection may occur independently of resource depletion, allowing for a time advantage for the root to prepare for potential interactions.

Model of directed lines for square ice with second-neighbor and third-neighbor interactions

Science.gov (United States)

Kirov, Mikhail V.

2018-02-01

The investigation of the properties of nanoconfined systems is one of the most rapidly developing scientific fields. Recently it has been established that water monolayer between two graphene sheets forms square ice. Because of the energetic disadvantage, in the structure of the square ice there are no longitudinally arranged molecules. The result is that the structure is formed by unidirectional straight-lines of hydrogen bonds only. A simple but accurate discrete model of square ice with second-neighbor and third-neighbor interactions is proposed. According to this model, the ground state includes all configurations which do not contain three neighboring unidirectional chains of hydrogen bonds. Each triplet increases the energy by the same value. This new model differs from an analogous model with long-range interactions where in the ground state all neighboring chains are antiparallel. The new model is suitable for the corresponding system of point electric (and magnetic) dipoles on the square lattice. It allows separately estimating the different contributions to the total binding energy and helps to understand the properties of infinite monolayers and finite nanostructures. Calculations of the binding energy for square ice and for point dipole system are performed using the packages TINKER and LAMMPS.

An extensive analysis of the hereditary hemochromatosis gene HFE and neighboring histone genes: associations with childhood leukemia.

Science.gov (United States)

Davis, Charronne F; Dorak, M Tevfik

2010-04-01

The most common mutation of the HFE gene C282Y has shown a risk association with childhood acute lymphoblastic leukemia (ALL) in Welsh and Scottish case-control studies. This finding has not been replicated outside Britain. Here, we present a thorough analysis of the HFE gene in a panel of HLA homozygous reference cell lines and in the original population sample from South Wales (117 childhood ALL cases and 414 newborn controls). The 21 of 24 variants analyzed were from the HFE gene region extending 52 kb from the histone gene HIST1H1C to HIST1H1T. We identified the single-nucleotide polymorphism (SNP) rs807212 as a tagging SNP for the most common HFE region haplotype, which contains wild-type alleles of all HFE variants examined. This intergenic SNP rs807212 yielded a strong male-specific protective association (per allele OR = 0.38, 95% CI = 0.22-0.64, P (trend) = 0.0002; P = 0.48 in females), which accounted for the original C282Y risk association. In the HapMap project data, rs807212 was in strong linkage disequilibrium with 25 other SNPs spanning 151 kb around HFE. Minor alleles of these 26 SNPs characterized the most common haplotype for the HFE region, which lacked all disease-associated HFE variants. The HapMap data suggested positive selection in this region even in populations where the HFE C282Y mutation is absent. These results have implications for the sex-specific associations observed in this region and suggest the inclusion of rs807212 in future studies of the HFE gene and the extended HLA class I region.

Fixations of the HIV-1 env gene refute neutralism: New evidence for pan-selective evolution

Directory of Open Access Journals (Sweden)

Carlos Y Valenzuela

2010-01-01

Full Text Available We examined 103 nucleotide sequences of the HIV-1 env gene, sampled from 35 countries and tested: I the random (neutral distribution of the number of nucleotide changes; II the proportion of bases at molecular equilibrium; III the neutral expected homogeneity of the distribution of new fxated bases; IV the hypothesis of the neighbor infuence on the mutation rates in a site. The expected random number of fxations per site was estimated by Bose-Einstein statistics, and the expected frequencies of bases by matrices of mutation-fxation rates. The homogeneity of new fxations was analyzed using χ2 and trinomial tests for homogeneity. Fixations of the central base in trinucleotides were used to test the neighbor infuence on base substitutions. Neither the number of fxations nor the frequencies of bases ftted the expected neutral distribution. There was a highly signifcant heterogeneity in the distribution of new fxations, and several sites showed more transversions than transitions, showing that each nucleotide site has its own pattern of change. These three independent results make the neutral theory, the nearly neutral and the neighbor infuence hypotheses untenable and indicate that evolution of env is rather highly selective.

The role of orthography in the semantic activation of neighbors.

Science.gov (United States)

Hino, Yasushi; Lupker, Stephen J; Taylor, Tamsen E

2012-09-01

There is now considerable evidence that a letter string can activate semantic information appropriate to its orthographic neighbors (e.g., Forster & Hector's, 2002, TURPLE effect). This phenomenon is the focus of the present research. Using Japanese words, we examined whether semantic activation of neighbors is driven directly by orthographic similarity alone or whether there is also a role for phonological similarity. In Experiment 1, using a relatedness judgment task in which a Kanji word-Katakana word pair was presented on each trial, an inhibitory effect was observed when the initial Kanji word was related to an orthographic and phonological neighbor of the Katakana word target but not when the initial Kanji word was related to a phonological but not orthographic neighbor of the Katakana word target. This result suggests that phonology plays little, if any, role in the activation of neighbors' semantics when reading familiar words. In Experiment 2, the targets were transcribed into Hiragana, a script they are typically not written in, requiring readers to engage in phonological coding. In that experiment, inhibitory effects were observed in both conditions. This result indicates that phonologically mediated semantic activation of neighbors will emerge when phonological processing is necessary in order to understand a written word (e.g., when that word is transcribed into an unfamiliar script). PsycINFO Database Record (c) 2012 APA, all rights reserved.

The distribution of the number of node neighbors in random hypergraphs

International Nuclear Information System (INIS)

López, Eduardo

2013-01-01

Hypergraphs, the generalization of graphs in which edges become conglomerates of r nodes called hyperedges of rank r ⩾ 2, are excellent models to study systems with interactions that are beyond the pairwise level. For hypergraphs, the node degree ℓ (number of hyperedges connected to a node) and the number of neighbors k of a node differ from each other in contrast to the case of graphs, where counting the number of edges is equivalent to counting the number of neighbors. In this paper, I calculate the distribution of the number of node neighbors in random hypergraphs in which hyperedges of uniform rank r have a homogeneous (equal for all hyperedges) probability p to appear. This distribution is equivalent to the degree distribution of ensembles of graphs created as projections of hypergraph or bipartite network ensembles, where the projection connects any two nodes in the projected graph when they are also connected in the hypergraph or bipartite network. The calculation is non-trivial due to the possibility that neighbor nodes belong simultaneously to multiple hyperedges (node overlaps). From the exact results, the traditional asymptotic approximation to the distribution in the sparse regime (small p) where overlaps are ignored is rederived and improved; the approximation exhibits Poisson-like behavior accompanied by strong fluctuations modulated by power-law decays in the system size N with decay exponents equal to the minimum number of overlapping nodes possible for a given number of neighbors. It is shown that the dense limit cannot be explained if overlaps are ignored, and the correct asymptotic distribution is provided. The neighbor distribution requires the calculation of a new combinatorial coefficient Q r−1 (k, ℓ), which counts the number of distinct labeled hypergraphs of k nodes, ℓ hyperedges of rank r − 1, and where every node is connected to at least one hyperedge. Some identities of Q r−1 (k, ℓ) are derived and applied to the

Weak doping dependence of the antiferromagnetic coupling between nearest-neighbor Mn2 + spins in (Ba1 -xKx) (Zn1-yMny) 2As2

Science.gov (United States)

Surmach, M. A.; Chen, B. J.; Deng, Z.; Jin, C. Q.; Glasbrenner, J. K.; Mazin, I. I.; Ivanov, A.; Inosov, D. S.

2018-03-01

Dilute magnetic semiconductors (DMS) are nonmagnetic semiconductors doped with magnetic transition metals. The recently discovered DMS material (Ba1 -xKx) (Zn1-yMny) 2As2 offers a unique and versatile control of the Curie temperature TC by decoupling the spin (Mn2 +, S =5 /2 ) and charge (K+) doping in different crystallographic layers. In an attempt to describe from first-principles calculations the role of hole doping in stabilizing ferromagnetic order, it was recently suggested that the antiferromagnetic exchange coupling J between the nearest-neighbor Mn ions would experience a nearly twofold suppression upon doping 20% of holes by potassium substitution. At the same time, further-neighbor interactions become increasingly ferromagnetic upon doping, leading to a rapid increase of TC. Using inelastic neutron scattering, we have observed a localized magnetic excitation at about 13 meV associated with the destruction of the nearest-neighbor Mn-Mn singlet ground state. Hole doping results in a notable broadening of this peak, evidencing significant particle-hole damping, but with only a minor change in the peak position. We argue that this unexpected result can be explained by a combined effect of superexchange and double-exchange interactions.

The PIN1 family gene PvPIN1 is involved in auxin-dependent root emergence and tillering in switchgrass

Directory of Open Access Journals (Sweden)

Kaijie Xu

2016-03-01

Full Text Available Abstract Switchgrass (Panicum virgatum L.; family Poaceae is a warm-season C4 perennial grass. Tillering plays an important role in determining the morphology of aboveground parts and the final biomass yield of switchgrass. Auxin distribution in plants can affect a variety of important growth and developmental processes, including the regulation of shoot and root branching, plant resistance and biological yield. Auxin transport and gradients in plants are mediated by influx and efflux carriers. PvPIN1, a switchgrass PIN1-like gene that is involved in regulating polar transport, is a putative auxin efflux carrier. Neighbor-joining analysis using sequences deposited in NCBI databases showed that the PvPIN1gene belongs to the PIN1 family and is evolutionarily closer to the Oryza sativa japonica group. Tiller emergence and development was significantly promoted in plants subjected toPvPIN1 RNA interference (RNAi, which yielded a phenotype similar to that of wild-type plants treated with the auxin transport inhibitor TIBA (2,3,5-triiodobenzoic acid. A transgenic approach that inducedPvPIN1 gene overexpression or suppression altered tiller number and the shoot/root ratio. These data suggest that PvPIN1plays an important role in auxin-dependent adventitious root emergence and tillering.

Recrafting the Neighbor-Joining Method

DEFF Research Database (Denmark)

Mailund; Brodal, Gerth Stølting; Fagerberg, Rolf

2006-01-01

Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implementations are based. Methods: In this paper we present techniques for speeding...... up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance...... matrices obtained from the Pfam collection of alignments. Results: The experiments indicate that the running time of our algorithms evolve as Θ(n2) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical...

Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids.

Science.gov (United States)

Liénard, Marjorie A; Araripe, Luciana O; Hartl, Daniel L

2016-07-19

Crosses between closely related animal species often result in male hybrids that are sterile, and the molecular and functional basis of genetic factors for hybrid male sterility is of great interest. Here, we report a molecular and functional analysis of HMS1, a region of 9.2 kb in chromosome 3 of Drosophila mauritiana, which results in virtually complete hybrid male sterility when homozygous in the genetic background of sibling species Drosophila simulans. The HMS1 region contains two strong candidate genes for the genetic incompatibility, agt and Taf1 Both encode unrelated DNA-binding proteins, agt for an alkyl-cysteine-S-alkyltransferase and Taf1 for a subunit of transcription factor TFIID that serves as a multifunctional transcriptional regulator. The contribution of each gene to hybrid male sterility was assessed by means of germ-line transformation, with constructs containing complete agt and Taf1 genomic sequences as well as various chimeric constructs. Both agt and Taf1 contribute about equally to HMS1 hybrid male sterility. Transgenes containing either locus rescue sterility in about one-half of the males, and among fertile males the number of offspring is in the normal range. This finding suggests compensatory proliferation of the rescued, nondysfunctional germ cells. Results with chimeric transgenes imply that the hybrid incompatibilities result from interactions among nucleotide differences residing along both agt and Taf1 Our results challenge a number of preliminary generalizations about the molecular and functional basis of hybrid male sterility, and strongly reinforce the role of DNA-binding proteins as a class of genes contributing to the maintenance of postzygotic reproductive isolation.

The Petunia GRAS Transcription Factor ATA/RAM1 Regulates Symbiotic Gene Expression and Fungal Morphogenesis in Arbuscular Mycorrhiza1

Science.gov (United States)

Rich, Mélanie K.

2015-01-01

Arbuscular mycorrhiza (AM) is a mutual symbiosis that involves a complex symbiotic interface over which nutrients are exchanged between the plant host and the AM fungus. Dozens of genes in the host are required for the establishment and functioning of the interaction, among them nutrient transporters that mediate the uptake of mineral nutrients delivered by the fungal arbuscules. We have isolated in a genetic mutant screen a petunia (Petunia hybrida) GIBBERELLIC ACID INSENSITIVE, REPRESSOR of GIBBERELLIC ACID INSENSITIVE, and SCARECROW (GRAS)-type transcription factor, ATYPICAL ARBUSCULE (ATA), that acts as the central regulator of AM-related genes and is required for the morphogenesis of arbuscules. Forced mycorrhizal inoculations from neighboring wild-type plants revealed an additional role of ATA in restricting mycorrhizal colonization of the root meristem. The lack of ATA, which represents the ortholog of REQUIRED FOR ARBUSCULAR MYCORRHIZA1 in Medicago truncatula, renders the interaction completely ineffective, hence demonstrating the central role of AM-related genes for arbuscule development and function. PMID:25971550

Genome-wide screening identifies Plasmodium chabaudi-induced modifications of DNA methylation status of Tlr1 and Tlr6 gene promoters in liver, but not spleen, of female C57BL/6 mice.

Science.gov (United States)

Al-Quraishy, Saleh; Dkhil, Mohamed A; Abdel-Baki, Abdel Azeem S; Delic, Denis; Santourlidis, Simeon; Wunderlich, Frank

2013-11-01

Epigenetic reprogramming of host genes via DNA methylation is increasingly recognized as critical for the outcome of diverse infectious diseases, but information for malaria is not yet available. Here, we investigate the effect of blood-stage malaria of Plasmodium chabaudi on the DNA methylation status of host gene promoters on a genome-wide scale using methylated DNA immunoprecipitation and Nimblegen microarrays containing 2,000 bp oligonucleotide features that were split into -1,500 to -500 bp Ups promoters and -500 to +500 bp Cor promoters, relative to the transcription site, for evaluation of differential DNA methylation. Gene expression was analyzed by Agilent and Affymetrix microarray technology. Challenging of female C57BL/6 mice with 10(6) P. chabaudi-infected erythrocytes resulted in a self-healing outcome of infections with peak parasitemia on day 8 p.i. These infections induced organ-specific modifications of DNA methylation of gene promoters. Among the 17,354 features on Nimblegen arrays, only seven gene promoters were identified to be hypermethylated in the spleen, whereas the liver exhibited 109 hyper- and 67 hypomethylated promoters at peak parasitemia in comparison with non-infected mice. Among the identified genes with differentially methylated Cor-promoters, only the 7 genes Pigr, Ncf1, Klkb1, Emr1, Ndufb11, and Tlr6 in the liver and Apol6 in the spleen were detected to have significantly changed their expression. Remarkably, the Cor promoter of the toll-like receptor Tlr6 became hypomethylated and Tlr6 expression increased by 3.4-fold during infection. Concomitantly, the Ups promoter of the Tlr1 was hypermethylated, but Tlr1 expression also increased by 11.3-fold. TLR6 and TLR1 are known as auxillary receptors to form heterodimers with TLR2 in plasma membranes of macrophages, which recognize different pathogen-associated molecular patterns (PAMPs), as, e.g., intact 3-acyl and sn-2-lyso-acyl glycosylphosphatidylinositols of P. falciparum

Simbologías del rostro representado: valores simbólicos del rostro en el arte contemporáneo

OpenAIRE

Tornero Sanchís, Josep

2016-01-01

Palabras clave: Rostro, máscara, prósopon, simbología, apolíneo, dionisiaco. Objetivos En esta investigación tratamos de aproximarnos a la reproducción artística del rostro, analizado desde una simbología de la ambigüedad entre lo apolíneo y dionisiaco, del mismo modo que su representación ha derivado en un conjunto de imágenes diversas y plurales, diversificando una complejidad que parece revelarse a modo de hipóstasis, reunida y universalizada en su propia etimología: el prósopon. ...

The evolution of gene expression in primates

OpenAIRE

Tashakkori Ghanbarian, Avazeh

2015-01-01

The evolution of a gene’s expression profile is commonly assumed to be independent of its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between expression of neighboring genes in extant taxa. Indeed, in all eukaryotic genomes, genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their e...

The prevalence of PAI-1 4G/5G gene variant in Serbian population

Directory of Open Access Journals (Sweden)

Đorđević Valentina

2013-01-01

Full Text Available Introduction: Plasminogen activator inhibitor 1 (PAI-1 has a major role in inhibition of firinolysis and normal haemostasis. The presence of the PAI-1 4G/4G genotype leads to increased expression of PAI-1. High blood level of PAI-1 is associated with many diseases such as thrombosis, cerebral insult, myocardial infarction, pregnancy loss, preeclampsia, insulin resistance, type 2 diabetes, breast cancer and asthma. In this study, the prevalence of PAI-1 4G/5G gene variant was determined in healthy subjects from Serbian population. Methods: The study was carried out in a group of 210 healthy subjects (105 women and 105 men. The presence of PAI-1 4G/5G gene variant was detected by PCR-RFLP analysis. Results: The prevalence of PAI-1 4G/4G genotype was 34.76% and it was increased compared to PAI-1 5G/5G genotype (19.05%. The most frequent was PAI-1 4G/5G genotype (46.19%. Allelic frequency for 4G allele was higher (0.58 compared to 5G allele (0.42. Conclusions: The prevalence of PAI-1 4G/5G gene variant in Serbian population is similar to the neighboring populations. Results of this study represent the first data for Serbian population. This study could be useful for further research where the role of PAI-1 4G/5G gene variant will be assessed in the pathogenesis of many diseases.

Mechanism of Trypanosoma brucei gambiense resistance to human serum

DEFF Research Database (Denmark)

Uzureau, Pierrick; Uzureau, Sophie; Lecordier, Laurence

2013-01-01

GP), which prevents APOL1 toxicity and induces stiffening of membranes upon interaction with lipids. Two additional features contribute to resistance to TLFs: reduction of sensitivity to APOL1 requiring cysteine protease activity, and TbHpHbR inactivation due to a L210S substitution. According...

Frog sound identification using extended k-nearest neighbor classifier

Science.gov (United States)

Mukahar, Nordiana; Affendi Rosdi, Bakhtiar; Athiar Ramli, Dzati; Jaafar, Haryati

2017-09-01

Frog sound identification based on the vocalization becomes important for biological research and environmental monitoring. As a result, different types of feature extractions and classifiers have been employed to evaluate the accuracy of frog sound identification. This paper presents a frog sound identification with Extended k-Nearest Neighbor (EKNN) classifier. The EKNN classifier integrates the nearest neighbors and mutual sharing of neighborhood concepts, with the aims of improving the classification performance. It makes a prediction based on who are the nearest neighbors of the testing sample and who consider the testing sample as their nearest neighbors. In order to evaluate the classification performance in frog sound identification, the EKNN classifier is compared with competing classifier, k -Nearest Neighbor (KNN), Fuzzy k -Nearest Neighbor (FKNN) k - General Nearest Neighbor (KGNN)and Mutual k -Nearest Neighbor (MKNN) on the recorded sounds of 15 frog species obtained in Malaysia forest. The recorded sounds have been segmented using Short Time Energy and Short Time Average Zero Crossing Rate (STE+STAZCR), sinusoidal modeling (SM), manual and the combination of Energy (E) and Zero Crossing Rate (ZCR) (E+ZCR) while the features are extracted by Mel Frequency Cepstrum Coefficient (MFCC). The experimental results have shown that the EKNCN classifier exhibits the best performance in terms of accuracy compared to the competing classifiers, KNN, FKNN, GKNN and MKNN for all cases.

Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding.

Science.gov (United States)

Rogals, Monique J; Greenwood, Alexander I; Kwon, Jeahoo; Lu, Kun Ping; Nicholson, Linda K

2016-12-01

The peptidyl prolyl isomerase Pin1 has two domains that are considered to be its binding (WW) and catalytic (PPIase) domains, both of which interact with phosphorylated Ser/Thr-Pro motifs. This shared specificity might influence substrate selection, as many known Pin1 substrates have multiple sequentially close phosphoSer/Thr-Pro motifs, including the protein interleukin-1 receptor-associated kinase-1 (IRAK1). The IRAK1 undefined domain (UD) contains two sets of such neighboring motifs (Ser131/Ser144 and Ser163/Ser173), suggesting possible bivalent interactions with Pin1. Using a series of NMR titrations with 15N-labeled full-length Pin1 (Pin1-FL), PPIase, or WW domain and phosphopeptides representing the Ser131/Ser144 and Ser163/Ser173 regions of IRAK1-UD, bivalent interactions were investigated. Binding studies using singly phosphorylated peptides showed that individual motifs displayed weak affinities (> 100 μm) for Pin1-FL and each isolated domain. Analysis of dually phosphorylated peptides binding to Pin1-FL showed that inclusion of bivalent states was necessary to fit the data. The resulting complex model and fitted parameters were applied to predict the impact of bivalent states at low micromolar concentrations, demonstrating significant affinity enhancement for both dually phosphorylated peptides (3.5 and 24 μm for peptides based on the Ser131/Ser144 and Ser163/Ser173 regions, respectively). The complementary technique biolayer interferometry confirmed the predicted affinity enhancement for a representative set of singly and dually phosphorylated Ser131/Ser144 peptides at low micromolar concentrations, validating model predictions. These studies provide novel insights regarding the complexity of interactions between Pin1 and activated IRAK1, and more broadly suggest that phosphorylation of neighboring Ser/Thr-Pro motifs in proteins might provide competitive advantage at cellular concentrations for engaging with Pin1. © 2016 Federation of European

Well-defined critical association concentration and rapid adsorption at the air/water interface of a short amphiphilic polymer, amphipol A8-35: a study by Förster resonance energy transfer and dynamic surface tension measurements.

Science.gov (United States)

Giusti, Fabrice; Popot, Jean-Luc; Tribet, Christophe

2012-07-17

Amphipols (APols) are short amphiphilic polymers designed to handle membrane proteins (MPs) in aqueous solutions as an alternative to small surfactants (detergents). APols adsorb onto the transmembrane, hydrophobic surface of MPs, forming small, water-soluble complexes, in which the protein is biochemically stabilized. At variance with MP/detergent complexes, MP/APol ones remain stable even at extreme dilutions. Pure APol solutions self-associate into well-defined micelle-like globules comprising a few APol molecules, a rather unusual behavior for amphiphilic polymers, which typically form ill-defined assemblies. The best characterized APol to date, A8-35, is a random copolymer of acrylic acid, isopropylacrylamide, and octylacrylamide. In the present work, the concentration threshold for self-association of A8-35 in salty buffer (NaCl 100 mM, Tris/HCl 20 mM, pH 8.0) has been studied by Förster resonance energy transfer (FRET) measurements and tensiometry. In a 1:1 mol/mol mixture of APols grafted with either rhodamine or 7-nitro-1,2,3-benzoxadiazole, the FRET signal as a function of A8-35 concentration is essentially zero below a threshold concentration of 0.002 g·L(-1) and increases linearly with concentration above this threshold. This indicates that assembly takes place in a narrow concentration interval around 0.002 g·L(-1). Surface tension measurements decreases regularly with concentration until a threshold of ca. 0.004 g·L(-1), beyond which it reaches a plateau at ca. 30 mN·m(-1). Within experimental uncertainties, the two techniques thus yield a comparable estimate of the critical self-assembly concentration. The kinetics of variation of the surface tension was analyzed by dynamic surface tension measurements in the time window 10 ms-100 s. The rate of surface tension decrease was similar in solutions of A8-35 and of the anionic surfactant sodium dodecylsulfate when both compounds were at a similar molar concentration of n-alkyl moieties. Overall, the

Carboxylesterase 1 genes

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Madsen, Majbritt Busk

2018-01-01

The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene.

Directory of Open Access Journals (Sweden)

Per Erixon

Full Text Available BACKGROUND: Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent. Non-synonymous rates are usually even slower due to purifying selection acting on the genes. Positive selection is expected to speed up non-synonymous substitution rates, whereas synonymous rates are expected to be unaffected. Until recently, positive selection has seldom been observed in chloroplast genes, and large-scale structural rearrangements leading to gene duplications are hitherto supposed to be rare. METHODOLOGY/PRINCIPLE FINDINGS: We found high substitution rates in the exons of the plastid clpP1 gene in Oenothera (the Evening Primrose family and three separate lineages in the tribe Sileneae (Caryophyllaceae, the Carnation family. Introns have been lost in some of the lineages, but where present, the intron sequences have substitution rates similar to those found in other introns of their genomes. The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny. In two of the lineages we found multiple copies of the gene. Neighboring genes present in the duplicated fragments do not show signs of elevated substitution rates or positive selection. Although non-synonymous substitutions account for most of the increase in substitution rates, synonymous rates are also markedly elevated in some lineages. Whereas plant clpP1 genes experiencing negative (purifying selection are characterized by having very conserved lengths, genes under positive selection often have large insertions of more or less repetitive amino acid sequence motifs. CONCLUSIONS/SIGNIFICANCE: We found positive selection of the clpP1 gene in various plant lineages to correlated with repeated duplication of the clpP1 gene and surrounding regions, repetitive amino acid sequences, and increase in synonymous substitution rates. The present study sheds light on the

Mixed random walks with a trap in scale-free networks including nearest-neighbor and next-nearest-neighbor jumps

Science.gov (United States)

Zhang, Zhongzhi; Dong, Yuze; Sheng, Yibin

2015-10-01

Random walks including non-nearest-neighbor jumps appear in many real situations such as the diffusion of adatoms and have found numerous applications including PageRank search algorithm; however, related theoretical results are much less for this dynamical process. In this paper, we present a study of mixed random walks in a family of fractal scale-free networks, where both nearest-neighbor and next-nearest-neighbor jumps are included. We focus on trapping problem in the network family, which is a particular case of random walks with a perfect trap fixed at the central high-degree node. We derive analytical expressions for the average trapping time (ATT), a quantitative indicator measuring the efficiency of the trapping process, by using two different methods, the results of which are consistent with each other. Furthermore, we analytically determine all the eigenvalues and their multiplicities for the fundamental matrix characterizing the dynamical process. Our results show that although next-nearest-neighbor jumps have no effect on the leading scaling of the trapping efficiency, they can strongly affect the prefactor of ATT, providing insight into better understanding of random-walk process in complex systems.

Scalable Nearest Neighbor Algorithms for High Dimensional Data.

Science.gov (United States)

Muja, Marius; Lowe, David G

2014-11-01

For many computer vision and machine learning problems, large training sets are key for good performance. However, the most computationally expensive part of many computer vision and machine learning algorithms consists of finding nearest neighbor matches to high dimensional vectors that represent the training data. We propose new algorithms for approximate nearest neighbor matching and evaluate and compare them with previous algorithms. For matching high dimensional features, we find two algorithms to be the most efficient: the randomized k-d forest and a new algorithm proposed in this paper, the priority search k-means tree. We also propose a new algorithm for matching binary features by searching multiple hierarchical clustering trees and show it outperforms methods typically used in the literature. We show that the optimal nearest neighbor algorithm and its parameters depend on the data set characteristics and describe an automated configuration procedure for finding the best algorithm to search a particular data set. In order to scale to very large data sets that would otherwise not fit in the memory of a single machine, we propose a distributed nearest neighbor matching framework that can be used with any of the algorithms described in the paper. All this research has been released as an open source library called fast library for approximate nearest neighbors (FLANN), which has been incorporated into OpenCV and is now one of the most popular libraries for nearest neighbor matching.

Lectures on the nearest neighbor method

CERN Document Server

Biau, Gérard

2015-01-01

This text presents a wide-ranging and rigorous overview of nearest neighbor methods, one of the most important paradigms in machine learning. Now in one self-contained volume, this book systematically covers key statistical, probabilistic, combinatorial and geometric ideas for understanding, analyzing and developing nearest neighbor methods. Gérard Biau is a professor at Université Pierre et Marie Curie (Paris). Luc Devroye is a professor at the School of Computer Science at McGill University (Montreal).   .

Dimensional testing for reverse k-nearest neighbor search

DEFF Research Database (Denmark)

Casanova, Guillaume; Englmeier, Elias; Houle, Michael E.

2017-01-01

Given a query object q, reverse k-nearest neighbor (RkNN) search aims to locate those objects of the database that have q among their k-nearest neighbors. In this paper, we propose an approximation method for solving RkNN queries, where the pruning operations and termination tests are guided...... by a characterization of the intrinsic dimensionality of the data. The method can accommodate any index structure supporting incremental (forward) nearest-neighbor search for the generation and verification of candidates, while avoiding impractically-high preprocessing costs. We also provide experimental evidence...

Performance modeling of neighbor discovery in proactive routing protocols

Directory of Open Access Journals (Sweden)

Andres Medina

2011-07-01

Full Text Available It is well known that neighbor discovery is a critical component of proactive routing protocols in wireless ad hoc networks. However there is no formal study on the performance of proposed neighbor discovery mechanisms. This paper provides a detailed model of key performance metrics of neighbor discovery algorithms, such as node degree and the distribution of the distance to symmetric neighbors. The model accounts for the dynamics of neighbor discovery as well as node density, mobility, radio and interference. The paper demonstrates a method for applying these models to the evaluation of global network metrics. In particular, it describes a model of network connectivity. Validation of the models shows that the degree estimate agrees, within 5% error, with simulations for the considered scenarios. The work presented in this paper serves as a basis for the performance evaluation of remaining performance metrics of routing protocols, vital for large scale deployment of ad hoc networks.

Synthesis of an oligonucleotide-derivatized amphipol and its use to trap and immobilize membrane proteins

DEFF Research Database (Denmark)

Bon, Christel Le; Della Pia, Eduardo Antonio; Giusti, Fabrice

2014-01-01

'OligAPol' have been investigated. Grafting was performed by reacting an ODN carrying an amine-terminated arm with the carboxylates of A8-35. The use of OligAPol for trapping MPs and immobilizing them onto solid supports was tested using bacteriorhodopsin (BR) and the transmembrane domain of Escherichia...... coli outer membrane protein A (tOmpA) as model proteins. BR and OligAPol form water-soluble complexes in which BR remains in its native conformation. Hybridization of the ODN arm with a complementary ODN was not hindered by the assembly of OligAPol into particles, nor by its association with BR. BR....../OligAPol and tOmpA/OligAPol complexes could be immobilized onto either magnetic beads or gold nanoparticles grafted with the complementary ODN, as shown by spectroscopic measurements, fluorescence microscopy and the binding of anti-BR and anti-tOmpA antibodies. OligAPols provide a novel, highly versatile...

Ligand binding turns moth pheromone-binding protein into a pH sensor: effect on the Antheraea polyphemus PBP1 conformation.

Science.gov (United States)

Katre, Uma V; Mazumder, Suman; Prusti, Rabi K; Mohanty, Smita

2009-11-13

In moths, pheromone-binding proteins (PBPs) are responsible for the transport of the hydrophobic pheromones to the membrane-bound receptors across the aqueous sensillar lymph. We report here that recombinant Antheraea polyphemus PBP1 (ApolPBP1) picks up hydrophobic molecule(s) endogenous to the Escherichia coli expression host that keeps the protein in the "open" (bound) conformation at high pH but switches to the "closed" (free) conformation at low pH. This finding has bearing on the solution structures of undelipidated lepidopteran moth PBPs determined thus far. Picking up a hydrophobic molecule from the host expression system could be a common feature for lipid-binding proteins. Thus, delipidation is critical for bacterially expressed lipid-binding proteins. We have shown for the first time that the delipidated ApolPBP1 exists primarily in the closed form at all pH levels. Thus, current views on the pH-induced conformational switch of PBPs hold true only for the ligand-bound open conformation of the protein. Binding of various ligands to delipidated ApolPBP1 studied by solution NMR revealed that the protein in the closed conformation switches to the open conformation only at or above pH 6.0 with a protein to ligand stoichiometry of approximately 1:1. Mutation of His(70) and His(95) to alanine drives the equilibrium toward the open conformation even at low pH for the ligand-bound protein by eliminating the histidine-dependent pH-induced conformational switch. Thus, the delipidated double mutant can bind ligand even at low pH in contrast to the wild type protein as revealed by fluorescence competitive displacement assay using 1-aminoanthracene and solution NMR.

Near Neighbor Distribution in Sets of Fractal Nature

Czech Academy of Sciences Publication Activity Database

Jiřina, Marcel

2013-01-01

Roč. 5, č. 1 (2013), s. 159-166 ISSN 2150-7988 R&D Projects: GA MŠk(CZ) LG12020 Institutional support: RVO:67985807 Keywords : nearest neighbor * fractal set * multifractal * Erlang distribution Subject RIV: BB - Applied Statistics, Operational Research http://www.mirlabs.org/ijcisim/regular_papers_2013/Paper91.pdf

First principle approach to correlation functions of spin-1/2 Heisenberg chain: fourth-neighbor correlators

International Nuclear Information System (INIS)

Boos, H.E.; Shiroishi, M.; Takahashi, M.

2005-01-01

We show how correlation functions of the spin-1/2 Heisenberg chain without magnetic field in the anti-ferromagnetic ground state can be explicitly calculated using information contained in the quantum Knizhnik-Zamolodchikov equation [qKZ]. We find several fundamental relations which the inhomogeneous correlations should fulfill. On the other hand, it turns out that these relations can fix the form of the correlations uniquely. Actually, applying this idea, we have obtained all the correlation functions on five sites. Particularly by taking the homogeneous limit, we have got the analytic form of the fourth-neighbor pair correlator j z S j+4 z >

Nearest Neighbor Search in the Metric Space of a Complex Network for Community Detection

Directory of Open Access Journals (Sweden)

Suman Saha

2016-03-01

Full Text Available The objective of this article is to bridge the gap between two important research directions: (1 nearest neighbor search, which is a fundamental computational tool for large data analysis; and (2 complex network analysis, which deals with large real graphs but is generally studied via graph theoretic analysis or spectral analysis. In this article, we have studied the nearest neighbor search problem in a complex network by the development of a suitable notion of nearness. The computation of efficient nearest neighbor search among the nodes of a complex network using the metric tree and locality sensitive hashing (LSH are also studied and experimented. For evaluation of the proposed nearest neighbor search in a complex network, we applied it to a network community detection problem. Experiments are performed to verify the usefulness of nearness measures for the complex networks, the role of metric tree and LSH to compute fast and approximate node nearness and the the efficiency of community detection using nearest neighbor search. We observed that nearest neighbor between network nodes is a very efficient tool to explore better the community structure of the real networks. Several efficient approximation schemes are very useful for large networks, which hardly made any degradation of results, whereas they save lot of computational times, and nearest neighbor based community detection approach is very competitive in terms of efficiency and time.

An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

Directory of Open Access Journals (Sweden)

Ling Liu

2009-03-01

Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

Association of food access and neighbor relationships with diet and underweight among community-dwelling older Japanese.

Science.gov (United States)

Nakamura, Hideko; Nakamura, Mieko; Okada, Eisaku; Ojima, Toshiyuki; Kondo, Katsunori

2017-11-01

Food access is important for maintaining dietary variety, which predicts underweight. The aim of this study was to examine the association of food access and neighbor relationships with eating and underweight. We analyzed cross-sectional data from 102,869 Japanese individuals aged 65 years or older. The perceived availability of food was assessed using the presence or absence of food stores within 1 km of the home. Level of relationships with neighbors was also assessed. The odds ratios (ORs) and 95% confidence intervals (CIs) for infrequent food intake and underweight were determined using logistic regression analysis. The proportion of men and women having low access to food was 25-30%. Having low food access (OR 1.18; 95% CI, 1.12-1.25 for men and OR 1.26; 95% CI, 1.19-1.33 for women) and a low level of relationship with neighbors (OR 1.38; 95% CI, 1.31-1.45 for men and OR 1.57; 95% CI, 1.48-1.67 for women) was associated with infrequent intake of fruits and vegetables in both sexes. Association between low food access and infrequent intake of fruits and vegetables was higher among men with low levels of neighbor relationship (OR 1.34; 95% CI, 1.23-1.46) than among men with high levels of relationship (OR 1.10; 95% CI, 1.03-1.18). Low perceived availability of food is a risk factor for low dietary variety among older people. Furthermore, high levels of relationship with neighbors may relieve the harmful effect of low food access. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

Neighbors United for Health

Science.gov (United States)

Westhoff, Wayne W.; Corvin, Jaime; Virella, Irmarie

2009-01-01

Modeled upon the ecclesiastic community group concept of Latin America to unite and strengthen the bond between the Church and neighborhoods, a community-based organization created Vecinos Unidos por la Salud (Neighbors United for Health) to bring health messages into urban Latino neighborhoods. The model is based on five tenants, and incorporates…

Pollinator-mediated interactions in experimental arrays vary with neighbor identity.

Science.gov (United States)

Ha, Melissa K; Ivey, Christopher T

2017-02-01

Local ecological conditions influence the impact of species interactions on evolution and community structure. We investigated whether pollinator-mediated interactions between coflowering plants vary with plant density, coflowering neighbor identity, and flowering season. We conducted a field experiment in which flowering time and floral neighborhood were manipulated in a factorial design. Early- and late-flowering Clarkia unguiculata plants were placed into arrays with C. biloba neighbors, noncongeneric neighbors, additional conspecific plants, or no additional plants as a density control. We compared whole-plant pollen limitation of seed set, pollinator behavior, and pollen deposition among treatments. Interactions mediated by shared pollinators depended on the identity of the neighbor and possibly changed through time, although flowering-season comparisons were compromised by low early-season plant survival. Interactions with conspecific neighbors were likely competitive late in the season. Interactions with C. biloba appeared to involve facilitation or neutral interactions. Interactions with noncongeners were more consistently competitive. The community composition of pollinators varied among treatment combinations. Pollinator-mediated interactions involved competition and likely facilitation, depending on coflowering neighbor. Experimental manipulation helped to reveal context-dependent variation in indirect biotic interactions. © 2017 Botanical Society of America.

The clinic as a good corporate neighbor.

Science.gov (United States)

Sass, Hans-Martin

2013-02-01

Clinics today specialize in health repair services similar to car repair shops; procedures and prices are standardized, regulated, and inflexibly uniform. Clinics of the future have to become Health Care Centers in order to be more respected and more effective corporate neighbors in offering outreach services in health education and preventive health care. The traditional concept of care for health is much broader than repair management and includes the promotion of lay health competence and responsibility in healthy social and natural environments. The corporate profile and ethics of the clinic as a good and competitive local neighbor will have to focus on [a] better personalized care, [b] education and services in preventive care, [c] direct or web-based information and advice for general, seasonal, or age related health risks, and on developing and improving trustworthy character traits of the clinic as a corporate person and a good neighbor.

Local biotic adaptation of trees and shrubs to plant neighbors

Science.gov (United States)

Grady, Kevin C.; Wood, Troy E.; Kolb, Thomas E.; Hersch-Green, Erika; Shuster, Stephen M.; Gehring, Catherine A.; Hart, Stephen C.; Allan, Gerard J.; Whitham, Thomas G.

2017-01-01

Natural selection as a result of plant–plant interactions can lead to local biotic adaptation. This may occur where species frequently interact and compete intensely for resources limiting growth, survival, and reproduction. Selection is demonstrated by comparing a genotype interacting with con- or hetero-specific sympatric neighbor genotypes with a shared site-level history (derived from the same source location), to the same genotype interacting with foreign neighbor genotypes (from different sources). Better genotype performance in sympatric than allopatric neighborhoods provides evidence of local biotic adaptation. This pattern might be explained by selection to avoid competition by shifting resource niches (differentiation) or by interactions benefitting one or more members (facilitation). We tested for local biotic adaptation among two riparian trees, Populus fremontii and Salix gooddingii, and the shrub Salix exigua by transplanting replicated genotypes from multiple source locations to a 17 000 tree common garden with sympatric and allopatric treatments along the Colorado River in California. Three major patterns were observed: 1) across species, 62 of 88 genotypes grew faster with sympatric neighbors than allopatric neighbors; 2) these growth rates, on an individual tree basis, were 44, 15 and 33% higher in sympatric than allopatric treatments for P. fremontii, S. exigua and S. gooddingii, respectively, and; 3) survivorship was higher in sympatric treatments for P. fremontiiand S. exigua. These results support the view that fitness of foundation species supporting diverse communities and dominating ecosystem processes is determined by adaptive interactions among multiple plant species with the outcome that performance depends on the genetic identity of plant neighbors. The occurrence of evolution in a plant-community context for trees and shrubs builds on ecological evolutionary research that has demonstrated co-evolution among herbaceous taxa, and

Org-1, the Drosophila ortholog of Tbx1, is a direct activator of known identity genes during muscle specification.

Science.gov (United States)

Schaub, Christoph; Nagaso, Hideyuki; Jin, Hong; Frasch, Manfred

2012-03-01

Members of the T-Box gene family of transcription factors are important players in regulatory circuits that generate myogenic and cardiogenic lineage diversities in vertebrates. We show that during somatic myogenesis in Drosophila, the single ortholog of vertebrate Tbx1, optomotor-blind-related-gene-1 (org-1), is expressed in a small subset of muscle progenitors, founder cells and adult muscle precursors, where it overlaps with the products of the muscle identity genes ladybird (lb) and slouch (slou). In addition, org-1 is expressed in the lineage of the heart-associated alary muscles. org-1 null mutant embryos lack Lb and Slou expression within the muscle lineages that normally co-express org-1. As a consequence, the respective muscle fibers and adult muscle precursors are either severely malformed or missing, as are the alary muscles. To address the mechanisms that mediate these regulatory interactions between Org-1, Lb and Slou, we characterized distinct enhancers associated with somatic muscle expression of lb and slou. We demonstrate that these lineage- and stage-specific cis-regulatory modules (CRMs) bind Org-1 in vivo, respond to org-1 genetically and require T-box domain binding sites for their activation. In summary, we propose that org-1 is a common and direct upstream regulator of slou and lb in the developmental pathway of these two neighboring muscle lineages. Cross-repression between slou and lb and combinatorial activation of lineage-specific targets by Org-1-Slou and Org-1-Lb, respectively, then leads to the distinction between the two lineages. These findings provide new insights into the regulatory circuits that control the proper pattering of the larval somatic musculature in Drosophila.

Diagnostic tools for nearest neighbors techniques when used with satellite imagery

Science.gov (United States)

Ronald E. McRoberts

2009-01-01

Nearest neighbors techniques are non-parametric approaches to multivariate prediction that are useful for predicting both continuous and categorical forest attribute variables. Although some assumptions underlying nearest neighbor techniques are common to other prediction techniques such as regression, other assumptions are unique to nearest neighbor techniques....

Microscopic theory of the nearest-neighbor valence bond sector of the spin-1/2 kagome antiferromagnet

Science.gov (United States)

Ralko, Arnaud; Mila, Frédéric; Rousochatzakis, Ioannis

2018-03-01

The spin-1/2 Heisenberg model on the kagome lattice, which is closely realized in layered Mott insulators such as ZnCu3(OH) 6Cl2 , is one of the oldest and most enigmatic spin-1/2 lattice models. While the numerical evidence has accumulated in favor of a quantum spin liquid, the debate is still open as to whether it is a Z2 spin liquid with very short-range correlations (some kind of resonating valence bond spin liquid), or an algebraic spin liquid with power-law correlations. To address this issue, we have pushed the program started by Rokhsar and Kivelson in their derivation of the effective quantum dimer model description of Heisenberg models to unprecedented accuracy for the spin-1/2 kagome, by including all the most important virtual singlet contributions on top of the orthogonalization of the nearest-neighbor valence bond singlet basis. Quite remarkably, the resulting picture is a competition between a Z2 spin liquid and a diamond valence bond crystal with a 12-site unit cell, as in the density-matrix renormalization group simulations of Yan et al. Furthermore, we found that, on cylinders of finite diameter d , there is a transition between the Z2 spin liquid at small d and the diamond valence bond crystal at large d , the prediction of the present microscopic description for the two-dimensional lattice. These results show that, if the ground state of the spin-1/2 kagome antiferromagnet can be described by nearest-neighbor singlet dimers, it is a diamond valence bond crystal, and, a contrario, that, if the system is a quantum spin liquid, it has to involve long-range singlets, consistent with the algebraic spin liquid scenario.

Unwanted Behaviors and Nuisance Behaviors Among Neighbors in a Belgian Community Sample.

Science.gov (United States)

Michaux, Emilie; Groenen, Anne; Uzieblo, Katarzyna

2015-06-30

Unwanted behaviors between (ex-)intimates have been extensively studied, while those behaviors within other contexts such as neighbors have received much less scientific consideration. Research indicates that residents are likely to encounter problem behaviors from their neighbors. Besides the lack of clarity in the conceptualization of problem behaviors among neighbors, little is known on which types of behaviors characterize neighbor problems. In this study, the occurrence of two types of problem behaviors encountered by neighbors was explored within a Belgian community sample: unwanted behaviors such as threats and neighbor nuisance issues such as noise nuisance. By clearly distinguishing those two types of behaviors, this study aimed at contributing to the conceptualization of neighbor problems. Next, the coping strategies used to deal with the neighbor problems were investigated. Our results indicated that unwanted behaviors were more frequently encountered by residents compared with nuisance problems. Four out of 10 respondents reported both unwanted pursuit behavior and nuisance problems. It was especially unlikely to encounter nuisance problems in isolation of unwanted pursuit behaviors. While different coping styles (avoiding the neighbor, confronting the neighbor, and enlisting help from others) were equally used by the stalked participants, none of them was perceived as being more effective in reducing the stalking behaviors. Strikingly, despite being aware of specialized help services such as community mediation services, only a very small subgroup enlisted this kind of professional help. © The Author(s) 2015.

Secure Nearest Neighbor Query on Crowd-Sensing Data

Directory of Open Access Journals (Sweden)

Ke Cheng

2016-09-01

Full Text Available Nearest neighbor queries are fundamental in location-based services, and secure nearest neighbor queries mainly focus on how to securely and quickly retrieve the nearest neighbor in the outsourced cloud server. However, the previous big data system structure has changed because of the crowd-sensing data. On the one hand, sensing data terminals as the data owner are numerous and mistrustful, while, on the other hand, in most cases, the terminals find it difficult to finish many safety operation due to computation and storage capability constraints. In light of they Multi Owners and Multi Users (MOMU situation in the crowd-sensing data cloud environment, this paper presents a secure nearest neighbor query scheme based on the proxy server architecture, which is constructed by protocols of secure two-party computation and secure Voronoi diagram algorithm. It not only preserves the data confidentiality and query privacy but also effectively resists the collusion between the cloud server and the data owners or users. Finally, extensive theoretical and experimental evaluations are presented to show that our proposed scheme achieves a superior balance between the security and query performance compared to other schemes.

Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

Directory of Open Access Journals (Sweden)

Qiang Zhang

Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

Two potential hookworm DAF-16 target genes, SNR-3 and LPP-1: gene structure, expression profile, and implications of a cis-regulatory element in the regulation of gene expression.

Science.gov (United States)

Gao, Xin; Goggin, Kevin; Dowling, Camille; Qian, Jason; Hawdon, John M

2015-01-08

Hookworms infect nearly 700 million people, causing anemia and developmental stunting in heavy infections. Little is known about the genomic structure or gene regulation in hookworms, although recent publication of draft genome assemblies has allowed the first investigations of these topics to be undertaken. The transcription factor DAF-16 mediates multiple developmental pathways in the free living nematode Caenorhabditis elegans, and is involved in the recovery from the developmentally arrested L3 in hookworms. Identification of downstream targets of DAF-16 will provide a better understanding of the molecular mechanism of hookworm infection. Genomic Fragment 2.23 containing a DAF-16 binding element (DBE) was used to identify overlapping complementary expressed sequence tags (ESTs). These sequences were used to search a draft assembly of the Ancylostoma caninum genome, and identified two neighboring genes, snr-3 and lpp-1, in a tail-to-tail orientation. Expression patterns of both genes during parasitic development were determined by qRT-PCR. DAF-16 dependent cis-regulatory activity of fragment 2.23 was investigated using an in vitro reporter system. The snr-3 gene spans approximately 5.6 kb in the genome and contains 3 exons and 2 introns, and contains the DBE in its 3' untranslated region. Downstream from snr-3 in a tail-to-tail arrangement is the gene lpp-1. The lpp-1 gene spans more than 6 kb and contains 10 exons and 9 introns. The A. caninum genome contains 2 apparent splice variants, but there are 7 splice variants in the A. ceylanicum genome. While the gene order is similar, the gene structures of the hookworm genes differ from their C. elegans orthologs. Both genes show peak expression in the late L4 stage. Using a cell culture based expression system, fragment 2.23 was found to have both DAF-16-dependent promoter and enhancer activity that required an intact DBE. Two putative DAF-16 targets were identified by genome wide screening for DAF-16 binding

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

Directory of Open Access Journals (Sweden)

Ye Zhi-Qiang

2011-08-01

Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

Amphipols from A to Z

DEFF Research Database (Denmark)

Popot, J-L; Althoff, T; Bagnard, D

2011-01-01

of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols...

Symmetric Link Key Management for Secure Neighbor Discovery in a Decentralized Wireless Sensor Network

Science.gov (United States)

2017-09-01

KEY MANAGEMENT FOR SECURE NEIGHBOR DISCOVERY IN A DECENTRALIZED WIRELESS SENSOR NETWORK by Kelvin T. Chew September 2017 Thesis Advisor...and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT...DATE September 2017 3. REPORT TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE SYMMETRIC LINK KEY MANAGEMENT FOR SECURE NEIGHBOR

Adenovirus-Mediated Delivery of Catalase to Retinal Pigment Epithelial Cells Protects Neighboring Photoreceptors from Photo-Oxidative Stress

OpenAIRE

Rex, T.S.; Tsui, I.; Hahn, P.; Maguire, A.M.; Duan, D.; Bennett, J.; Dunaief, J.L.

2004-01-01

Oxidative stress is involved in the pathogenesis of many diseases. Overexpression of antioxidant enzymes by gene therapy may protect tissues from oxidative damage. Because the reactive oxygen species hydrogen peroxide can diffuse across cell membranes, we hypothesized that overexpression of the antioxidant catalase within certain cells might protect neighboring cells. To test this hypothesis, we transduced retinal pigment epithelial (RPE) cells in vitro and in vivo with adenovirus carrying th...

A Novel Preferential Diffusion Recommendation Algorithm Based on User’s Nearest Neighbors

Directory of Open Access Journals (Sweden)

Fuguo Zhang

2017-01-01

Full Text Available Recommender system is a very efficient way to deal with the problem of information overload for online users. In recent years, network based recommendation algorithms have demonstrated much better performance than the standard collaborative filtering methods. However, most of network based algorithms do not give a high enough weight to the influence of the target user’s nearest neighbors in the resource diffusion process, while a user or an object with high degree will obtain larger influence in the standard mass diffusion algorithm. In this paper, we propose a novel preferential diffusion recommendation algorithm considering the significance of the target user’s nearest neighbors and evaluate it in the three real-world data sets: MovieLens 100k, MovieLens 1M, and Epinions. Experiments results demonstrate that the novel preferential diffusion recommendation algorithm based on user’s nearest neighbors can significantly improve the recommendation accuracy and diversity.

Color and neighbor edge directional difference feature for image retrieval

Institute of Scientific and Technical Information of China (English)

Chaobing Huang; Shengsheng Yu; Jingli Zhou; Hongwei Lu

2005-01-01

@@ A novel image feature termed neighbor edge directional difference unit histogram is proposed, in which the neighbor edge directional difference unit is defined and computed for every pixel in the image, and is used to generate the neighbor edge directional difference unit histogram. This histogram and color histogram are used as feature indexes to retrieve color image. The feature is invariant to image scaling and translation and has more powerful descriptive for the natural color images. Experimental results show that the feature can achieve better retrieval performance than other color-spatial features.

Nearest neighbors by neighborhood counting.

Science.gov (United States)

Wang, Hui

2006-06-01

Finding nearest neighbors is a general idea that underlies many artificial intelligence tasks, including machine learning, data mining, natural language understanding, and information retrieval. This idea is explicitly used in the k-nearest neighbors algorithm (kNN), a popular classification method. In this paper, this idea is adopted in the development of a general methodology, neighborhood counting, for devising similarity functions. We turn our focus from neighbors to neighborhoods, a region in the data space covering the data point in question. To measure the similarity between two data points, we consider all neighborhoods that cover both data points. We propose to use the number of such neighborhoods as a measure of similarity. Neighborhood can be defined for different types of data in different ways. Here, we consider one definition of neighborhood for multivariate data and derive a formula for such similarity, called neighborhood counting measure or NCM. NCM was tested experimentally in the framework of kNN. Experiments show that NCM is generally comparable to VDM and its variants, the state-of-the-art distance functions for multivariate data, and, at the same time, is consistently better for relatively large k values. Additionally, NCM consistently outperforms HEOM (a mixture of Euclidean and Hamming distances), the "standard" and most widely used distance function for multivariate data. NCM has a computational complexity in the same order as the standard Euclidean distance function and NCM is task independent and works for numerical and categorical data in a conceptually uniform way. The neighborhood counting methodology is proven sound for multivariate data experimentally. We hope it will work for other types of data.

Local randomization in neighbor selection improves PRM roadmap quality

KAUST Repository

McMahon, Troy; Jacobs, Sam; Boyd, Bryan; Tapia, Lydia; Amato, Nancy M.

2012-01-01

Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K'), that first computes the K' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

Local randomization in neighbor selection improves PRM roadmap quality

KAUST Repository

McMahon, Troy

2012-10-01

Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K\\'), that first computes the K\\' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K\\'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

The Islands Approach to Nearest Neighbor Querying in Spatial Networks

DEFF Research Database (Denmark)

Huang, Xuegang; Jensen, Christian Søndergaard; Saltenis, Simonas

2005-01-01

, and versatile approach to k nearest neighbor computation that obviates the need for using several k nearest neighbor approaches for supporting a single service scenario. The experimental comparison with the existing techniques uses real-world road network data and considers both I/O and CPU performance...

Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

2007-12-20

Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved after the transfer.Conclusions: Our results highlight the rapid evolution of niche-specificgene regulation in bacteria.

Handling Neighbor Discovery and Rendezvous Consistency with Weighted Quorum-Based Approach.

Science.gov (United States)

Own, Chung-Ming; Meng, Zhaopeng; Liu, Kehan

2015-09-03

Neighbor discovery and the power of sensors play an important role in the formation of Wireless Sensor Networks (WSNs) and mobile networks. Many asynchronous protocols based on wake-up time scheduling have been proposed to enable neighbor discovery among neighboring nodes for the energy saving, especially in the difficulty of clock synchronization. However, existing researches are divided two parts with the neighbor-discovery methods, one is the quorum-based protocols and the other is co-primality based protocols. Their distinction is on the arrangements of time slots, the former uses the quorums in the matrix, the latter adopts the numerical analysis. In our study, we propose the weighted heuristic quorum system (WQS), which is based on the quorum algorithm to eliminate redundant paths of active slots. We demonstrate the specification of our system: fewer active slots are required, the referring rate is balanced, and remaining power is considered particularly when a device maintains rendezvous with discovered neighbors. The evaluation results showed that our proposed method can effectively reschedule the active slots and save the computing time of the network system.

Handling Neighbor Discovery and Rendezvous Consistency with Weighted Quorum-Based Approach

Directory of Open Access Journals (Sweden)

Chung-Ming Own

2015-09-01

Full Text Available Neighbor discovery and the power of sensors play an important role in the formation of Wireless Sensor Networks (WSNs and mobile networks. Many asynchronous protocols based on wake-up time scheduling have been proposed to enable neighbor discovery among neighboring nodes for the energy saving, especially in the difficulty of clock synchronization. However, existing researches are divided two parts with the neighbor-discovery methods, one is the quorum-based protocols and the other is co-primality based protocols. Their distinction is on the arrangements of time slots, the former uses the quorums in the matrix, the latter adopts the numerical analysis. In our study, we propose the weighted heuristic quorum system (WQS, which is based on the quorum algorithm to eliminate redundant paths of active slots. We demonstrate the specification of our system: fewer active slots are required, the referring rate is balanced, and remaining power is considered particularly when a device maintains rendezvous with discovered neighbors. The evaluation results showed that our proposed method can effectively reschedule the active slots and save the computing time of the network system.

Accelerating distributed average consensus by exploring the information of second-order neighbors

Energy Technology Data Exchange (ETDEWEB)

Yuan Deming [School of Automation, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu (China); Xu Shengyuan, E-mail: syxu02@yahoo.com.c [School of Automation, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu (China); Zhao Huanyu [School of Automation, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu (China); Chu Yuming [Department of Mathematics, Huzhou Teacher' s College, Huzhou 313000, Zhejiang (China)

2010-05-17

The problem of accelerating distributed average consensus by using the information of second-order neighbors in both the discrete- and continuous-time cases is addressed in this Letter. In both two cases, when the information of second-order neighbors is used in each iteration, the network will converge with a speed faster than the algorithm only using the information of first-order neighbors. Moreover, the problem of using partial information of second-order neighbors is considered, and the edges are not chosen randomly from second-order neighbors. In the continuous-time case, the edges are chosen by solving a convex optimization problem which is formed by using the convex relaxation method. In the discrete-time case, for small network the edges are chosen optimally via the brute force method. Finally, simulation examples are provided to demonstrate the effectiveness of the proposed algorithm.

Finger vein identification using fuzzy-based k-nearest centroid neighbor classifier

Science.gov (United States)

Rosdi, Bakhtiar Affendi; Jaafar, Haryati; Ramli, Dzati Athiar

2015-02-01

In this paper, a new approach for personal identification using finger vein image is presented. Finger vein is an emerging type of biometrics that attracts attention of researchers in biometrics area. As compared to other biometric traits such as face, fingerprint and iris, finger vein is more secured and hard to counterfeit since the features are inside the human body. So far, most of the researchers focus on how to extract robust features from the captured vein images. Not much research was conducted on the classification of the extracted features. In this paper, a new classifier called fuzzy-based k-nearest centroid neighbor (FkNCN) is applied to classify the finger vein image. The proposed FkNCN employs a surrounding rule to obtain the k-nearest centroid neighbors based on the spatial distributions of the training images and their distance to the test image. Then, the fuzzy membership function is utilized to assign the test image to the class which is frequently represented by the k-nearest centroid neighbors. Experimental evaluation using our own database which was collected from 492 fingers shows that the proposed FkNCN has better performance than the k-nearest neighbor, k-nearest-centroid neighbor and fuzzy-based-k-nearest neighbor classifiers. This shows that the proposed classifier is able to identify the finger vein image effectively.

On Competitiveness of Nearest-Neighbor-Based Music Classification: A Methodological Critique

DEFF Research Database (Denmark)

Pálmason, Haukur; Jónsson, Björn Thór; Amsaleg, Laurent

2017-01-01

The traditional role of nearest-neighbor classification in music classification research is that of a straw man opponent for the learning approach of the hour. Recent work in high-dimensional indexing has shown that approximate nearest-neighbor algorithms are extremely scalable, yielding results...... of reasonable quality from billions of high-dimensional features. With such efficient large-scale classifiers, the traditional music classification methodology of aggregating and compressing the audio features is incorrect; instead the approximate nearest-neighbor classifier should be given an extensive data...... collection to work with. We present a case study, using a well-known MIR classification benchmark with well-known music features, which shows that a simple nearest-neighbor classifier performs very competitively when given ample data. In this position paper, we therefore argue that nearest...

Beyond formal groups: neighboring acts and watershed protection in Appalachia

Directory of Open Access Journals (Sweden)

Heather Lukacs

2016-09-01

Full Text Available This paper explores how watershed organizations in Appalachia have persisted in addressing water quality issues in areas with a history of coal mining. We identified two watershed groups that have taken responsibility for restoring local creeks that were previously highly degraded and sporadically managed. These watershed groups represent cases of self-organized commons governance in resource-rich, economically poor Appalachian communities. We describe the extent and characteristics of links between watershed group volunteers and watershed residents who are not group members. Through surveys, participant observation, and key-informant consultation, we found that neighbors – group members as well as non-group-members – supported the group's function through informal neighboring acts. Past research has shown that local commons governance institutions benefit from being nested in supportive external structures. We found that the persistence and success of community watershed organizations depends on the informal participation of local residents, affirming the necessity of looking beyond formal, organized groups to understand the resources, expertise, and information needed to address complex water pollution at the watershed level. Our findings augment the concept of nestedness in commons governance to include that of a formal organization acting as a neighbor that exchanges informal neighboring acts with local residents. In this way, we extend the concept of neighboring to include interactions between individuals and a group operating in the same geographic area.

Effect of Genetic African Ancestry on eGFR and Kidney Disease

Science.gov (United States)

Nadkarni, Girish N.; Belbin, Gillian; Lotay, Vaneet; Wyatt, Christina; Gottesman, Omri; Bottinger, Erwin P.; Kenny, Eimear E.; Peter, Inga

2015-01-01

Self-reported ancestry, genetically determined ancestry, and APOL1 polymorphisms are associated with variation in kidney function and related disease risk, but the relative importance of these factors remains unclear. We estimated the global proportion of African ancestry for 9048 individuals at Mount Sinai Medical Center in Manhattan (3189 African Americans, 1721 European Americans, and 4138 Hispanic/Latino Americans by self-report) using genome-wide genotype data. CKD-EPI eGFR and genotypes of three APOL1 coding variants were available. In admixed African Americans and Hispanic/Latino Americans, serum creatinine values increased as African ancestry increased (per 10% increase in African ancestry, creatinine values increased 1% in African Americans and 0.9% in Hispanic/Latino Americans; P≤1x10−7). eGFR was likewise significantly associated with African genetic ancestry in both populations. In contrast, APOL1 risk haplotypes were significantly associated with CKD, eGFRblack on the basis of ≥50% African ancestry resulted in higher eGFR for 14.7% of Hispanic/Latino Americans and lower eGFR for 4.1% of African Americans, affecting CKD staging in 4.3% and 1% of participants, respectively. Reclassified individuals had electrolyte values consistent with their newly assigned CKD stage. In summary, proportion of African ancestry was significantly associated with normal-range creatinine and eGFR, whereas APOL1 risk haplotypes drove the associations with CKD. Recalculation of eGFR on the basis of genetic ancestry affected CKD staging and warrants additional investigation. PMID:25349204

Plant neighbor identity influences plant biochemistry and physiology related to defense.

Science.gov (United States)

Broz, Amanda K; Broeckling, Corey D; De-la-Peña, Clelia; Lewis, Matthew R; Greene, Erick; Callaway, Ragan M; Sumner, Lloyd W; Vivanco, Jorge M

2010-06-17

Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors. In the greenhouse, C. maculosa individuals were paired with either conspecific (C. maculosa) or heterospecific (Festuca idahoensis) plant neighbors and elicited with the plant defense signaling molecule methyl jasmonate to mimic insect herbivory. We found that elicited C. maculosa plants grown with conspecific neighbors exhibited increased levels of total phenolics, whereas those grown with heterospecific neighbors allocated more resources towards growth. To further investigate these results in the field, we conducted a metabolomics analysis to explore chemical differences between individuals of C. maculosa growing in naturally occurring conspecific and heterospecific field stands. Similar to the greenhouse results, C. maculosa individuals accumulated higher levels of defense-related secondary metabolites and lower levels of primary metabolites when growing in conspecific versus heterospecific field stands. Leaf herbivory was similar in both stand types; however, a separate field study positively correlated specialist herbivore load with higher densities of C. maculosa conspecifics. Our results suggest that an individual C. maculosa plant can change its defensive strategy based on the identity of its plant neighbors. This is likely to have important consequences for individual and community success.

Dimensionality reduction with unsupervised nearest neighbors

CERN Document Server

Kramer, Oliver

2013-01-01

This book is devoted to a novel approach for dimensionality reduction based on the famous nearest neighbor method that is a powerful classification and regression approach. It starts with an introduction to machine learning concepts and a real-world application from the energy domain. Then, unsupervised nearest neighbors (UNN) is introduced as efficient iterative method for dimensionality reduction. Various UNN models are developed step by step, reaching from a simple iterative strategy for discrete latent spaces to a stochastic kernel-based algorithm for learning submanifolds with independent parameterizations. Extensions that allow the embedding of incomplete and noisy patterns are introduced. Various optimization approaches are compared, from evolutionary to swarm-based heuristics. Experimental comparisons to related methodologies taking into account artificial test data sets and also real-world data demonstrate the behavior of UNN in practical scenarios. The book contains numerous color figures to illustr...

Does a pear growl? Interference from semantic properties of orthographic neighbors.

Science.gov (United States)

Pecher, Diane; de Rooij, Jimmy; Zeelenberg, René

2009-07-01

In this study, we investigated whether semantic properties of a word's orthographic neighbors are activated during visual word recognition. In two experiments, words were presented with a property that was not true for the word itself. We manipulated whether the property was true for an orthographic neighbor of the word. Our results showed that rejection of the property was slower and less accurate when the property was true for a neighbor than when the property was not true for a neighbor. These findings indicate that semantic information is activated before orthographic processing is finished. The present results are problematic for the links model (Forster, 2006; Forster & Hector, 2002) that was recently proposed in order to bring form-first models of visual word recognition into line with previously reported findings (Forster & Hector, 2002; Pecher, Zeelenberg, & Wagenmakers, 2005; Rodd, 2004).

The Petunia GRAS Transcription Factor ATA/RAM1 Regulates Symbiotic Gene Expression and Fungal Morphogenesis in Arbuscular Mycorrhiza.

Science.gov (United States)

Rich, Mélanie K; Schorderet, Martine; Bapaume, Laure; Falquet, Laurent; Morel, Patrice; Vandenbussche, Michiel; Reinhardt, Didier

2015-07-01

Arbuscular mycorrhiza (AM) is a mutual symbiosis that involves a complex symbiotic interface over which nutrients are exchanged between the plant host and the AM fungus. Dozens of genes in the host are required for the establishment and functioning of the interaction, among them nutrient transporters that mediate the uptake of mineral nutrients delivered by the fungal arbuscules. We have isolated in a genetic mutant screen a petunia (Petunia hybrida) Gibberellic Acid Insensitive, Repressor of Gibberellic Acid Insensitive, and Scarecrow (GRAS)-type transcription factor, Atypical Arbuscule (ATA), that acts as the central regulator of AM-related genes and is required for the morphogenesis of arbuscules. Forced mycorrhizal inoculations from neighboring wild-type plants revealed an additional role of ATA in restricting mycorrhizal colonization of the root meristem. The lack of ATA, which represents the ortholog of Required For Arbuscular Mycorrhiza1 in Medicago truncatula, renders the interaction completely ineffective, hence demonstrating the central role of AM-related genes for arbuscule development and function. © 2015 American Society of Plant Biologists. All Rights Reserved.

Detect thy neighbor: Identity recognition at the root level in plants

NARCIS (Netherlands)

Chen, B.J.W.; During, H.J.; Anten, N.P.R.

2012-01-01

Some plant species increase root allocation at the expense of reproduction in the presence of non-self and non-kin neighbors, indicating the capacity of neighbor-identityrecognition at the rootlevel. Yet in spite of the potential consequences of rootidentityrecognition for the relationship between

Tricriticality in the q-neighbor Ising model on a partially duplex clique.

Science.gov (United States)

Chmiel, Anna; Sienkiewicz, Julian; Sznajd-Weron, Katarzyna

2017-12-01

We analyze a modified kinetic Ising model, a so-called q-neighbor Ising model, with Metropolis dynamics [Phys. Rev. E 92, 052105 (2015)PLEEE81539-375510.1103/PhysRevE.92.052105] on a duplex clique and a partially duplex clique. In the q-neighbor Ising model each spin interacts only with q spins randomly chosen from its whole neighborhood. In the case of a duplex clique the change of a spin is allowed only if both levels simultaneously induce this change. Due to the mean-field-like nature of the model we are able to derive the analytic form of transition probabilities and solve the corresponding master equation. The existence of the second level changes dramatically the character of the phase transition. In the case of the monoplex clique, the q-neighbor Ising model exhibits a continuous phase transition for q=3, discontinuous phase transition for q≥4, and for q=1 and q=2 the phase transition is not observed. On the other hand, in the case of the duplex clique continuous phase transitions are observed for all values of q, even for q=1 and q=2. Subsequently we introduce a partially duplex clique, parametrized by r∈[0,1], which allows us to tune the network from monoplex (r=0) to duplex (r=1). Such a generalized topology, in which a fraction r of all nodes appear on both levels, allows us to obtain the critical value of r=r^{*}(q) at which a tricriticality (switch from continuous to discontinuous phase transition) appears.

Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

Science.gov (United States)

Hubert, Nathaniel A; Gehring, Catherine A

2008-09-01

Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

Reduction in predator defense in the presence of neighbors in a colonial fish.

Directory of Open Access Journals (Sweden)

Franziska C Schädelin

Full Text Available Predation pressure has long been considered a leading explanation of colonies, where close neighbors may reduce predation via dilution, alarming or group predator attacks. Attacking predators may be costly in terms of energy and survival, leading to the question of how neighbors contribute to predator deterrence in relationship to each other. Two hypotheses explaining the relative efforts made by neighbors are byproduct-mutualism, which occurs when breeders inadvertently attack predators by defending their nests, and reciprocity, which occurs when breeders deliberately exchange predator defense efforts with neighbors. Most studies investigating group nest defense have been performed with birds. However, colonial fish may constitute a more practical model system for an experimental approach because of the greater ability of researchers to manipulate their environment. We investigated in the colonial fish, Neolamprologus caudopunctatus, whether prospecting pairs preferred to breed near conspecifics or solitarily, and how breeders invested in anti-predator defense in relation to neighbors. In a simple choice test, prospecting pairs selected breeding sites close to neighbors versus a solitary site. Predators were then sequentially presented to the newly established test pairs, the previously established stimulus pairs or in between the two pairs. Test pairs attacked the predator eight times more frequently when they were presented on their non-neighbor side compared to between the two breeding sites, where stimulus pairs maintained high attack rates. Thus, by joining an established pair, test pairs were able to reduce their anti-predator efforts near neighbors, at no apparent cost to the stimulus pairs. These findings are unlikely to be explained by reciprocity or byproduct-mutualism. Our results instead suggest a commensal relationship in which new pairs exploit the high anti-predator efforts of established pairs, which invest similarly with or

Seismic clusters analysis in Northeastern Italy by the nearest-neighbor approach

Science.gov (United States)

Peresan, Antonella; Gentili, Stefania

2018-01-01

The main features of earthquake clusters in Northeastern Italy are explored, with the aim to get new insights on local scale patterns of seismicity in the area. The study is based on a systematic analysis of robustly and uniformly detected seismic clusters, which are identified by a statistical method, based on nearest-neighbor distances of events in the space-time-energy domain. The method permits us to highlight and investigate the internal structure of earthquake sequences, and to differentiate the spatial properties of seismicity according to the different topological features of the clusters structure. To analyze seismicity of Northeastern Italy, we use information from local OGS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. A preliminary reappraisal of the earthquake bulletins is carried out and the area of sufficient completeness is outlined. Various techniques are considered to estimate the scaling parameters that characterize earthquakes occurrence in the region, namely the b-value and the fractal dimension of epicenters distribution, required for the application of the nearest-neighbor technique. Specifically, average robust estimates of the parameters of the Unified Scaling Law for Earthquakes, USLE, are assessed for the whole outlined region and are used to compute the nearest-neighbor distances. Clusters identification by the nearest-neighbor method turn out quite reliable and robust with respect to the minimum magnitude cutoff of the input catalog; the identified clusters are well consistent with those obtained from manual aftershocks identification of selected sequences. We demonstrate that the earthquake clusters have distinct preferred geographic locations, and we identify two areas that differ substantially in the examined clustering properties. Specifically, burst-like sequences are associated with the north-western part and swarm-like sequences with the south-eastern part of the study

Plant neighbor identity influences plant biochemistry and physiology related to defense

Directory of Open Access Journals (Sweden)

Callaway Ragan M

2010-06-01

Full Text Available Abstract Background Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors. Results In the greenhouse, C. maculosa individuals were paired with either conspecific (C. maculosa or heterospecific (Festuca idahoensis plant neighbors and elicited with the plant defense signaling molecule methyl jasmonate to mimic insect herbivory. We found that elicited C. maculosa plants grown with conspecific neighbors exhibited increased levels of total phenolics, whereas those grown with heterospecific neighbors allocated more resources towards growth. To further investigate these results in the field, we conducted a metabolomics analysis to explore chemical differences between individuals of C. maculosa growing in naturally occurring conspecific and heterospecific field stands. Similar to the greenhouse results, C. maculosa individuals accumulated higher levels of defense-related secondary metabolites and lower levels of primary metabolites when growing in conspecific versus heterospecific field stands. Leaf herbivory was similar in both stand types; however, a separate field study positively correlated specialist herbivore load with higher densities of C. maculosa conspecifics. Conclusions Our results suggest that an individual C. maculosa plant can change its defensive strategy based on the identity of its plant neighbors. This is likely to have important consequences for individual and community success.

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

Science.gov (United States)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

Effects of second neighbor interactions on skyrmion lattices in chiral magnets

International Nuclear Information System (INIS)

Oliveira, E A S; Silva, R L; Silva, R C; Pereira, A R

2017-01-01

In this paper we investigate the influences of the second neighbor interactions on a skyrmion lattice in two-dimensional chiral magnets. Such a system contains the exchange and the Dzyaloshinskii–Moriya for the spin interactions and therefore, we analyse three situations: firstly, the second neighbor interaction is present only in the exchange coupling; secondly, it is present only in the Dzyaloshinskii–Moriya coupling. Finally, the second neighbor interactions are present in both exchange and Dzyaloshinskii–Moriya couplings. We show that such effects cause important modifications to the helical and skyrmion phases when an external magnetic field is applied. (paper)

Improving Fraudster Detection in Online Auctions by Using Neighbor-Driven Attributes

Directory of Open Access Journals (Sweden)

Jun-Lin Lin

2015-12-01

Full Text Available Online auction websites use a simple reputation system to help their users to evaluate the trustworthiness of sellers and buyers. However, to improve their reputation in the reputation system, fraudulent users can easily deceive the reputation system by creating fake transactions. This inflated-reputation fraud poses a major problem for online auction websites because it can lead legitimate users into scams. Numerous approaches have been proposed in the literature to address this problem, most of which involve using social network analysis (SNA to derive critical features (e.g., k-core, center weight, and neighbor diversity for distinguishing fraudsters from legitimate users. This paper discusses the limitations of these SNA features and proposes a class of SNA features referred to as neighbor-driven attributes (NDAs. The NDAs of users are calculated from the features of their neighbors. Because fraudsters require collusive neighbors to provide them with positive ratings in the reputation system, using NDAs can be helpful for detecting fraudsters. Although the idea of NDAs is not entirely new, experimental results on a real-world dataset showed that using NDAs improves classification accuracy compared with state-of-the-art methods that use the k-core, center weight, and neighbor diversity.

Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model.

Directory of Open Access Journals (Sweden)

Daniel Ting

2010-04-01

Full Text Available Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes. These include: 1 input data size and criteria for structure inclusion (resolution, R-factor, etc.; 2 filtering of suspect conformations and outliers using B-factors or other features; 3 secondary structure of input data (e.g., whether helix and sheet are included; whether beta turns are included; 4 the method used for determining probability densities ranging from simple histograms to modern nonparametric density estimation; and 5 whether they include nearest neighbor effects on the distribution of conformations in different regions of the Ramachandran map. In this work, Ramachandran probability distributions are presented for residues in protein loops from a high-resolution data set with filtering based on calculated electron densities. Distributions for all 20 amino acids (with cis and trans proline treated separately have been determined, as well as 420 left-neighbor and 420 right-neighbor dependent distributions. The neighbor-independent and neighbor-dependent probability densities have been accurately estimated using Bayesian nonparametric statistical analysis based on the Dirichlet process. In particular, we used hierarchical Dirichlet process priors, which allow sharing of information between densities for a particular residue type and different neighbor residue types. The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp.

The nearest neighbor and the bayes error rates.

Science.gov (United States)

Loizou, G; Maybank, S J

1987-02-01

The (k, l) nearest neighbor method of pattern classification is compared to the Bayes method. If the two acceptance rates are equal then the asymptotic error rates satisfy the inequalities Ek,l + 1 ¿ E*(¿) ¿ Ek,l dE*(¿), where d is a function of k, l, and the number of pattern classes, and ¿ is the reject threshold for the Bayes method. An explicit expression for d is given which is optimal in the sense that for some probability distributions Ek,l and dE* (¿) are equal.

Incidence and Prevalence of Tuberculosis in Iran and Neighboring Countries

Directory of Open Access Journals (Sweden)

Arezoo Tavakoli

2017-07-01

Full Text Available Background Tuberculosis is one of the major public health concerns in many countries, however the available and effective treatment is known. Tuberculosis typically determined with socio-economic problems such as war, malnutrition and HIV prevalence. In Iran, many progresses are carried to control tuberculosis but, different factors such as immigration from neighboring countries are affective to tuberculosis infection. Objectives In this paper, the incidence and prevalence of tuberculosis is evaluated in different regions of Iran and neighboring countries. Methods The data are collected from different and valid sources such as Scopus, Pubmed and also many reports from world health organization (WHO and center of disease control and prevention (CDC for a period of 25 years (1990 - 2015 evaluated for Iran and neighboring countries. Results This study as a descriptive- analytical research is conducted cross- sectional among Iran and neighboring countries since 1990. The information is obtained from exact and valid informative data from web of sciences. The east and west border countries of Iran which are faced with war and immigration in Afghanistan, Pakistan and Iraq are source of tuberculosis infection that effect on tuberculosis prevalence in Iran. The data were analyzed by SPSS 22 and Excel 2013. Conclusions The incidence of tuberculosis in Iran has been decreased because of many controlling actions such as BCG vaccination, electronic reporting system for tuberculosis and free access to tuberculosis medication. Some of Iran neighboring countries such as Tajikistan and Pakistan have the highest incidence of tuberculosis which known as a challenge for tuberculosis control in Iran while Saudi Arabia and Turkey have the lowest incidence.

Neighboring Hetero-Atom Assistance of Sacrificial Amines to Hydrogen Evolution Using Pt-Loaded TiO2-Photocatalyst

Directory of Open Access Journals (Sweden)

Masahide Yasuda

2014-05-01

Full Text Available Photocatalytic H2 evolution was examined using Pt-loaded TiO2-photocatalyst in the presence of amines as sacrificial agents. In the case of amines with all of the carbon attached to the hetero-atom such as 2-aminoethanol, 1,2-diamonoethane, 2-amino-1,3-propanediol, and 3-amino-1,2-propanediol, they were completely decomposed into CO2 and water to quantitatively evolve H2. On the other hand, the amines with both hetero-atoms and one methyl group at the β-positions (neighboring carbons of amino group such as 2-amino-1-propanol and 1,2-diaminopropane were partially decomposed. Also, the photocatalytic H2 evolution using amines without the hetero-atoms at the β-positions such as ethylamine, propylamine, 1-butylamine, 1,3-diaminopropane, 2-propylamine, and 2-butylamine was inefficient. Thus, it was found that the neighboring hetero-atom strongly assisted the degradation of sacrificial amines. Moreover, rate constants for H2 evolution were compared among amines. In conclusion, the neighboring hetero-atom did not affect the rate constants but enhanced the yield of hydrogen evolution.

Cryptosporidiosis in Saudi Arabia and neighboring countries

International Nuclear Information System (INIS)

Areeshi, Mohammed Y.; Hart, C.A.; Beeching, N.J.

2007-01-01

Cryptosporidium is a coccidian protozoan parasite of the intestinal tract that causes severe and sometimes fatal watery diarrhea in immunocompromised patients and self-limiting but prolonged diarrheal disease in immunocompetent individuals. It exists naturally in animals and can be zoonotic. Although cryptosporidiosis is a significant cause of diarrheal disease in both developing and developed countries, it is more prevalent in developing countries and in tropical environments. We examined the epidemiology and disease burden of Cryptosporidium in Saudi Arabia and neighboring countries by reviewing 23 published studies of Cryptosporidium and etiology of diarrhea in between 1986 and 2006. The prevalence of Cryptosporidium infection in human's ranged from 1% to 37% with a median of 4%, while in animals it was for different species of animals and geographic locations of the studies. Most cases of cryptosporidiosis occurred among children less than 7 years of age and particularly in the first two years of life. The seasonality of Cryptosporidium varied depending on the geographic locations of the studies but it generally most prevalent in the rainy season. The most commonly identified species was Cryptosporidium parvum while C.hominis was detected only in one study from Kuwait. The cumulative experience from Saudi Arabia and four neighboring countries (Kuwait, Oman, Jordan and Iraq) suggest that Cryptosporidium is an important cause of diarrhea in human and cattle. However, the findings of this review also demonstrate the limitations of the available data regarding Cryptosporidium species and strains in circulation in these countries. (author)

Evidence for cultural differences between neighboring chimpanzee communities.

Science.gov (United States)

Luncz, Lydia V; Mundry, Roger; Boesch, Christophe

2012-05-22

The majority of evidence for cultural behavior in animals has come from comparisons between populations separated by large geographical distances that often inhabit different environments. The difficulty of excluding ecological and genetic variation as potential explanations for observed behaviors has led some researchers to challenge the idea of animal culture. Chimpanzees (Pan troglodytes verus) in the Taï National Park, Côte d'Ivoire, crack Coula edulis nuts using stone and wooden hammers and tree root anvils. In this study, we compare for the first time hammer selection for nut cracking across three neighboring chimpanzee communities that live in the same forest habitat, which reduces the likelihood of ecological variation. Furthermore, the study communities experience frequent dispersal of females at maturity, which eliminates significant genetic variation. We compared key ecological factors, such as hammer availability and nut hardness, between the three neighboring communities and found striking differences in group-specific hammer selection among communities despite similar ecological conditions. Differences were found in the selection of hammer material and hammer size in response to changes in nut resistance over time. Our findings highlight the subtleties of cultural differences in wild chimpanzees and illustrate how cultural knowledge is able to shape behavior, creating differences among neighboring social groups. Copyright © 2012 Elsevier Ltd. All rights reserved.

Knowing Our Neighbors: 2MASS 2306-0502 (TRAPPIST-1) Revisited

Science.gov (United States)

Bartlett, Jennifer Lynn; Lurie, John; Jao, W.-C.; Ianna, P. A.; Riedel, A.; Finch, C.; Winters, J.; Subasavage, J.; Henry, T.

2018-01-01

Obtaining a well-understood, volume-limited (and ultimately volume-complete) sample of stellar systems within 25 pc is essential for determining the stellar luminosity function, the mass-luminosity relationship, the stellar velocity distribution, and the stellar multiplicity fraction. Such a sample also provides insight into the local star formation history. Towards that end, Research Consortium On Nearby Stars (RECONS) measures trigonometric parallaxes to establish which systems truly lie within the 25-pc radius of the Solar Neighborhood. Recent observations with the CTIO/SMARTS 0.9-m telescope allow us to update the astrometry and VRI photometry for 2MASS J23062928-0502285 (TRAPPIST-1). Extrasolar planet searches by others detected 7 Earth-sized planets transiting this cool dwarf.Based on our 2004—2016 observations, we measure a parallax of 78.76 ± 1.04 mas with a proper motion of 1034.8 ± 0.3 mas/yr in 118.5○ ± 0.03○ for 2MASS 2306-0502. During this 12.2-year period, we did not detect any perturbations in the astrometric residuals. Because this parallax is independent of the earlier CTIOPI/SMARTS 1.5-m result, we calculate its weighted mean parallax to be 79.29 ± 0.96 mas (12.6 ± 0.2 pc), which is ~4% farther than the original distance. Our improved parallax implies its radii and that of its planets would be ~4% larger than previously reported.During our astrometric observations, 2MASS 2306-0502 demonstrated an overall photometric variability of 11.6 mmag in I-band, which is less than the 20-mmag limit for significant variability. Removing a July 2009 flaring event drops the mean variability to 8.2 mmag.Our VRI photometry indicates the brightness of 2MASS 2306-0502 is 18.75, 16.54, 14.10 mag, respectively, based on 3 nights.Even as we continue to look for new neighbors, we should also keep an eye on old friends.NSF grants AST 05-07711 and AST 09-08402, NASA-SIM, Georgia State University, the University of Virginia, Hampden-Sydney College, and the

A Classification Framework Applied to Cancer Gene Expression Profiles

Directory of Open Access Journals (Sweden)

Hussein Hijazi

2013-01-01

Full Text Available Classification of cancer based on gene expression has provided insight into possible treatment strategies. Thus, developing machine learning methods that can successfully distinguish among cancer subtypes or normal versus cancer samples is important. This work discusses supervised learning techniques that have been employed to classify cancers. Furthermore, a two-step feature selection method based on an attribute estimation method (e.g., ReliefF and a genetic algorithm was employed to find a set of genes that can best differentiate between cancer subtypes or normal versus cancer samples. The application of different classification methods (e.g., decision tree, k-nearest neighbor, support vector machine (SVM, bagging, and random forest on 5 cancer datasets shows that no classification method universally outperforms all the others. However, k-nearest neighbor and linear SVM generally improve the classification performance over other classifiers. Finally, incorporating diverse types of genomic data (e.g., protein-protein interaction data and gene expression increase the prediction accuracy as compared to using gene expression alone.

Robust gene network analysis reveals alteration of the STAT5a network as a hallmark of prostate cancer.

Science.gov (United States)

Reddy, Anupama; Huang, C Chris; Liu, Huiqing; Delisi, Charles; Nevalainen, Marja T; Szalma, Sandor; Bhanot, Gyan

2010-01-01

We develop a general method to identify gene networks from pair-wise correlations between genes in a microarray data set and apply it to a public prostate cancer gene expression data from 69 primary prostate tumors. We define the degree of a node as the number of genes significantly associated with the node and identify hub genes as those with the highest degree. The correlation network was pruned using transcription factor binding information in VisANT (http://visant.bu.edu/) as a biological filter. The reliability of hub genes was determined using a strict permutation test. Separate networks for normal prostate samples, and prostate cancer samples from African Americans (AA) and European Americans (EA) were generated and compared. We found that the same hubs control disease progression in AA and EA networks. Combining AA and EA samples, we generated networks for low low (cancer (e.g. possible turning on of oncogenes). (ii) Some hubs reduced their degree in the tumor network compared to their degree in the normal network, suggesting that these genes are associated with loss of regulatory control in cancer (e.g. possible loss of tumor suppressor genes). A striking result was that for both AA and EA tumor samples, STAT5a, CEBPB and EGR1 are major hubs that gain neighbors compared to the normal prostate network. Conversely, HIF-lα is a major hub that loses connections in the prostate cancer network compared to the normal prostate network. We also find that the degree of these hubs changes progressively from normal to low grade to high grade disease, suggesting that these hubs are master regulators of prostate cancer and marks disease progression. STAT5a was identified as a central hub, with ~120 neighbors in the prostate cancer network and only 81 neighbors in the normal prostate network. Of the 120 neighbors of STAT5a, 57 are known cancer related genes, known to be involved in functional pathways associated with tumorigenesis. Our method is general and can easily

The chromosomal organization of horizontal gene transfer in bacteria.

Science.gov (United States)

Oliveira, Pedro H; Touchon, Marie; Cury, Jean; Rocha, Eduardo P C

2017-10-10

Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

Transcriptional changes common to human cocaine, cannabis and phencyclidine abuse.

Directory of Open Access Journals (Sweden)

Elin Lehrmann

2006-12-01

Full Text Available A major goal of drug abuse research is to identify and understand drug-induced changes in brain function that are common to many or all drugs of abuse. As these may underlie drug dependence and addiction, the purpose of the present study was to examine if different drugs of abuse effect changes in gene expression that converge in common molecular pathways. Microarray analysis was employed to assay brain gene expression in postmortem anterior prefrontal cortex (aPFC from 42 human cocaine, cannabis and/or phencyclidine abuse cases and 30 control cases, which were characterized by toxicology and drug abuse history. Common transcriptional changes were demonstrated for a majority of drug abuse cases (N = 34, representing a number of consistently changed functional classes: Calmodulin-related transcripts (CALM1, CALM2, CAMK2B were decreased, while transcripts related to cholesterol biosynthesis and trafficking (FDFT1, APOL2, SCARB1, and Golgi/endoplasmic reticulum (ER functions (SEMA3B, GCC1 were all increased. Quantitative PCR validated decreases in calmodulin 2 (CALM2 mRNA and increases in apolipoprotein L, 2 (APOL2 and semaphorin 3B (SEMA3B mRNA for individual cases. A comparison between control cases with and without cardiovascular disease and elevated body mass index indicated that these changes were not due to general cellular and metabolic stress, but appeared specific to the use of drugs. Therefore, humans who abused cocaine, cannabis and/or phencyclidine share a decrease in transcription of calmodulin-related genes and increased transcription related to lipid/cholesterol and Golgi/ER function. These changes represent common molecular features of drug abuse, which may underlie changes in synaptic function and plasticity that could have important ramifications for decision-making capabilities in drug abusers.

Multiple k Nearest Neighbor Query Processing in Spatial Network Databases

DEFF Research Database (Denmark)

Xuegang, Huang; Jensen, Christian Søndergaard; Saltenis, Simonas

2006-01-01

This paper concerns the efficient processing of multiple k nearest neighbor queries in a road-network setting. The assumed setting covers a range of scenarios such as the one where a large population of mobile service users that are constrained to a road network issue nearest-neighbor queries...... for points of interest that are accessible via the road network. Given multiple k nearest neighbor queries, the paper proposes progressive techniques that selectively cache query results in main memory and subsequently reuse these for query processing. The paper initially proposes techniques for the case...... where an upper bound on k is known a priori and then extends the techniques to the case where this is not so. Based on empirical studies with real-world data, the paper offers insight into the circumstances under which the different proposed techniques can be used with advantage for multiple k nearest...

Improving Recommendations in Tag-based Systems with Spectral Clustering of Tag Neighbors

DEFF Research Database (Denmark)

Pan, Rong; Xu, Guandong; Dolog, Peter

2012-01-01

Tag as a useful metadata reflects the collaborative and conceptual features of documents in social collaborative annotation systems. In this paper, we propose a collaborative approach for expanding tag neighbors and investigate the spectral clustering algorithm to filter out noisy tag neighbors...... in order to get appropriate recommendation for users. The preliminary experiments have been conducted on MovieLens dataset to compare our proposed approach with the traditional collaborative filtering recommendation approach and naive tag neighbors expansion approach in terms of precision, and the result...... demonstrates that our approach could considerably improve the performance of recommendations....

The effect of near laterally and vertically neighboring quantum dots on the composition of uncapped InxGa1−xAs/GaAs quantum dots

International Nuclear Information System (INIS)

Donglin, Wang; Zhongyuan, Yu; Yumin, Liu; Han, Ye; Pengfei, Lu; Xiaotao, Guo; Long, Zhao; Xia, Xin

2010-01-01

The composition of quantum dots has a direct effect on the optical and electronic properties of quantum-dot-based devices. In this paper, we combine the method of moving asymptotes and finite element tools to compute the composition distribution by minimizing the Gibbs free energy of quantum dots, and use this method to study the effect of near laterally and vertically neighboring quantum dots on the composition distribution. The simulation results indicate that the effect from the laterally neighboring quantum dot is very small, and the vertically neighboring quantum dot can significantly influence the composition by the coupled strain field

Dynamical correlation functions of the S=1/2 nearest-neighbor and Haldane-Shastry Heisenberg antiferromagnetic chains in zero and applied fields

DEFF Research Database (Denmark)

Lefmann, K.; Rischel, C.

1996-01-01

We present a numerical diagonalization study of two one-dimensional S=1/2 antiferromagnetic Heisenberg chains, having nearest-neighbor and Haldane-Shastry (1/r(2)) interactions, respectively. We have obtained the T=0 dynamical correlation function, S-alpha alpha(q,omega), for chains of length N=8......-28. We have studied S-zz(q,omega) for the Heisenberg chain in zero field, and from finite-size scaling we have obtained a limiting behavior that for large omega deviates from the conjecture proposed earlier by Muller ct al. For both chains we describe the behavior of S-zz(q,omega) and S...

Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species

Directory of Open Access Journals (Sweden)

Stone Joshua K

2012-11-01

Full Text Available Abstract Background Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS as a potential vaccine target because it is known as one of the most important antigenic epitopes in B. pseudomallei. Complicating this strategy are the four different B. pseudomallei LPS O-antigen types: A, B, B2, and rough. Sero-crossreactivity is common among O-antigens of Burkholderia species. Here, we identified the presence of multiple B. pseudomallei O-antigen types and sero-crossreactivity in its near-neighbor species. Results PCR screening of O-antigen biosynthesis genes, phenotypic characterization using SDS-PAGE, and immunoblot analysis showed that majority of B. mallei and B. thailandensis strains contained the typical O-antigen type A. In contrast, most of B. ubonensis and B. thailandensis-like strains expressed the atypical O-antigen types B and B2, respectively. Most B. oklahomensis strains expressed a distinct and non-seroreactive O-antigen type, except strain E0147 which expressed O-antigen type A. O-antigen type B2 was also detected in B. thailandensis 82172, B. ubonensis MSMB108, and Burkholderia sp. MSMB175. Interestingly, B. thailandensis-like MSMB43 contained a novel serotype B positive O-antigen. Conclusions This study expands the number of species which express B. pseudomallei O-antigen types. Further work is required to elucidate the full structures and how closely these are to the B. pseudomallei O-antigens, which will ultimately determine the efficacy of the near-neighbor B serotypes for vaccine development.

Working with Family, Friend, and Neighbor Caregivers: Lessons from Four Diverse Communities

Science.gov (United States)

Powell, Douglas R.

2011-01-01

This article is excerpted from "Who's Watching the Babies? Improving the Quality of Family, Friend, and Neighbor Care" by Douglas R. Powell ("ZERO TO THREE," 2008). The article explores questions about program development and implementation strategies for supporting Family, Friend, and Neighbor (FFN) caregivers: How do programs and their host…

Dual-therapeutic reporter genes fusion for enhanced cancer gene therapy and imaging.

Science.gov (United States)

Sekar, T V; Foygel, K; Willmann, J K; Paulmurugan, R

2013-05-01

Two of the successful gene-directed enzyme prodrug therapies include herpes simplex virus-thymidine kinase (HSV1-TK) enzyme-ganciclovir prodrug and the Escherichia coli nitroreductase (NTR) enzyme-CB1954 prodrug strategies; these enzyme-prodrug combinations produce activated cytotoxic metabolites of the prodrugs capable of tumor cell death by inhibiting DNA synthesis and killing quiescent cells, respectively. Both these strategies also affect significant bystander cell killing of neighboring tumor cells that do not express these enzymes. We have developed a dual-combination gene strategy, where we identified HSV1-TK and NTR fused in a particular orientation can effectively kill tumor cells when the tumor cells are treated with a fusion HSV1-TK-NTR gene- along with a prodrug combination of GCV and CB1954. In order to determine whether the dual-system demonstrate superior therapeutic efficacy than either HSV1-TK or NTR systems alone, we conducted both in vitro and in vivo tumor xenograft studies using triple negative SUM159 breast cancer cells, by evaluating the efficacy of cell death by apoptosis and necrosis upon treatment with the dual HSV1-TK genes-GCV-CB1954 prodrugs system, and compared the efficiency to HSV1-TK-GCV and NTR-CB1954. Our cell-based studies, tumor regression studies in xenograft mice, histological analyses of treated tumors and bystander studies indicate that the dual HSV1-TK-NTR-prodrug system is two times more efficient even with half the doses of both prodrugs than the respective single gene-prodrug system, as evidenced by enhanced apoptosis and necrosis of tumor cells in vitro in culture and xenograft of tumor tissues in animals.

The Application of Determining Students’ Graduation Status of STMIK Palangkaraya Using K-Nearest Neighbors Method

Science.gov (United States)

Rusdiana, Lili; Marfuah

2017-12-01

K-Nearest Neighbors method is one of methods used for classification which calculate a value to find out the closest in distance. It is used to group a set of data such as students’ graduation status that are got from the amount of course credits taken by them, the grade point average (AVG), and the mini-thesis grade. The study is conducted to know the results of using K-Nearest Neighbors method on the application of determining students’ graduation status, so it can be analyzed from the method used, the data, and the application constructed. The aim of this study is to find out the application results by using K-Nearest Neighbors concept to determine students’ graduation status using the data of STMIK Palangkaraya students. The development of the software used Extreme Programming, since it was appropriate and precise for this study which was to quickly finish the project. The application was created using Microsoft Office Excel 2007 for the training data and Matlab 7 to implement the application. The result of K-Nearest Neighbors method on the application of determining students’ graduation status was 92.5%. It could determine the predicate graduation of 94 data used from the initial data before the processing as many as 136 data which the maximal training data was 50data. The K-Nearest Neighbors method is one of methods used to group a set of data based on the closest value, so that using K-Nearest Neighbors method agreed with this study. The results of K-Nearest Neighbors method on the application of determining students’ graduation status was 92.5% could determine the predicate graduation which is the maximal training data. The K-Nearest Neighbors method is one of methods used to group a set of data based on the closest value, so that using K-Nearest Neighbors method agreed with this study.

Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India

Science.gov (United States)

Peddayelachagiri, Bhavani V.; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H.; Batra, Harsh V.

2016-01-01

Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

Modeling the effect of neighboring grains on twin growth in HCP polycrystals

Science.gov (United States)

Kumar, M. Arul; Beyerlein, I. J.; Lebensohn, R. A.; Tomé, C. N.

2017-09-01

In this paper, we study the dependence of neighboring grain orientation on the local stress state around a deformation twin in a hexagonal close packed (HCP) crystal and its effects on the resistance against twin thickening. We use a recently developed, full-field elasto-visco-plastic formulation based on fast Fourier transforms that account for the twinning shear transformation imposed by the twin lamella. The study is applied to Mg, Zr and Ti, since these HCP metals tend to deform by activation of different types of slip modes. The analysis shows that the local stress along the twin boundary are strongly controlled by the relative orientation of the easiest deformation modes in the neighboring grain with respect to the twin lamella in the parent grain. A geometric expression that captures this parent-neighbor relationship is proposed and incorporated into a larger scale, mean-field visco-plastic self-consistent model to simulate the role of neighboring grain orientation on twin thickening. We demonstrate that the approach improves the prediction of twin area fraction distribution when compared with experimental observations.

Carbon-hydrogen defects with a neighboring oxygen atom in n-type Si

Science.gov (United States)

Gwozdz, K.; Stübner, R.; Kolkovsky, Vl.; Weber, J.

2017-07-01

We report on the electrical activation of neutral carbon-oxygen complexes in Si by wet-chemical etching at room temperature. Two deep levels, E65 and E75, are observed by deep level transient spectroscopy in n-type Czochralski Si. The activation enthalpies of E65 and E75 are obtained as EC-0.11 eV (E65) and EC-0.13 eV (E75). The electric field dependence of their emission rates relates both levels to single acceptor states. From the analysis of the depth profiles, we conclude that the levels belong to two different defects, which contain only one hydrogen atom. A configuration is proposed, where the CH1BC defect, with hydrogen in the bond-centered position between neighboring C and Si atoms, is disturbed by interstitial oxygen in the second nearest neighbor position to substitutional carbon. The significant reduction of the CH1BC concentration in samples with high oxygen concentrations limits the use of this defect for the determination of low concentrations of substitutional carbon in Si samples.

Efficient in vivo gene transfer to xenotransplanted human skin by lentivirus-mediated, but not by AAV-directed, gene delivery

DEFF Research Database (Denmark)

Jakobsen, Maria Vad; Askou, Anne Louise; Dokkedahl, Karin Stenderup

skin graft, and firefly luciferase expression was observed primarily in neighboring tissue beneath or surrounding the graft. In contrast, gene delivery by intradermally injected lentiviral vectors was efficient and led to extensive and persistent firefly luciferase expression within the human skin...... graft only. The study demonstrates limited capacity of single-stranded AAV vectors of six commonly used serotypes for gene delivery to human skin in vivo....

Maximum Gene-Support Tree

Directory of Open Access Journals (Sweden)

Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

A concerted action of a paired-type homeobox gene, aristaless, and a homolog of Hox11/tlx homeobox gene, clawless, is essential for the distal tip development of the Drosophila leg.

Science.gov (United States)

Kojima, Tetsuya; Tsuji, Takuya; Saigo, Kaoru

2005-03-15

The subdivision of the developing field by region-specific expression of genes encoding transcription factors is an essential step during appendage development in arthropod and vertebrates. In Drosophila leg development, the distal-most region (pretarsus) is specified by the expression of homeobox genes, aristaless and Lim1, and its immediate neighbor (distal tarsus) is specified by the expression of a pair of Bar homeobox genes. Here, we show that one additional gene, clawless, which is a homolog of vertebrate Hox11/tlx homeobox gene family and formerly known as C15, is specifically expressed in the pretarsus and cooperatively acts with aristaless to repress Bar and possibly to activate Lim1. Similar to aristaless, the maximal expression of clawless requires Lim1 and its co-factor, Chip. Bar attenuates aristaless and clawless expression through Lim1 repression. Aristaless and Clawless proteins form a complex capable of binding to specific DNA targets, which cannot be well recognized solely by Aristaless or Clawless.

Text Categorization Using Weight Adjusted k-Nearest Neighbor Classification

National Research Council Canada - National Science Library

Han, Euihong; Karypis, George; Kumar, Vipin

1999-01-01

.... The authors present a nearest neighbor classification scheme for text categorization in which the importance of discriminating words is learned using mutual information and weight adjustment techniques...

SibRank: Signed bipartite network analysis for neighbor-based collaborative ranking

Science.gov (United States)

Shams, Bita; Haratizadeh, Saman

2016-09-01

Collaborative ranking is an emerging field of recommender systems that utilizes users' preference data rather than rating values. Unfortunately, neighbor-based collaborative ranking has gained little attention despite its more flexibility and justifiability. This paper proposes a novel framework, called SibRank that seeks to improve the state of the art neighbor-based collaborative ranking methods. SibRank represents users' preferences as a signed bipartite network, and finds similar users, through a novel personalized ranking algorithm in signed networks.

ENTROPY CHARACTERISTICS IN MODELS FOR COORDINATION OF NEIGHBORING ROAD SECTIONS

Directory of Open Access Journals (Sweden)

N. I. Kulbashnaya

2016-01-01

Full Text Available The paper considers an application of entropy characteristics as criteria to coordinate traffic conditions at neighboring road sections. It has been proved that the entropy characteristics are widely used in the methods that take into account information influence of the environment on drivers and in the mechanisms that create such traffic conditions which ensure preservation of the optimal level of driver’s emotional tension during the drive. Solution of such problem is considered in the aspect of coordination of traffic conditions at neighboring road sections that, in its turn, is directed on exclusion of any driver’s transitional processes. Methodology for coordination of traffic conditions at neighboring road sections is based on the E. V. Gavrilov’s concept on coordination of some parameters of road sections which can be expressed in the entropy characteristics. The paper proposes to execute selection of coordination criteria according to accident rates because while moving along neighboring road sections traffic conditions change drastically that can result in creation of an accident situation. Relative organization of a driver’s perception field and driver’s interaction with the traffic environment has been selected as entropy characteristics. Therefore, the given characteristics are made conditional to the road accidents rate. The investigation results have revealed a strong correlation between the relative organization of the driver’s perception field and the relative organization of the driver’s interaction with the traffic environment and the accident rate. Results of the executed experiment have proved an influence of the accident rate on the investigated entropy characteristics.

Do alcohol compliance checks decrease underage sales at neighboring establishments?

Science.gov (United States)

Erickson, Darin J; Smolenski, Derek J; Toomey, Traci L; Carlin, Bradley P; Wagenaar, Alexander C

2013-11-01

Underage alcohol compliance checks conducted by law enforcement agencies can reduce the likelihood of illegal alcohol sales at checked alcohol establishments, and theory suggests that an alcohol establishment that is checked may warn nearby establishments that compliance checks are being conducted in the area. In this study, we examined whether the effects of compliance checks diffuse to neighboring establishments. We used data from the Complying with the Minimum Drinking Age trial, which included more than 2,000 compliance checks conducted at more than 900 alcohol establishments. The primary outcome was the sale of alcohol to a pseudo-underage buyer without the need for age identification. A multilevel logistic regression was used to model the effect of a compliance check at each establishment as well as the effect of compliance checks at neighboring establishments within 500 m (stratified into four equal-radius concentric rings), after buyer, license, establishment, and community-level variables were controlled for. We observed a decrease in the likelihood of establishments selling alcohol to underage youth after they had been checked by law enforcement, but these effects quickly decayed over time. Establishments that had a close neighbor (within 125 m) checked in the past 90 days were also less likely to sell alcohol to young-appearing buyers. The spatial effect of compliance checks on other establishments decayed rapidly with increasing distance. Results confirm the hypothesis that the effects of police compliance checks do spill over to neighboring establishments. These findings have implications for the development of an optimal schedule of police compliance checks.

Kinetic Models for Topological Nearest-Neighbor Interactions

Science.gov (United States)

Blanchet, Adrien; Degond, Pierre

2017-12-01

We consider systems of agents interacting through topological interactions. These have been shown to play an important part in animal and human behavior. Precisely, the system consists of a finite number of particles characterized by their positions and velocities. At random times a randomly chosen particle, the follower, adopts the velocity of its closest neighbor, the leader. We study the limit of a system size going to infinity and, under the assumption of propagation of chaos, show that the limit kinetic equation is a non-standard spatial diffusion equation for the particle distribution function. We also study the case wherein the particles interact with their K closest neighbors and show that the corresponding kinetic equation is the same. Finally, we prove that these models can be seen as a singular limit of the smooth rank-based model previously studied in Blanchet and Degond (J Stat Phys 163:41-60, 2016). The proofs are based on a combinatorial interpretation of the rank as well as some concentration of measure arguments.

Nearest unlike neighbor (NUN): an aid to decision confidence estimation

Science.gov (United States)

Dasarathy, Belur V.

1995-09-01

The concept of nearest unlike neighbor (NUN), proposed and explored previously in the design of nearest neighbor (NN) based decision systems, is further exploited in this study to develop a measure of confidence in the decisions made by NN-based decision systems. This measure of confidence, on the basis of comparison with a user-defined threshold, may be used to determine the acceptability of the decision provided by the NN-based decision system. The concepts, associated methodology, and some illustrative numerical examples using the now classical Iris data to bring out the ease of implementation and effectiveness of the proposed innovations are presented.

Cloning of the rat Waf1/Cip1 gene

International Nuclear Information System (INIS)

Belinsky, S.A.; Middleton, S.K.

1994-01-01

The progression of eukaryotic cells through the cell cycle involves the sequential expression of specific genes. This process is regulated by both external and internal stimuli that prevent the cell from prematurely entering the next phase before all macromolecular events have been completed. The activation and subsequent inactivation of cyclin dependent kinases (Cdks) represent one internal stimuli required to regulate the transit of cells from one stage of the cell cycle to the next. Another member of this regulatory cascade is the p53 tumor suppressor gene, which controls a G 1 checkpoint at which the cell cycle can be arrested prior to the initiation of DNA synthesis. Following DNA damage, p53 protein levels rise, and entry into S phase is delayed, presumably to allow time for repair of the lesions. When p53 function is lost, cells containing damaged DNA template enter S phase leading to fixation and propagation of genetic alterations. Recently, evidence linking the growth-suppressing activity of p53 and inactivation of Cdks has been provided by the cloning of the Waf1/Cip1 gene. Waf1/Cip1 encodes a protein of M r 21,000 (p21), which inhibits Cdks in vitro. The overexpression of Waf1/Cip1 in cells inhibits cell growth, suggesting that p21 is a downstream mediator of p53 function. Loss of Waf1/Cip1 gene function could lead to deregulation of the cell cycle and contribute to the development of the neoplastic phenotype in tumors that do not contain mutations in the p53 gene. The purpose of the present investigation was to clone the rat Waf1/Cip1 gene,then determine the frequency for alteration of this gene in lung tumors induced by X-rays

[Galaxy/quasar classification based on nearest neighbor method].

Science.gov (United States)

Li, Xiang-Ru; Lu, Yu; Zhou, Jian-Ming; Wang, Yong-Jun

2011-09-01

With the wide application of high-quality CCD in celestial spectrum imagery and the implementation of many large sky survey programs (e. g., Sloan Digital Sky Survey (SDSS), Two-degree-Field Galaxy Redshift Survey (2dF), Spectroscopic Survey Telescope (SST), Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) program and Large Synoptic Survey Telescope (LSST) program, etc.), celestial observational data are coming into the world like torrential rain. Therefore, to utilize them effectively and fully, research on automated processing methods for celestial data is imperative. In the present work, we investigated how to recognizing galaxies and quasars from spectra based on nearest neighbor method. Galaxies and quasars are extragalactic objects, they are far away from earth, and their spectra are usually contaminated by various noise. Therefore, it is a typical problem to recognize these two types of spectra in automatic spectra classification. Furthermore, the utilized method, nearest neighbor, is one of the most typical, classic, mature algorithms in pattern recognition and data mining, and often is used as a benchmark in developing novel algorithm. For applicability in practice, it is shown that the recognition ratio of nearest neighbor method (NN) is comparable to the best results reported in the literature based on more complicated methods, and the superiority of NN is that this method does not need to be trained, which is useful in incremental learning and parallel computation in mass spectral data processing. In conclusion, the results in this work are helpful for studying galaxies and quasars spectra classification.

Plant Clonal Integration Mediates the Horizontal Redistribution of Soil Resources, Benefiting Neighboring Plants.

Science.gov (United States)

Ye, Xue-Hua; Zhang, Ya-Lin; Liu, Zhi-Lan; Gao, Shu-Qin; Song, Yao-Bin; Liu, Feng-Hong; Dong, Ming

2016-01-01

Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor) microsite could be translocated within a clonal network, released into different (recipient) microsites and subsequently used by neighbor plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbors. The isotopes [(15)N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighboring A. ordosica, which increased growth of the neighboring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighboring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes.

Appendix 1：Upregulated genes in gene expression profile （P<0.05 ...

Indian Academy of Sciences (India)

lazi

Appendix 1: Upregulated genes in gene expression profile«P2）. Probe_s. Gene_Symbol pvalues foldchange. Probe_S. et_ID. Gene_Symbol pvalues foldchange. et_ID. 1370355. 1393751. Scd1. 1.35E-04. 25.77. Loc1009122508.06E-03. 2.55. -at at. 1398250. 1370870. Acot1. 2.43E-02. 12.18. Me1.

Antiferromagnetic geometric frustration under the influence of the next-nearest-neighbor interaction. An exactly solvable model

Science.gov (United States)

Jurčišinová, E.; Jurčišin, M.

2018-02-01

The influence of the next-nearest-neighbor interaction on the properties of the geometrically frustrated antiferromagnetic systems is investigated in the framework of the exactly solvable antiferromagnetic spin- 1 / 2 Ising model in the external magnetic field on the square-kagome recursive lattice, where the next-nearest-neighbor interaction is supposed between sites within each elementary square of the lattice. The thermodynamic properties of the model are investigated in detail and it is shown that the competition between the nearest-neighbor antiferromagnetic interaction and the next-nearest-neighbor ferromagnetic interaction changes properties of the single-point ground states but does not change the frustrated character of the basic model. On the other hand, the presence of the antiferromagnetic next-nearest-neighbor interaction leads to the enhancement of the frustration effects with the formation of additional plateau and single-point ground states at low temperatures. Exact expressions for magnetizations and residual entropies of all ground states of the model are found. It is shown that the model exhibits various ground states with the same value of magnetization but different macroscopic degeneracies as well as the ground states with different values of magnetization but the same value of the residual entropy. The specific heat capacity is investigated and it is shown that the model exhibits the Schottky-type anomaly behavior in the vicinity of each single-point ground state value of the magnetic field. The formation of the field-induced double-peak structure of the specific heat capacity at low temperatures is demonstrated and it is shown that its very existence is directly related to the presence of highly macroscopically degenerated single-point ground states in the model.

Gene Ontology and KEGG Enrichment Analyses of Genes Related to Age-Related Macular Degeneration

Directory of Open Access Journals (Sweden)

Jian Zhang

2014-01-01

Full Text Available Identifying disease genes is one of the most important topics in biomedicine and may facilitate studies on the mechanisms underlying disease. Age-related macular degeneration (AMD is a serious eye disease; it typically affects older adults and results in a loss of vision due to retina damage. In this study, we attempt to develop an effective method for distinguishing AMD-related genes. Gene ontology and KEGG enrichment analyses of known AMD-related genes were performed, and a classification system was established. In detail, each gene was encoded into a vector by extracting enrichment scores of the gene set, including it and its direct neighbors in STRING, and gene ontology terms or KEGG pathways. Then certain feature-selection methods, including minimum redundancy maximum relevance and incremental feature selection, were adopted to extract key features for the classification system. As a result, 720 GO terms and 11 KEGG pathways were deemed the most important factors for predicting AMD-related genes.

Neighbor Discovery Algorithm in Wireless Local Area Networks Using Multi-beam Directional Antennas

Science.gov (United States)

Wang, Jin; Peng, Wei; Liu, Song

2017-10-01

Neighbor discovery is an important step for Wireless Local Area Networks (WLAN) and the use of multi-beam directional antennas can greatly improve the network performance. However, most neighbor discovery algorithms in WLAN, based on multi-beam directional antennas, can only work effectively in synchronous system but not in asynchro-nous system. And collisions at AP remain a bottleneck for neighbor discovery. In this paper, we propose two asynchrono-us neighbor discovery algorithms: asynchronous hierarchical scanning (AHS) and asynchronous directional scanning (ADS) algorithm. Both of them are based on three-way handshaking mechanism. AHS and ADS reduce collisions at AP to have a good performance in a hierarchical way and directional way respectively. In the end, the performance of the AHS and ADS are tested on OMNeT++. Moreover, it is analyzed that different application scenarios and the factors how to affect the performance of these algorithms. The simulation results show that AHS is suitable for the densely populated scenes around AP while ADS is suitable for that most of the neighborhood nodes are far from AP.

Using K-Nearest Neighbor in Optical Character Recognition

Directory of Open Access Journals (Sweden)

Veronica Ong

2016-03-01

Full Text Available The growth in computer vision technology has aided society with various kinds of tasks. One of these tasks is the ability of recognizing text contained in an image, or usually referred to as Optical Character Recognition (OCR. There are many kinds of algorithms that can be implemented into an OCR. The K-Nearest Neighbor is one such algorithm. This research aims to find out the process behind the OCR mechanism by using K-Nearest Neighbor algorithm; one of the most influential machine learning algorithms. It also aims to find out how precise the algorithm is in an OCR program. To do that, a simple OCR program to classify alphabets of capital letters is made to produce and compare real results. The result of this research yielded a maximum of 76.9% accuracy with 200 training samples per alphabet. A set of reasons are also given as to why the program is able to reach said level of accuracy.

An Improvement To The k-Nearest Neighbor Classifier For ECG Database

Science.gov (United States)

Jaafar, Haryati; Hidayah Ramli, Nur; Nasir, Aimi Salihah Abdul

2018-03-01

The k nearest neighbor (kNN) is a non-parametric classifier and has been widely used for pattern classification. However, in practice, the performance of kNN often tends to fail due to the lack of information on how the samples are distributed among them. Moreover, kNN is no longer optimal when the training samples are limited. Another problem observed in kNN is regarding the weighting issues in assigning the class label before classification. Thus, to solve these limitations, a new classifier called Mahalanobis fuzzy k-nearest centroid neighbor (MFkNCN) is proposed in this study. Here, a Mahalanobis distance is applied to avoid the imbalance of samples distribition. Then, a surrounding rule is employed to obtain the nearest centroid neighbor based on the distributions of training samples and its distance to the query point. Consequently, the fuzzy membership function is employed to assign the query point to the class label which is frequently represented by the nearest centroid neighbor Experimental studies from electrocardiogram (ECG) signal is applied in this study. The classification performances are evaluated in two experimental steps i.e. different values of k and different sizes of feature dimensions. Subsequently, a comparative study of kNN, kNCN, FkNN and MFkCNN classifier is conducted to evaluate the performances of the proposed classifier. The results show that the performance of MFkNCN consistently exceeds the kNN, kNCN and FkNN with the best classification rates of 96.5%.

HIV-1 subtypes among intravenous drug users from two neighboring cities in São Paulo State, Brazil

Directory of Open Access Journals (Sweden)

M.A.A. Rossini

2001-01-01

Full Text Available In order to assess the molecular epidemiology of HIV-1 in two neighboring cities located near the epicenter of the HIV-1 epidemics in Brazil (Santos and São Paulo, we investigated 83 HIV-1 strains obtained from samples collected in 1995 from intravenous drug users. The V3 through V5 region of the envelope of gp 120 was analyzed by heteroduplex mobility analysis. Of the 95 samples, 12 (12.6% were PCR negative (6 samples from each group; low DNA concentration was the reason for non-amplification in half of these cases. Of the 42 typed cases from São Paulo, 34 (81%, 95% confidence limits 74.9 to 87.0% were B and 8 (19%, 95% confidence limits 12.9 to 25.0% were F, whereas of the 41 typed cases from Santos, 39 (95%, 95% confidence limits 91.6 to 98.4% were B and 2 (5%, 95% confidence limits 1.6 to 8.4% were C. We therefore confirm the relationship between clade F and intravenous drug use in São Paulo, and the presence of clade C in Santos. The fact that different genetic subtypes of HIV-1 are co-circulating indicates a need for continuous surveillance for these subtypes as well as for recombinant viruses in Brazil.

Neighbor discovery in multi-hop wireless networks: evaluation and dimensioning with interferences considerations

Directory of Open Access Journals (Sweden)

Elyes Ben Hamida

2008-04-01

Full Text Available In this paper, we study the impact of collisions and interferences on a neighbor discovery process in the context of multi-hop wireless networks. We consider three models in which interferences and collisions are handled in very different ways. From an ideal channel where simultaneous transmissions do not interfere, we derive an alternate channel where simultaneous transmissions are considered two-by-two under the form of collisions, to finally reach a more realistic channel where simultaneous transmissions are handled under the form of shot-noise interferences. In these models, we analytically compute the link probability success between two neighbors as well as the expected number of nodes that correctly receive a Hello packet. Using this analysis, we show that if the neighbor discovery process is asymptotically equivalent in the three models, it offers very different behaviors locally in time. In particular, the scalability of the process is not the same depending on the way interferences are handled. Finally, we apply our results to the dimensioning of a Hello protocol parameters. We propose a method to adapt the protocol parameters to meet application constraints on the neighbor discovery process and to minimize the protocol energy consumption.

Disentangling neighbors and extended range density oscillations in monatomic amorphous semiconductors.

Science.gov (United States)

Roorda, S; Martin, C; Droui, M; Chicoine, M; Kazimirov, A; Kycia, S

2012-06-22

High energy x-ray diffraction measurements of pure amorphous Ge were made and its radial distribution function (RDF) was determined at high resolution, revealing new information on the atomic structure of amorphous semiconductors. Fine structure in the second peak in the RDF provides evidence that a fraction of third neighbors are closer than some second neighbors; taking this into account leads to a narrow distribution of tetrahedral bond angles, (8.5 ± 0.1)°. A small peak which appears near 5 Å upon thermal annealing shows that some ordering in the dihedral bond-angle distribution takes place during structural relaxation. Extended range order is detected (in both a-Ge and a-Si) which persists to beyond 20 Å, and both the periodicity and its decay length increase upon thermal annealing. Previously, the effect of structural relaxation was only detected at intermediate range, involving reduced tetrahedral bond-angle distortions. These results enhance our understanding of the atomic order in continuous random networks and place significantly more stringent requirements on computer models intending to describe these networks, or their alternatives which attempt to describe the structure in terms of an arrangement of paracrystals.

Genome-wide analysis of central corneal thickness in primary open-angle glaucoma cases in the NEIGHBOR and GLAUGEN consortia.

Science.gov (United States)

Ulmer, Megan; Li, Jun; Yaspan, Brian L; Ozel, Ayse Bilge; Richards, Julia E; Moroi, Sayoko E; Hawthorne, Felicia; Budenz, Donald L; Friedman, David S; Gaasterland, Douglas; Haines, Jonathan; Kang, Jae H; Lee, Richard; Lichter, Paul; Liu, Yutao; Pasquale, Louis R; Pericak-Vance, Margaret; Realini, Anthony; Schuman, Joel S; Singh, Kuldev; Vollrath, Douglas; Weinreb, Robert; Wollstein, Gadi; Zack, Donald J; Zhang, Kang; Young, Terri; Allingham, R Rand; Wiggs, Janey L; Ashley-Koch, Allison; Hauser, Michael A

2012-07-03

To investigate the effects of central corneal thickness (CCT)-associated variants on primary open-angle glaucoma (POAG) risk using single nucleotide polymorphisms (SNP) data from the Glaucoma Genes and Environment (GLAUGEN) and National Eye Institute (NEI) Glaucoma Human Genetics Collaboration (NEIGHBOR) consortia. A replication analysis of previously reported CCT SNPs was performed in a CCT dataset (n = 1117) and these SNPs were then tested for association with POAG using a larger POAG dataset (n = 6470). Then a CCT genome-wide association study (GWAS) was performed. Top SNPs from this analysis were selected and tested for association with POAG. cDNA libraries from fetal and adult brain and ocular tissue samples were generated and used for candidate gene expression analysis. Association with one of 20 previously published CCT SNPs was replicated: rs12447690, near the ZNF469 gene (P = 0.001; β = -5.08 μm/allele). None of these SNPs were significantly associated with POAG. In the CCT GWAS, no SNPs reached genome-wide significance. After testing 50 candidate SNPs for association with POAG, one SNP was identified, rs7481514 within the neurotrimin (NTM) gene, that was significantly associated with POAG in a low-tension subset (P = 0.00099; Odds Ratio [OR] = 1.28). Additionally, SNPs in the CNTNAP4 gene showed suggestive association with POAG (top SNP = rs1428758; P = 0.018; OR = 0.84). NTM and CNTNAP4 were shown to be expressed in ocular tissues. The results suggest previously reported CCT loci are not significantly associated with POAG susceptibility. By performing a quantitative analysis of CCT and a subsequent analysis of POAG, SNPs in two cell adhesion molecules, NTM and CNTNAP4, were identified and may increase POAG susceptibility in a subset of cases.

Velocity correlations and spatial dependencies between neighbors in a unidirectional flow of pedestrians

Science.gov (United States)

Porzycki, Jakub; WÄ s, Jarosław; Hedayatifar, Leila; Hassanibesheli, Forough; Kułakowski, Krzysztof

2017-08-01

The aim of the paper is an analysis of self-organization patterns observed in the unidirectional flow of pedestrians. On the basis of experimental data from Zhang et al. [J. Zhang et al., J. Stat. Mech. (2011) P06004, 10.1088/1742-5468/2011/06/P06004], we analyze the mutual positions and velocity correlations between pedestrians when walking along a corridor. The angular and spatial dependencies of the mutual positions reveal a spatial structure that remains stable during the crowd motion. This structure differs depending on the value of n , for the consecutive n th -nearest-neighbor position set. The preferred position for the first-nearest neighbor is on the side of the pedestrian, while for further neighbors, this preference shifts to the axis of movement. The velocity correlations vary with the angle formed by the pair of neighboring pedestrians and the direction of motion and with the time delay between pedestrians' movements. The delay dependence of the correlations shows characteristic oscillations, produced by the velocity oscillations when striding; however, a filtering of the main frequency of individual striding out reduces the oscillations only partially. We conclude that pedestrians select their path directions so as to evade the necessity of continuously adjusting their speed to their neighbors'. They try to keep a given distance, but follow the person in front of them, as well as accepting and observing pedestrians on their sides. Additionally, we show an empirical example that illustrates the shape of a pedestrian's personal space during movement.

Error Analysis for RADAR Neighbor Matching Localization in Linear Logarithmic Strength Varying Wi-Fi Environment

Directory of Open Access Journals (Sweden)

Mu Zhou

2014-01-01

Full Text Available This paper studies the statistical errors for the fingerprint-based RADAR neighbor matching localization with the linearly calibrated reference points (RPs in logarithmic received signal strength (RSS varying Wi-Fi environment. To the best of our knowledge, little comprehensive analysis work has appeared on the error performance of neighbor matching localization with respect to the deployment of RPs. However, in order to achieve the efficient and reliable location-based services (LBSs as well as the ubiquitous context-awareness in Wi-Fi environment, much attention has to be paid to the highly accurate and cost-efficient localization systems. To this end, the statistical errors by the widely used neighbor matching localization are significantly discussed in this paper to examine the inherent mathematical relations between the localization errors and the locations of RPs by using a basic linear logarithmic strength varying model. Furthermore, based on the mathematical demonstrations and some testing results, the closed-form solutions to the statistical errors by RADAR neighbor matching localization can be an effective tool to explore alternative deployment of fingerprint-based neighbor matching localization systems in the future.

Error Analysis for RADAR Neighbor Matching Localization in Linear Logarithmic Strength Varying Wi-Fi Environment

Science.gov (United States)

Tian, Zengshan; Xu, Kunjie; Yu, Xiang

2014-01-01

This paper studies the statistical errors for the fingerprint-based RADAR neighbor matching localization with the linearly calibrated reference points (RPs) in logarithmic received signal strength (RSS) varying Wi-Fi environment. To the best of our knowledge, little comprehensive analysis work has appeared on the error performance of neighbor matching localization with respect to the deployment of RPs. However, in order to achieve the efficient and reliable location-based services (LBSs) as well as the ubiquitous context-awareness in Wi-Fi environment, much attention has to be paid to the highly accurate and cost-efficient localization systems. To this end, the statistical errors by the widely used neighbor matching localization are significantly discussed in this paper to examine the inherent mathematical relations between the localization errors and the locations of RPs by using a basic linear logarithmic strength varying model. Furthermore, based on the mathematical demonstrations and some testing results, the closed-form solutions to the statistical errors by RADAR neighbor matching localization can be an effective tool to explore alternative deployment of fingerprint-based neighbor matching localization systems in the future. PMID:24683349

Reduction of Conflicts in Mining Development Using "Good Neighbor Agreements"

Science.gov (United States)

Masaitis, A.

2013-05-01

New environmental and social challenges for the mining industry in both developed and developing countries show the obvious need to implement "responsible" mining practices that include improved community involvement. Good Neighbor Agreements (GNA's) are a relatively new mechanism for improving communication and trust between a mining company and the community. The focus of a GNA will be to provide a written and enforceable agreement, negotiated between the concerned public and the respective mining company to respond to concerns from the public, and also provide a mechanism for conflict resolution, when there is mutual benefit to maintain a working relationship. Development of GNA's, a recently evolving process that promotes environmentally sound relationships between mines and the surrounding communities. Modify and apply the resulting GNA formulas to the developing countries and countries with transitional economies. This is particularly important for countries that have poorly functioning regulatory systems that cannot guarantee a healthy and safe environment for the communities. The fundamental questions addressed by this research. 1. This is a three-year research project started in August 2012 at the University of Nevada, Reno (UNR) to develop a Good Neighbor Agreements standards as well as to investigate the details of mine development. 2. Identify spheres of possible cooperation between mining companies, government organizations, and the Non-Governmental Organizations (NGO's). Use this cooperation to develop international standards for the GNA, to promote exchange of environmental information, and exchange of successful environmental, health, and safety practices between mining operations from different countries. Discussion: The Good Neighbor Agreement currently evolving will address the following: 1. Provide an economically viable mechanism for developing a partnership between mining operations and the local communities that will increase mining industry

ACTION RECOGNITION USING SALIENT NEIGHBORING HISTOGRAMS

DEFF Research Database (Denmark)

Ren, Huamin; Moeslund, Thomas B.

2013-01-01

Combining spatio-temporal interest points with Bag-of-Words models achieves state-of-the-art performance in action recognition. However, existing methods based on “bag-ofwords” models either are too local to capture the variance in space/time or fail to solve the ambiguity problem in spatial...... and temporal dimensions. Instead, we propose a salient vocabulary construction algorithm to select visual words from a global point of view, and form compact descriptors to represent discriminative histograms in the neighborhoods. Those salient neighboring histograms are then trained to model different actions...

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease.

Science.gov (United States)

Chiba, Hirofumi; Kakuta, Yoichi; Kinouchi, Yoshitaka; Kawai, Yosuke; Watanabe, Kazuhiro; Nagao, Munenori; Naito, Takeo; Onodera, Motoyuki; Moroi, Rintaro; Kuroha, Masatake; Kanazawa, Yoshitake; Kimura, Tomoya; Shiga, Hisashi; Endo, Katsuya; Negoro, Kenichi; Nagasaki, Masao; Unno, Michiaki; Shimosegawa, Tooru

2018-01-01

Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). We confirmed the existence of cis-regulated ASM around

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease

Science.gov (United States)

Chiba, Hirofumi; Kakuta, Yoichi; Kinouchi, Yoshitaka; Kawai, Yosuke; Watanabe, Kazuhiro; Nagao, Munenori; Naito, Takeo; Onodera, Motoyuki; Moroi, Rintaro; Kuroha, Masatake; Kanazawa, Yoshitake; Kimura, Tomoya; Shiga, Hisashi; Endo, Katsuya; Negoro, Kenichi; Nagasaki, Masao; Unno, Michiaki; Shimosegawa, Tooru

2018-01-01

Background Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. Methods CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score (ΔRAS¯) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing ΔRAS¯ >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. Results We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of ΔRAS¯ (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 (ΔRAS¯ = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). Conclusions We confirmed the existence of cis-regulated ASM around IBD

Gene-gene interactions of IRF5, STAT4, IKZF1 and ETS1 in systemic lupus erythematosus.

Science.gov (United States)

Dang, J; Shan, S; Li, J; Zhao, H; Xin, Q; Liu, Y; Bian, X; Liu, Q

2014-06-01

Interferon (IFN) activation signaling and T helper 17 (Th17)-cell/B-cell regulation play a critical role in the pathogenesis of systemic lupus erythematosus (SLE). Several studies have provided convincing evidence that polymorphisms in IRF5, STAT4, IKZF1 and ETS1 from these pathways may be involved in SLE by affecting gene expression or epistasis. We analyzed the genetic interaction in known SLE susceptibility loci from the four genes in northern Han Chinese. A total of 946 northern Han Chinese participated in this study (370 unrelated SLE patients and 576 healthy controls). Subjects underwent genotyping for the single-nucleotide polymorphisms (SNPs) rs2004640 in IRF5, rs7574865 in STAT4, rs4917014 in IKZF1 and rs1128334 in ETS1 by use of a TaqMan SNP genotyping assay and direct sequencing. Gene-gene interaction analysis involved direct counting, multifactor dimensionality reduction (MDR) and linear regression analysis. SLE patients and controls differed in allele frequencies of rs7574865, rs1128334 (P < 0.001) and rs4917014 (P < 0.01). Direct counting revealed that the frequency of risk homozygote combinations was higher for SLE patients than controls (P < 0.01). Furthermore, 2-, 3- and 4-way gene-gene epistasis in SLE was confirmed by parametric methods and MDR analysis. Gene expression analysis partially supported the findings. Our study confirmed the association of the IFN pathway or Th17/B-cells and the pathogenesis of SLE, and gene-gene interaction in this pathway may increase the risk of SLE. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A Novel AMR-WB Speech Steganography Based on Diameter-Neighbor Codebook Partition

Directory of Open Access Journals (Sweden)

Junhui He

2018-01-01

Full Text Available Steganography is a means of covert communication without revealing the occurrence and the real purpose of communication. The adaptive multirate wideband (AMR-WB is a widely adapted format in mobile handsets and is also the recommended speech codec for VoLTE. In this paper, a novel AMR-WB speech steganography is proposed based on diameter-neighbor codebook partition algorithm. Different embedding capacity may be achieved by adjusting the iterative parameters during codebook division. The experimental results prove that the presented AMR-WB steganography may provide higher and flexible embedding capacity without inducing perceptible distortion compared with the state-of-the-art methods. With 48 iterations of cluster merging, twice the embedding capacity of complementary-neighbor-vertices-based embedding method may be obtained with a decrease of only around 2% in speech quality and much the same undetectability. Moreover, both the quality of stego speech and the security regarding statistical steganalysis are better than the recent speech steganography based on neighbor-index-division codebook partition.

Roles of bHLH genes in neural stem cell differentiation

International Nuclear Information System (INIS)

Kageyama, Ryoichiro; Ohtsuka, Toshiyuki; Hatakeyama, Jun; Ohsawa, Ryosuke

2005-01-01

Neural stem cells change their characteristics over time during development: they initially proliferate only and then give rise to neurons first and glial cells later. In the absence of the repressor-type basic helix-loop-helix (bHLH) genes Hes1, Hes3 and Hes5, neural stem cells do not proliferate sufficiently but prematurely differentiate into neurons and become depleted without making the later born cell types such as astrocytes and ependymal cells. Thus, Hes genes are essential for maintenance of neural stem cells to make cells not only in correct numbers but also in full diversity. Hes genes antagonize the activator-type bHLH genes, which include Mash1, Math and Neurogenin. The activator-type bHLH genes promote the neuronal fate determination and induce expression of Notch ligands such as Delta. These ligands activate Notch signaling and upregulate Hes1 and Hes5 expression in neighboring cells, thereby maintaining these cells undifferentiated. Thus, the activator-type and repressor-type bHLH genes regulate each other, allowing only subsets of cells to undergo differentiation while keeping others to stay neural stem cells. This regulation is essential for generation of complex brain structures of appropriate size, shape and cell arrangement

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is an ideal method in mammary gland bioreactor research. For this purpose, a gene targeting vector was constructed to targeting the human lysozyme gene on bovine αs1-casein gene locus. In this case, the ...

Forest structure of Mediterranean yew (Taxus baccata L. populations and neighbor effects on juvenile yew performance in the NE Iberian Peninsula

Directory of Open Access Journals (Sweden)

Pere Casals

2015-12-01

Full Text Available Aim of study: In the Mediterranean region, yew (Taxus baccata L. usually grows with other tree species in mixed forests. Yew recruitment and juvenile growth may depend on the structure of the forest and the net balance between competition for soil water and nutrients with neighbors and facilitation that these neighbors exert by protecting the plants from direct sun exposure. This study aims, at a regional scale, to analyze the structure of forests containing yew, and, on an individual level, to analyze the effect of the surrounding vegetation structure on the performance of yew juveniles.Area of study: The structural typologies of yew populations were defined based on field inventories conducted in 55 plots distributed in 14 localities in the North-Eastern (NE Iberian Peninsula, covering a wide range of yew distribution in the area. In a second step, an analysis of neighboring species' effects on juveniles was conducted based on the data from 103 plots centered in yew juveniles in five localities.Main Results: A cluster analysis classified the inventoried stands into four forest structural types: two multi-stratified forests with scattered yew and two yew groves. Multiple regression modeling showed that the δ13C measured in last year's leaves positively relates to the basal area of conifer neighbors, but negatively with the cover of the yew crown by other trees.Research highlights: At a stand-level, the density of recruits and juveniles (625 ± 104 recruits ha-1, 259 ± 55 juveniles ha-1 in mixed forests was found to be higher than that on yew dominant stands (181 ± 88 recruits ha-1 and 57 ± 88 juveniles ha-1. At an individual-level, the water stress (estimated from leaf δ13C of yew juveniles seems alleviated by the crown cover by neighbors while it increases with the basal area of conifers. Yew conservation should focus on selective felling for the reduction of basal area of neighbors surrounding the target tree, but avoid affecting the

Grain price spikes and beggar-thy-neighbor policy responses

DEFF Research Database (Denmark)

Boysen, Ole; Jensen, Hans Grinsted

on the agenda of various international policy fora, including the annual meetings of G20 countries in recent years. For that reason, recent studies have attempted to quantify the extent to which such policy actions contributed to the rise in food prices. A study by Jensen & Anderson (2014) uses the global AGE...... model GTAP and the corresponding database to quantify the global policy actions contributions to the raise in food prices by modeling the changes in distortions to agricultural incentives in the period 2006 to 2008. We link the results from this global model into a national AGE model, highlighting how...... global "Beggar-thy-Neighbor Policy Responses" impacted on poor households in Uganda. More specifically we examine the following research questions: What were the Ugandan economy-wide and poverty impacts of the price spikes? What was the impact of other countries "Beggar-thy-Neighbor Policy Responses...

Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.

Science.gov (United States)

Varrault, Annie; Dantec, Christelle; Le Digarcher, Anne; Chotard, Laëtitia; Bilanges, Benoit; Parrinello, Hugues; Dubois, Emeric; Rialle, Stéphanie; Severac, Dany; Bouschet, Tristan; Journot, Laurent

2017-10-13

PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Generalized Approach for Measuring Relationships Among Genes.

Science.gov (United States)

Wang, Lijun; Ahsan, Md Asif; Chen, Ming

2017-07-21

Several methods for identifying relationships among pairs of genes have been developed. In this article, we present a generalized approach for measuring relationships between any pairs of genes, which is based on statistical prediction. We derive two particular versions of the generalized approach, least squares estimation (LSE) and nearest neighbors prediction (NNP). According to mathematical proof, LSE is equivalent to the methods based on correlation; and NNP is approximate to one popular method called the maximal information coefficient (MIC) according to the performances in simulations and real dataset. Moreover, the approach based on statistical prediction can be extended from two-genes relationships to multi-genes relationships. This application would help to identify relationships among multi-genes.

Collective Behaviors of Mobile Robots Beyond the Nearest Neighbor Rules With Switching Topology.

Science.gov (United States)

Ning, Boda; Han, Qing-Long; Zuo, Zongyu; Jin, Jiong; Zheng, Jinchuan

2018-05-01

This paper is concerned with the collective behaviors of robots beyond the nearest neighbor rules, i.e., dispersion and flocking, when robots interact with others by applying an acute angle test (AAT)-based interaction rule. Different from a conventional nearest neighbor rule or its variations, the AAT-based interaction rule allows interactions with some far-neighbors and excludes unnecessary nearest neighbors. The resulting dispersion and flocking hold the advantages of scalability, connectivity, robustness, and effective area coverage. For the dispersion, a spring-like controller is proposed to achieve collision-free coordination. With switching topology, a new fixed-time consensus-based energy function is developed to guarantee the system stability. An upper bound of settling time for energy consensus is obtained, and a uniform time interval is accordingly set so that energy distribution is conducted in a fair manner. For the flocking, based on a class of generalized potential functions taking nonsmooth switching into account, a new controller is proposed to ensure that the same velocity for all robots is eventually reached. A co-optimizing problem is further investigated to accomplish additional tasks, such as enhancing communication performance, while maintaining the collective behaviors of mobile robots. Simulation results are presented to show the effectiveness of the theoretical results.

Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

Directory of Open Access Journals (Sweden)

Xiaoling Zhang

2013-01-01

Full Text Available We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs at a false discovery rate (FDR <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.

The Influence of Neighbor Effect and Urbanization Toward Organ Donation in Thailand.

Science.gov (United States)

Wongboonsin, Kua; Jindahra, Pavitra; Teerakapibal, Surat

2018-03-01

Toward population wellness, an extreme scarcity of organ supply is proven to be an enormous hindrance. Preferences toward organ donation are vital to raise the organ donation rate. Notably, the area people live in can address the social influence on individual preference toward organ donation. This article studies the impact of the neighbor effect on organ donation decisions, addressing the social influence of urbanization on preferences. How neighborhood-specific variables, population density, and socioeconomic status drive the neighbor effect is investigated. The pursuit of organ donor traits is to be answered. The study uses organ donation interview survey data and neighborhood-specific data from Thailand to estimate a series of logistic regression models. Individuals residing in urban areas exhibit a greater likelihood to sign the donor card than those in rural areas. The neighborhood socioeconomic status is the key driver. An individual is more willing to be an organ donor when having neighbors with higher socioeconomic statuses. Results also reveal positive influences of males and education on the organ donation rate. This article documents the "neighbor effect" on the organ donation decision via living area type, offering an alternative exposition in raising the organ donation rate. In shifting the society norm toward organ donation consent, policy-makers should acknowledge the benefit of urbanization on organ donation decision derived from resourceful urban areas. Moreover, raising education levels does improve not only citizens' well-being but also their tendency to exhibit an altruistic act toward others.

The influence of neighbors' family size preference on progression to high parity births in rural Nepal.

Science.gov (United States)

Jennings, Elyse A; Barber, Jennifer S

2013-03-01

Large families can have a negative impact on the health and well-being of women, children, and their communities. Seventy-three percent of the individuals in our rural Nepalese sample report that two children is their ideal number, yet about half of the married women continue childbearing after their second child. Using longitudinal data from the Chitwan Valley Family Study, we explore the influence of women's and neighbors' family size preferences on women's progression to high parity births, comparing this influence across two cohorts. We find that neighbors' family size preferences influence women's fertility, that older cohorts of women are more influenced by their neighbors' preferences than are younger cohorts of women, and that the influence of neighbors' preferences is independent of women's own preferences. © 2013 The Population Council, Inc.

Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

Science.gov (United States)

Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

2007-07-01

Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?

Science.gov (United States)

Kaur, Simranjeet; Pociot, Flemming

2015-07-13

Despite numerous studies implicating Alu repeat elements in various diseases, there is sparse information available with respect to the potential functional and biological roles of the repeat elements in Type 1 diabetes (T1D). Therefore, we performed a genome-wide sequence analysis of T1D candidate genes to identify embedded Alu elements within these genes. We observed significant enrichment of Alu elements within the T1D genes (p-value genes harboring Alus revealed significant enrichment for immune-mediated processes (p-value genes harboring inverted Alus (IRAlus) within their 3' untranslated regions (UTRs) that are known to regulate the expression of host mRNAs by generating double stranded RNA duplexes. Our in silico analysis predicted the formation of duplex structures by IRAlus within the 3'UTRs of T1D genes. We propose that IRAlus might be involved in regulating the expression levels of the host T1D genes.

Construction Of An Optimized Lentiviral Vector Containing Pdx-1 Gene For Transduction Of Stem Cells Towards Gene Therapy Diabetes Type 1

Directory of Open Access Journals (Sweden)

S Rahmati

2013-02-01

Full Text Available Abstract Background & aim: Nowadays, most of gene therapy protocols are performed by lentiviral vectors. One of the most important factors which is involved in pancreas development and transcription of insulin gene is pancreatic & duodenal homeobox 1 (PDX-1 transcription factor. The goal of this study was to optimize a lentiviral construct, containing pdx-1 gene, to transfect stem cells towards gene therapy of type-1 diabetes. Methods: In this experimental study, first, the pdx-1 gene was multiplied by PCR from pcDNA3.1-pdx-1 and cloned into pTG19-T vector. Then, pdx-1 was subcloned on upstream of IRES-EGFP gene into IRES2-EGFP vector. At the next step, the cloned parts of IRES-EGFP and pdx-1 were isolated and cloned into the lentiviral expression vector pSINTREM in upstream of TRE-CMV gene. After sequencing, final construct was transfected into HEK 293 cells and gene expression of pdx-1 was evaluated using flow cytometry analysis and reverse fluorescent microscopy. Results: Flow cytometry results and inverted fluorescent microscopy observing showed that pdx-1 and GFP genes are expressed in cells transfected with final recombinant construct. Conclusion: Regarding the design of this construct, to ensure long time expression with higher in vivo and in vitro expression efficiency for stem cells and also use of Tet on induced optimized system, it seems that the current construct can be among the best ones to transfect stem cells. Key words: Gene therapy, Diabetes, Stem cells

Clustered K nearest neighbor algorithm for daily inflow forecasting

NARCIS (Netherlands)

Akbari, M.; Van Overloop, P.J.A.T.M.; Afshar, A.

2010-01-01

Instance based learning (IBL) algorithms are a common choice among data driven algorithms for inflow forecasting. They are based on the similarity principle and prediction is made by the finite number of similar neighbors. In this sense, the similarity of a query instance is estimated according to

Contrasting demographic histories of the neighboring bonobo and chimpanzee

DEFF Research Database (Denmark)

Hvilsom, Christina; Carlsen, Frands; Heller, Rasmus

2014-01-01

of the neighboring bonobo remained constant. The changes in population size are likely linked to changes in habitat area due to climate oscillations during the late Pleistocene. Furthermore, the timing of population expansion for the rainforest-adapted chimpanzee is concurrent with the expansion of the savanna...

Genetic variability in L1 and L2 genes of HPV-16 and HPV-58 in Southwest China.

Directory of Open Access Journals (Sweden)

Yaofei Yue

Full Text Available HPV account for most of the incidence of cervical cancer. Approximately 90% of anal cancers and a smaller subset (<50% of other cancers (oropharyngeal, penile, vaginal, vulvar are also attributed to HPV. The L1 protein comprising HPV vaccine formulations elicits high-titre neutralizing antibodies and confers type restricted protection. The L2 protein is a promising candidate for a broadly protective HPV vaccine. In our previous study, we found the most prevalent high-risk HPV infectious serotypes were HPV-16 and HPV-58 among women of Southwest China. To explore gene polymorphisms and intratypic variations of HPV-16 and HPV-58 L1/L2 genes originating in Southwest China, HPV-16 (L1: n = 31, L2: n = 28 and HPV-58 (L1: n = 21, L2: n = 21 L1/L2 genes were sequenced and compared to others described and submitted to GenBank. Phylogenetic trees were then constructed by Neighbor-Joining and the Kimura 2-parameters methods (MEGA software, followed by an analysis of the diversity of secondary structure. Then selection pressures acting on the L1/L2 genes were estimated by PAML software. Twenty-nine single nucleotide changes were observed in HPV-16 L1 sequences with 16/29 non-synonymous mutations and 13/29 synonymous mutations (six in alpha helix and two in beta turns. Seventeen single nucleotide changes were observed in HPV-16 L2 sequences with 8/17 non-synonymous mutations (one in beta turn and 9/17 synonymous mutations. Twenty-four single nucleotide changes were observed in HPV-58 L1 sequences with 10/24 non-synonymous mutations and 14/24 synonymous mutations (eight in alpha helix and four in beta turn. Seven single nucleotide changes were observed in HPV-58 L2 sequences with 4/7 non-synonymous mutations and 3/7 synonymous mutations. The result of selective pressure analysis showed that most of these mutations were of positive selection. This study may help understand the intrinsic geographical relatedness and biological differences of HPV-16/HPV-58 and

Network analysis of differential expression for the identification of disease-causing genes.

Directory of Open Access Journals (Sweden)

Daniela Nitsch

Full Text Available Genetic studies (in particular linkage and association studies identify chromosomal regions involved in a disease or phenotype of interest, but those regions often contain many candidate genes, only a few of which can be followed-up for biological validation. Recently, computational methods to identify (prioritize the most promising candidates within a region have been proposed, but they are usually not applicable to cases where little is known about the phenotype (no or few confirmed disease genes, fragmentary understanding of the biological cascades involved. We seek to overcome this limitation by replacing knowledge about the biological process by experimental data on differential gene expression between affected and healthy individuals. Considering the problem from the perspective of a gene/protein network, we assess a candidate gene by considering the level of differential expression in its neighborhood under the assumption that strong candidates will tend to be surrounded by differentially expressed neighbors. We define a notion of soft neighborhood where each gene is given a contributing weight, which decreases with the distance from the candidate gene on the protein network. To account for multiple paths between genes, we define the distance using the Laplacian exponential diffusion kernel. We score candidates by aggregating the differential expression of neighbors weighted as a function of distance. Through a randomization procedure, we rank candidates by p-values. We illustrate our approach on four monogenic diseases and successfully prioritize the known disease causing genes.

Quality and efficiency in high dimensional Nearest neighbor search

KAUST Repository

Tao, Yufei; Yi, Ke; Sheng, Cheng; Kalnis, Panos

2009-01-01

Nearest neighbor (NN) search in high dimensional space is an important problem in many applications. Ideally, a practical solution (i) should be implementable in a relational database, and (ii) its query cost should grow sub-linearly with the dataset size, regardless of the data and query distributions. Despite the bulk of NN literature, no solution fulfills both requirements, except locality sensitive hashing (LSH). The existing LSH implementations are either rigorous or adhoc. Rigorous-LSH ensures good quality of query results, but requires expensive space and query cost. Although adhoc-LSH is more efficient, it abandons quality control, i.e., the neighbor it outputs can be arbitrarily bad. As a result, currently no method is able to ensure both quality and efficiency simultaneously in practice. Motivated by this, we propose a new access method called the locality sensitive B-tree (LSB-tree) that enables fast highdimensional NN search with excellent quality. The combination of several LSB-trees leads to a structure called the LSB-forest that ensures the same result quality as rigorous-LSH, but reduces its space and query cost dramatically. The LSB-forest also outperforms adhoc-LSH, even though the latter has no quality guarantee. Besides its appealing theoretical properties, the LSB-tree itself also serves as an effective index that consumes linear space, and supports efficient updates. Our extensive experiments confirm that the LSB-tree is faster than (i) the state of the art of exact NN search by two orders of magnitude, and (ii) the best (linear-space) method of approximate retrieval by an order of magnitude, and at the same time, returns neighbors with much better quality. © 2009 ACM.

Spatial correlations between browsing on balsam fir by white-tailed deer and the nutritional value of neighboring winter forage.

Science.gov (United States)

Champagne, Emilie; Moore, Ben D; Côté, Steeve D; Tremblay, Jean-Pierre

2018-03-01

Associational effects, that is, the influence of neighboring plants on herbivory suffered by a plant, are an outcome of forage selection. Although forage selection is a hierarchical process, few studies have investigated associational effects at multiple spatial scales. Because the nutritional quality of plants can be spatially structured, it might differently influence associational effects across multiple scales. Our objective was to determine the radius of influence of neighbor density and nutritional quality on balsam fir ( Abies balsamea ) herbivory by white-tailed deer ( Odocoileus virginianus ) in winter. We quantified browsing rates on fir and the density and quality of neighboring trees in a series of 10-year-old cutovers on Anticosti Island (Canada). We used cross-correlations to investigate relationships between browsing rates and the density and nutritional quality of neighboring trees at distances up to 1,000 m. Balsam fir and white spruce ( Picea glauca ) fiber content and dry matter in vitro true digestibility were correlated with fir browsing rate at the finest extra-patch scale (across distance of up to 50 m) and between cutover areas (300-400 m). These correlations suggest associational effects, that is, low nutritional quality of neighbors reduces the likelihood of fir herbivory (associational defense). Our results may indicate associational effects mediated by intraspecific variation in plant quality and suggest that these effects could occur at scales from tens to hundreds of meters. Understanding associational effects could inform strategies for restoration or conservation; for example, planting of fir among existing natural regeneration could be concentrated in areas of low nutritional quality.

Who's Watching the Babies? Improving the Quality of Family, Friend, and Neighbor Child Care

Science.gov (United States)

Powell, Douglas R.

2008-01-01

One of the important influences on a child's development is the quality of his or her early care and education experiences. It is estimated that more than 1 million children in the U.S. are cared for while their parents are at work by nonlicensed caregivers who are family, friends, or neighbors - and these caregivers can be difficult to reach…

Regulation of the Apolipoprotein Gene Cluster by a Long Noncoding RNA

Directory of Open Access Journals (Sweden)

Paul Halley

2014-01-01

Full Text Available Apolipoprotein A1 (APOA1 is the major protein component of high-density lipoprotein (HDL in plasma. We have identified an endogenously expressed long noncoding natural antisense transcript, APOA1-AS, which acts as a negative transcriptional regulator of APOA1 both in vitro and in vivo. Inhibition of APOA1-AS in cultured cells resulted in the increased expression of APOA1 and two neighboring genes in the APO cluster. Chromatin immunoprecipitation (ChIP analyses of a ∼50 kb chromatin region flanking the APOA1 gene demonstrated that APOA1-AS can modulate distinct histone methylation patterns that mark active and/or inactive gene expression through the recruitment of histone-modifying enzymes. Targeting APOA1-AS with short antisense oligonucleotides also enhanced APOA1 expression in both human and monkey liver cells and induced an increase in hepatic RNA and protein expression in African green monkeys. Furthermore, the results presented here highlight the significant local modulatory effects of long noncoding antisense RNAs and demonstrate the therapeutic potential of manipulating the expression of these transcripts both in vitro and in vivo.

Protein function prediction using neighbor relativity in protein-protein interaction network.

Science.gov (United States)

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

OpenAIRE

Richaud, F; Richaud, C; Ratet, P; Patte, J C

1986-01-01

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amin...

Radionuclide content of an exhumed canyon vessel and neighboring soil

International Nuclear Information System (INIS)

Holcomb, H.P.

1976-11-01

The long-term hazard potential associated with burial of process equipment from radiochemical separations plants is being evaluated. As part of this evaluation, a feed adjustment tank was exhumed eighteen years after burial. The tank had been in service in the fuel reprocessing plant for twenty-nine months before it was retired. Assay of the exhumed tank indicated that 7 mg (0.4 mCi) of 239 Pu and 1 mCi of 137 Cs remained on its surfaces; 1.1 mg (0.07 mCi) 239 Pu, 0.4 mCi 137 Cs, and 3.5 mCi 90 Sr were found in neighboring soil. The vessel and surrounding soil have met the present guidelines (less than or equal to 10 nCi/g) of the U. S. Energy Research and Development Administration (ERDA) for nonretrievable waste

Perceptual inequality between two neighboring time intervals defined by sound markers: correspondence between neurophysiological and psychological data

Directory of Open Access Journals (Sweden)

Takako eMitsudo

2014-09-01

Full Text Available Brain activity related to time estimation processes in humans was analyzed using a perceptual phenomenon called auditory temporal assimilation. In a typical stimulus condition, two neighboring time intervals (T1 and T2 in this order are perceived as equal even when the physical lengths of these time intervals are considerably different. Our previous event-related potential (ERP study demonstrated that a slow negative component (SNCt appears in the right-frontal brain area (around the F8 electrode after T2, which is associated with judgment of the equality/inequality of T1 and T2. In the present study, we conducted two ERP experiments to further confirm the robustness of the SNCt. The stimulus patterns consisted of two neighboring time intervals marked by three successive tone bursts. Thirteen participants only listened to the patterns in the first session, and judged the equality/inequality of T1 and T2 in the next session. Behavioral data showed typical temporal assimilation. The ERP data revealed that three components (N1; contingent negative variation, CNV; and SNCt emerged related to the temporal judgment. The N1 appeared in the central area, and its peak latencies corresponded to the physical timing of each marker onset. The CNV component appeared in the frontal area during T2 presentation, and its amplitude increased as a function of T1. The SNCt appeared in the right-frontal area after the presentation of T1 and T2, and its magnitude was larger for the temporal patterns causing perceptual inequality. The SNCt was also correlated with the perceptual equality/inequality of the same stimulus pattern, and continued up to about 400 ms after the end of T2. These results suggest that the SNCt can be a signature of equality/inequality judgment, which derives from the comparison of the two neighboring time intervals.

ANN-Benchmarks: A Benchmarking Tool for Approximate Nearest Neighbor Algorithms

DEFF Research Database (Denmark)

Aumüller, Martin; Bernhardsson, Erik; Faithfull, Alexander

2017-01-01

This paper describes ANN-Benchmarks, a tool for evaluating the performance of in-memory approximate nearest neighbor algorithms. It provides a standard interface for measuring the performance and quality achieved by nearest neighbor algorithms on different standard data sets. It supports several...... visualise these as images, Open image in new window plots, and websites with interactive plots. ANN-Benchmarks aims to provide a constantly updated overview of the current state of the art of k-NN algorithms. In the short term, this overview allows users to choose the correct k-NN algorithm and parameters...... for their similarity search task; in the longer term, algorithm designers will be able to use this overview to test and refine automatic parameter tuning. The paper gives an overview of the system, evaluates the results of the benchmark, and points out directions for future work. Interestingly, very different...

What Will the Neighbors Think? Building Large-Scale Science Projects Around the World

International Nuclear Information System (INIS)

Jones, Craig; Mrotzek, Christian; Toge, Nobu; Sarno, Doug

2007-01-01

Public participation is an essential ingredient for turning the International Linear Collider into a reality. Wherever the proposed particle accelerator is sited in the world, its neighbors -- in any country -- will have something to say about hosting a 35-kilometer-long collider in their backyards. When it comes to building large-scale physics projects, almost every laboratory has a story to tell. Three case studies from Japan, Germany and the US will be presented to examine how community relations are handled in different parts of the world. How do particle physics laboratories interact with their local communities? How do neighbors react to building large-scale projects in each region? How can the lessons learned from past experiences help in building the next big project? These and other questions will be discussed to engage the audience in an active dialogue about how a large-scale project like the ILC can be a good neighbor.

A new approach to very short term wind speed prediction using k-nearest neighbor classification

International Nuclear Information System (INIS)

Yesilbudak, Mehmet; Sagiroglu, Seref; Colak, Ilhami

2013-01-01

Highlights: ► Wind speed parameter was predicted in an n-tupled inputs using k-NN classification. ► The effects of input parameters, nearest neighbors and distance metrics were analyzed. ► Many useful and reasonable inferences were uncovered using the developed model. - Abstract: Wind energy is an inexhaustible energy source and wind power production has been growing rapidly in recent years. However, wind power has a non-schedulable nature due to wind speed variations. Hence, wind speed prediction is an indispensable requirement for power system operators. This paper predicts wind speed parameter in an n-tupled inputs using k-nearest neighbor (k-NN) classification and analyzes the effects of input parameters, nearest neighbors and distance metrics on wind speed prediction. The k-NN classification model was developed using the object oriented programming techniques and includes Manhattan and Minkowski distance metrics except from Euclidean distance metric on the contrary of literature. The k-NN classification model which uses wind direction, air temperature, atmospheric pressure and relative humidity parameters in a 4-tupled space achieved the best wind speed prediction for k = 5 in the Manhattan distance metric. Differently, the k-NN classification model which uses wind direction, air temperature and atmospheric pressure parameters in a 3-tupled inputs gave the worst wind speed prediction for k = 1 in the Minkowski distance metric

The square Ising model with second-neighbor interactions and the Ising chain in a transverse field

International Nuclear Information System (INIS)

Grynberg, M.D.; Tanatar, B.

1991-06-01

We consider the thermal and critical behaviour of the square Ising lattice with frustrated first - and second-neighbor interactions. A low-temperature domain wall analysis including kinks and dislocations shows that there is a close relation between this classical model and the Hamiltonian of an Ising chain in a transverse field provided that the ratio of the next-nearest to nearest-neighbor coupling, is close to 1/2. Due to the field inversion symmetry of the Ising chain Hamiltonian, the thermal properties of the classical system are symmetrical with respect to this coupling ratio. In the neighborhood of this regime critical exponents of the model turn out to belong to the Ising universality class. Our results are compared with previous Monte Carlo simulations. (author). 23 refs, 6 figs

Optimizing Neighbor Discovery for Ad hoc Networks based on the Bluetooth PAN Profile

DEFF Research Database (Denmark)

Kuijpers, Gerben; Nielsen, Thomas Toftegaard; Prasad, Ramjee

2002-01-01

IP layer neighbor discovery mechanisms rely highly on broadcast/multicast capabilities of the underlying link layer. The Bluetooth personal area network (PAN) profile has no native link layer broadcast/multicast capabilities and can only emulate this by repeatedly unicast link layer frames....... This paper introduces a neighbor discovery mechanism that utilizes the resources in the Bluetooth PAN profile more efficient. The performance of the new mechanism is investigated using a IPv6 network simulator and compared with emulated broadcasting. It is shown that the signaling overhead can...

Integration and analysis of neighbor discovery and link quality estimation in wireless sensor networks.

Science.gov (United States)

Radi, Marjan; Dezfouli, Behnam; Abu Bakar, Kamalrulnizam; Abd Razak, Shukor

2014-01-01

Network connectivity and link quality information are the fundamental requirements of wireless sensor network protocols to perform their desired functionality. Most of the existing discovery protocols have only focused on the neighbor discovery problem, while a few number of them provide an integrated neighbor search and link estimation. As these protocols require a careful parameter adjustment before network deployment, they cannot provide scalable and accurate network initialization in large-scale dense wireless sensor networks with random topology. Furthermore, performance of these protocols has not entirely been evaluated yet. In this paper, we perform a comprehensive simulation study on the efficiency of employing adaptive protocols compared to the existing nonadaptive protocols for initializing sensor networks with random topology. In this regard, we propose adaptive network initialization protocols which integrate the initial neighbor discovery with link quality estimation process to initialize large-scale dense wireless sensor networks without requiring any parameter adjustment before network deployment. To the best of our knowledge, this work is the first attempt to provide a detailed simulation study on the performance of integrated neighbor discovery and link quality estimation protocols for initializing sensor networks. This study can help system designers to determine the most appropriate approach for different applications.

Integration and Analysis of Neighbor Discovery and Link Quality Estimation in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Marjan Radi

2014-01-01

Full Text Available Network connectivity and link quality information are the fundamental requirements of wireless sensor network protocols to perform their desired functionality. Most of the existing discovery protocols have only focused on the neighbor discovery problem, while a few number of them provide an integrated neighbor search and link estimation. As these protocols require a careful parameter adjustment before network deployment, they cannot provide scalable and accurate network initialization in large-scale dense wireless sensor networks with random topology. Furthermore, performance of these protocols has not entirely been evaluated yet. In this paper, we perform a comprehensive simulation study on the efficiency of employing adaptive protocols compared to the existing nonadaptive protocols for initializing sensor networks with random topology. In this regard, we propose adaptive network initialization protocols which integrate the initial neighbor discovery with link quality estimation process to initialize large-scale dense wireless sensor networks without requiring any parameter adjustment before network deployment. To the best of our knowledge, this work is the first attempt to provide a detailed simulation study on the performance of integrated neighbor discovery and link quality estimation protocols for initializing sensor networks. This study can help system designers to determine the most appropriate approach for different applications.

Transfer-Efficient Face Routing Using the Planar Graphs of Neighbors in High Density WSNs

Directory of Open Access Journals (Sweden)

Eun-Seok Cho

2017-10-01

Full Text Available Face routing has been adopted in wireless sensor networks (WSNs where topological changes occur frequently or maintaining full network information is difficult. For message forwarding in networks, a planar graph is used to prevent looping, and because long edges are removed by planarization and the resulting planar graph is composed of short edges, and messages are forwarded along multiple nodes connected by them even though they can be forwarded directly. To solve this, face routing using information on all nodes within 2-hop range was adopted to forward messages directly to the farthest node within radio range. However, as the density of the nodes increases, network performance plunges because message transfer nodes receive and process increased node information. To deal with this problem, we propose a new face routing using the planar graphs of neighboring nodes to improve transfer efficiency. It forwards a message directly to the farthest neighbor and reduces loads and processing time by distributing network graph construction and planarization to the neighbors. It also decreases the amount of location information to be transmitted by sending information on the planar graph nodes rather than on all neighboring nodes. Simulation results show that it significantly improves transfer efficiency.

A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates

DEFF Research Database (Denmark)

Hobolth, Asger

2008-01-01

The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous rate of substitution at a site depends on the states of the neighboring sites. Neighbor...

Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

Science.gov (United States)

Richaud, F; Richaud, C; Ratet, P; Patte, J C

1986-04-01

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons.

Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

Science.gov (United States)

Richaud, F; Richaud, C; Ratet, P; Patte, J C

1986-01-01

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons. Images PMID:3514578

75 FR 62412 - Notice of Proposed Information Collection: Comment Request; HUD-Owned Real Estate-Good Neighbor...

Science.gov (United States)

2010-10-08

... DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT [Docket No. FR-5380-N-36] Notice of Proposed Information Collection: Comment Request; HUD- Owned Real Estate-Good Neighbor Next Door Program AGENCY: Office... information: Title of Proposal: HUD-Owned Real Estate-Good Neighbor Next Door Program. OMB Control Number, if...

Local and neighboring patch conditions alter sex-specific movement in banana weevils.

Science.gov (United States)

Carval, Dominique; Perrin, Benjamin; Duyck, Pierre-François; Tixier, Philippe

2015-12-01

Understanding the mechanisms underlying the movements and spread of a species over time and space is a major concern of ecology. Here, we assessed the effects of an individual's sex and the density and sex ratio of conspecifics in the local and neighboring environment on the movement probability of the banana weevil, Cosmopolites sordidus. In a "two patches" experiment, we used radiofrequency identification tags to study the C. sordidus movement response to patch conditions. We showed that local and neighboring densities of conspecifics affect the movement rates of individuals but that the density-dependent effect can be either positive or negative depending on the relative densities of conspecifics in local and neighboring patches. We demonstrated that sex ratio also influences the movement of C. sordidus, that is, the weevil exhibits nonfixed sex-biased movement strategies. Sex-biased movement may be the consequence of intrasexual competition for resources (i.e., oviposition sites) in females and for mates in males. We also detected a high individual variability in the propensity to move. Finally, we discuss the role of demographic stochasticity, sex-biased movement, and individual heterogeneity in movement on the colonization process.

Clock gene modulates roles of OXTR and AVPR1b genes in prosociality.

Directory of Open Access Journals (Sweden)

Haipeng Ci

Full Text Available BACKGROUND: The arginine vasopressin receptor (AVPR and oxytocin receptor (OXTR genes have been demonstrated to contribute to prosocial behavior. Recent research has focused on the manner by which these simple receptor genes influence prosociality, particularly with regard to the AVP system, which is modulated by the clock gene. The clock gene is responsible for regulating the human biological clock, affecting sleep, emotion and behavior. The current study examined in detail whether the influences of the OXTR and AVPR1b genes on prosociality are dependent on the clock gene. METHODOLOGY/PRINCIPAL FINDINGS: This study assessed interactions between the clock gene (rs1801260, rs6832769 and the OXTR (rs1042778, rs237887 and AVPR1b (rs28373064 genes in association with individual differences in prosociality in healthy male Chinese subjects (n = 436. The Prosocial Tendencies Measure (PTM-R was used to assess prosociality. Participants carrying both the GG/GA variant of AVPR1b rs28373064 and the AA variant of clock rs6832769 showed the highest scores on the Emotional PTM. Carriers of both the T allele of OXTR rs1042778 and the C allele of clock rs1801260 showed the lowest total PTM scores compared with the other groups. CONCLUSIONS: The observed interaction effects provide converging evidence that the clock gene and OXT/AVP systems are intertwined and contribute to human prosociality.

Clock gene modulates roles of OXTR and AVPR1b genes in prosociality.

Science.gov (United States)

Ci, Haipeng; Wu, Nan; Su, Yanjie

2014-01-01

The arginine vasopressin receptor (AVPR) and oxytocin receptor (OXTR) genes have been demonstrated to contribute to prosocial behavior. Recent research has focused on the manner by which these simple receptor genes influence prosociality, particularly with regard to the AVP system, which is modulated by the clock gene. The clock gene is responsible for regulating the human biological clock, affecting sleep, emotion and behavior. The current study examined in detail whether the influences of the OXTR and AVPR1b genes on prosociality are dependent on the clock gene. This study assessed interactions between the clock gene (rs1801260, rs6832769) and the OXTR (rs1042778, rs237887) and AVPR1b (rs28373064) genes in association with individual differences in prosociality in healthy male Chinese subjects (n = 436). The Prosocial Tendencies Measure (PTM-R) was used to assess prosociality. Participants carrying both the GG/GA variant of AVPR1b rs28373064 and the AA variant of clock rs6832769 showed the highest scores on the Emotional PTM. Carriers of both the T allele of OXTR rs1042778 and the C allele of clock rs1801260 showed the lowest total PTM scores compared with the other groups. The observed interaction effects provide converging evidence that the clock gene and OXT/AVP systems are intertwined and contribute to human prosociality.

Impact of Training Bolivian Farmers on Integrated Pest Management and Diffusion of Knowledge to Neighboring Farmers.

Science.gov (United States)

Jørs, Erik; Konradsen, Flemming; Huici, Omar; Morant, Rafael C; Volk, Julie; Lander, Flemming

2016-01-01

Teaching farmers integrated pest management (IPM) in farmer field schools (FFS) has led to reduced pesticide use and safer handling. This article evaluates the long-term impact of training farmers on IPM and the diffusion of knowledge from trained farmers to neighboring farmers, a subject of importance to justify training costs and to promote a healthy and sustainable agriculture. Training on IPM of farmers took place from 2002 to 2004 in their villages in La Paz County, Bolivia, whereas dissemination of knowledge from trained farmer to neighboring farmer took place until 2009. To evaluate the impact of the intervention, self-reported knowledge and practice on pesticide handling and IPM among trained farmers (n = 23) and their neighboring farmers (n = 47) were analyzed in a follow-up study and compared in a cross-sectional analysis with a control group of farmers (n = 138) introduced in 2009. Variables were analyzed using χ2 test and analysis of variance (ANOVA). Trained farmers improved and performed significantly better in all tested variables than their neighboring farmers, although the latter also improved their performance from 2002 to 2009. Including a control group showed an increasing trend in all variables, with the control farmers having the poorest performance and trained farmers the best. The same was seen in an aggregated variable where trained farmers had a mean score of 16.55 (95% confidence interval [CI]: 15.45-17.65), neighboring farmers a mean score of 11.97 (95% CI: 10.56-13.38), and control farmers a mean score of 9.18 (95% CI: 8.55-9.80). Controlling for age and living altitude did not change these results. Trained farmers and their neighboring farmers improved and maintained knowledge and practice on IPM and pesticide handling. Diffusion of knowledge from trained farmers might explain the better performance of the neighboring farmers compared with the control farmers. Dissemination of knowledge can contribute to justify the cost and convince

Studying nearest neighbor correlations by atom probe tomography (APT) in metallic glasses as exemplified for Fe40Ni40B20 glassy ribbons

KAUST Repository

Shariq, Ahmed

2012-01-01

A next nearest neighbor evaluation procedure of atom probe tomography data provides distributions of the distances between atoms. The width of these distributions for metallic glasses studied so far is a few Angstrom reflecting the spatial resolution of the analytical technique. However, fitting Gaussian distributions to the distribution of atomic distances yields average distances with statistical uncertainties of 2 to 3 hundredth of an Angstrom. Fe 40Ni40B20 metallic glass ribbons are characterized this way in the as quenched state and for a state heat treated at 350 °C for 1 h revealing a change in the structure on the sub-nanometer scale. By applying the statistical tool of the χ2 test a slight deviation from a random distribution of B-atoms in the as quenched sample is perceived, whereas a pronounced elemental inhomogeneity of boron is detected for the annealed state. In addition, the distance distribution of the first fifteen atomic neighbors is determined by using this algorithm for both annealed and as quenched states. The next neighbor evaluation algorithm evinces a steric periodicity of the atoms when the next neighbor distances are normalized by the first next neighbor distance. A comparison of the nearest neighbor atomic distribution for as quenched and annealed state shows accumulation of Ni and B. Moreover, it also reveals the tendency of Fe and B to move slightly away from each other, an incipient step to Ni rich boride formation. © 2011 Elsevier B.V.

PPB | What is the DICER1 gene?

Science.gov (United States)

DICER1 is a gene that manages the function of other genes. Inherited changes in DICER1 can result in a variety of tumors, including pleuropulmonary blastoma (PPB). The PPB DICER1 Syndrome Study ‹an observational clinical research study is enrolling children with PPB and their families.

RNAi-Based Identification of Gene-Specific Nuclear Cofactor Networks Regulating Interleukin-1 Target Genes

Directory of Open Access Journals (Sweden)

Johanna Meier-Soelch

2018-04-01

Full Text Available The potent proinflammatory cytokine interleukin (IL-1 triggers gene expression through the NF-κB signaling pathway. Here, we investigated the cofactor requirements of strongly regulated IL-1 target genes whose expression is impaired in p65 NF-κB-deficient murine embryonic fibroblasts. By two independent small-hairpin (shRNA screens, we examined 170 genes annotated to encode nuclear cofactors for their role in Cxcl2 mRNA expression and identified 22 factors that modulated basal or IL-1-inducible Cxcl2 levels. The functions of 16 of these factors were validated for Cxcl2 and further analyzed for their role in regulation of 10 additional IL-1 target genes by RT-qPCR. These data reveal that each inducible gene has its own (quantitative requirement of cofactors to maintain basal levels and to respond to IL-1. Twelve factors (Epc1, H2afz, Kdm2b, Kdm6a, Mbd3, Mta2, Phf21a, Ruvbl1, Sin3b, Suv420h1, Taf1, and Ube3a have not been previously implicated in inflammatory cytokine functions. Bioinformatics analysis indicates that they are components of complex nuclear protein networks that regulate chromatin functions and gene transcription. Collectively, these data suggest that downstream from the essential NF-κB signal each cytokine-inducible target gene has further subtle requirements for individual sets of nuclear cofactors that shape its transcriptional activation profile.

Effect of Floquet engineering on the p-wave superconductor with second-neighbor couplings

Science.gov (United States)

Li, X. P.; Li, C. F.; Wang, L. C.; Zhou, L.

2018-06-01

The influence of the Floquet engineering on a particular one-dimensional p-wave superconductor, Kitaev model, with second-neighbor couplings is investigated in this paper. The effective Hamiltonians in the rotated reference frames have been obtained, and the convergent regions of the approximated Hamiltonian as well as the topological phase diagrams have been analyzed and discussed. We show that by modulating the external driving field amplitude, frequency as well as the second-neighbor hopping amplitude, the rich phase diagrams and transitions between different topological phases can be obtained.

Classification of EEG Signals using adaptive weighted distance nearest neighbor algorithm

Directory of Open Access Journals (Sweden)

E. Parvinnia

2014-01-01

Full Text Available Electroencephalogram (EEG signals are often used to diagnose diseases such as seizure, alzheimer, and schizophrenia. One main problem with the recorded EEG samples is that they are not equally reliable due to the artifacts at the time of recording. EEG signal classification algorithms should have a mechanism to handle this issue. It seems that using adaptive classifiers can be useful for the biological signals such as EEG. In this paper, a general adaptive method named weighted distance nearest neighbor (WDNN is applied for EEG signal classification to tackle this problem. This classification algorithm assigns a weight to each training sample to control its influence in classifying test samples. The weights of training samples are used to find the nearest neighbor of an input query pattern. To assess the performance of this scheme, EEG signals of thirteen schizophrenic patients and eighteen normal subjects are analyzed for the classification of these two groups. Several features including, fractal dimension, band power and autoregressive (AR model are extracted from EEG signals. The classification results are evaluated using Leave one (subject out cross validation for reliable estimation. The results indicate that combination of WDNN and selected features can significantly outperform the basic nearest-neighbor and the other methods proposed in the past for the classification of these two groups. Therefore, this method can be a complementary tool for specialists to distinguish schizophrenia disorder.

The genomic structure of the DMBT1 gene

DEFF Research Database (Denmark)

Mollenhauer, J; Holmskov, U; Wiemann, S

1999-01-01

Increasing evidence has accumulated for an involvement of the inactivation of tumour suppressor genes at chromosome 10q in the carcinogenesis of brain tumours, melanomas, and carcinomas of the lung, the prostate, the pancreas, and the endometrium. The gene DMBT1 (Deleted in Malignant Brain Tumours...... 1) is located at chromosome 10q25.3-q26.1, within one of the putative intervals for tumour suppressor genes. DMBT1 is a member of the scavenger-receptor cysteine-rich (SRCR) superfamily and displays homozygous deletions or lack of expression in glioblastoma multiforme, medulloblastoma......, and in gastrointestinal and lung cancers. Based on these properties, DMBT1 has been proposed to be a candidate tumour suppressor gene. We have determined the genomic sequence of DMBT1 to allow analyses of mutations. The gene has at least 54 exons that span a genomic region of about 80 kb. We have identified a putative...

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

ajl yemi

2011-11-28

Nov 28, 2011 ... Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is ... case, the expression of human lysozyme could be regulated by the endogenous cis-element of αs1- casein gene in .... Mouse mammary epithelial C127 cells (Cell Bank, Chinese. Academy of ...

Cloning, characterization, and expression of the dapE gene of Escherichia coli.

OpenAIRE

Bouvier, J; Richaud, C; Higgins, W; Bögler, O; Stragier, P

1992-01-01

The dapE gene of Escherichia coli encodes N-succinyl-L-diaminopimelic acid desuccinylase, an enzyme that catalyzes the synthesis of LL-diaminopimelic acid, one of the last steps in the diaminopimelic acid-lysine pathway. The dapE gene region was previously purified from a lambda bacteriophage transducing the neighboring purC gene (J. Parker, J. Bacteriol. 157:712-717, 1984). Various subcloning steps led to the identification of a 2.3-kb fragment that complemented several dapE mutants and allo...

Alteration of the SETBP1 gene and splicing pathway genes SF3B1, U2AF1, and SRSF2 in childhood acute myeloid leukemia.

Science.gov (United States)

Choi, Hyun-Woo; Kim, Hye-Ran; Baek, Hee-Jo; Kook, Hoon; Cho, Duck; Shin, Jong-Hee; Suh, Soon-Pal; Ryang, Dong-Wook; Shin, Myung-Geun

2015-01-01

Recurrent somatic SET-binding protein 1 (SETBP1) and splicing pathway gene mutations have recently been found in atypical chronic myeloid leukemia and other hematologic malignancies. These mutations have been comprehensively analyzed in adult AML, but not in childhood AML. We investigated possible alteration of the SETBP1, splicing factor 3B subunit 1 (SF3B1), U2 small nuclear RNA auxiliary factor 1 (U2AF1), and serine/arginine-rich splicing factor 2 (SRSF2) genes in childhood AML. Cytogenetic and molecular analyses were performed to reveal chromosomal and genetic alterations. Sequence alterations in the SETBP1, SF3B1, U2AF1, and SRSF2 genes were examined by using direct sequencing in a cohort of 53 childhood AML patients. Childhood AML patients did not harbor any recurrent SETBP1 gene mutations, although our study did identify a synonymous mutation in one patient. None of the previously reported aberrations in the mutational hotspot of SF3B1, U2AF1, and SRSF2 were identified in any of the 53 patients. Alterations of the SETBP1 gene or SF3B1, U2AF1, and SRSF2 genes are not common genetic events in childhood AML, implying that the mutations are unlikely to exert a driver effect in myeloid leukemogenesis during childhood.

Genetic polymorphisms in CYP1A1, GSTM1, GSTP1 and GSTT1 metabolic genes and risk of lung cancer in Asturias

International Nuclear Information System (INIS)

López-Cima, M Felicitas; Álvarez-Avellón, Sara M; Pascual, Teresa; Fernández-Somoano, Ana; Tardón, Adonina

2012-01-01

Metabolic genes have been associated with the function of metabolizing and detoxifying environmental carcinogens. Polymorphisms present in these genes could lead to changes in their metabolizing and detoxifying ability and thus may contribute to individual susceptibility to different types of cancer. We investigated if the individual and/or combined modifying effects of the CYP1A1 MspI T6235C, GSTM1 present/null, GSTT1 present/null and GSTP1 Ile105Val polymorphisms are related to the risk of developing lung cancer in relation to tobacco consumption and occupation in Asturias, Northern Spain. A hospital-based case–control study (CAPUA Study) was designed including 789 lung cancer patients and 789 control subjects matched in ethnicity, age, sex, and hospital. Genotypes were determined by PCR or PCR-RFLP. Individual and combination effects were analysed using an unconditional logistic regression adjusting for age, pack-years, family history of any cancer and occupation. No statistically significant main effects were observed for the carcinogen metabolism genes in relation to lung cancer risk. In addition, the analysis did not reveal any significant gene-gene, gene-tobacco smoking or gene-occupational exposure interactions relative to lung cancer susceptibility. Lastly, no significant gene-gene combination effects were observed. These results suggest that genetic polymorphisms in the CYP1A1, GSTM1, GSTT1 and GSTP1 metabolic genes were not significantly associated with lung cancer risk in the current study. The results of the analysis of gene-gene interactions of CYP1A1 MspI T6235C, GSTM1 present/null, GSTT1 present/null and GSTP1 Ile105Val polymorphisms in lung cancer risk indicate that these genes do not interact in lung cancer development

Raman scattering mediated by neighboring molecules

Science.gov (United States)

Williams, Mathew D.; Bradshaw, David S.; Andrews, David L.

2016-05-01

Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

Raman scattering mediated by neighboring molecules

Energy Technology Data Exchange (ETDEWEB)

Williams, Mathew D.; Bradshaw, David S.; Andrews, David L., E-mail: david.andrews@physics.org [School of Chemistry, University of East Anglia, Norwich NR4 7TJ (United Kingdom)

2016-05-07

Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development.

Science.gov (United States)

Ding, Mingquan; Jiang, Yurong; Cao, Yuefen; Lin, Lifeng; He, Shae; Zhou, Wei; Rong, Junkang

2014-02-10

Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1. Copyright © 2013 Elsevier B.V. All rights reserved.

Gene-gene combination effect and interactions among ABCA1, APOA1, SR-B1, and CETP polymorphisms for serum high-density lipoprotein-cholesterol in the Japanese population.

Directory of Open Access Journals (Sweden)

Akihiko Nakamura

Full Text Available BACKGROUND/OBJECTIVE: Gene-gene interactions in the reverse cholesterol transport system for high-density lipoprotein-cholesterol (HDL-C are poorly understood. The present study observed gene-gene combination effect and interactions between single nucleotide polymorphisms (SNPs in ABCA1, APOA1, SR-B1, and CETP in serum HDL-C from a cross-sectional study in the Japanese population. METHODS: The study population comprised 1,535 men and 1,515 women aged 35-69 years who were enrolled in the Japan Multi-Institutional Collaborative Cohort (J-MICC Study. We selected 13 SNPs in the ABCA1, APOA1, CETP, and SR-B1 genes in the reverse cholesterol transport system. The effects of genetic and environmental factors were assessed using general linear and logistic regression models after adjusting for age, sex, and region. PRINCIPAL FINDINGS: Alcohol consumption and daily activity were positively associated with HDL-C levels, whereas smoking had a negative relationship. The T allele of CETP, rs3764261, was correlated with higher HDL-C levels and had the highest coefficient (2.93 mg/dL/allele among the 13 SNPs, which was statistically significant after applying the Bonferroni correction (p<0.001. Gene-gene combination analysis revealed that CETP rs3764261 was associated with high HDL-C levels with any combination of SNPs from ABCA1, APOA1, and SR-B1, although no gene-gene interaction was apparent. An increasing trend for serum HDL-C was also observed with an increasing number of alleles (p<0.001. CONCLUSIONS: The present study identified a multiplier effect from a polymorphism in CETP with ABCA1, APOA1, and SR-B1, as well as a dose-dependence according to the number of alleles present.

Detecting PM2.5's Correlations between Neighboring Cities Using a Time-Lagged Cross-Correlation Coefficient.

Science.gov (United States)

Wang, Fang; Wang, Lin; Chen, Yuming

2017-08-31

In order to investigate the time-dependent cross-correlations of fine particulate (PM2.5) series among neighboring cities in Northern China, in this paper, we propose a new cross-correlation coefficient, the time-lagged q-L dependent height crosscorrelation coefficient (denoted by p q (τ, L)), which incorporates the time-lag factor and the fluctuation amplitude information into the analogous height cross-correlation analysis coefficient. Numerical tests are performed to illustrate that the newly proposed coefficient ρ q (τ, L) can be used to detect cross-correlations between two series with time lags and to identify different range of fluctuations at which two series possess cross-correlations. Applying the new coefficient to analyze the time-dependent cross-correlations of PM2.5 series between Beijing and the three neighboring cities of Tianjin, Zhangjiakou, and Baoding, we find that time lags between the PM2.5 series with larger fluctuations are longer than those between PM2.5 series withsmaller fluctuations. Our analysis also shows that cross-correlations between the PM2.5 series of two neighboring cities are significant and the time lags between two PM2.5 series of neighboring cities are significantly non-zero. These findings providenew scientific support on the view that air pollution in neighboring cities can affect one another not simultaneously but with a time lag.

Cloning and sequencing of phenol oxidase 1 (pox1) gene from ...

African Journals Online (AJOL)

The gene (pox1) encoding a phenol oxidase 1 from Pleurotus ostreatus was sequenced and the corresponding pox1-cDNA was also synthesized, cloned and sequenced. The isolated gene is flanked by an upstream region called the promoter (399 bp) prior to the start codon (ATG). The putative metalresponsive elements ...

Social dilemma alleviated by sharing the gains with immediate neighbors

Science.gov (United States)

Wu, Zhi-Xi; Yang, Han-Xin

2014-01-01

We study the evolution of cooperation in the evolutionary spatial prisoner's dilemma game (PDG) and snowdrift game (SG), within which a fraction α of the payoffs of each player gained from direct game interactions is shared equally by the immediate neighbors. The magnitude of the parameter α therefore characterizes the degree of the relatedness among the neighboring players. By means of extensive Monte Carlo simulations as well as an extended mean-field approximation method, we trace the frequency of cooperation in the stationary state. We find that plugging into relatedness can significantly promote the evolution of cooperation in the context of both studied games. Unexpectedly, cooperation can be more readily established in the spatial PDG than that in the spatial SG, given that the degree of relatedness and the cost-to-benefit ratio of mutual cooperation are properly formulated. The relevance of our model with the stakeholder theory is also briefly discussed.

Genome-wide identification of KANADI1 target genes.

Directory of Open Access Journals (Sweden)

Paz Merelo

Full Text Available Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV. A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.

Electronic transport of molecular nanowires by considering of electron hopping energy between the second neighbors

Directory of Open Access Journals (Sweden)

H Rabani

2015-07-01

Full Text Available In this paper, we study the electronic conductance of molecular nanowires by considering the electron hopping between the first and second neighbors with the help Green’s function method at the tight-binding approach. We investigate three types of structures including linear uniform and periodic chains as well as poly(p-phenylene molecule which are embedded between two semi-infinite metallic leads. The results show that in the second neighbor approximation, the resonance, anti-resonance and Fano phenomena occur in the conductance spectra of these structures. Moreover, a new gap is observed at edge of the lead energy band wich its width depends on the value of the electron hopping energy between the second neighbors. In the systems including intrinsic gap, this hopping energy shifts the gap in the energy spectra.

Multi-strategy based quantum cost reduction of linear nearest-neighbor quantum circuit

Science.gov (United States)

Tan, Ying-ying; Cheng, Xue-yun; Guan, Zhi-jin; Liu, Yang; Ma, Haiying

2018-03-01

With the development of reversible and quantum computing, study of reversible and quantum circuits has also developed rapidly. Due to physical constraints, most quantum circuits require quantum gates to interact on adjacent quantum bits. However, many existing quantum circuits nearest-neighbor have large quantum cost. Therefore, how to effectively reduce quantum cost is becoming a popular research topic. In this paper, we proposed multiple optimization strategies to reduce the quantum cost of the circuit, that is, we reduce quantum cost from MCT gates decomposition, nearest neighbor and circuit simplification, respectively. The experimental results show that the proposed strategies can effectively reduce the quantum cost, and the maximum optimization rate is 30.61% compared to the corresponding results.

Role of NPR1 dependent and NPR1 independent genes in response to Salicylic acid

Directory of Open Access Journals (Sweden)

Neha Agarwal

2017-10-01

Full Text Available NPR1 (Nonexpressor of pathogenesis-related gene is a transcription coactivator and central regulator of systemic acquired resistance (SAR pathway. It controls wide range of pathogenesis related genes involved in various defense responses, acts by sensing SAR signal molecule, Salicylic acid (SA. Mutation in NPR1 results in increased susceptibility to pathogen infection and less expression of pathogenesis related genes. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction. For this RNA-seq was performed in Arabidopsis thaliana Col-0 and npr1-1 in response to Salicylic acid. RNA-seq analysis revealed a total of 3811 differentially expressed gene in which 2109 genes are up-regulated and 1702 genes are down-regulated. We have divided these genes in 6 categories SA induced (SI, SA repressed (SR, NPR1 dependent SI (ND-SI, NPR1 dependent SR (ND-SR, NPR1 independent SI (NI-SI, NPR1 independent SR (NI-SR. Further, Gene ontology and MapMan pathway analysis of differentially expressed genes suggested variety of biological processes and metabolic pathways that are enriched during SAR defense pathway. These results contribute to shed light on importance of both NPR1-dependent (ND and NPR1-independent (NI gene acting downstream to Salicylic acid induction in SAR pathway. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction.

Studies of Neurofibromatosis-1 Modifier Genes

Science.gov (United States)

2005-06-01

characterize patients of the FANCD1 complementation group (Howlett et al., 2002), and FANCA , which is the most frequently mutated FA gene , maps to a 650 kb...associations, we genotyped a total of 16 SNPs in FANCA and three immediately adjacent genes and collaborated with statistical geneticist Dr. Mark Daly at MIT to...across 15 SNPs in FANCA and the adjacent FLJ12547, CDKIO, and SPG7 genes . Red/pink coloration indicates statistical significance (LOD=3). The number in

Identification of Phosphoglycerate Kinase 1 (PGK1 as a reference gene for quantitative gene expression measurements in human blood RNA

Directory of Open Access Journals (Sweden)

Unger Elizabeth R

2011-09-01

Full Text Available Abstract Background Blood is a convenient sample and increasingly used for quantitative gene expression measurements with a variety of diseases including chronic fatigue syndrome (CFS. Quantitative gene expression measurements require normalization of target genes to reference genes that are stable and independent from variables being tested in the experiment. Because there are no genes that are useful for all situations, reference gene selection is an essential step to any quantitative reverse transcription-PCR protocol. Many publications have described appropriate genes for a wide variety of tissues and experimental conditions, however, reference genes that may be suitable for the analysis of CFS, or human blood RNA derived from whole blood as well as isolated peripheral blood mononuclear cells (PBMCs, have not been described. Findings Literature review and analyses of our unpublished microarray data were used to narrow down the pool of candidate reference genes to six. We assayed whole blood RNA from Tempus tubes and cell preparation tube (CPT-collected PBMC RNA from 46 subjects, and used the geNorm and NormFinder algorithms to select the most stable reference genes. Phosphoglycerate kinase 1 (PGK1 was one of the optimal normalization genes for both whole blood and PBMC RNA, however, additional genes differed for the two sample types; Ribosomal protein large, P0 (RPLP0 for PBMC RNA and Peptidylprolyl isomerase B (PPIB for whole blood RNA. We also show that the use of a single reference gene is sufficient for normalization when the most stable candidates are used. Conclusions We have identified PGK1 as a stable reference gene for use with whole blood RNA and RNA derived from PBMC. When stable genes are selected it is possible to use a single gene for normalization rather than two or three. Optimal normalization will improve the ability of results from PBMC RNA to be compared with those from whole blood RNA and potentially allows comparison of

A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates

DEFF Research Database (Denmark)

Hobolth, Asger

2008-01-01

-dimensional integrals required in the EM algorithm are estimated using MCMC sampling. The MCMC sampler requires simulation of sample paths from a continuous time Markov process, conditional on the beginning and ending states and the paths of the neighboring sites. An exact path sampling algorithm is developed......The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous rate of substitution at a site depends on the states of the neighboring sites. Neighbor......-dependent substitution models are analytically intractable and must be analyzed using either approximate or simulation-based methods. We describe statistical inference of neighbor-dependent models using a Markov chain Monte Carlo expectation maximization (MCMC-EM) algorithm. In the MCMC-EM algorithm, the high...

Thermodynamic systematics of oxides of americium, curium, and neighboring elements

International Nuclear Information System (INIS)

Morss, L.R.

1984-01-01

Recently-obtained calorimetric data on the sesquioxides and dioxides of americium and curium are summarized. These data are combined with other properties of the actinide elements to elucidate the stability relationships among these oxides and to predict the behavior of neighboring actinide oxides. 45 references, 4 figures, 5 tables

Flagellar-phase variation: isolation of the rh1 gene

International Nuclear Information System (INIS)

Silverman, M.; Zieg, J.; Simon, M.

1979-01-01

In Salmonella, expression of flagellar antigen alternates between two serotypes (phases) encoded by two genes, H1 and H2. The mechanism which controls the alternative expression of the H1 and H2 genes was examined by cloning these genes and the genetic elements which control their activity on hybrid vehicles in Escherichia coli. H2 gene activity was shown to be controlled by a recombinational switch located adjacent to the H2 gene. Activity of the H1 gene is thought to be repressed, when the H2 gene is expressed, by the product of another gene, rhl (repressor of H1), which is controlled coordinately with the H2 gene. In this report, we describe the construction of hybrid lambda vehicles which contain, in addition to the H2 gene, a genetic activity corresponding to rhl. Variation of flagellar antigens analogous to that observed in Salmonella was observed when E. coli strains were transduced with the hybrid lambda. By using the lambda H2rhl hybrid to program protein syntheis in uv-irradiated cells, the synthesis of a polypeptide was correlated with rhl gene product activity. We conclude that the H2 region consists of two cotranscribed genes, H2 and rhl. The expression of both gene products is regulated by the same recombinational event

A Hybrid Instance Selection Using Nearest-Neighbor for Cross-Project Defect Prediction

Institute of Scientific and Technical Information of China (English)

Duksan Ryu; Jong-In Jang; Jongmoon Baik; Member; ACM; IEEE

2015-01-01

Software defect prediction (SDP) is an active research field in software engineering to identify defect-prone modules. Thanks to SDP, limited testing resources can be effectively allocated to defect-prone modules. Although SDP requires suffcient local data within a company, there are cases where local data are not available, e.g., pilot projects. Companies without local data can employ cross-project defect prediction (CPDP) using external data to build classifiers. The major challenge of CPDP is different distributions between training and test data. To tackle this, instances of source data similar to target data are selected to build classifiers. Software datasets have a class imbalance problem meaning the ratio of defective class to clean class is far low. It usually lowers the performance of classifiers. We propose a Hybrid Instance Selection Using Nearest-Neighbor (HISNN) method that performs a hybrid classification selectively learning local knowledge (via k-nearest neighbor) and global knowledge (via na¨ıve Bayes). Instances having strong local knowledge are identified via nearest-neighbors with the same class label. Previous studies showed low PD (probability of detection) or high PF (probability of false alarm) which is impractical to use. The experimental results show that HISNN produces high overall performance as well as high PD and low PF.

In Silico Analysis of FMR1 Gene Missense SNPs.

Science.gov (United States)

Tekcan, Akin

2016-06-01

The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases.

Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

Directory of Open Access Journals (Sweden)

Chen Chuang

2012-10-01

Full Text Available Abstract Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms. Results Real-time quantitative PCR using DNA from the animal whose genome was sequenced (“Dominette” and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR “a” pattern of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms. Conclusion The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Poulsen, Flemming Martin

2011-01-01

Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

Behavior change communication activities improve infant and young child nutrition knowledge and practice of neighboring non-participants in a cluster-randomized trial in rural Bangladesh.

Science.gov (United States)

Hoddinott, John; Ahmed, Ishita; Ahmed, Akhter; Roy, Shalini

2017-01-01

To examine the impact on infant and young child nutrition knowledge and practice of mothers who were neighbors of mothers participating in a nutrition Behavior Change Communication (BCC) intervention in rural Bangladesh. We analyzed data from 300 mothers whose neighbor participated in a nutrition BCC intervention and 600 mothers whose neighbor participated in an intervention that did not include BCC. We constructed measures capturing mothers' knowledge of infant and young child nutrition (IYCN) and measures of food consumption by children 6-24m. The effect on these outcomes of exposure to a neighbor receiving a nutrition BCC intervention was estimated using ordinary least squares and probit regressions. The study was registered with ClinicalTrials.gov (Study ID: NCT02237144). Having a neighboring mother participate in a nutrition BCC intervention increased non-participant mothers' IYCN knowledge by 0.17 SD (translating to 0.3 more correct answers). They were 14.1 percentage points more likely to feed their 6-24m children legumes and nuts; 11.6 percentage points more likely to feed these children vitamin A rich fruits and vegetables; and 10.0 percentage points more likely to feed these children eggs. Children of non-participant mothers who had a neighboring mother participate in a nutrition BCC intervention were 13.8 percentage points more likely to meet World Health Organization (WHO) guidelines for minimum diet diversity, 11.9 percentage points more likely to meet WHO guidelines for minimum acceptable diet, and 10.3 percentage points more likely to meet WHO guidelines for minimum meal frequency for children who continue to be breastfed after age 6m. Children aged 0-6m of non-participant mothers who are neighbors of mothers receiving BCC were 7.1 percentage points less likely to have ever consumed water-based liquids. Studies of nutrition BCC that do not account for information spillovers to non-participants may underestimate its benefits in terms of IYCN knowledge

Behavior change communication activities improve infant and young child nutrition knowledge and practice of neighboring non-participants in a cluster-randomized trial in rural Bangladesh.

Directory of Open Access Journals (Sweden)

John Hoddinott

Full Text Available To examine the impact on infant and young child nutrition knowledge and practice of mothers who were neighbors of mothers participating in a nutrition Behavior Change Communication (BCC intervention in rural Bangladesh.We analyzed data from 300 mothers whose neighbor participated in a nutrition BCC intervention and 600 mothers whose neighbor participated in an intervention that did not include BCC. We constructed measures capturing mothers' knowledge of infant and young child nutrition (IYCN and measures of food consumption by children 6-24m. The effect on these outcomes of exposure to a neighbor receiving a nutrition BCC intervention was estimated using ordinary least squares and probit regressions. The study was registered with ClinicalTrials.gov (Study ID: NCT02237144.Having a neighboring mother participate in a nutrition BCC intervention increased non-participant mothers' IYCN knowledge by 0.17 SD (translating to 0.3 more correct answers. They were 14.1 percentage points more likely to feed their 6-24m children legumes and nuts; 11.6 percentage points more likely to feed these children vitamin A rich fruits and vegetables; and 10.0 percentage points more likely to feed these children eggs. Children of non-participant mothers who had a neighboring mother participate in a nutrition BCC intervention were 13.8 percentage points more likely to meet World Health Organization (WHO guidelines for minimum diet diversity, 11.9 percentage points more likely to meet WHO guidelines for minimum acceptable diet, and 10.3 percentage points more likely to meet WHO guidelines for minimum meal frequency for children who continue to be breastfed after age 6m. Children aged 0-6m of non-participant mothers who are neighbors of mothers receiving BCC were 7.1 percentage points less likely to have ever consumed water-based liquids.Studies of nutrition BCC that do not account for information spillovers to non-participants may underestimate its benefits in terms of

A γ dose distribution evaluation technique using the k-d tree for nearest neighbor searching

International Nuclear Information System (INIS)

Yuan Jiankui; Chen Weimin

2010-01-01

Purpose: The authors propose an algorithm based on the k-d tree for nearest neighbor searching to improve the γ calculation time for 2D and 3D dose distributions. Methods: The γ calculation method has been widely used for comparisons of dose distributions in clinical treatment plans and quality assurances. By specifying the acceptable dose and distance-to-agreement criteria, the method provides quantitative measurement of the agreement between the reference and evaluation dose distributions. The γ value indicates the acceptability. In regions where γ≤1, the predefined criterion is satisfied and thus the agreement is acceptable; otherwise, the agreement fails. Although the concept of the method is not complicated and a quick naieve implementation is straightforward, an efficient and robust implementation is not trivial. Recent algorithms based on exhaustive searching within a maximum radius, the geometric Euclidean distance, and the table lookup method have been proposed to improve the computational time for multidimensional dose distributions. Motivated by the fact that the least searching time for finding a nearest neighbor can be an O(log N) operation with a k-d tree, where N is the total number of the dose points, the authors propose an algorithm based on the k-d tree for the γ evaluation in this work. Results: In the experiment, the authors found that the average k-d tree construction time per reference point is O(log N), while the nearest neighbor searching time per evaluation point is proportional to O(N 1/k ), where k is between 2 and 3 for two-dimensional and three-dimensional dose distributions, respectively. Conclusions: Comparing with other algorithms such as exhaustive search and sorted list O(N), the k-d tree algorithm for γ evaluation is much more efficient.

Sistem Rekomendasi Pada E-Commerce Menggunakan K-Nearest Neighbor

Directory of Open Access Journals (Sweden)

Chandra Saha Dewa Prasetya

2017-09-01

The growing number of product information available on the internet brings challenges to both customer and online businesses in the e-commerce environment. Customer often have difficulty when looking for products on the internet because of the number of products sold on the internet. In addition, online businessman often experience difficulties because they has much data about products, customers and transactions, thus causing online businessman have difficulty to promote the right product to a particular customer target. A recommendation system was developed to address those problem with various methods such as Collaborative Filtering, ContentBased, and Hybrid. Collaborative filtering method uses customer’s rating data, content based using product content such as title or description, and hybrid using both as the basis of the recommendation. In this research, the k-nearest neighbor algorithm is used to determine the top-n product recommendations for each buyer. The result of this research method Content Based outperforms other methods because the sparse data, that is the condition where the number of rating given by the customers is relatively little compared the number of products available in e-commerce. Keywords: recomendation system, k-nearest neighbor, collaborative filtering, content based.

Nomenclature for alleles of the human carboxylesterase 1 gene

DEFF Research Database (Denmark)

Rasmussen, Henrik B.; Madsen, Majbritt B.; Bjerre, Ditte

2017-01-01

The carboxylesterase 1 gene (CES1) in humans encodes a hydrolase, which is implicated in the metabolism of several commonly used drugs 1. This gene is located on chromosome 16 with a highly homologous pseudogene, CES1P1, in its proximity. A duplicated segment of CES1 replaces most of CES1P1 in some...... appears to be low 8,13. The formation of hybrids consisting of a gene and a related pseudogene has been reported for other genes than CES1. This includes the hybrids of the gene encoding cytochrome P450 2D6 (CYP2D6) and pseudogene CYP2D7, that is, the so-called CYP2D7/D6 hybrids 14......,15. These are categorized as CYP2D6 variants and not as variants of pseudogene CYP2D716....

Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

KAUST Repository

Abusamra, Heba

2016-07-20

The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

Crimean-Congo hemorrhagic fever in Iran and neighboring countries

DEFF Research Database (Denmark)

Chinikar, S; Ghiasi, Seyed Mojtaba; Hewson, R

2010-01-01

Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic viral disease that is asymptomatic in infected livestock, but a serious threat to humans. Human infections begin with nonspecific febrile symptoms, but progress to a serious hemorrhagic syndrome with a case fatality rate of 2-50%. Although the ...... in Iran and neighboring countries and provide evidence of over 5000 confirmed cases of CCHF in a single period/season....

Use of the neighboring orbital model for analysis of electronic coupling in Class III intervalence compounds

International Nuclear Information System (INIS)

Nelsen, Stephen F.; Weaver, Michael N.; Luo Yun; Lockard, Jenny V.; Zink, Jeffrey I.

2006-01-01

Symmetrical charge-delocalized intervalence radical ions should not be described by the traditional two-state model that has been so successful for their localized counterparts. If they lack direct overlap between their charge-bearing units (M), their diabatic orbitals have an equal energy pair of symmetrized M-centered combination orbitals that are symmetric (S) or antisymmetric (A) with respect to a symmetry element at the center of the molecule. The M combination orbitals will mix separately with bridge orbitals of the same symmetry. We call the simplest useful model for this situation the neighboring orbital model, which uses the S and A bridge orbitals of high overlap that lie closest in energy to the M orbital pair, resulting in two two-state models that have a common energy for one pair. This model is developed quantitatively, and examples having 1, 3, 5, and 7 electrons in the neighboring orbitals are illustrated

Gene program-specific regulation of PGC-1{alpha} activity

DEFF Research Database (Denmark)

Schmidt, Søren F; Mandrup, Susanne

2011-01-01

Peroxisome proliferator-activated receptor γ (PPARγ) coactivator 1 α (PGC-1α) activation coordinates induction of the hepatic fasting response through coactivation of numerous transcription factors and gene programs. In the June 15, 2011, issue of Genes & Development, Lustig and colleagues (pp....... 1232-1244) demonstrated that phosphorylation of PGC-1α by the p70 ribosomal protein S6 kinase 1 (S6K1) specifically interfered with the interaction between PGC-1α and HNF4α in liver and blocked the coactivation of the gluconeogenic target genes. This demonstrates how independent fine-tuning of gene...

The surprising power of neighborly advice.

Science.gov (United States)

Gilbert, Daniel T; Killingsworth, Matthew A; Eyre, Rebecca N; Wilson, Timothy D

2009-03-20

Two experiments revealed that (i) people can more accurately predict their affective reactions to a future event when they know how a neighbor in their social network reacted to the event than when they know about the event itself and (ii) people do not believe this. Undergraduates made more accurate predictions about their affective reactions to a 5-minute speed date (n = 25) and to a peer evaluation (n = 88) when they knew only how another undergraduate had reacted to these events than when they had information about the events themselves. Both participants and independent judges mistakenly believed that predictions based on information about the event would be more accurate than predictions based on information about how another person had reacted to it.

The impact of vacant, tax-delinquent, and foreclosed property on sales prices of neighboring homes

OpenAIRE

Stephan Whitaker; Thomas J. Fitzpatrick

2012-01-01

In this empirical analysis, we estimate the impact of vacancy, neglect associated with property-tax delinquency, and foreclosures on the value of neighboring homes using parcel-level observations. Numerous studies have estimated the impact of foreclosures on neighboring properties, and these papers theorize that the foreclosure impact works partially through creating vacant and neglected homes. To our knowledge, this is only the second attempt to estimate the impact of vacancy itself and the ...

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.

Science.gov (United States)

Davarniya, Behzad; Hu, Hao; Kahrizi, Kimia; Musante, Luciana; Fattahi, Zohreh; Hosseini, Masoumeh; Maqsoud, Fariba; Farajollahi, Reza; Wienker, Thomas F; Ropers, H Hilger; Najmabadi, Hossein

2015-01-01

Cognitive impairment or intellectual disability (ID) is a widespread neurodevelopmental disorder characterized by low IQ (below 70). ID is genetically heterogeneous and is estimated to affect 1-3% of the world's population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID), we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831), encodes the metabotropic glutamate receptor1 (mGluR1). This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011). We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder.

Resampling nucleotide sequences with closest-neighbor trimming and its comparison to other methods.

Directory of Open Access Journals (Sweden)

Kouki Yonezawa

Full Text Available A large number of nucleotide sequences of various pathogens are available in public databases. The growth of the datasets has resulted in an enormous increase in computational costs. Moreover, due to differences in surveillance activities, the number of sequences found in databases varies from one country to another and from year to year. Therefore, it is important to study resampling methods to reduce the sampling bias. A novel algorithm-called the closest-neighbor trimming method-that resamples a given number of sequences from a large nucleotide sequence dataset was proposed. The performance of the proposed algorithm was compared with other algorithms by using the nucleotide sequences of human H3N2 influenza viruses. We compared the closest-neighbor trimming method with the naive hierarchical clustering algorithm and [Formula: see text]-medoids clustering algorithm. Genetic information accumulated in public databases contains sampling bias. The closest-neighbor trimming method can thin out densely sampled sequences from a given dataset. Since nucleotide sequences are among the most widely used materials for life sciences, we anticipate that our algorithm to various datasets will result in reducing sampling bias.

Hemoglobin is a co-factor of human trypanosome lytic factor

DEFF Research Database (Denmark)

Widener, Justin; Nielsen, Marianne Jensby; Shiflett, April

2007-01-01

Trypanosome lytic factor (TLF) is a high-density lipoprotein (HDL) subclass providing innate protection to humans against infection by the protozoan parasite Trypanosoma brucei brucei. Two primate-specific plasma proteins, haptoglobin-related protein (Hpr) and apolipoprotein L-1 (ApoL-1), have be...

Regional gene expression of LOX-1, VCAM-1, and ICAM-1 in aorta of HIV-1 transgenic rats.

Directory of Open Access Journals (Sweden)

Anne Mette Fisker Hag

Full Text Available BACKGROUND: Increased prevalence of atherosclerotic cardiovascular disease in HIV-infected patients has been observed. The cause of this accelerated atherosclerosis is a matter of controversy. As clinical studies are complicated by a multiplicity of risk-factors and a low incidence of hard endpoints, studies in animal models could be attractive alternatives. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated gene expression of lectin-like oxidized-low-density-lipoprotein receptor-1 (LOX-1, vascular cell adhesion molecule-1 (VCAM-1, and intercellular adhesion molecule-1 (ICAM-1 in HIV-1 transgenic (HIV-1Tg rats; these genes are all thought to play important roles in early atherogenesis. Furthermore, the plasma level of sICAM-1 was measured. We found that gene expressions of LOX-1 and VCAM-1 were higher in the aortic arch of HIV-1Tg rats compared to controls. Also, the level of sICAM-1 was elevated in the HIV-1Tg rats compared to controls, but the ICAM-1 gene expression profile did not show any differences between the groups. CONCLUSIONS/SIGNIFICANCE: HIV-1Tg rats have gene expression patterns indicating endothelial dysfunction and accelerated atherosclerosis in aorta, suggesting that HIV-infection per se may cause atherosclerosis. This transgenic rat model may be a very promising model for further studies of the pathophysiology behind HIV-associated cardiovascular disease.

The neighbor enclosed area tracking algorithm and its application to cyclone merger in the midlatitudes

Science.gov (United States)

Inatsu, Masaru; Amada, Shotarou; Satake, Yuya

2010-05-01

The neighbor enclosed area tracking (NEAT) algorithm is proposed as an alternative method to conventional point-to-point cyclone tracking approaches. Most automated Lagrangian tracking algorithms contain three procedures: cyclone identification, cyclone tracking, and quantification of cyclone intensity and activity. The cyclone identification was simply based on a comparison of neighboring grid points; cyclone tracking mainly employed a near-neighbor point search to neighbor-time cyclone-center datasets; and cyclone intensity and activity are mainly quantified as cyclone track density, and other accompanying products such as genesis and lysis densities, mean lifetime, average moving vector, and mean growth rate can also be obtained in the final procedure. But a crucial problem in the above technique is its requirement of some complicated connecting conditions for near-neighbor tracking. To overcome the problem, NEAT completes cyclone identification and cyclone tracking in a single process of equivalent labeling for spatiotemporally connected domains, i.e., if two spatially enclosed areas in a neighboring time frame overlap, they should be connected. NEAT enables us to count the genesis and tracks of individual cyclones as the conventional tracking. Moreover, NEAT has the ability to produce fruitful information on cyclone mergers and separations, cyclone shape, and material transport by individual eddies (the latter two features will be reported elsewhere). There are many possible applications of NEAT to meteorology and oceanography, but now we focus on the situation, well-known by Japanese synopticians, that two cyclones pass respectively over the north and south of Japan and then they frequently merge and are rapidly deepened in the western Pacific. For the case, the southern cyclones tend to be stimulated just above the sea surface temperature front to the north of oceanic western boundary currents, while the northern cyclones, moving eastward along the polar

Stuttering Attitudes among Turkish Family Generations and Neighbors from Representative Samples

Science.gov (United States)

Ozdemir, R. Sertan; St. Louis, Kenneth O.; Topbas, Seyhun

2011-01-01

Purpose: Attitudes toward stuttering, measured by the "Public Opinion Survey of Human Attributes-Stuttering" ("POSHA-S"), are compared among (a) two different representative samples; (b) family generations (children, parents, and either grandparents or uncles and aunts) and neighbors; (c) children, parents, grandparents/adult…

Level crossing, spin structure factor and quantum phases of the frustrated spin-1/2 chain with first and second neighbor exchange.

Science.gov (United States)

Kumar, Manoranjan; Parvej, Aslam; Soos, Zoltán G

2015-08-12

The spin-1/2 chain with isotropic Heisenberg exchange J1, J2  >  0 between first and second neighbors is frustrated for either sign of J1. Its quantum phase diagram has critical points at fixed J1/J2 between gapless phases with nondegenerate ground state (GS) and quasi-long-range order (QLRO) and gapped phases with doubly degenerate GS and spin correlation functions of finite range. In finite chains, exact diagonalization (ED) estimates critical points as level crossing of excited states. GS spin correlations enter in the spin structure factor S(q) that diverges at wave vector qm in QLRO(q(m)) phases with periodicity 2π/q(m) but remains finite in gapped phases. S(q(m)) is evaluated using ED and density matrix renormalization group (DMRG) calculations. Level crossing and the magnitude of S(q(m)) are independent and complementary probes of quantum phases, based respectively on excited and ground states. Both indicate a gapless QLRO(π/2) phase between  -1.2  quantum critical points at small frustration J2 but disagree in the sector of weak exchange J1 between Heisenberg antiferromagnetic chains on sublattices of odd and even-numbered sites.

The Patient-Centered Medical Home Neighbor: A Critical Concept for a Redesigned Healthcare Delivery System

Science.gov (United States)

2011-01-25

Sharing Knowledge: Achieving Breakthrough Performance 2010 Military Health System Conference The Patient -Centered Medical Home Neighbor: A Critical...DATE 25 JAN 2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE The Patient -Centered Medical Home Neighbor: A...Conference What is the Patient -Centered Medical Home?  …a vision of health care as it should be  …a framework for organizing systems of care at both the

A two-step nearest neighbors algorithm using satellite imagery for predicting forest structure within species composition classes

Science.gov (United States)

Ronald E. McRoberts

2009-01-01

Nearest neighbors techniques have been shown to be useful for predicting multiple forest attributes from forest inventory and Landsat satellite image data. However, in regions lacking good digital land cover information, nearest neighbors selected to predict continuous variables such as tree volume must be selected without regard to relevant categorical variables such...

Domestication-driven Gossypium profilin 1 (GhPRF1) gene transduces early flowering phenotype in tobacco by spatial alteration of apical/floral-meristem related gene expression.

Science.gov (United States)

Pandey, Dhananjay K; Chaudhary, Bhupendra

2016-05-13

Plant profilin genes encode core cell-wall structural proteins and are evidenced for their up-regulation under cotton domestication. Notwithstanding striking discoveries in the genetics of cell-wall organization in plants, little is explicit about the manner in which profilin-mediated molecular interplay and corresponding networks are altered, especially during cellular signalling of apical meristem determinacy and flower development. Here we show that the ectopic expression of GhPRF1 gene in tobacco resulted in the hyperactivation of apical meristem and early flowering phenotype with increased flower number in comparison to the control plants. Spatial expression alteration in CLV1, a key meristem-determinacy gene, is induced by the GhPRF1 overexpression in a WUS-dependent manner and mediates cell signalling to promote flowering. But no such expression alterations are recorded in the GhPRF1-RNAi lines. The GhPRF1 transduces key positive flowering regulator AP1 gene via coordinated expression of FT4, SOC1, FLC1 and FT1 genes involved in the apical-to-floral meristem signalling cascade which is consistent with our in silico profilin interaction data. Remarkably, these positive and negative flowering regulators are spatially controlled by the Actin-Related Protein (ARP) genes, specifically ARP4 and ARP6 in proximate association with profilins. This study provides a novel and systematic link between GhPRF1 gene expression and the flower primordium initiation via up-regulation of the ARP genes, and an insight into the functional characterization of GhPRF1 gene acting upstream to the flowering mechanism. Also, the transgenic plants expressing GhPRF1 gene show an increase in the plant height, internode length, leaf size and plant vigor. Overexpression of GhPRF1 gene induced early and increased flowering in tobacco with enhanced plant vigor. During apical meristem determinacy and flower development, the GhPRF1 gene directly influences key flowering regulators through ARP-genes

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.

Directory of Open Access Journals (Sweden)

Behzad Davarniya

Full Text Available Cognitive impairment or intellectual disability (ID is a widespread neurodevelopmental disorder characterized by low IQ (below 70. ID is genetically heterogeneous and is estimated to affect 1-3% of the world's population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID, we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831, encodes the metabotropic glutamate receptor1 (mGluR1. This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011. We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder.

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families

Science.gov (United States)

Kahrizi, Kimia; Musante, Luciana; Fattahi, Zohreh; Hosseini, Masoumeh; Maqsoud, Fariba; Farajollahi, Reza; Wienker, Thomas F.; Ropers, H. Hilger; Najmabadi, Hossein

2015-01-01

Cognitive impairment or intellectual disability (ID) is a widespread neurodevelopmental disorder characterized by low IQ (below 70). ID is genetically heterogeneous and is estimated to affect 1–3% of the world’s population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID), we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831), encodes the metabotropic glutamate receptor1 (mGluR1). This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011). We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder. PMID:26308914

Linear perturbation renormalization group for the two-dimensional Ising model with nearest- and next-nearest-neighbor interactions in a field

Science.gov (United States)

Sznajd, J.

2016-12-01

The linear perturbation renormalization group (LPRG) is used to study the phase transition of the weakly coupled Ising chains with intrachain (J ) and interchain nearest-neighbor (J1) and next-nearest-neighbor (J2) interactions forming the triangular and rectangular lattices in a field. The phase diagrams with the frustration point at J2=-J1/2 for a rectangular lattice and J2=-J1 for a triangular lattice have been found. The LPRG calculations support the idea that the phase transition is always continuous except for the frustration point and is accompanied by a divergence of the specific heat. For the antiferromagnetic chains, the external field does not change substantially the shape of the phase diagram. The critical temperature is suppressed to zero according to the power law when approaching the frustration point with an exponent dependent on the value of the field.

Influenza NA and PB1 Gene Segments Interact during the Formation of Viral Progeny: Localization of the Binding Region within the PB1 Gene

Directory of Open Access Journals (Sweden)

Brad Gilbertson

2016-08-01

Full Text Available The influenza A virus genome comprises eight negative-sense viral RNAs (vRNAs that form individual ribonucleoprotein (RNP complexes. In order to incorporate a complete set of each of these vRNAs, the virus uses a selective packaging mechanism that facilitates co-packaging of specific gene segments but whose molecular basis is still not fully understood. Recently, we used a competitive transfection model where plasmids encoding the A/Puerto Rico/8/34 (PR8 and A/Udorn/307/72 (Udorn PB1 gene segments were competed to show that the Udorn PB1 gene segment is preferentially co-packaged into progeny virions with the Udorn NA gene segment. Here we created chimeric PB1 genes combining both Udorn and PR8 PB1 sequences to further define the location within the Udorn PB1 gene that drives co-segregation of these genes and show that nucleotides 1776–2070 of the PB1 gene are crucial for preferential selection. In vitro assays examining specific interactions between Udorn NA vRNA and purified vRNAs transcribed from chimeric PB1 genes also supported the importance of this region in the PB1-NA interaction. Hence, this work identifies an association between viral genes that are co-selected during packaging. It also reveals a region potentially important in the RNP-RNP interactions within the supramolecular complex that is predicted to form prior to budding to allow one of each segment to be packaged in the viral progeny. Our study lays the foundation to understand the co-selection of specific genes, which may be critical to the emergence of new viruses with pandemic potential.

Differentially expressed genes in embryonic cardiac tissues of mice lacking Folr1 gene activity

Directory of Open Access Journals (Sweden)

Schwartz Robert J

2007-11-01

Full Text Available Abstract Background Heart anomalies are the most frequently observed among all human congenital defects. As with the situation for neural tube defects (NTDs, it has been demonstrated that women who use multivitamins containing folic acid peri-conceptionally have a reduced risk for delivering offspring with conotruncal heart defects 123. Cellular folate transport is mediated by a receptor or binding protein and by an anionic transporter protein system. Defective function of the Folr1 (also known as Folbp1; homologue of human FRα gene in mice results in inadequate transport, accumulation, or metabolism of folate during cardiovascular morphogenesis. Results We have observed cardiovascular abnormalities including outflow tract and aortic arch arterial defects in genetically compromised Folr1 knockout mice. In order to investigate the molecular mechanisms underlying the failure to complete development of outflow tract and aortic arch arteries in the Folr1 knockout mouse model, we examined tissue-specific gene expression difference between Folr1 nullizygous embryos and morphologically normal heterozygous embryos during early cardiac development (14-somite stage, heart tube looping (28-somite stage, and outflow track septation (38-somite stage. Microarray analysis was performed as a primary screening, followed by investigation using quantitative real-time PCR assays. Gene ontology analysis highlighted the following ontology groups: cell migration, cell motility and localization of cells, structural constituent of cytoskeleton, cell-cell adhesion, oxidoreductase, protein folding and mRNA processing. This study provided preliminary data and suggested potential candidate genes for further description and investigation. Conclusion The results suggested that Folr1 gene ablation and abnormal folate homeostasis altered gene expression in developing heart and conotruncal tissues. These changes affected normal cytoskeleton structures, cell migration and

Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model.

Science.gov (United States)

Bao, Yanyan; Gao, Yingjie; Shi, Yujing; Cui, Xiaolan

2017-06-01

H1N1, a major pathogenic subtype of influenza A virus, causes a respiratory infection in humans and livestock that can range from a mild infection to more severe pneumonia associated with acute respiratory distress syndrome. Understanding the dynamic changes in the genome and the related functional changes induced by H1N1 influenza virus infection is essential to elucidating the pathogenesis of this virus and thereby determining strategies to prevent future outbreaks. In this study, we filtered the significantly expressed genes in mouse pneumonia using mRNA microarray analysis. Using STC analysis, seven significant gene clusters were revealed, and using STC-GO analysis, we explored the significant functions of these seven gene clusters. The results revealed GOs related to H1N1 virus-induced inflammatory and immune functions, including innate immune response, inflammatory response, specific immune response, and cellular response to interferon-beta. Furthermore, the dynamic regulation relationships of the key genes in mouse pneumonia were revealed by dynamic gene network analysis, and the most important genes were filtered, including Dhx58, Cxcl10, Cxcl11, Zbp1, Ifit1, Ifih1, Trim25, Mx2, Oas2, Cd274, Irgm1, and Irf7. These results suggested that during mouse pneumonia, changes in the expression of gene clusters and the complex interactions among genes lead to significant changes in function. Dynamic gene expression analysis revealed key genes that performed important functions. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology, as well as the use of mice as a model organism for human H1N1 influenza virus infection studies.

Novel mutations in the SCNN1A gene causing Pseudohypoaldosteronism type 1.

Directory of Open Access Journals (Sweden)

Jian Wang

Full Text Available Pseudohypoaldosteronism type 1 (PHA1 is a rare inherited disease characterized by resistance to the actions of aldosterone. Mutations in the subunit genes (SCNN1A, SCNN1B, SCNN1G of the epithelial sodium channel (ENaC and the NR3C2 gene encoding the mineralocorticoid receptor, result in systemic PHA1 and renal PHA1 respectively. Common clinical manifestations of PHA1 include salt wasting, hyperkalaemia, metabolic acidosis and elevated plasma aldosterone levels in the neonatal period. In this study, we describe the clinical and biochemical manifestations in two Chinese patients with systemic PHA1. Sequence analysis of the SCNN1A gene revealed a compound heterozygous mutation (c.1311delG and c.1439+1G>C in one patient and a homozygous mutation (c.814_815insG in another patient, all three variants are novel. Further analysis of the splicing pattern in a minigene construct showed that the c.1439+1G>C mutation can lead to the retainment of intron 9 as the 5'-donor splice site disappears during post-transcriptional processing of mRNA. In conclusion, our study identified three novel SCNN1A gene mutations in two Chinese patients with systemic PHA1.

Numerical Simulation of the Diffusion Processes in Nanoelectrode Arrays Using an Axial Neighbor Symmetry Approximation.

Science.gov (United States)

Peinetti, Ana Sol; Gilardoni, Rodrigo S; Mizrahi, Martín; Requejo, Felix G; González, Graciela A; Battaglini, Fernando

2016-06-07

Nanoelectrode arrays have introduced a complete new battery of devices with fascinating electrocatalytic, sensitivity, and selectivity properties. To understand and predict the electrochemical response of these arrays, a theoretical framework is needed. Cyclic voltammetry is a well-fitted experimental technique to understand the undergoing diffusion and kinetics processes. Previous works describing microelectrode arrays have exploited the interelectrode distance to simulate its behavior as the summation of individual electrodes. This approach becomes limited when the size of the electrodes decreases to the nanometer scale due to their strong radial effect with the consequent overlapping of the diffusional fields. In this work, we present a computational model able to simulate the electrochemical behavior of arrays working either as the summation of individual electrodes or being affected by the overlapping of the diffusional fields without previous considerations. Our computational model relays in dividing a regular electrode array in cells. In each of them, there is a central electrode surrounded by neighbor electrodes; these neighbor electrodes are transformed in a ring maintaining the same active electrode area than the summation of the closest neighbor electrodes. Using this axial neighbor symmetry approximation, the problem acquires a cylindrical symmetry, being applicable to any diffusion pattern. The model is validated against micro- and nanoelectrode arrays showing its ability to predict their behavior and therefore to be used as a designing tool.

Congenital Hypopituitarism due to POU1F1 Gene Mutation

Directory of Open Access Journals (Sweden)

Ni-Chung Lee

2011-01-01

Full Text Available POU1F1 (Pit-1; Gene ID 5449 is an anterior pituitary transcriptional factor, and POU1F1 mutation is known to cause anterior pituitary hypoplasia, growth hormone and prolactin deficiency and various degree of hypothyroidism. We report here a patient who presented with growth failure and central hypothyroidism since early infancy. However, treatment with thyroxine gave no effect and he subsequently developed calf muscle pseudohypertrophy (Kocher-Debre-Semelaigne syndrome, elevation of creatinine kinase, dilated cardiomyopathy and pericardial effusion. Final diagnosis was made by combined pituitary function test and sequencing analysis that revealed POU1F1 gene C.698T > C (p.F233S mutation. The rarity of the disease can result in delayed diagnosis and treatment.

Codon usage and amino acid usage influence genes expression level.

Science.gov (United States)

Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

2018-02-01

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

Locus-specific ribosomal RNA gene silencing in nucleolar dominance.

Directory of Open Access Journals (Sweden)

Michelle S Lewis

2007-08-01

Full Text Available The silencing of one parental set of rRNA genes in a genetic hybrid is an epigenetic phenomenon known as nucleolar dominance. We showed previously that silencing is restricted to the nucleolus organizer regions (NORs, the loci where rRNA genes are tandemly arrayed, and does not spread to or from neighboring protein-coding genes. One hypothesis is that nucleolar dominance is the net result of hundreds of silencing events acting one rRNA gene at a time. A prediction of this hypothesis is that rRNA gene silencing should occur independent of chromosomal location. An alternative hypothesis is that the regulatory unit in nucleolar dominance is the NOR, rather than each individual rRNA gene, in which case NOR localization may be essential for rRNA gene silencing. To test these alternative hypotheses, we examined the fates of rRNA transgenes integrated at ectopic locations. The transgenes were accurately transcribed in all independent transgenic Arabidopsis thaliana lines tested, indicating that NOR localization is not required for rRNA gene expression. Upon crossing the transgenic A. thaliana lines as ovule parents with A. lyrata to form F1 hybrids, a new system for the study of nucleolar dominance, the endogenous rRNA genes located within the A. thaliana NORs are silenced. However, rRNA transgenes escaped silencing in multiple independent hybrids. Collectively, our data suggest that rRNA gene activation can occur in a gene-autonomous fashion, independent of chromosomal location, whereas rRNA gene silencing in nucleolar dominance is locus-dependent.

Effect of electrode design on crosstalk between neighboring organic field-effect transistors based on one single crystal

Science.gov (United States)

Li, Mengjie; Tang, Qingxin; Tong, Yanhong; Zhao, Xiaoli; Zhou, Shujun; Liu, Yichun

2018-03-01

The design of high-integration organic circuits must be such that the interference between neighboring devices is eliminated. Here, rubrene crystals were used to study the effect of the electrode design on crosstalk between neighboring organic field-effect transistors (OFETs). Results show that a decreased source/drain interval and gate electrode width can decrease the diffraction distance of the current, and therefore can weaken the crosstalk. In addition, the inherent low carrier concentration in organic semiconductors can create a high-resistance barrier at the space between gate electrodes of neighboring devices, limiting or even eliminating the crosstalk as a result of the gate electrode width being smaller than the source/drain electrode width.

Attribute Weighting Based K-Nearest Neighbor Using Gain Ratio

Science.gov (United States)

Nababan, A. A.; Sitompul, O. S.; Tulus

2018-04-01

K- Nearest Neighbor (KNN) is a good classifier, but from several studies, the result performance accuracy of KNN still lower than other methods. One of the causes of the low accuracy produced, because each attribute has the same effect on the classification process, while some less relevant characteristics lead to miss-classification of the class assignment for new data. In this research, we proposed Attribute Weighting Based K-Nearest Neighbor Using Gain Ratio as a parameter to see the correlation between each attribute in the data and the Gain Ratio also will be used as the basis for weighting each attribute of the dataset. The accuracy of results is compared to the accuracy acquired from the original KNN method using 10-fold Cross-Validation with several datasets from the UCI Machine Learning repository and KEEL-Dataset Repository, such as abalone, glass identification, haberman, hayes-roth and water quality status. Based on the result of the test, the proposed method was able to increase the classification accuracy of KNN, where the highest difference of accuracy obtained hayes-roth dataset is worth 12.73%, and the lowest difference of accuracy obtained in the abalone dataset of 0.07%. The average result of the accuracy of all dataset increases the accuracy by 5.33%.

Tandemly Arrayed Genes in Vertebrate Genomes

Directory of Open Access Journals (Sweden)

Deng Pan

2008-01-01

Full Text Available Tandemly arrayed genes (TAGs are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94% have parallel transcription orientation (i.e., they are encoded on the same strand in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

New insights on the evolution of Leafy cotyledon1 (LEC1) type genes in vascular plants.

Science.gov (United States)

Cagliari, Alexandro; Turchetto-Zolet, Andreia Carina; Korbes, Ana Paula; Maraschin, Felipe Dos Santos; Margis, Rogerio; Margis-Pinheiro, Marcia

2014-01-01

NF-Y is a conserved oligomeric transcription factor found in all eukaryotes. In plants, this regulator evolved with a broad diversification of the genes coding for its three subunits (NF-YA, NF-YB and NF-YC). The NF-YB members can be divided into Leafy Cotyledon1 (LEC1) and non-LEC1 types. Here we presented a comparative genomic study using phylogenetic analyses to validate an evolutionary model for the origin of LEC-type genes in plants and their emergence from non-LEC1-type genes. We identified LEC1-type members in all vascular plant genomes, but not in amoebozoa, algae, fungi, metazoa and non-vascular plant representatives, which present exclusively non-LEC1-type genes as constituents of their NF-YB subunits. The non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) between LEC1 and non-LEC1-type genes indicate the presence of positive selection acting on LEC1-type members to the fixation of LEC1-specific amino acid residues. The phylogenetic analyses demonstrated that plant LEC1-type genes are evolutionary divergent from the non-LEC1-type genes of plants, fungi, amoebozoa, algae and animals. Our results point to a scenario in which LEC1-type genes have originated in vascular plants after gene expansion in plants. We suggest that processes of neofunctionalization and/or subfunctionalization were responsible for the emergence of a versatile role for LEC1-type genes in vascular plants, especially in seed plants. LEC1-type genes besides being phylogenetic divergent also present different expression profile when compared with non-LEC1-type genes. Altogether, our data provide new insights about the LEC1 and non-LEC1 evolutionary relationship during the vascular plant evolution. Copyright © 2014 Elsevier Inc. All rights reserved.

Regional gene expression of LOX-1, VCAM-1, and ICAM-1 in aorta of HIV-1 transgenic rats

DEFF Research Database (Denmark)

Hag, Anne Mette Fisker; Kristoffersen, Ulrik Sloth; Pedersen, Sune Folke

2009-01-01

endpoints, studies in animal models could be attractive alternatives. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated gene expression of lectin-like oxidized-low-density-lipoprotein receptor-1 (LOX-1), vascular cell adhesion molecule-1 (VCAM-1), and intercellular adhesion molecule-1 (ICAM-1) in HIV-1...... transgenic (HIV-1Tg) rats; these genes are all thought to play important roles in early atherogenesis. Furthermore, the plasma level of sICAM-1 was measured. We found that gene expressions of LOX-1 and VCAM-1 were higher in the aortic arch of HIV-1Tg rats compared to controls. Also, the level of sICAM-1......-infection per se may cause atherosclerosis. This transgenic rat model may be a very promising model for further studies of the pathophysiology behind HIV-associated cardiovascular disease....

RCSD1-ABL1 Translocation Associated with IKZF1 Gene Deletion in B-Cell Acute Lymphoblastic Leukemia

Directory of Open Access Journals (Sweden)

Shawana Kamran

2015-01-01

Full Text Available The RCSD1 gene has recently been identified as a novel gene fusion partner of the ABL1 gene in cases of B-cell Acute Lymphoblastic Leukemia (B-ALL. The RCSD1 gene is located at 1q23 and ABL1 is located at 9q34, so that the RCSD1-ABL1 fusion typically arises through a rare reciprocal translocation t(1;9(q23;q34. Only a small number of RCSD1-ABL1 positive cases of B-ALL have been described in the literature, and the full spectrum of clinical, morphological, immunophenotypic, and molecular features associated with this genetic abnormality has not been defined. We describe extensive genetic characterization of a case of B-ALL with RCSD1-ABL1 fusion, by using conventional cytogenetic analysis, Fluorescence In Situ Hybridization (FISH studies, and Chromosomal Microarray Analysis (CMA. The use of CMA resulted in detection of an approximately 70 kb deletion at 7p12.2, which caused a disruption of the IKZF1 gene. Deletions and mutations of IKZF1 are recurring abnormalities in B-ALL and are associated with a poor prognosis. Our findings highlight the association of the deletion of IKZF1 gene with the t(1;9(q24;q34 and illustrate the importance of comprehensive cytogenetic and molecular evaluation for accurate prediction of prognosis in patients with B-cell ALL.

Insulin gene therapy for type 1 diabetes mellitus.

Science.gov (United States)

Handorf, Andrew M; Sollinger, Hans W; Alam, Tausif

2015-04-01

Type 1 diabetes mellitus is an autoimmune disease resulting from the destruction of pancreatic β cells. Current treatments for patients with type 1 diabetes mellitus include daily insulin injections or whole pancreas transplant, each of which are associated with profound drawbacks. Insulin gene therapy, which has shown great efficacy in correcting hyperglycemia in animal models, holds great promise as an alternative strategy to treat type 1 diabetes mellitus in humans. Insulin gene therapy refers to the targeted expression of insulin in non-β cells, with hepatocytes emerging as the primary therapeutic target. In this review, we present an overview of the current state of insulin gene therapy to treat type 1 diabetes mellitus, including the need for an alternative therapy, important features dictating the success of the therapy, and current obstacles preventing the translation of this treatment option to a clinical setting. In so doing, we hope to shed light on insulin gene therapy as a viable option to treat type 1 diabetes mellitus.

Learn good from bad: Effects of good and bad neighbors in spatial prisoners' dilemma games

Science.gov (United States)

Lu, Peng

2015-10-01

Cooperation is vital for the human society and this study focuses on how to promote cooperation. In our stratification model, there exist three classes: two minorities are elites who are prone to cooperate and scoundrels who are born to defect; one majority is the class of common people. Agents of these three classes interact with each other on a square lattice. Commons' cooperation and its factors are investigated. Contradicting our common sense, it indicates that elites play a negative role while scoundrels play a positive one in promoting commons' cooperation. Besides, effects of good and bad neighbors vary with temptation. When the temptation is smaller the positive effect is able to overcome the negative effect, but the later prevails when the temptation is larger. It concludes that common people are more prone to cooperate in harsh environment with bad neighbors, and a better environment with good neighbors merely leads to laziness and free riding of commons.

Neurotensin receptor 1 gene (NTSR1 polymorphism is associated with working memory.

Directory of Open Access Journals (Sweden)

Jin Li

Full Text Available BACKGROUND: Recent molecular genetics studies showed significant associations between dopamine-related genes (including genes for dopamine receptors, transporters, and degradation and working memory, but little is known about the role of genes for dopamine modulation, such as those related to neurotensin (NT, in working memory. A recent animal study has suggested that NT antagonist administration impaired working memory in a learning task. The current study examined associations between NT genes and working memory among humans. METHODS: Four hundred and sixty healthy undergraduate students were assessed with a 2-back working memory paradigm. 5 SNPs in the NTSR1 gene were genotyped. 5 ANOVA tests were conducted to examine whether and how working memory differed by NTSR1 genotype, with each SNP variant as the independent variable and the average accuracy on the working memory task as the dependent variable. RESULTS: ANOVA results suggested that two SNPs in the NTSR1 gene (rs4334545 and rs6090453 were significantly associated with working memory. These results survived corrections for multiple comparisons. CONCLUSIONS: Our results demonstrated that NTSR1 SNP polymorphisms were significantly associated with variance in working memory performance among healthy adults. This result extended previous rodent studies showing that the NT deficiency impairs the working memory function. Future research should replicate our findings and extend to an examination of other dopamine modulators.

Cell membrane disruption stimulates cAMP and Ca2+ signaling to potentiate cell membrane resealing in neighboring cells

Directory of Open Access Journals (Sweden)

Tatsuru Togo

2017-12-01

Full Text Available Disruption of cellular plasma membranes is a common event in many animal tissues, and the membranes are usually rapidly resealed. Moreover, repeated membrane disruptions within a single cell reseal faster than the initial wound in a protein kinase A (PKA- and protein kinase C (PKC-dependent manner. In addition to wounded cells, recent studies have demonstrated that wounding of Madin-Darby canine kidney (MDCK cells potentiates membrane resealing in neighboring cells in the short-term by purinergic signaling, and in the long-term by nitric oxide/protein kinase G signaling. In the present study, real-time imaging showed that cell membrane disruption stimulated cAMP synthesis and Ca2+ mobilization from intracellular stores by purinergic signaling in neighboring MDCK cells. Furthermore, inhibition of PKA and PKC suppressed the ATP-mediated short-term potentiation of membrane resealing in neighboring cells. These results suggest that cell membrane disruption stimulates PKA and PKC via purinergic signaling to potentiate cell membrane resealing in neighboring MDCK cells.

Phylogenetic relationships among Perissodactyla: secretoglobin 1A1 gene duplication and triplication in the Equidae family.

Science.gov (United States)

Côté, Olivier; Viel, Laurent; Bienzle, Dorothee

2013-12-01

Secretoglobin family 1A member 1 (SCGB 1A1) is a small anti-inflammatory and immunomodulatory protein that is abundantly secreted in airway surface fluids. We recently reported the existence of three distinct SCGB1A1 genes in the domestic horse genome as opposed to the single gene copy consensus present in other mammals. The origin of SCGB1A1 gene triplication and the evolutionary relationship of the three genes amongst Equidae family members are unknown. For this study, SCGB1A1 genomic data were collected from various Equus individuals including E. caballus, E. przewalskii, E. asinus, E. grevyi, and E. quagga. Three SCGB1A1 genes in E. przewalskii, two SCGB1A1 genes in E. asinus, and a single SCGB1A1 gene in E. grevyi and E. quagga were identified. Sequence analysis revealed that the non-synonymous nucleotide substitutions between the different equid genes coded for 17 amino acid changes. Most of these changes localized to the SCGB 1A1 central cavity that binds hydrophobic ligands, suggesting that this area of SCGB 1A1 evolved to accommodate diverse molecular interactions. Three-dimensional modeling of the proteins revealed that the size of the SCGB 1A1 central cavity is larger than that of SCGB 1A1A. Altogether, these findings suggest that evolution of the SCGB1A1 gene may parallel the separation of caballine and non-caballine species amongst Equidae, and may indicate an expansion of function for SCGB1A1 gene products. Copyright © 2013 Elsevier Inc. All rights reserved.

Fast Most Similar Neighbor (MSN) classifiers for Mixed Data

OpenAIRE

Hernández Rodríguez, Selene

2010-01-01

The k nearest neighbor (k-NN) classifier has been extensively used in Pattern Recognition because of its simplicity and its good performance. However, in large datasets applications, the exhaustive k-NN classifier becomes impractical. Therefore, many fast k-NN classifiers have been developed; most of them rely on metric properties (usually the triangle inequality) to reduce the number of prototype comparisons. Hence, the existing fast k-NN classifiers are applicable only when the comparison f...

Genes affecting β-cell function in type 1 diabetes

DEFF Research Database (Denmark)

Fløyel, Tina; Kaur, Simranjeet; Pociot, Flemming

2015-01-01

Type 1 diabetes (T1D) is a multifactorial disease resulting from an immune-mediated destruction of the insulin-producing pancreatic β cells. Several environmental and genetic risk factors predispose to the disease. Genome-wide association studies (GWAS) have identified around 50 genetic regions...... that affect the risk of developing T1D, but the disease-causing variants and genes are still largely unknown. In this review, we discuss the current status of T1D susceptibility loci and candidate genes with focus on the β cell. At least 40 % of the genes in the T1D susceptibility loci are expressed in human...... islets and β cells, where they according to recent studies modulate the β-cell response to the immune system. As most of the risk variants map to noncoding regions of the genome, i.e., promoters, enhancers, intergenic regions, and noncoding genes, their possible involvement in T1D pathogenesis as gene...

Neurospora crassa glucose - repressible gene -1(Grg-1) promoter controls the expression of neurospora tyrosinase gene in a clock-controlled manner

International Nuclear Information System (INIS)

Tarawneh, A. K

1997-01-01

In this study sphareroplastes of white Neurospora crassa mutant auxotroph for aromatic am no acids a rom 9 q a-2 inv, was transformed by the pKF-Tyr7-wt DNA construct. This construct contains the promoter of neurospora crassa glucose-repressible gene-1 (G rg-1) usp stream of Neurospora tyrosinase gene. The co transformation of this mutant with pKF-Tyr-7-wt cincture's and the pKAL-1, a plasmid which contains the Neurospora q a-2+ gene transform it to photophor. The transform ant contains the tyrosinase gene which catalyzes the unique step in the synthesis of the black pigment melanin. The activity of the tyrosinase in this transform ant was followed by measuring the absorbance of the dark coloured pigment at 332 nm. The maximum of the tyrosinase activity was shown at 16.36 and 56 hours after the shift of the transformed mycelia from constant light (L L) to constant dark (Dd). The rate of the enzyme activity was changed according to ci radian cycle of 20 hours. This G rg 1/tyrosinase construct provides a good system to study to study the temporal control of gene expression and the interaction between the different environmental c uses that affects gene expression. (author). 20 refs., 4 figs

Chromosomal evolution of the PKD1 gene family in primates

Directory of Open Access Journals (Sweden)

Krawczak Michael

2008-09-01

Full Text Available Abstract Background The autosomal dominant polycystic kidney disease (ADPKD is mostly caused by mutations in the PKD1 (polycystic kidney disease 1 gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1-containing genomic BAC clone and a PKD1-cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. Results Comparative FISH with the PKD1-cDNA clone clearly shows that in all primate species studied distinct single signals map in subtelomeric chromosomal positions orthologous to the short arm of human chromosome 16 harbouring the master PKD1 gene. Only in human and African great apes, but not in orangutan, FISH with both BAC and cDNA clones reveals additional signal clusters located proximal of and clearly separated from the PKD1 master genes indicating the chromosomal position of PKD1 pseudogenes in 16p of these species, respectively. Indeed, this is in accordance with sequencing data in human, chimpanzee and orangutan. Apart from the master PKD1 gene, six pseudogenes are identified in both, human and chimpanzee, while only a single-copy gene is present in the whole-genome sequence of orangutan. The phylogenetic reconstruction of the PKD1-tree reveals that all human pseudogenes are closely related to the human PKD1 gene, and all chimpanzee pseudogenes are closely related to the chimpanzee PKD1 gene. However, our statistical analyses provide strong indication that gene conversion events may have occurred within the PKD1 family members of human and chimpanzee, respectively. Conclusion PKD1 must have undergone amplification very recently in hominid evolution. Duplicative

The PCDH1 gene and asthma in early childhood

DEFF Research Database (Denmark)

Mortensen, Li J; Kreiner-Møller, Eskil; Hakonarson, Hakon

2014-01-01

Previous studies have suggested that variants in the protocadherin-1 (PCDH1) gene, which is important for cell-cell adhesion, are associated with asthma, bronchial, hyperresponsiveness and atopic dermatitis in school children. Our aim was to associate common variants of the PCDH1 gene with longit......Previous studies have suggested that variants in the protocadherin-1 (PCDH1) gene, which is important for cell-cell adhesion, are associated with asthma, bronchial, hyperresponsiveness and atopic dermatitis in school children. Our aim was to associate common variants of the PCDH1 gene...... with longitudinally assessed asthma phenotypes and atopic dermatitis in early childhood. We analysed eight single-nucleotide polymorphisms in PCDH1 from 411 children born to asthmatic mothers from the Copenhagen Prospective Studies on Asthma in Childhood birth cohort. Asthma and atopic dermatitis were diagnosed...

Analysis of the reptile CD1 genes: evolutionary implications.

Science.gov (United States)

Yang, Zhi; Wang, Chunyan; Wang, Tao; Bai, Jianhui; Zhao, Yu; Liu, Xuhan; Ma, Qingwei; Wu, Xiaobing; Guo, Ying; Zhao, Yaofeng; Ren, Liming

2015-06-01

CD1, as the third family of antigen-presenting molecules, is previously only found in mammals and chickens, which suggests that the chicken and mammalian CD1 shared a common ancestral gene emerging at least 310 million years ago. Here, we describe CD1 genes in the green anole lizard and Crocodylia, demonstrating that CD1 is ubiquitous in mammals, birds, and reptiles. Although the reptilian CD1 protein structures are predicted to be similar to human CD1d and chicken CD1.1, CD1 isotypes are not found to be orthologous between mammals, birds, and reptiles according to phylogenetic analyses, suggesting an independent diversification of CD1 isotypes during the speciation of mammals, birds, and reptiles. In the green anole lizard, although the single CD1 locus and MHC I gene are located on the same chromosome, there is an approximately 10-Mb-long sequence in between, and interestingly, several genes flanking the CD1 locus belong to the MHC paralogous region on human chromosome 19. The CD1 genes in Crocodylia are located in two loci, respectively linked to the MHC region and MHC paralogous region (corresponding to the MHC paralogous region on chromosome 19). These results provide new insights for studying the origin and evolution of CD1.

River Flow Prediction Using the Nearest Neighbor Probabilistic Ensemble Method

Directory of Open Access Journals (Sweden)

H. Sanikhani

2016-02-01

Full Text Available Introduction: In the recent years, researchers interested on probabilistic forecasting of hydrologic variables such river flow.A probabilistic approach aims at quantifying the prediction reliability through a probability distribution function or a prediction interval for the unknown future value. The evaluation of the uncertainty associated to the forecast is seen as a fundamental information, not only to correctly assess the prediction, but also to compare forecasts from different methods and to evaluate actions and decisions conditionally on the expected values. Several probabilistic approaches have been proposed in the literature, including (1 methods that use resampling techniques to assess parameter and model uncertainty, such as the Metropolis algorithm or the Generalized Likelihood Uncertainty Estimation (GLUE methodology for an application to runoff prediction, (2 methods based on processing the forecast errors of past data to produce the probability distributions of future values and (3 methods that evaluate how the uncertainty propagates from the rainfall forecast to the river discharge prediction, as the Bayesian forecasting system. Materials and Methods: In this study, two different probabilistic methods are used for river flow prediction.Then the uncertainty related to the forecast is quantified. One approach is based on linear predictors and in the other, nearest neighbor was used. The nonlinear probabilistic ensemble can be used for nonlinear time series analysis using locally linear predictors, while NNPE utilize a method adapted for one step ahead nearest neighbor methods. In this regard, daily river discharge (twelve years of Dizaj and Mashin Stations on Baranduz-Chay basin in west Azerbijan and Zard-River basin in Khouzestan provinces were used, respectively. The first six years of data was applied for fitting the model. The next three years was used to calibration and the remained three yeas utilized for testing the models

Innate immune genes including a mucin-like gene, mul-1, induced by ionizing radiation in Caenorhabditis elegans.

Science.gov (United States)

Kimura, Takafumi; Takanami, Takako; Sakashita, Tetsuya; Wada, Seiichi; Kobayashi, Yasuhiko; Higashitani, Atsushi

2012-10-01

The effect of radiation on the intestine has been studied for more than one hundred years. It remains unclear, however, whether this organ uses specific defensive mechanisms against ionizing radiation. The infection with Pseudomonas aeruginosa (PA14) in Caenorhabditis elegans induces up-regulation of innate immune response genes. Here, we found that exposure to ionizing radiation also induces certain innate immune response genes such as F49F1.6 (termed mul-1), clec-4, clec-67, lys-1 and lys-2 in the intestine. Moreover, pre-treatment with ionizing radiation before seeding on PA14 lawn plate significantly increased survival rate in the nematode. We also studied transcription pathway of the mul-1 in response to ionizing radiation. Induction of mul-1 gene was highly dependent on the ELT-2 transcription factor and p38 MAPK. Moreover, the insulin/IGF-1 signal pathway works to enhance induction of this gene. The mul-1 gene showed a different induction pattern from the DNA damage response gene, ced-13, which implies that the expression of this gene might be triggered as an indirect effect of radiation. Silencing of the mul-1 gene led to growth retardation after treatment with ionizing radiation. We describe the cross-tolerance between the response to radiation exposure and the innate immune system.

Phase Transition and Critical Values of a Nearest-Neighbor System with Uncountable Local State Space on Cayley Trees

International Nuclear Information System (INIS)

Jahnel, Benedikt; Külske, Christof; Botirov, Golibjon I.

2014-01-01

We consider a ferromagnetic nearest-neighbor model on a Cayley tree of degree k ⩾ 2 with uncountable local state space [0,1] where the energy function depends on a parameter θ ∊[0, 1). We show that for 0 ⩽ θ ⩽ 5 3 k the model has a unique translation-invariant Gibbs measure. If 5 3 k < θ < 1 , there is a phase transition, in particular there are three translation-invariant Gibbs measures

Unsynchronized influenza epidemics in two neighboring subtropical cities

Directory of Open Access Journals (Sweden)

Xiujuan Tang

2018-04-01

Full Text Available Objective: The aim of this study was to examine the synchrony of influenza epidemics between Hong Kong and Shenzhen, two neighboring subtropical cities in South China. Methods: Laboratory-confirmed influenza data for the period January 2006 to December 2016 were obtained from the Shenzhen Center for Disease Control and Prevention and the Department of Health in Hong Kong. The population data were retrieved from the 2011 population censuses. The weekly rates of laboratory-confirmed influenza cases were compared between Shenzhen and Hong Kong. Results: Unsynchronized influenza epidemics between Hong Kong and Shenzhen were frequently observed during the study period. Influenza A/H1N1 caused a more severe pandemic in Hong Kong in 2009, but the subsequent seasonal epidemics showed similar magnitudes in both cities. Two influenza A/H3N2 dominant epidemic waves were seen in Hong Kong in 2015, but these epidemics were very minor in Shenzhen. More influenza B epidemics occurred in Shenzhen than in Hong Kong. Conclusions: Influenza epidemics appeared to be unsynchronized between Hong Kong and Shenzhen most of the time. Given the close geographical locations of these two cities, this could be due to the strikingly different age structures of their populations. Keywords: Influenza epidemics, Synchrony, Shenzhen, Hong Kong

LOS GENES BRCA1 y BRCA2. ESTUDIO MOLECULAR

Directory of Open Access Journals (Sweden)

N. Alonso

2006-11-01

Full Text Available RESUMENEn los últimos años, se realizaron numerosos estudios para establecer la predisposición hereditaria al cáncer y las alteraciones mutacionales a nivel de genes susceptibles de originar cáncer de mama y ovario. En 1994 se identificaron los genes BRCA1 (Breast Cancer Gene 1 y BRCA2 (Breast Cancer Gene 2 como susceptibles de cáncer de mama y ovario. En la actualidad se sabe que las mutaciones en BRCA1 y BRCA2 están lejos de explicar la totalidad de los casos de cáncer de mama y/o ovario, y a pesar de que se postulan alteraciones mutacionales en otros genes como CHEK2, TP53 y PTEN, el BRCA1 y BRCA2, siguen teniendo su importancia y utilidad en la valoración del riesgo de predisposición hereditaria. Aunque las cifras son variables según los distintos estudios y autores, se trata en cualquier caso de porcentajes importantes. Entre el 15 y el 85% de las mujeres portadoras de mutación BRCA 1 o BRCA 2 tienen riesgo de desarrollar un cáncer de mama y entre un 10 y 60% de desarrollar un cáncer de ovario. ABSTRACT:In the last years, numerous studies were made to establish the hereditary predisposition to the cancer and the mutationals alterations at level of genes susceptible to originate breast and ovarian cancers. In 1994 genes BRCA1 (Breast Cancer Gene 1 and BRCA2 were identified (Breast Cancer Gene 2 as susceptible of both of breast and ovarian cancers. At the present time, it is knows that the mutations in BRCA 1 and BRCA 2 are far from explaining the totality of the cases of breast cancer and/or ovary, and although mutationals alterations in other genes like CHEK2, TP53 and PTEN, the BRCA1 and BRCA2 are postulated, they continue having his importance and utility in the valuation of the risk of hereditary predisposition. Correlations between both BRCA1 and BRCA2 levels with tumour grade metastasis and prognostic accuracy. Between 15 and 85% of the carrying women of mutation BRCA 1 or BRCA 2 have risk of developing a cancer of breast

Herpes simplex virus type 1 (HSV-1)-derived recombinant vectors for gene transfer and gene therapy.

Science.gov (United States)

Marconi, Peggy; Fraefel, Cornel; Epstein, Alberto L

2015-01-01

Herpes simplex virus type 1 (HSV-1 ) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153-kilobase pair (kbp) double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes the approach most commonly used to prepare recombinant HSV-1 vectors through homologous recombination, either in eukaryotic cells or in bacteria.

Incorporating the information from direct and indirect neighbors into fitness evaluation enhances the cooperation in the social dilemmas

International Nuclear Information System (INIS)

Hu, Menglong; Wang, Juan; Kong, Lingcong; An, Kang; Bi, Tao; Guo, Baohong; Dong, Enzeng

2015-01-01

Highlights: •A novel fitness evaluation method integrating environmental information is presented. •The introduction of neighbors’ payoff favors the promotion of cooperation in the PDG. •The role of direct neighbors becomes much more prominent. •In the SDG, the cooperative behavior is also improved by this new mechanism. -- Abstract: We propose an improved fitness evaluation method to investigate the evolution of cooperation in the spatial social dilemmas. In our model, a focal player’s fitness is calculated as the linear combination of his own payoff, the average payoffs of direct and indirect neighbors in which two independent selection parameters (α and β) are used to control the proportion of various payoff contribution to the current fitness. Then, the fitness-based strategy update rule is still Fermi-like, and asynchronous update is adopted here. A large plethora of numerical simulations are performed to validate the behaviors of the current model, and the results unambiguously demonstrate that the cooperation level is greatly enhanced by introducing the payoffs from the surrounding players. In particular, the influence of direct neighbors become more evident when compared with indirect neighbors since the correlation between focal players and their direct neighbors is much closer. Current outcomes are significant for us to further illustrate the origin and emergence of cooperation within a wide variety of natural and man-made systems

Gene Expression of Glucose Transporter 1 (GLUT1), Hexokinase 1 and Hexokinase 2 in Gastroenteropancreatic Neuroendocrine Tumors

DEFF Research Database (Denmark)

Binderup, Tina; Knigge, Ulrich; Federspiel, Birgitte Hartnack

2013-01-01

-associated genes and to compare this with FDG-PET imaging as well as with the cellular proliferation index in two cancer entities with different malignant potential. Using real-time PCR, gene expression of GLUT1, HK1 and HK2 were studied in 34 neuroendocrine tumors (NETs) in comparison with 14 colorectal...... adenocarcinomas (CRAs). The Ki67 proliferation index and, when available, FDG-PET imaging was compared with gene expression. Overexpression of GLUT1 gene expression was less frequent in NETs (38%) compared to CRAs (86%), P = 0.004. HK1 was overexpressed in 41% and 71% of NETs and CRAs, respectively (P = 0.......111) and HK2 was overexpressed in 50% and 64% of NETs and CRAs, respectively (P = 0.53). There was a significant correlation between the Ki67 proliferation index and GLUT1 gene expression for the NETs (R = 0.34, P = 0.047), but no correlation with the hexokinases. FDG-PET identified foci in significantly...

Congenital hypopituitarism due to POU1F1 gene mutation.

Science.gov (United States)

Lee, Ni-Chung; Tsai, Wen-Yu; Peng, Shinn-Forng; Tung, Yi-Ching; Chien, Yin-Hsiu; Hwu, Wuh-Liang

2011-01-01

POU1F1 (Pit-1; Gene ID 5449) is an anterior pituitary transcriptional factor, and POU1F1 mutation is known to cause anterior pituitary hypoplasia, growth hormone and prolactin deficiency and various degree of hypothyroidism. We report here a patient who presented with growth failure and central hypothyroidism since early infancy. However, treatment with thyroxine gave no effect and he subsequently developed calf muscle pseudohypertrophy (Kocher-Debre-Semelaigne syndrome), elevation of creatinine kinase, dilated cardiomyopathy and pericardial effusion. Final diagnosis was made by combined pituitary function test and sequencing analysis that revealed POU1F1 gene C.698T > C (p.F233S) mutation. The rarity of the disease can result in delayed diagnosis and treatment. Copyright © 2011 Formosan Medical Association & Elsevier. Published by Elsevier B.V. All rights reserved.

An Alcohol Dehydrogenase Gene from Synechocystis sp. Confers Salt Tolerance in Transgenic Tobacco

Directory of Open Access Journals (Sweden)

So Young Yi

2017-11-01

Full Text Available Synechocystis salt-responsive gene 1 (sysr1 was engineered for expression in higher plants, and gene construction was stably incorporated into tobacco plants. We investigated the role of Sysr1 [a member of the alcohol dehydrogenase (ADH superfamily] by examining the salt tolerance of sysr1-overexpressing (sysr1-OX tobacco plants using quantitative real-time polymerase chain reactions, gas chromatography-mass spectrometry, and bioassays. The sysr1-OX plants exhibited considerably increased ADH activity and tolerance to salt stress conditions. Additionally, the expression levels of several stress-responsive genes were upregulated. Moreover, airborne signals from salt-stressed sysr1-OX plants triggered salinity tolerance in neighboring wild-type (WT plants. Therefore, Sysr1 enhanced the interconversion of aldehydes to alcohols, and this occurrence might affect the quality of green leaf volatiles (GLVs in sysr1-OX plants. Actually, the Z-3-hexenol level was approximately twofold higher in sysr1-OX plants than in WT plants within 1–2 h of wounding. Furthermore, analyses of WT plants treated with vaporized GLVs indicated that Z-3-hexenol was a stronger inducer of stress-related gene expression and salt tolerance than E-2-hexenal. The results of the study suggested that increased C6 alcohol (Z-3-hexenol induced the expression of resistance genes, thereby enhancing salt tolerance of transgenic plants. Our results revealed a role for ADH in salinity stress responses, and the results provided a genetic engineering strategy that could improve the salt tolerance of crops.

A dual resistance gene system prevents infection by three distinct pathogens.

Science.gov (United States)

Narusaka, Mari; Kubo, Yasuyuki; Shiraishi, Tomonori; Iwabuchi, Masaki; Narusaka, Yoshihiro

2009-10-01

Colletotrichum higginsianum causes typical anthracnose lesions on the leaves, petioles, and stems of cruciferous plants. Inoculation of Arabidopsis thaliana ecotype Columbia leaves with C. higginsianum results in fungal growth and disease symptoms reminiscent of those induced in other cruciferous plants. We performed map-based cloning and natural variation analysis of 19 A. thaliana ecotypes to identify a dominant resistance locus against C. higginsianum. We found that the A. thaliana RCH2 (for recognition of C. higginsianum) locus encodes two NB-LRR proteins, both of which are required for resistance to C. higginsianum in the A. thaliana ecotype Ws-0. Both proteins are well-characterized R proteins involved in resistance against bacterial pathogens; RRS1 (resistance to Ralstonia solanacearum 1) confers resistance to strain Rs1000 of R. solanacearum and RPS4 to Pseudomonas syringae pv. tomato strain DC3000 expressing avrRps4 (Pst-avrRps4). Furthermore, we found that both RRS1-Ws and RPS4-Ws genes are required for resistance to Pst-avrRps4 and to Rs1002 R. solanacearum. We therefore demonstrate that a pair of neighboring genes, RRS1-Ws and RPS4-Ws, function cooperatively as a dual R-gene system against at least three distinct pathogens.

Feasibility of sodium/iodide symporter gene as a new imaging reporter gene: comparison with HSV1-tk

International Nuclear Information System (INIS)

Shin, Jae Hoon; Chung, June-Key; Lee, Yong Jin; Kim, Kwang Il; Kang, Joo Hyun; Jeong, Jae Min; Lee, Dong Soo; Kim, Chul Woo; Lee, Myung Chul

2004-01-01

Positron emission tomography (PET) imaging reporter genes, such as HSV1-tk and D 2 receptor genes, make it possible to visualise gene expression non-invasively and repetitively in vivo. However, these systems require the synthesis of complicated substrates and the availability of expensive PET equipment. Expression of the sodium/iodide symporter (NIS) gene can be easily monitored with radioiodines and technetium-99m using a gamma camera. To evaluate the possibility of using NIS as an imaging reporter gene, we compared its characteristics with those of the conventional HSV1-tk gene. The CM cell line was made by transfecting the HSV1-tk gene into CT-26 (mouse colon carcinoma cell line). The CTN and CMN cell lines were then made by transfecting the NIS gene into CT-26 and CM. We measured the uptake of iodine-125 iodovinyldeoxyuridine ([ 125 I]IVDU) and 125 I to evaluate the expression of the HSV1-tk and NIS genes, respectively. Each cell line was injected into four flank sites in Balb/c mice. The biodistribution study was performed after intravenously injecting [ 125 I]IVDU and 131 I, and 131 I scintigraphy was performed for the evaluation of NIS expression. In vitro studies indicated that CTN and CMN had 40- to 79-fold and 150- to 256-fold higher uptake of 125 I than CT-26 and CM, respectively. Furthermore, CM and CMN showed 57- to 69-fold higher uptake of [ 125 I]IVDU than CT-26 and CTN. NIS gene expression and 125 I accumulation were found to be directly correlated (R 2 =0.923), as were HSV1-tk gene expression and [ 125 I]IVDU accumulation (R 2 =0.956). Calculated signal per unit NIS and HSV1-tk mRNA expression was 23,240±3,755 cpm and 34,039±5,346 cpm, respectively. In vivo study indicated that CTN and CMN had 2.3- and 5.8-fold higher uptake of 131 I than CT-26 and CM, and 1.8- and 3.5-fold higher uptake of [ 125 I]IVDU than CT-26 and CTN. Scintigraphy using 131 I easily visualised CTN and CMN tumours. In conclusion, the NIS gene may be viewed as an imaging

Establishment of mitochondrial pyruvate carrier 1 (MPC1) gene knockout mice with preliminary gene function analyses

Science.gov (United States)

Li, Xiaoli; Li, Yaqing; Han, Gaoyang; Li, Xiaoran; Ji, Yasai; Fan, Zhirui; Zhong, Yali; Cao, Jing; Zhao, Jing; Mariusz, Goscinski; Zhang, Mingzhi; Wen, Jianguo; Nesland, Jahn M.; Suo, Zhenhe

2016-01-01

Pyruvate plays a critical role in the mitochondrial tricarboxylic acid (TCA) cycle, and it is the center product for the synthesis of amino acids, carbohydrates and fatty acids. Pyruvate transported across the inner mitochondrial membrane appears to be essential in anabolic and catabolic intermediary metabolism. The mitochondrial pyruvate carrier (MPC) mounted in the inner membrane of mitochondria serves as the channel to facilitate pyruvate permeating. In mammals, the MPC is formed by two paralogous subunits, MPC1 and MPC2. It is known that complete ablation of MPC2 in mice causes death on the 11th or 12th day of the embryonic period. However, MPC1 deletion and the knowledge of gene function in vivo are lacking. Using the new technology of gene manipulation known as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) systems, we gained stable MPC1 gene heterozygous mutation mice models, and the heterozygous mutations could be stably maintained in their offsprings. Only one line with homozygous 27 bases deletion in the first exon was established, but no offsprings could be obtained after four months of mating experiments, indicating infertility of the mice with such homozygous deletion. The other line of MPC1 knockout (KO) mice was only heterozygous, which mutated in the first exon with a terminator shortly afterwards. These two lines of MPC1 KO mice showed lower fertility and significantly higher bodyweight in the females. We concluded that heterozygous MPC1 KO weakens fertility and influences the metabolism of glucose and fatty acid and bodyweight in mice. PMID:27835892

Knowledgeable Neighbors: a mobile clinic model for disease prevention and screening in underserved communities.

Science.gov (United States)

Hill, Caterina; Zurakowski, David; Bennet, Jennifer; Walker-White, Rainelle; Osman, Jamie L; Quarles, Aaron; Oriol, Nancy

2012-03-01

The Family Van mobile health clinic uses a "Knowledgeable Neighbor" model to deliver cost-effective screening and prevention activities in underserved neighborhoods in Boston, MA. We have described the Knowledgeable Neighbor model and used operational data collected from 2006 to 2009 to evaluate the service. The Family Van successfully reached mainly minority low-income men and women. Of the clients screened, 60% had previously undetected elevated blood pressure, 14% had previously undetected elevated blood glucose, and 38% had previously undetected elevated total cholesterol. This represents an important model for reaching underserved communities to deliver proven cost-effective prevention activities, both to help control health care costs and to reduce health disparities.

Linkage relationship between semi-dwarfing gene sd-1 and gene for grain shattering in rice

International Nuclear Information System (INIS)

Oba, S.; Kikuchi, F.

1990-01-01

Full text: Most semidwarf rice cultivars carry the same gene sd-1. We observed an association between semi-dwarfness and grain shattering in isogenic lines carrying sd-1 from different sources in the background of the Japanese tall cultivar 'Norin 28'. The shattering was found to be caused by a single recessive gene, sh-2, linked to the sd-1 locus. The shattering gene seems to have been transmitted to many semi-dwarf cultivars together with sd-1, not only from 'Dee-geo-woo-gen' but also from the indica-cultivar 'Ai-jio-nan-te' and the japonica cultivar 'Shiranui'. (author)

Nearest Neighbor Estimates of Entropy for Multivariate Circular Distributions

Directory of Open Access Journals (Sweden)

Neeraj Misra

2010-05-01

Full Text Available In molecular sciences, the estimation of entropies of molecules is important for the understanding of many chemical and biological processes. Motivated by these applications, we consider the problem of estimating the entropies of circular random vectors and introduce non-parametric estimators based on circular distances between n sample points and their k th nearest neighbors (NN, where k (≤ n – 1 is a fixed positive integer. The proposed NN estimators are based on two different circular distances, and are proven to be asymptotically unbiased and consistent. The performance of one of the circular-distance estimators is investigated and compared with that of the already established Euclidean-distance NN estimator using Monte Carlo samples from an analytic distribution of six circular variables of an exactly known entropy and a large sample of seven internal-rotation angles in the molecule of tartaric acid, obtained by a realistic molecular-dynamics simulation.

Study on the polymorphism of POU1F1 gene in sheep

Directory of Open Access Journals (Sweden)

Jun Yan Bai

Full Text Available ABSTRACT In this study, POU1F1 gene polymorphism was detected in five sheep populations (large-tailed Han, small-tailed Han, Yuxi fat-tailed, Lanzhou large-tailed, and Mongolian sheep, using DNA pooling and sequencing, to provide theoretical basis for the breeding of excellent sheep varieties. Three single-nucleotide polymorphism (SNP loci of POU1F1 gene were detected in five sheep populations, namely C355T (C/T, C71G (C/G, and C330G (C/G. C and T frequencies of C355T were 0.67/0.33, 0.81/0.19, 0.67/0.33, 1.00/0.00, and 0.93/0.07, respectively, in large-tailed Han, small-tailed Han, Yuxi fat-tailed, Mongolian, and Lanzhou large-tailed sheep. C of C355T locus was the dominant allele in five sheep populations. C and G allele frequencies of C330G locus were detected in Yuxi fat-tailed sheep; their frequencies were 0.75 and 0.25, respectively. C and G allele of C71G locus were only detected in Yuxi fat-tailed and large-tailed Han sheep; their frequencies were 0.87/0.13 and 0.87/0.13, respectively. The cluster analysis based on POU1F1 gene sequence showed that bactrian camel, dromedary, and wild camel clustered first, and dolphin and killer whales clustered according to taxonomy. Although the four species Tibetan antelope, buffalo, goat, and sheep were alone, they got close and the relative genetic relationship was intimate according to the dendrogram. The mutation site analysis of the POU1F1 gene in five sheep populations in this study would be favorable for uncovering the function of POU1F1 gene deeply.

Response properties of neighboring neurons in the auditory midbrain for pure-tone stimulation: a tetrode study.

Science.gov (United States)

Seshagiri, Chandran V; Delgutte, Bertrand

2007-10-01

The complex anatomical structure of the central nucleus of the inferior colliculus (ICC), the principal auditory nucleus in the midbrain, may provide the basis for functional organization of auditory information. To investigate this organization, we used tetrodes to record from neighboring neurons in the ICC of anesthetized cats and studied the similarity and difference among the responses of these neurons to pure-tone stimuli using widely used physiological characterizations. Consistent with the tonotopic arrangement of neurons in the ICC and reports of a threshold map, we found a high degree of correlation in the best frequencies (BFs) of neighboring neurons, which were mostly binaural beats. However, the characteristic phases (CPs) of neighboring neurons revealed a significant correlation. Because the CP is related to the neural mechanisms generating the ITD sensitivity, this result is consistent with segregation of inputs to the ICC from the lateral and medial superior olives.

The progress of tumor gene-radiotherapy induced by Egr-1 promoter

International Nuclear Information System (INIS)

Guo Rui; Li Biao

2010-01-01

The promoter of early growth response gene-1 (Egr-1) is a cis-acting element of Egr-1, and its activity is regulated by inducers such as ionizing radiation, free radical. In designated gene-radiotherapy system, radiation combined with therapeutic gene (such as tumor necrosis factor-α gene, suicide gene) can spatially and temporally regulate therapeutic gene expression in the irradiated field, produced a marked effect, while little systemic toxicities were observed. The combination of radiotherapy and gene therapy is promising in tumor therapy. (authors)

BRCA1-mediated repression of select X chromosome genes

Directory of Open Access Journals (Sweden)

Ropers H Hilger

2004-09-01

Full Text Available Abstract Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary DNA microarrays were used to compare the expression levels of X chromosome genes in 18 BRCA1-associated ovarian cancers to those of the 13 "BRCA1-like" and 14 "BRCA2-like" sporadic tumors (as defined by previously reported expression profiling. Significance was determined using parametric statistics with P

Implementation of the k -Neighbors Technique in a recommender algorithm for a purchasing system using NFC and Android

Directory of Open Access Journals (Sweden)

Oscar Arley Riveros

2017-01-01

Full Text Available Introduction: This paper aims to present the design of a mobile application involving NFC technology and a collaborative recommendation algorithm under the K-neighbors technique, allowing to observe personalized suggestions for each client. Objective: Design and develop a mobile application, using NFC technologies and K-Neighbors Technique in a recommendation algorithm, for a Procurement System. Methodology: The process followed for the design and development of the application focuses on: • Review of the state of the art in mobile shopping systems. • State-of-the-art construction in the use of NFC technology and AI techniques for recommending systems focused on K-Neighbors Algorithms • Proposed system design • Parameterization and implementation of the K-Neighbors Technique and integration of NFC Technology • Proposed System Implementation and Testing. Results: Among the results obtained are detailed: • Mobile application that integrates Android, NFC Technologies and a Technique of Algorithm Recommendation • Parameterization of the K-Neighbors Technique, to be used within the recommended algorithm. • Implementation of functional requirements that allow the generation of personalized recommendations for purchase to the user, user ratings Conclusions: The k-neighbors technique in a recommendation algorithm allows the client to provide a series of recommendations with a level of security, since this algorithm performs calculations taking into account multiple parameters and contrasts the results obtained for other users, finding the articles with a Greater degree of similarity with the customer profile. This algorithm starts from a sample of similar, complementary and other unrelated products, applying its respective formulation, we obtain that the recommendation is made only with the complementary products that obtained higher qualification; Making a big difference with most recommending systems on the market, which are limited to

Id-1 gene and gene products as therapeutic targets for treatment of breast cancer and other types of carcinoma

Science.gov (United States)

Desprez, Pierre-Yves; Campisi, Judith

2014-08-19

A method for treatment of breast cancer and other types of cancer. The method comprises targeting and modulating Id-1 gene expression, if any, for the Id-1 gene, or gene products in breast or other epithelial cancers in a patient by delivering products that modulate Id-1 gene expression. When expressed, Id-1 gene is a prognostic indicator that cancer cells are invasive and metastatic.

Chirality dependence of dipole matrix element of carbon nanotubes in axial magnetic field: A third neighbor tight binding approach

Science.gov (United States)

Chegel, Raad; Behzad, Somayeh

2014-02-01

We have studied the electronic structure and dipole matrix element, D, of carbon nanotubes (CNTs) under magnetic field, using the third nearest neighbor tight binding model. It is shown that the 1NN and 3NN-TB band structures show differences such as the spacing and mixing of neighbor subbands. Applying the magnetic field leads to breaking the degeneracy behavior in the D transitions and creates new allowed transitions corresponding to the band modifications. It is found that |D| is proportional to the inverse tube radius and chiral angle. Our numerical results show that amount of filed induced splitting for the first optical peak is proportional to the magnetic field by the splitting rate ν11. It is shown that ν11 changes linearly and parabolicly with the chiral angle and radius, respectively.

Nidogen-1 regulates laminin-1-dependent mammary-specific gene expression

Energy Technology Data Exchange (ETDEWEB)

Pujuguet, Philippe; Simian, Marina; Liaw, Jane; Timpl, Rupert; Werb, Zena; Bissell, Mina J..

2000-02-01

Nidogen-1 (entactin) acts as a bridge between the extracellular matrix molecules laminin-1 and type IV collagen, and thus participates in the assembly of basement membranes. To investigate the role of nidogen-1 in regulating cell-type-specific gene expression in mammary epithelium, we designed a culture microecosystem in which each component, including epithelial cells, mesenchymal cells, lactogenic hormones and extracellular matrix, could be controlled. We found that primary and established mesenchymal and myoepithelial cells synthesized and secreted nidogen-1, whereas expression was absent in primary and established epithelial cells. In an epithelial cell line containing mesenchymal cells, nidogen-1 was produced by the mesenchymal cells but deposited between the epithelial cells. In this mixed culture, mammary epithelial cells express b-casein in the presence of lactogenic hormones. Addition of either laminin-1 plus nidogen-1, or laminin-1 alone to mammary epithelial cells induced b- casein production. We asked whether recombinant nidogen-1 alone could signal directly for b-casein. Nidogen-1 did not induce b-casein synthesis in epithelial cells, but it augmented the inductive capacity of laminin-1. These data suggest that nidogen-1 can cooperate with laminin-1 to regulate b-casein expression. Addition of full length nidogen-1 to the mixed cultures had no effect on b-casein gene expression; however, a nidogen-1 fragment containing the laminin-1 binding domain, but lacking the type IV collagen-binding domain, had a dominant negative effect on b-casein expression. These data point to a physiological role for nidogen-1 in the basement membrane-induced gene expression by epithelial cells.

Neighboring Structure Visualization on a Grid-based Layout.

Science.gov (United States)

Marcou, G; Horvath, D; Varnek, A

2017-10-01

Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi- or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

MSX1 gene in the etiology orofacial deformities

Directory of Open Access Journals (Sweden)

Anna Paradowska-Stolarz

2015-12-01

Full Text Available The muscle segment homeobox (MSX1 gene plays a crucial role in epithelial-mesenchymal tissue interactions in craniofacial development. It plays a regulative role in cellular proliferation, differentiation and cell death. The human MSX1 domain was also found in cow (Bt 302906, mouse (Mm 123311, rat (Rn13592001, chicken (Gg 170873 and clawed toad (XI 547690. Cleft lip and palate is the most common anomaly of the facial part of the skull. The etiology is not fully understood, but it is believed that the key role is played by the genetic factor activated by environmental factors. Among the candidate genes whose mutations could lead to formation of the cleft, the MSX1 homeobox gene is mentioned. Mutations in the gene MSX1 can lead to isolated cleft deformities, but also cause other dismorphic changes. Among the most frequently mentioned is loss of permanent tooth buds (mostly of less than 4 teeth – hypodontia, including second premolars. Mutations of MSX1 are observed in the Pierre- Robin sequence, which may be one of the features of congenital defects or is observed as an isolated defect. Mutation of the gene can lead to the occurrence of a rare congenital defect Wiktop (dental-nail syndrome. Deletion of a fragment MSX1 (4p16.3 located in the WHS critical region, may be a cause of some symptoms of Wolf-Hirschhorn syndrome.

Multidimensional k-nearest neighbor model based on EEMD for financial time series forecasting

Science.gov (United States)

Zhang, Ningning; Lin, Aijing; Shang, Pengjian

2017-07-01

In this paper, we propose a new two-stage methodology that combines the ensemble empirical mode decomposition (EEMD) with multidimensional k-nearest neighbor model (MKNN) in order to forecast the closing price and high price of the stocks simultaneously. The modified algorithm of k-nearest neighbors (KNN) has an increasingly wide application in the prediction of all fields. Empirical mode decomposition (EMD) decomposes a nonlinear and non-stationary signal into a series of intrinsic mode functions (IMFs), however, it cannot reveal characteristic information of the signal with much accuracy as a result of mode mixing. So ensemble empirical mode decomposition (EEMD), an improved method of EMD, is presented to resolve the weaknesses of EMD by adding white noise to the original data. With EEMD, the components with true physical meaning can be extracted from the time series. Utilizing the advantage of EEMD and MKNN, the new proposed ensemble empirical mode decomposition combined with multidimensional k-nearest neighbor model (EEMD-MKNN) has high predictive precision for short-term forecasting. Moreover, we extend this methodology to the case of two-dimensions to forecast the closing price and high price of the four stocks (NAS, S&P500, DJI and STI stock indices) at the same time. The results indicate that the proposed EEMD-MKNN model has a higher forecast precision than EMD-KNN, KNN method and ARIMA.

Investigation of associations between NR1D1, RORA and RORB genes and bipolar disorder.

Directory of Open Access Journals (Sweden)

Yin-Chieh Lai

Full Text Available Several genes that are involved in the regulation of circadian rhythms are implicated in the susceptibility to bipolar disorder (BD. The current study aimed to investigate the relationships between genetic variants in NR1D1 RORA, and RORB genes and BD in the Han Chinese population. We conducted a case-control genetic association study with two samples of BD patients and healthy controls. Sample I consisted of 280 BD patients and 200 controls. Sample II consisted of 448 BD patients and 1770 healthy controls. 27 single nucleotide polymorphisms in the NR1D1, RORA, and RORB genes were genotyped using GoldenGate VeraCode assays in sample I, and 492 markers in the three genes were genotyped using Affymetrix Genome-Wide CHB Array in sample II. Single marker and gene-based association analyses were performed using PLINK. A combined p-value for the joining effects of all markers within a gene was calculated using the rank truncated product method. Multifactor dimensionality reduction (MDR method was also applied to test gene-gene interactions in sample I. All markers were in Hardy-Weinberg equilibrium (P>0.001. In sample I, the associations with BD were observed for rs4774388 in RORA (OR = 1.53, empirical p-value, P = 0.024, and rs1327836 in RORB (OR = 1.75, P = 0.003. In Sample II, there were 45 SNPs showed associations with BD, and the most significant marker in RORA was rs11639084 (OR = 0.69, P = 0.002, and in RORB was rs17611535 (OR = 3.15, P = 0.027. A combined p-value of 1.6×10-6, 0.7, and 1.0 was obtained for RORA, RORB and NR1D1, respectively, indicting a strong association for RORA with the risk of developing BD. A four way interaction was found among markers in NR1D1, RORA, and RORB with the testing accuracy 53.25% and a cross-validation consistency of 8 out of 10. In sample II, 45 markers had empirical p-values less than 0.05. The most significant markers in RORA and RORB genes were rs11639084 (OR = 0.69, P = 0.002, and rs17611535 (OR = 3

DIA1R is an X-linked gene related to Deleted In Autism-1.

Directory of Open Access Journals (Sweden)

Azhari Aziz

Full Text Available BACKGROUND: Autism spectrum disorders (ASDS are frequently occurring disorders diagnosed by deficits in three core functional areas: social skills, communication, and behaviours and/or interests. Mental retardation frequently accompanies the most severe forms of ASDs, while overall ASDs are more commonly diagnosed in males. Most ASDs have a genetic origin and one gene recently implicated in the etiology of autism is the Deleted-In-Autism-1 (DIA1 gene. METHODOLOGY/PRINCIPAL FINDINGS: Using a bioinformatics-based approach, we have identified a human gene closely related to DIA1, we term DIA1R (DIA1-Related. While DIA1 is autosomal (chromosome 3, position 3q24, DIA1R localizes to the X chromosome at position Xp11.3 and is known to escape X-inactivation. The gene products are of similar size, with DIA1 encoding 430, and DIA1R 433, residues. At the amino acid level, DIA1 and DIA1R are 62% similar overall (28% identical, and both encode signal peptides for targeting to the secretory pathway. Both genes are ubiquitously expressed, including in fetal and adult brain tissue. CONCLUSIONS/SIGNIFICANCE: Examination of published literature revealed point mutations in DIA1R are associated with X-linked mental retardation (XLMR and DIA1R deletion is associated with syndromes with ASD-like traits and/or XLMR. Together, these results support a model where the DIA1 and DIA1R gene products regulate molecular traffic through the cellular secretory pathway or affect the function of secreted factors, and functional deficits cause disorders with ASD-like symptoms and/or mental retardation.

Observing Literacy Practices in Neighbor Institutions

DEFF Research Database (Denmark)

Reusch, Charlotte

’procedures on language and literacy. Based on this material, we developed an observation scheme and a guide for preschool teachers to follow, inspired by an action learning concept.During fall 2015, a pilot project is carried out. Preschool teachers from one institution visit a neighbor institution one by one during...... work hours, in order to observe and register how language and literacy events look like there. Afterwards, they share their registrations at a team meeting, and discuss and decide which procedures to test in their own institution. Thus, they form a professional learning network. In the pilot project......The Danish National Centre for Reading and a municipality in southern Denmark cooperate to develop a program to improve preschool children’s early literacy skills. The project aims to support preschool teachers’ ability to create a rich literacy environment for children age 3‒6. Recent research...

Integrative analysis of RUNX1 downstream pathways and target genes

Directory of Open Access Journals (Sweden)

Liu Marjorie

2008-07-01

Full Text Available Abstract Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML. The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. Results Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1 cell lines with RUNX1 mutations from FPD-AML patients, 2 over-expression of RUNX1 and CBFβ, and 3 Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFβ. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. Conclusion This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease

DNMT1-interacting RNAs block gene specific DNA methylation

Science.gov (United States)

Di Ruscio, Annalisa; Ebralidze, Alexander K.; Benoukraf, Touati; Amabile, Giovanni; Goff, Loyal A.; Terragni, Joylon; Figueroa, Maria Eugenia; De Figureido Pontes, Lorena Lobo; Alberich-Jorda, Meritxell; Zhang, Pu; Wu, Mengchu; D’Alò, Francesco; Melnick, Ari; Leone, Giuseppe; Ebralidze, Konstantin K.; Pradhan, Sriharsa; Rinn, John L.; Tenen, Daniel G.

2013-01-01

Summary DNA methylation was described almost a century ago. However, the rules governing its establishment and maintenance remain elusive. Here, we present data demonstrating that active transcription regulates levels of genomic methylation. We identified a novel RNA arising from the CEBPA gene locus critical in regulating the local DNA methylation profile. This RNA binds to DNMT1 and prevents CEBPA gene locus methylation. Deep sequencing of transcripts associated with DNMT1 combined with genome-scale methylation and expression profiling extended the generality of this finding to numerous gene loci. Collectively, these results delineate the nature of DNMT1-RNA interactions and suggest strategies for gene selective demethylation of therapeutic targets in disease. PMID:24107992

Introduction to machine learning: k-nearest neighbors.

Science.gov (United States)

Zhang, Zhongheng

2016-06-01

Machine learning techniques have been widely used in many scientific fields, but its use in medical literature is limited partly because of technical difficulties. k-nearest neighbors (kNN) is a simple method of machine learning. The article introduces some basic ideas underlying the kNN algorithm, and then focuses on how to perform kNN modeling with R. The dataset should be prepared before running the knn() function in R. After prediction of outcome with kNN algorithm, the diagnostic performance of the model should be checked. Average accuracy is the mostly widely used statistic to reflect the kNN algorithm. Factors such as k value, distance calculation and choice of appropriate predictors all have significant impact on the model performance.

Multiplex PCR detection of GSTM1, GSTT1, and GSTP1 gene variants: simultaneously detecting GSTM1 and GSTT1 gene copy number and the allelic status of the GSTP1 Ile105Val genetic variant

DEFF Research Database (Denmark)

Buchard, Anders; Sanchez Sanchez, Juan Jose; Dalhoff, Kim

2007-01-01

, the enzyme activity of GSTM1 and GSTT1 is absent in approximately 50 and 15% of the population, respectively, due to deletions of both chromosomal copies of the genes. A trimodal phenotype pattern exists in which individuals with two, one, or no functional genes are fast, intermediate, or slow "conjugators...

Long-term effect of September 11 on the political behavior of victims’ families and neighbors

Science.gov (United States)

Hersh, Eitan D.

2013-01-01

This article investigates the long-term effect of September 11, 2001 on the political behaviors of victims’ families and neighbors. Relative to comparable individuals, family members and residential neighbors of victims have become—and have stayed—significantly more active in politics in the last 12 years, and they have become more Republican on account of the terrorist attacks. The method used to demonstrate these findings leverages the random nature of the terrorist attack to estimate a causal effect and exploits new techniques to link multiple, individual-level, governmental databases to measure behavioral change without relying on surveys or aggregate analysis. PMID:24324145

Long-term effect of September 11 on the political behavior of victims' families and neighbors.

Science.gov (United States)

Hersh, Eitan D

2013-12-24

This article investigates the long-term effect of September 11, 2001 on the political behaviors of victims' families and neighbors. Relative to comparable individuals, family members and residential neighbors of victims have become--and have stayed--significantly more active in politics in the last 12 years, and they have become more Republican on account of the terrorist attacks. The method used to demonstrate these findings leverages the random nature of the terrorist attack to estimate a causal effect and exploits new techniques to link multiple, individual-level, governmental databases to measure behavioral change without relying on surveys or aggregate analysis.

The Schizosaccharomyces pombe map1 gene encodes an SRF/MCM1-related protein required for P-cell specific gene expression

DEFF Research Database (Denmark)

Nielsen, O; Friis, T; Kjaerulff, S

1996-01-01

Cells of Schizosaccharomyces pombe undergo mating and meiosis when starved for a nitrogen source. In this process a P and and M cell first mate to generate a diploid zygote, which subsequently enters meiosis and sporulates. The P mating type is controlled by the mat1-Pc gene at the mating type lo...... cerevisiae MCM1. The Mat1-Pc protein contains a motif characteristic for proteins that interact with MADS-box factors, suggesting that Mat-Pc and Map1 may form a heterodimer that activates the P-specific map3 gene....

GABA metabolism pathway genes, UGA1 and GAD1, regulate replicative lifespan in Saccharomycescerevisiae

Energy Technology Data Exchange (ETDEWEB)

Kamei, Yuka; Tamura, Takayuki [Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829 (Japan); Yoshida, Ryo [Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ohta, Shinji [Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829 (Japan); Fukusaki, Eiichiro [Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Mukai, Yukio, E-mail: y_mukai@nagahama-i-bio.ac.jp [Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829 (Japan)

2011-04-01

Highlights: {yields}We demonstrate that two genes in the yeast GABA metabolism pathway affect aging. {yields} Deletion of the UGA1 or GAD1 genes extends replicative lifespan. {yields} Addition of GABA to wild-type cultures has no effect on lifespan. {yields} Intracellular GABA levels do not differ in longevity mutants and wild-type cells. {yields} Levels of tricarboxylic acid cycle intermediates positively correlate with lifespan. -- Abstract: Many of the genes involved in aging have been identified in organisms ranging from yeast to human. Our previous study showed that deletion of the UGA3 gene-which encodes a zinc-finger transcription factor necessary for {gamma}-aminobutyric acid (GABA)-dependent induction of the UGA1 (GABA aminotransferase), UGA2 (succinate semialdehyde dehydrogenase), and UGA4 (GABA permease) genes-extends replicative lifespan in the budding yeast Saccharomycescerevisiae. Here, we found that deletion of UGA1 lengthened the lifespan, as did deletion of UGA3; in contrast, strains with UGA2 or UGA4 deletions exhibited no lifespan extension. The {Delta}uga1 strain cannot deaminate GABA to succinate semialdehyde. Deletion of GAD1, which encodes the glutamate decarboxylase that converts glutamate into GABA, also increased lifespan. Therefore, two genes in the GABA metabolism pathway, UGA1 and GAD1, were identified as aging genes. Unexpectedly, intracellular GABA levels in mutant cells (except for {Delta}uga2 cells) did not differ from those in wild-type cells. Addition of GABA to culture media, which induces transcription of the UGA structural genes, had no effect on replicative lifespan of wild-type cells. Multivariate analysis of {sup 1}H nuclear magnetic resonance spectra for the whole-cell metabolite levels demonstrated a separation between long-lived and normal-lived strains. Gas chromatography-mass spectrometry analysis of identified metabolites showed that levels of tricarboxylic acid cycle intermediates positively correlated with lifespan

GABA metabolism pathway genes, UGA1 and GAD1, regulate replicative lifespan in Saccharomycescerevisiae

International Nuclear Information System (INIS)

Kamei, Yuka; Tamura, Takayuki; Yoshida, Ryo; Ohta, Shinji; Fukusaki, Eiichiro; Mukai, Yukio

2011-01-01

Highlights: →We demonstrate that two genes in the yeast GABA metabolism pathway affect aging. → Deletion of the UGA1 or GAD1 genes extends replicative lifespan. → Addition of GABA to wild-type cultures has no effect on lifespan. → Intracellular GABA levels do not differ in longevity mutants and wild-type cells. → Levels of tricarboxylic acid cycle intermediates positively correlate with lifespan. -- Abstract: Many of the genes involved in aging have been identified in organisms ranging from yeast to human. Our previous study showed that deletion of the UGA3 gene-which encodes a zinc-finger transcription factor necessary for γ-aminobutyric acid (GABA)-dependent induction of the UGA1 (GABA aminotransferase), UGA2 (succinate semialdehyde dehydrogenase), and UGA4 (GABA permease) genes-extends replicative lifespan in the budding yeast Saccharomycescerevisiae. Here, we found that deletion of UGA1 lengthened the lifespan, as did deletion of UGA3; in contrast, strains with UGA2 or UGA4 deletions exhibited no lifespan extension. The Δuga1 strain cannot deaminate GABA to succinate semialdehyde. Deletion of GAD1, which encodes the glutamate decarboxylase that converts glutamate into GABA, also increased lifespan. Therefore, two genes in the GABA metabolism pathway, UGA1 and GAD1, were identified as aging genes. Unexpectedly, intracellular GABA levels in mutant cells (except for Δuga2 cells) did not differ from those in wild-type cells. Addition of GABA to culture media, which induces transcription of the UGA structural genes, had no effect on replicative lifespan of wild-type cells. Multivariate analysis of 1 H nuclear magnetic resonance spectra for the whole-cell metabolite levels demonstrated a separation between long-lived and normal-lived strains. Gas chromatography-mass spectrometry analysis of identified metabolites showed that levels of tricarboxylic acid cycle intermediates positively correlated with lifespan extension. These results strongly suggest

Estimating forest attribute parameters for small areas using nearest neighbors techniques

Science.gov (United States)

Ronald E. McRoberts

2012-01-01

Nearest neighbors techniques have become extremely popular, particularly for use with forest inventory data. With these techniques, a population unit prediction is calculated as a linear combination of observations for a selected number of population units in a sample that are most similar, or nearest, in a space of ancillary variables to the population unit requiring...

Applying an efficient K-nearest neighbor search to forest attribute imputation

Science.gov (United States)

Andrew O. Finley; Ronald E. McRoberts; Alan R. Ek

2006-01-01

This paper explores the utility of an efficient nearest neighbor (NN) search algorithm for applications in multi-source kNN forest attribute imputation. The search algorithm reduces the number of distance calculations between a given target vector and each reference vector, thereby, decreasing the time needed to discover the NN subset. Results of five trials show gains...

Transcriptional regulation of the HMGA1 gene by octamer-binding proteins Oct-1 and Oct-2.

Directory of Open Access Journals (Sweden)

Eusebio Chiefari

Full Text Available The High-Mobility Group AT-Hook 1 (HMGA1 protein is an architectural transcription factor that binds to AT-rich sequences in the promoter region of DNA and functions as a specific cofactor for gene activation. Previously, we demonstrated that HMGA1 is a key regulator of the insulin receptor (INSR gene and an important downstream target of the INSR signaling cascade. Moreover, from a pathogenic point of view, overexpression of HMGA1 has been associated with human cancer, whereas functional variants of the HMGA1 gene have been recently linked to type 2 diabetes mellitus and metabolic syndrome. However, despite of this biological and pathological relevance, the mechanisms that control HMGA1 gene expression remain unknown. In this study, to define the molecular mechanism(s that regulate HMGA1 gene expression, the HMGA1 gene promoter was investigated by transient transfection of different cell lines, either before or after DNA and siRNA cotransfections. An octamer motif was identified as an important element of transcriptional regulation of this gene, the interaction of which with the octamer transcription factors Oct-1 and Oct-2 is crucial in modulating HMGA1 gene and protein expression. Additionally, we demonstrate that HMGA1 binds its own promoter and contributes to its transactivation by Oct-2 (but not Oct-1, supporting its role in an auto-regulatory circuit. Overall, our results provide insight into the transcriptional regulation of the HMGA1 gene, revealing a differential control exerted by both Oct-1 and Oct-2. Furthermore, they consistently support the hypothesis that a putative defect in Oct-1 and/or Oct-2, by affecting HMGA1 expression, may cause INSR dysfunction, leading to defects of the INSR signaling pathway.

A part of patients with autism spectrum disorder has haploidy of HPC-1/syntaxin1A gene that possibly causes behavioral disturbance as in experimentally gene ablated mice.

Science.gov (United States)

Kofuji, Takefumi; Hayashi, Yuko; Fujiwara, Tomonori; Sanada, Masumi; Tamaru, Masao; Akagawa, Kimio

2017-03-22

Autism spectrum disorder (ASD) is highly heritable and encompasses a various set of neuropsychiatric disorders with a wide-ranging presentation. HPC-1/syntaxin1A (STX1A) encodes a neuronal plasma membrane protein that regulates the secretion of neurotransmitters and neuromodulators. STX1A gene ablated mice (null and heterozygote mutant) exhibit abnormal behavioral profiles similar to human autistic symptoms, accompanied by reduction of monoamine secretion. To determine whether copy number variation of STX1A gene and the change of its expression correlate with ASD as in STX1A gene ablated mice, we performed copy number assay and real-time quantitative RT-PCR using blood or saliva samples from ASD patients. We found that some ASD patients were haploid for the STX1A gene similar to STX1A heterozygote mutant mice. However, copy number of STX1A gene was normal in the parents and siblings of ASD patients with STX1A gene haploidy. In ASD patients with gene haploidy, STX1A mRNA expression was reduced to about half of their parents. Thus, a part of ASD patients had haploidy of STX1A gene and lower STX1A gene expression. Copyright © 2017 Elsevier B.V. All rights reserved.

A hybrid network-based method for the detection of disease-related genes

Science.gov (United States)

Cui, Ying; Cai, Meng; Dai, Yang; Stanley, H. Eugene

2018-02-01

Detecting disease-related genes is crucial in disease diagnosis and drug design. The accepted view is that neighbors of a disease-causing gene in a molecular network tend to cause the same or similar diseases, and network-based methods have been recently developed to identify novel hereditary disease-genes in available biomedical networks. Despite the steady increase in the discovery of disease-associated genes, there is still a large fraction of disease genes that remains under the tip of the iceberg. In this paper we exploit the topological properties of the protein-protein interaction (PPI) network to detect disease-related genes. We compute, analyze, and compare the topological properties of disease genes with non-disease genes in PPI networks. We also design an improved random forest classifier based on these network topological features, and a cross-validation test confirms that our method performs better than previous similar studies.

[Differential expression of DTSsa4 Tc1-like transposons in closely related populations of Baikal ciscoes].

Science.gov (United States)

Bychenko, O S; Sukhanova, L V; Azhikina, T L; Sverdlov, E D

2009-01-01

Two representatives of Baikal ciscoes - lake cisco and omul - diverged from a common ancestor as recently as 10-20 thousand years ago. We have found an increasing expression level of DTSsa4 Tc1-like DNA transposons in cisco and omul brains. The mapping of the sequences of these transposons from Salmo salar and Danio rerio genomes has shown that in some cases, these transposons are located in the 5' and 3' regions, as well as in the promoter regions of various genes. Probably, Tc1-like transposons affect the activity of neighboring genes, providing the adaptive divergence of the cisco population.

NF-1 Dependent Gene Regulation in Drosophila Melanogaster

National Research Council Canada - National Science Library

Zhong, Yi

2004-01-01

.... We have used an Affymetrix whole genome chip, containing all 13,500 genes of the fruit fly Drosophila, to identify 93 genes with altered expression patterns in flies that have no NF1 protein compared...

Tank-Binding Kinase 1 (TBK1) Gene and Open-Angle Glaucomas (An American Ophthalmological Society Thesis).

Science.gov (United States)

Fingert, John H; Robin, Alan L; Scheetz, Todd E; Kwon, Young H; Liebmann, Jeffrey M; Ritch, Robert; Alward, Wallace L M

2016-08-01

To investigate the role of TANK-binding kinase 1 ( TBK1 ) gene copy-number variations (ie, gene duplications and triplications) in the pathophysiology of various open-angle glaucomas. In previous studies, we discovered that copy-number variations in the TBK1 gene are associated with normal-tension glaucoma. Here, we investigated the prevalence of copy-number variations in cohorts of patients with other open-angle glaucomas-juvenile-onset open-angle glaucoma (n=30), pigmentary glaucoma (n=209), exfoliation glaucoma (n=225), and steroid-induced glaucoma (n=79)-using a quantitative polymerase chain reaction assay. No TBK1 gene copy-number variations were detected in patients with juvenile-onset open-angle glaucoma, pigmentary glaucoma, or steroid-induced glaucoma. A TBK1 gene duplication was detected in one (0.44%) of the 225 exfoliation glaucoma patients. TBK1 gene copy-number variations (gene duplications and triplications) have been previously associated with normal-tension glaucoma. An exploration of other open-angle glaucomas detected a TBK1 copy-number variation in a patient with exfoliation glaucoma, which is the first example of a TBK1 mutation in a glaucoma patient with a diagnosis other than normal-tension glaucoma. A broader phenotypic range may be associated with TBK1 copy-number variations, although mutations in this gene are most often detected in patients with normal-tension glaucoma.

Power-Controlled MAC Protocols with Dynamic Neighbor Prediction for Ad hoc Networks

Institute of Scientific and Technical Information of China (English)

LI Meng; ZHANG Lin; XIAO Yong-kang; SHAN Xiu-ming

2004-01-01

Energy and bandwidth are the scarce resources in ad hoc networks because most of the mobile nodes are battery-supplied and share the exclusive wireless medium. Integrating the power control into MAC protocol is a promising technique to fully exploit these precious resources of ad hoc wireless networks. In this paper, a new intelligent power-controlled Medium Access Control (MAC) (iMAC) protocol with dynamic neighbor prediction is proposed. Through the elaborate design of the distributed transmit-receive strategy of mobile nodes, iMAC greatly outperforms the prevailing IEEE 802.11 MAC protocols in not only energy conservation but also network throughput. Using the Dynamic Neighbor Prediction (DNP), iMAC performs well in mobile scenes. To the best of our knowledge, iMAC is the first protocol that considers the performance deterioration of power-controlled MAC protocols in mobile scenes and then proposes a solution. Simulation results indicate that DNP is important and necessary for power-controlled MAC protocols in mobile ad hoc networks.

Characterisation of the NUCKS gene on human chromosome 1q32.1 and the presence of a homologous gene in different species

International Nuclear Information System (INIS)

Grundt, Kirsten; Haga, Ingvild Vagslid; Aleporou-Marinou, Vasiliki; Drosos, Yiannis; Wanvik, Birgit; Ostvold, Anne Carine

2004-01-01

The NUCKS gene is located on human chromosome 1q32.1 and consists of seven exons and six introns. The gene lacks a TATA box but contains two Inr elements, two GC boxes, and one consensus-binding site for E2F-1. NUCKS is expressed in all human adult and foetal tissues investigated, and has all the features of being a housekeeping gene. Both data searches and Western immunoblotting experiments show that a homologous protein is present in fish, amphibians, and birds but not in insects and yeast, suggesting that NUCKS is a vertebrate specific gene. In all the species investigated, the protein contains several consensus phosphorylation sites for cyclin-dependent kinases and CK-2, and we have shown that the fish protein (like mammalian NUCKS) indeed is a substrate for CDK1 and CK-2 in vitro. The NUCKS protein is also conserved with respect to a DNA-binding domain previously characterised in mammals, and two putative bipartite nuclear localisation signals

Gene conversion homogenizes the CMT1A paralogous repeats

Directory of Open Access Journals (Sweden)

Hurles Matthew E

2001-12-01

Full Text Available Abstract Background Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Results Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10-4 and 5.1 × 10-5 per generation for the alternative models. Conclusions This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them.

Functional characterisation of an Arabidopsis gene strongly induced by ionising radiation: the gene coding the poly(ADP-ribose)polymerase-1 (AthPARP-1)

International Nuclear Information System (INIS)

Doucet-Chabeaud, G.

2000-01-01

Arabidopsis thaliana, the model-system in plant genetics, has been used to study the responses to DNA damage, experimentally introduced by γ-irradiation. We have characterised a radiation-induced gene coding a 111 kDa protein, AthPARP-1, homologous to the human poly(ADP-ribose)polymerase-1 (hPARP-1). As hPARP-1 is composed by three functional domain with characteristic motifs, AthPARP-1 binds to DNA bearing single-strand breaks and shows DNA damage-dependent poly(ADP-ribosyl)ation. The preferential expression of AthPARP-1 in mitotically active tissues is in agreement with a potential role in the maintenance of genome integrity during DNA replication, as proposed for its human counterpart. Transcriptional gene activation by ionising radiation of AthPARP-1 and AthPARP-2 genes is to date plant specific activation. Our expression analyses after exposure to various stress indicate that 1) AthPARP-1 and AthPARP-2 play an important role in the response to DNA lesions, particularly they are activated by genotoxic agents implicating the BER DNA repair pathway 2) AthPARP-2 gene seems to play an additional role in the signal transduction induced by oxidative stress 3) the observed expression profile of AthPARP-1 is in favour of the regulation of AthPARP-1 gene expression at the level of transcription and translation. This mode of regulation of AthPARP-1 protein biosynthesis, clearly distinct from that observed in animals, needs the implication of a so far unidentified transcription factor that is activated by the presence of DNA lesions. The major outcome of this work resides in the isolation and characterisation of such new transcription factor, which will provide new insight on the regulation of plant gene expression by genotoxic stress. (author) [fr

Mountain tourism development in Serbia and neighboring countries

Directory of Open Access Journals (Sweden)

Krunić Nikola

2010-01-01

Full Text Available Mountain areas with their surroundings are important parts of tourism regions with potentials for all-season tourism development and complementary activities. Development possibilities are based on size of high mountain territory, nature protection regimes, infrastructural equipment, provided conditions for leisure and recreation as well as involvement of local population in processes of development and protection. This paper analyses the key aspects of tourism development, winter tourism in high-mountain areas of Serbia and some neighboring countries (Slovakia, Romania, Bulgaria, and Greece. Common determinants of cohesion between nature protection and mountain tourism development, national development policies, applied models and concepts and importance of trans-border cooperation are indicated.

An interactive cooperation model for neighboring virtual power plants

International Nuclear Information System (INIS)

Shabanzadeh, Morteza; Sheikh-El-Eslami, Mohammad-Kazem; Haghifam, Mahmoud-Reza

2017-01-01

Highlights: •The trading strategies of a VPP in cooperation with its neighboring VPPs are addressed. •A portfolio of inter-regional contracts is considered to model this cooperation scheme. •A novel mathematical formulation for possible inadvertent transactions is provided. •A two-stage stochastic programming approach is applied to characterize the uncertainty. •Two efficient risk measures, SSD and CVaR, are implemented in the VPP decision-making problem. -- Abstract: Future distribution systems will accommodate an increasing share of distributed energy resources (DERs). Facing with this new reality, virtual power plants (VPPs) play a key role to aggregate DERs with the aim of facilitating their involvement in wholesale electricity markets. In this paper, the trading strategies of a VPP in cooperation with its neighboring VPPs are addressed. Toward this aim, a portfolio of inter-regional contracts is considered to model this cooperation and maximize the energy trade opportunities of the VPP within a medium-term horizon. To hedge against profit variability caused by market price uncertainties, two efficient risk management approaches are also implemented in the VPP decision-making problem based on the concepts of conditional value at risk (CVaR) and second-order stochastic dominance constraints (SSD). The resulting models are formulated as mixed-integer linear programming (MILP) problems that can be solved using off-the-shelf software packages. The efficiency of the proposed risk-hedging models is analyzed through a detailed case study, and thereby relevant conclusions are drawn.

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

International Nuclear Information System (INIS)

Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

2015-01-01

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

Energy Technology Data Exchange (ETDEWEB)

Thompson, Aidan P. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Multiscale Science Dept.; Swiler, Laura P. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Optimization and Uncertainty Quantification Dept.; Trott, Christian R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Scalable Algorithms Dept.; Foiles, Stephen M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computational Materials and Data Science Dept.; Tucker, Garritt J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computational Materials and Data Science Dept.; Drexel Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering

2015-03-15

Here, we present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

Energy Technology Data Exchange (ETDEWEB)

Thompson, A.P., E-mail: athomps@sandia.gov [Multiscale Science Department, Sandia National Laboratories, PO Box 5800, MS 1322, Albuquerque, NM 87185 (United States); Swiler, L.P., E-mail: lpswile@sandia.gov [Optimization and Uncertainty Quantification Department, Sandia National Laboratories, PO Box 5800, MS 1318, Albuquerque, NM 87185 (United States); Trott, C.R., E-mail: crtrott@sandia.gov [Scalable Algorithms Department, Sandia National Laboratories, PO Box 5800, MS 1322, Albuquerque, NM 87185 (United States); Foiles, S.M., E-mail: foiles@sandia.gov [Computational Materials and Data Science Department, Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185 (United States); Tucker, G.J., E-mail: gtucker@coe.drexel.edu [Computational Materials and Data Science Department, Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185 (United States); Department of Materials Science and Engineering, Drexel University, Philadelphia, PA 19104 (United States)

2015-03-15

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

Functional study of the novel multidrug resistance gene HA117 and its comparison to multidrug resistance gene 1

Directory of Open Access Journals (Sweden)

Chen Tingfu

2010-07-01

Full Text Available Abstract Background The novel gene HA117 is a multidrug resistance (MDR gene expressed by all-trans retinoic acid-resistant HL-60 cells. In the present study, we compared the multidrug resistance of the HA117 with that of the classical multidrug resistance gene 1 (MDR1 in breast cancer cell line 4T1. Methods Transduction of the breast cancer cell line 4T1 with adenoviral vectors encoding the HA117 gene and the green fluorescence protein gene (GFP (Ad-GFP-HA117, the MDR1 and GFP (Ad-GFP-MDR1 or GFP (Ad-GFP was respectively carried out. The transduction efficiency and the multiplicity of infection (MOI were detected by fluorescence microscope and flow cytometry. The transcription of HA117 gene and MDR1 gene were detected by reverse transcription polymerase chain reaction (RT-PCR. Western blotting analysis was used to detect the expression of P-glycoprotein (P-gp but the expression of HA117 could not be analyzed as it is a novel gene and its antibody has not yet been synthesized. The drug-excretion activity of HA117 and MDR1 were determined by daunorubicin (DNR efflux assay. The drug sensitivities of 4T1/HA117 and 4T1/MDR1 to chemotherapeutic agents were detected by Methyl-Thiazolyl-Tetrazolium (MTT assay. Results The transducted efficiency of Ad-GFP-HA117 and Ad-GFP-MDR1 were 75%-80% when MOI was equal to 50. The transduction of Ad-GFP-HA117 and Ad-GFP-MDR1 could increase the expression of HA117 and MDR1. The drug resistance index to Adriamycin (ADM, vincristine (VCR, paclitaxel (Taxol and bleomycin (BLM increased to19.8050, 9.0663, 9.7245, 3.5650 respectively for 4T1/HA117 and 24.2236, 11.0480, 11.3741, 0.9630 respectively for 4T1/MDR1 as compared to the control cells. There were no significant differences in drug sensitivity between 4T1/HA117 and 4T1/MDR1 for the P-gp substrates (ADM, VCR and Taxol (P Conclusions These results confirm that HA117 is a strong MDR gene in both HL-60 and 4T1 cells. Furthermore, our results indicate that the MDR

The Tyrosyl-DNA Phosphodiesterase 1β (Tdp1β Gene Discloses an Early Response to Abiotic Stresses

Directory of Open Access Journals (Sweden)

Maria Elisa Sabatini

2017-11-01

Full Text Available Tyrosyl-DNA phosphodiesterase 1 (Tdp1 is involved in DNA repair pathways as it mends the topoisomerase I—DNA covalent complexes. In plants, a small Tdp1 gene family, composed by Tdp1α and Tdp1β genes, was identified, but the roles of these genes in abiotic stress responses are not fully understood. To investigate their specific stress response patterns, the present study made use of bioinformatic and molecular tools to look into the Tdp1β gene function, so far described only in the plant kingdom, and compare it with Tdp1α gene coding for the canonical, highly conserved α isoform. The expression profiles of Tdp1α and Tdp1β genes were examined under abiotic stress conditions (cold, heat, high osmolarity, salt, and UV-B in two model species, Arabidopsis thaliana and Medicago truncatula. The two isoforms of topoisomerase I (TOP1α and TOP1β were also taken into consideration in view of their known roles in DNA metabolism and cell proliferation. Data relative to gene expression in Arabidopsis were retrieved from the AtGenExpress microarray dataset, while quantitative Real-Time PCR was carried out to evaluate the stress response in M. truncatula cell cultures. These analyses revealed that Tdp1β gene expression was enhanced during the first hour of treatment, whereas Tdp1α enhanced expression succeeded at subsequent timepoints. In agreement with the gene-specific responses to abiotic stress conditions, the promoter regions of Tdp1α and Tdp1β genes are well equipped with stress-related cis-elements. An in-depth bioinformatic characterization of the HIRAN motif, a distinctive feature of the Tdp1β protein, showed its wide distribution in chromatin remodeling and DNA repair proteins. The reported data suggests that Tdp1β functions in the early response to abiotic stresses.

Wound healing genes and susceptibility to cutaneous leishmaniasis in Brazil: Role of COL1A1

Science.gov (United States)

Almeida, Lucas; Oliveira, Joyce; Guimarães, Luiz Henrique; Carvalho, Edgar M; Blackwell, Jenefer M

2015-01-01

Previous studies have demonstrated a role for wound healing genes in resolution of cutaneous lesions caused by Leishmania spp. in both mice and humans, including the gene FLI1 encoding Friend leukaemia virus integration 1. Reduction of Fli1 expression in mice has been shown to result in up-regulation of collagen type I alpha 1 (Col1a1) and alpha 2 (Col1a2) genes and, conversely, in down-regulation of the matrix metalloproteinase 1 (Mmp1) gene, suggesting that Fli1 suppression is involved in activation of the profibrotic gene program. Here we examined single nucleotide polymorphisms (SNPs) in these genes as risk factors for cutaneous (CL) and mucosal leishmaniasis (ML), and leishmaniasis per se, caused by L. braziliensis in humans. SNPs were genotyped in 168 nuclear families (250 CL; 87 ML cases) and replicated in 157 families (402 CL; 39 ML cases). Family-based association tests (FBAT) showed the strongest association between SNPs rs1061237 (combined P=0.002) and rs2586488 (combined P=0.027) at COL1A1 and CL disease. This contributes to our further understanding of the role of wound healing in the resolution of CL disease, providing potential for therapies modulating COL1A1 via drugs acting on FLI1. PMID:25562121

Cultural macroevolution on neighbor graphs : vertical and horizontal transmission among Western North American Indian societies.

Science.gov (United States)

Towner, Mary C; Grote, Mark N; Venti, Jay; Borgerhoff Mulder, Monique

2012-09-01

What are the driving forces of cultural macroevolution, the evolution of cultural traits that characterize societies or populations? This question has engaged anthropologists for more than a century, with little consensus regarding the answer. We develop and fit autologistic models, built upon both spatial and linguistic neighbor graphs, for 44 cultural traits of 172 societies in the Western North American Indian (WNAI) database. For each trait, we compare models including or excluding one or both neighbor graphs, and for the majority of traits we find strong evidence in favor of a model which uses both spatial and linguistic neighbors to predict a trait's distribution. Our results run counter to the assertion that cultural trait distributions can be explained largely by the transmission of traits from parent to daughter populations and are thus best analyzed with phylogenies. In contrast, we show that vertical and horizontal transmission pathways can be incorporated in a single model, that both transmission modes may indeed operate on the same trait, and that for most traits in the WNAI database, accounting for only one mode of transmission would result in a loss of information.

Efficient and accurate nearest neighbor and closest pair search in high-dimensional space

KAUST Repository

Tao, Yufei; Yi, Ke; Sheng, Cheng; Kalnis, Panos

2010-01-01

Nearest Neighbor (NN) search in high-dimensional space is an important problem in many applications. From the database perspective, a good solution needs to have two properties: (i) it can be easily incorporated in a relational database, and (ii

Determination of taste receptor type 1 member 1 (TAS1R1) gene ...

African Journals Online (AJOL)

In this article, the objective was to investigate variations in goat TAS1R1 gene and their associations with growth traits in 317 goats by PCR-SSCP and DNA sequencing methods. The results showed two novel single nucleotide polymorphisms (SNPs): HM449123:g. [T3974C, C4037T]. In detail, two different alleles, A and B, ...

Inferring Phylogenetic Networks from Gene Order Data

Directory of Open Access Journals (Sweden)

Alexey Anatolievich Morozov

2013-01-01

Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

2010-09-15

To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

Myeloid cell leukemia-1 (Mc1-1 is a candidate target gene of hypoxia-inducible factor-1 (HIF-1 in the testis

Directory of Open Access Journals (Sweden)

Palladino Michael A

2012-12-01

Full Text Available Abstract Background Spermatic cord torsion can lead to testis ischemia (I and subsequent ischemia-reperfusion (I/R causing germ cell-specific apoptosis. Previously, we demonstrated that the hypoxia-inducible factor-1 (HIF-1 transcription factor, a key regulator of physiological responses to hypoxia, is abundant in Leydig cells in normoxic and ischemic testes. We hypothesize that testicular HIF-1 activates the expression of antiapoptotic target genes to protect Leydig cells from apoptosis. In silico analysis of testis genes containing a consensus hypoxia response element (HRE, 5’-RCGTG-3’ identified myeloid cell leukemia-1 (Mcl-1 as a potential HIF-1 target gene. The purpose of this study was to determine whether HIF-1 shows DNA-binding activity in normoxic and ischemic testes and whether Mcl-1 is a target gene of testicular HIF-1. Methods The testicular HIF-1 DNA-binding capacity was analyzed in vitro using a quantitative enzyme-linked immunosorbent assay (ELISA and electrophoretic mobility shift assays (EMSA. MCL-1 protein expression was evaluated by immunoblot analysis and immunohistochemistry. The binding of testicular HIF-1 to the Mcl-1 gene was examined via chromatin immunoprecipitation (ChIP analysis. Results The ELISA and EMSA assays demonstrated that testicular HIF-1 from normoxic and ischemic testes binds DNA equally strongly, suggesting physiological roles for HIF-1 in the normoxic testis, unlike most tissues in which HIF-1 is degraded under normoxic conditions and is only activated by hypoxia. MCL-1 protein was determined to be abundant in both normoxic and ischemic testes and expressed in Leydig cells. In a pattern identical to that of HIF-1 expression, the steady-state levels of MCL-1 were not significantly affected by I or I/R and MCL-1 co-localized with HIF-1α in Leydig cells. Chromatin immunoprecipitation (ChIP analysis using a HIF-1 antibody revealed sequences enriched for the Mcl-1 promoter. Conclusions The results

Isolation and characterization of the human CDX1 gene: A candidate gene for diastrophic dysplasia

Energy Technology Data Exchange (ETDEWEB)

Bonner, C.; Loftus, S.; Wasmuth, J.J. [Univ. of California, Irvine, CA (United States)

1994-09-01

Diastrophic dysplasia is an autosomal recessive disorder characterized by short stature, dislocation of the joints, spinal deformities and malformation of the hands and feet. Multipoint linkage analysis places the diastrophic dysplasia (DTD) locus in 5q31-5q34. Linkage disequilibrium mapping places the DTD locus near CSFIR in the direction of PDGFRB (which is tandem to CSFIR). This same study tentatively placed PDGFRB and DTD proximal to CSFIR. Our results, as well as recently reported work from other laboratories, suggest that PDGFRB (and possibly DTD) is distal rather than proximal to CSFIR. We have constructed a cosmid contig covering approximately 200 kb of the region containing CSFIR. Several exons have been {open_quotes}trapped{close_quotes} from these cosmids using exon amplification. One of these exons was trapped from a cosmid isolated from a walk from PDGFRB, approximately 80 kb from CSFIR. This exon was sequenced and was determined to be 89% identical to the nucleotide sequence of exon two of the murine CDX1 gene (100% amino acid identity). The exon was used to isolate the human CDX gene. Sequence analysis of the human CDX1 gene indicates a very high degree of homology to the murine gene. CDX1 is a caudal type homeobox gene expressed during gastrulation. In the mouse, expression during gastrulation begins in the primitive streak and subsequently localizes to the ectodermal and mesodermal cells of the primitive streak, neural tube, somites, and limb buds. Later in gastrulation, CDX1 expression becomes most prominent in the mesoderm of the forelimbs, and, to a lesser extent, the hindlimbs. CDX1 is an intriguing candidate gene for diastrophic dysplasia. We are currently screening DNA from affected individuals and hope to shortly determine whether CDX1 is involved in this disorder.

Humanitarian Cleft Lip/Palate Surgeries in Buddhist Thailand and Neighboring Countries.

Science.gov (United States)

Uemura, Tetsuji; Preeyanont, Piyoros; Udnoon, Sopridee

2015-06-01

This study evaluates surgeries done on patients with cleft lip and/or palate in Thailand and its neighboring countries from 1988 to 2008. This 21-year-long volunteer surgical mission was sponsored by Duang-Kaew Foundation, a volunteer organization. Countries involved, besides Thailand, were Vietnam, Myanmar, Laos, Cambodia, China, Sri Lanka, Bhutan, and India. The same surgical method for primary and secondary repair of lip and/or palate was used throughout: Onizuka method by single surgeon, the second author mainly. We assessed, by way of the patients' medical records including their background, the results of surgeries. The healing rates and complication rates associated with patients for primary and secondary repair of lip and/or palate. The study consisted of a total of 6832 patients: 3120 with cleft lip (CL); 2190 with cleft palate (CP); and 1522 with cleft lip and palate (CLP). Their primary cases were 675 (CL), 799 (CP), and 301 (CLP). All CP operations were done under general anesthesia. Of the CL surgeries, 10% of adult cases were done under local anesthesia. Of all the patients, 78%, or 5329, had one surgery; and 22%, or 1503, had 2 or more surgeries. Good healing was seen in 73.3%, whereas wound infection was noted in 2.0% and healing by second intention was in 1.2% of all cases. It is important that the Onizuka method was the only method used in all the countries throughout the mission period. The method has an advantage over other methods in that its design is simple enough so that even a beginning plastic surgeon can easily master, and operative results are constantly good regardless of who did the operation. The Duang-Kaew Foundation's long-term surgical program helped reduce the number of untreated patients to manageable levels for local health care providers in Thailand and neighboring countries for as long as 21 years.

Association between Insulin Like Growth Factor-1 (IGF-1) gene ...

African Journals Online (AJOL)

The insulin-like growth factor-1 (IGF1) is a key regulator of muscle development and metabolism in birds and other vertebrate. Our objective was to determine the association between IGF1 gene polymorphism and carcass traits in FUNAAB Alpha chicken. Genomic DNA was extracted from the blood of 50 normal feathered ...

Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation.

Directory of Open Access Journals (Sweden)

Alexandra Dumitriu

2012-06-01

Full Text Available Parkinson disease (PD is a complex neurodegenerative disorder with largely unknown genetic mechanisms. While the degeneration of dopaminergic neurons in PD mainly takes place in the substantia nigra pars compacta (SN region, other brain areas, including the prefrontal cortex, develop Lewy bodies, the neuropathological hallmark of PD. We generated and analyzed expression data from the prefrontal cortex Brodmann Area 9 (BA9 of 27 PD and 26 control samples using the 44K One-Color Agilent 60-mer Whole Human Genome Microarray. All samples were male, without significant Alzheimer disease pathology and with extensive pathological annotation available. 507 of the 39,122 analyzed expression probes were different between PD and control samples at false discovery rate (FDR of 5%. One of the genes with significantly increased expression in PD was the forkhead box O1 (FOXO1 transcription factor. Notably, genes carrying the FoxO1 binding site were significantly enriched in the FDR-significant group of genes (177 genes covered by 189 probes, suggesting a role for FoxO1 upstream of the observed expression changes. Single-nucleotide polymorphisms (SNPs selected from a recent meta-analysis of PD genome-wide association studies (GWAS were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. A significant association was observed between a SNP in the cyclin G associated kinase (GAK gene and a probe in the spermine oxidase (SMOX gene. Further examination of the FOXO1 region in a meta-analysis of six available GWAS showed two SNPs significantly associated with age at onset of PD. These results implicate FOXO1 as a PD-relevant gene and warrant further functional analyses of its transcriptional regulatory mechanisms.

The genetic alteration of MTS1/CDKN2 gene in esophageal cancer

International Nuclear Information System (INIS)

Zo, Jae Ill; Paik, Hee Jong; Park, Jong Ho; Kim, Mi Hee

1996-12-01

MTS1/CDKN2 gene plays a key role in cell cycle regulation, and there have been many studies about the significance of this gene in tumorigenesis. To investigate the frequency of MTS1/CDKN2 gene alteration in Korean esophageal cancer, we studied 36 esophageal cancer tissues with paired PCR analysis to detect homozygous deletion and PCR-SSCP methods to find minute mutations, if any. In the cases with abnormalities, the nucleotide sequence analysis was performed. And in cases without RB gene a alterations, direct sequence analysis was also done. There was no homozygous deletions. Mobility shift by PCR-SSCP was observed in four cases at exon 2, which showed 1 bp deletion in codon 97 of mutation in codon 100 which changed TAT (Tyr) from GAT (Asp). But there were not MTS1/CDKN2 gene alterations in cases without Rb gene alterations. Analysis of clinical data did not show any differences depending upon MTS1/CDKN2 gene alterations. Therefore the MTS1/CDKN2 gene mutations were infrequent events and do not play a major role in the group of patients examined. More study for contribution of methylation in MTS1/CDKN2 gene for inactivation of p16 should be done before evaluation and application of MTS1/CDKN2 gene in tumorigenesis and as an candidate of gene therapy. (author). 15 refs

The genetic alteration of MTS1/CDKN2 gene in esophageal cancer

Energy Technology Data Exchange (ETDEWEB)

Zo, Jae Ill; Paik, Hee Jong; Park, Jong Ho; Kim, Mi Hee [Korea Cancer Center Hospital, Seoul (Korea, Republic of)

1996-12-01

MTS1/CDKN2 gene plays a key role in cell cycle regulation, and there have been many studies about the significance of this gene in tumorigenesis. To investigate the frequency of MTS1/CDKN2 gene alteration in Korean esophageal cancer, we studied 36 esophageal cancer tissues with paired PCR analysis to detect homozygous deletion and PCR-SSCP methods to find minute mutations, if any. In the cases with abnormalities, the nucleotide sequence analysis was performed. And in cases without RB gene a alterations, direct sequence analysis was also done. There was no homozygous deletions. Mobility shift by PCR-SSCP was observed in four cases at exon 2, which showed 1 bp deletion in codon 97 of mutation in codon 100 which changed TAT (Tyr) from GAT (Asp). But there were not MTS1/CDKN2 gene alterations in cases without Rb gene alterations. Analysis of clinical data did not show any differences depending upon MTS1/CDKN2 gene alterations. Therefore the MTS1/CDKN2 gene mutations were infrequent events and do not play a major role in the group of patients examined. More study for contribution of methylation in MTS1/CDKN2 gene for inactivation of p16 should be done before evaluation and application of MTS1/CDKN2 gene in tumorigenesis and as an candidate of gene therapy. (author). 15 refs.

Gastronomy Tourism in Several Neighbor Countries of Indonesia: a Brief Review

Directory of Open Access Journals (Sweden)

Kurniasih Sukenti

2014-04-01

Full Text Available Gastronomy tourism, also called culinary tourism or food tourism, is a kind of tourism that provide attractions based on the culinary aspect owned by a country, region, or area. It is not only offers food and beverages as the main objects in its attractions, but also everything related to food activities ranging from food ingredients, preparation, processing, serving, as well as the cultural and local values. A well-managed culinary tourism will be a supportive program in developing and enhancing the tourism sector in a country. The objective of this paper is to describe the profile of gastronomy tourism in several neighbor countries of Indonesia, i.e. Hongkong, Singapore, Thailand, and Malaysia. This brief review is also discussed the potential of Indonesia gastronomy in supporting government’s tourism program. Basically, Indonesia has more enormous potential asset in managing its cultural heritages in term of culinary than its neighbor countries. A well-managed gastronomy tourism plays not only an important role in enhancing the economic sector, but also contribute in preserving the natural and cultural resources. Keywords: gastronomy tourism, culinary tourism, food tourism.

Evolution and Expression Patterns of CYC/TB1 Genes in Anacyclus: Phylogenetic Insights for Floral Symmetry Genes in Asteraceae

Science.gov (United States)

Bello, María A.; Cubas, Pilar; Álvarez, Inés; Sanjuanbenito, Guillermo; Fuertes-Aguilar, Javier

2017-01-01

Homologs of the CYC/TB1 gene family have been independently recruited many times across the eudicots to control aspects of floral symmetry The family Asteraceae exhibits the largest known diversification in this gene paralog family accompanied by a parallel morphological floral richness in its specialized head-like inflorescence. In Asteraceae, whether or not CYC/TB1 gene floral symmetry function is preserved along organismic and gene lineages is unknown. In this study, we used phylogenetic, structural and expression analyses focused on the highly derived genus Anacyclus (tribe Anthemidae) to address this question. Phylogenetic reconstruction recovered eight main gene lineages present in Asteraceae: two from CYC1, four from CYC2 and two from CYC3-like genes. The species phylogeny was recovered in most of the gene lineages, allowing the delimitation of orthologous sets of CYC/TB1 genes in Asteraceae. Quantitative real-time PCR analysis indicated that in Anacyclus three of the four isolated CYC2 genes are more highly expressed in ray flowers. The expression of the four AcCYC2 genes overlaps in several organs including the ligule of ray flowers, as well as in anthers and ovules throughout development. PMID:28487706

Involvement of Resveratrol and ω-3 Polyunsaturated Fatty Acids on Sirtuin 1 Gene Expression in THP1 Cells.

Science.gov (United States)

Tsuchiya, Takafumi; Endo, Ayano; Tsujikado, Kyoko; Inukai, Toshihiko

2017-10-01

Resveratrol, a kind of polyphenol, has the potential to activate the longevity gene in several cells, in the same manner as calorie restriction. We investigated the effect of resveratrol and ω-3-line polyunsaturated fatty acid on surtuin 1 (SIRT1) gene expression in human monocytes (THP1) cells. We examined the gene expression of THP1 cells using real-time polymerase chain reaction and Western blotting analysis. Resveratol, eicosapentaenoic acid (EPA) and docosahexaeanoic acid (DHA) as n-3 polyunsaturated fatty acid were added on THP1 cells. We observed the changes in the SIRT1 gene expression in those cells, under various doses of agents and in time courses. Then, we examined the interaction of glucose and mannitol on those agents׳ effect of the gene expression. The concentration range of glucose and mannitol was from 5-20mM, respectively. The SIRT1 gene expression could be defined in 24 and 48 hours both in real-time polymerase chain reaction analysis and in Western blotting. Resveratrol showed SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. Although EPA at 10μM showed marked increase in SIRT1 gene expression compared to control condition in Western blotting, this phenomenon was not in dose-dependent manner. DHA did not exhibit any augmentation of SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. We refined the dose-dependent inhibition of the SIRT1 gene expression within 20mM glucose medium. Although 20mM did not exhibit any inhibition, 10μM resveratrol induced the gene expression compared to control medium. Both 5 and 15mM mannitol medium did not significantly alter basic gene expression and 10μM resveratrol-induced gene expression. The present results suggest that resveratrol and EPA, but not DHA, markedly activated the SIRT1 gene expression in THP1 cells, and that high glucose medium could inhibit the basic gene expression, but not powerful resveratrol-induced gene

Identification of novel risk genes associated with type 1 diabetes mellitus using a genome-wide gene-based association analysis.

Science.gov (United States)

Qiu, Ying-Hua; Deng, Fei-Yan; Li, Min-Jing; Lei, Shu-Feng

2014-11-01

Type 1 diabetes mellitus is a serious disorder characterized by destruction of pancreatic β-cells, culminating in absolute insulin deficiency. Genetic factors contribute to the susceptibility of type 1 diabetes mellitus. The aim of the present study was to identify more susceptibility genes of type 1 diabetes mellitus. We carried out an initial gene-based genome-wide association study in a total of 4,075 type 1 diabetes mellitus cases and 2,604 controls by using the Gene-based Association Test using Extended Simes procedure. Furthermore, we carried out replication studies, differential expression analysis and functional annotation clustering analysis to support the significance of the identified susceptibility genes. We identified 452 genes associated with type 1 diabetes mellitus, even after adapting the genome-wide threshold for significance (P diabetes mellitus, which were ignored in single-nucleotide polymorphism-based association analysis and were not previously reported. We found that 53 genes have supportive evidence from replication studies and/or differential expression studies. In particular, seven genes including four non-human leukocyte antigen (HLA) genes (RASIP1, STRN4, BCAR1 and MYL2) are replicated in at least one independent population and also differentially expressed in peripheral blood mononuclear cells or monocytes. Furthermore, the associated genes tend to enrich in immune-related pathways or Gene Ontology project terms. The present results suggest the high power of gene-based association analysis in detecting disease-susceptibility genes. Our findings provide more insights into the genetic basis of type 1 diabetes mellitus.

Equivalent charge source model based iterative maximum neighbor weight for sparse EEG source localization.

Science.gov (United States)

Xu, Peng; Tian, Yin; Lei, Xu; Hu, Xiao; Yao, Dezhong

2008-12-01

How to localize the neural electric activities within brain effectively and precisely from the scalp electroencephalogram (EEG) recordings is a critical issue for current study in clinical neurology and cognitive neuroscience. In this paper, based on the charge source model and the iterative re-weighted strategy, proposed is a new maximum neighbor weight based iterative sparse source imaging method, termed as CMOSS (Charge source model based Maximum neighbOr weight Sparse Solution). Different from the weight used in focal underdetermined system solver (FOCUSS) where the weight for each point in the discrete solution space is independently updated in iterations, the new designed weight for each point in each iteration is determined by the source solution of the last iteration at both the point and its neighbors. Using such a new weight, the next iteration may have a bigger chance to rectify the local source location bias existed in the previous iteration solution. The simulation studies with comparison to FOCUSS and LORETA for various source configurations were conducted on a realistic 3-shell head model, and the results confirmed the validation of CMOSS for sparse EEG source localization. Finally, CMOSS was applied to localize sources elicited in a visual stimuli experiment, and the result was consistent with those source areas involved in visual processing reported in previous studies.

The bromodomain protein LEX-1 acts with TAM-1 to modulate gene expression in C. elegans.

Science.gov (United States)

Tseng, Rong-Jeng; Armstrong, Kristin R; Wang, Xiaodong; Chamberlin, Helen M

2007-11-01

In many organisms, repetitive DNA serves as a trigger for gene silencing. However, some gene expression is observed from repetitive genomic regions such as heterochromatin, suggesting mechanisms exist to modulate the silencing effects. From a genetic screen in C. elegans, we have identified mutations in two genes important for expression of repetitive sequences: lex-1 and tam-1. Here we show that lex-1 encodes a protein containing an ATPase domain and a bromodomain. LEX-1 is similar to the yeast Yta7 protein, which maintains boundaries between silenced and active chromatin. tam-1 has previously been shown to encode a RING finger/B-box protein that modulates gene expression from repetitive DNA. We find that lex-1, like tam-1, acts as a class B synthetic multivulva (synMuv) gene. However, since lex-1 and tam-1 mutants have normal P granule localization, it suggests they act through a mechanism distinct from other class B synMuvs. We observe intragenic (interallelic) complementation with lex-1 and a genetic interaction between lex-1 and tam-1, data consistent with the idea that the gene products function in the same biological process, perhaps as part of a protein complex. We propose that LEX-1 and TAM-1 function together to influence chromatin structure and to promote expression from repetitive sequences.