WorldWideScience

Sample records for detect allelic imbalances

  1. AllelicImbalance: An R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing

    DEFF Research Database (Denmark)

    Gådin, Jesper R.; van't Hooft, Ferdinand M.; Eriksson, Per

    2015-01-01

    the possible biases. Results: We present AllelicImblance, a software program that is designed to detect, manage, and visualize allelic imbalances comprehensively. The purpose of this software is to allow users to pose genetic questions in any RNA sequencing experiment quickly, enhancing the general utility...... of RNA sequencing. The visualization features can reveal notable, non-trivial allelic imbalance behavior over specific regions, such as exons. Conclusions: The software provides a complete framework to perform allelic imbalance analyses of aligned RNA sequencing data, from detection to visualization...

  2. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis.

    Science.gov (United States)

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-07-01

    Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5'- and 3'-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients.Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3'-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5'-UTR polymorphisms).For neither the 3'- nor the 5'-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance.The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold, in our population

  3. Intrinsic MYH7 expression regulation contributes to tissue level allelic imbalance in hypertrophic cardiomyopathy.

    Science.gov (United States)

    Montag, Judith; Syring, Mandy; Rose, Julia; Weber, Anna-Lena; Ernstberger, Pia; Mayer, Anne-Kathrin; Becker, Edgar; Keyser, Britta; Dos Remedios, Cristobal; Perrot, Andreas; van der Velden, Jolanda; Francino, Antonio; Navarro-Lopez, Francesco; Ho, Carolyn Yung; Brenner, Bernhard; Kraft, Theresia

    2017-08-01

    HCM, the most common inherited cardiac disease, is mainly caused by mutations in sarcomeric genes. More than a third of the patients are heterozygous for mutations in the MYH7 gene encoding for the β-myosin heavy chain. In HCM-patients, expression of the mutant and the wildtype allele can be unequal, thus leading to fractions of mutant and wildtype mRNA and protein which deviate from 1:1. This so-called allelic imbalance was detected in whole tissue samples but also in individual cells. There is evidence that the severity of HCM not only depends on the functional effect of the mutation itself, but also on the fraction of mutant protein in the myocardial tissue. Allelic imbalance has been shown to occur in a broad range of genes. Therefore, we aimed to examine whether the MYH7-alleles are intrinsically expressed imbalanced or whether the allelic imbalance is solely associated with the disease. We compared the expression of MYH7-alleles in non-HCM donors and in HCM-patients with different MYH7-missense mutations. In the HCM-patients, we identified imbalanced as well as equal expression of both alleles. Also at the protein level, allelic imbalance was determined. Most interestingly, we also discovered allelic imbalance and balance in non-HCM donors. Our findings therefore strongly indicate that apart from mutation-specific mechanisms, also non-HCM associated allelic-mRNA expression regulation may account for the allelic imbalance of the MYH7 gene in HCM-patients. Since the relative amount of mutant mRNA and protein or the extent of allelic imbalance has been associated with the severity of HCM, individual analysis of the MYH7-allelic expression may provide valuable information for the prognosis of each patient.

  4. Erasure and reestablishment of random allelic expression imbalance after epigenetic reprogramming.

    Science.gov (United States)

    Jeffries, Aaron Richard; Uwanogho, Dafe Aghogho; Cocks, Graham; Perfect, Leo William; Dempster, Emma; Mill, Jonathan; Price, Jack

    2016-10-01

    Clonal level random allelic expression imbalance and random monoallelic expression provides cellular heterogeneity within tissues by modulating allelic dosage. Although such expression patterns have been observed in multiple cell types, little is known about when in development these stochastic allelic choices are made. We examine allelic expression patterns in human neural progenitor cells before and after epigenetic reprogramming to induced pluripotency, observing that loci previously characterized by random allelic expression imbalance (0.63% of expressed genes) are generally reset to a biallelic state in induced pluripotent stem cells (iPSCs). We subsequently neuralized the iPSCs and profiled isolated clonal neural stem cells, observing that significant random allelic expression imbalance is reestablished at 0.65% of expressed genes, including novel loci not found to show allelic expression imbalance in the original parental neural progenitor cells. Allelic expression imbalance was associated with altered DNA methylation across promoter regulatory regions, with clones characterized by skewed allelic expression being hypermethylated compared to their biallelic sister clones. Our results suggest that random allelic expression imbalance is established during lineage commitment and is associated with increased DNA methylation at the gene promoter. © 2016 Jeffries et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.

    Directory of Open Access Journals (Sweden)

    Brian B Tuch

    Full Text Available Due to growing throughput and shrinking cost, massively parallel sequencing is rapidly becoming an attractive alternative to microarrays for the genome-wide study of gene expression and copy number alterations in primary tumors. The sequencing of transcripts (RNA-Seq should offer several advantages over microarray-based methods, including the ability to detect somatic mutations and accurately measure allele-specific expression. To investigate these advantages we have applied a novel, strand-specific RNA-Seq method to tumors and matched normal tissue from three patients with oral squamous cell carcinomas. Additionally, to better understand the genomic determinants of the gene expression changes observed, we have sequenced the tumor and normal genomes of one of these patients. We demonstrate here that our RNA-Seq method accurately measures allelic imbalance and that measurement on the genome-wide scale yields novel insights into cancer etiology. As expected, the set of genes differentially expressed in the tumors is enriched for cell adhesion and differentiation functions, but, unexpectedly, the set of allelically imbalanced genes is also enriched for these same cancer-related functions. By comparing the transcriptomic perturbations observed in one patient to his underlying normal and tumor genomes, we find that allelic imbalance in the tumor is associated with copy number mutations and that copy number mutations are, in turn, strongly associated with changes in transcript abundance. These results support a model in which allele-specific deletions and duplications drive allele-specific changes in gene expression in the developing tumor.

  6. Allelic imbalance and cytogenetic deletion of 1p in colorectal adenomas: a target region identified between DIS199 and DIS234

    DEFF Research Database (Denmark)

    Bomme, L; Heim, S; Bardi, G

    1998-01-01

    short-term cultured and karyotyped colorectal adenomas for allelic imbalance at eight microsatellite loci in 1p. Allelic imbalances were detected in seven of the 12 adenomas that had cytogenetically visible abnormalities of chromosome 1, as well as in four adenomas that either had a normal karyotype...... region. This genomic area contains the human homologue of the tumor modifier gene Mom1 (1p35-36.1), which, in mice, modifies the number of intestinal tumors in multiple intestinal neoplasia (Min)-mutated animals. To evaluate whether the imbalances corresponded to interstitial deletions of 1p material, we...

  7. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome

    Science.gov (United States)

    Pinter, Stefan F.; Colognori, David; Beliveau, Brian J.; Sadreyev, Ruslan I.; Payer, Bernhard; Yildirim, Eda; Wu, Chao-ting; Lee, Jeannie T.

    2015-01-01

    In mammals, several classes of monoallelic genes have been identified, including those subject to X-chromosome inactivation (XCI), genomic imprinting, and random monoallelic expression (RMAE). However, the extent to which these epigenetic phenomena are influenced by underlying genetic variation is unknown. Here we perform a systematic classification of allelic imbalance in mouse hybrids derived from reciprocal crosses of divergent strains. We observe that deviation from balanced biallelic expression is common, occurring in ∼20% of the mouse transcriptome in a given tissue. Allelic imbalance attributed to genotypic variation is by far the most prevalent class and typically is tissue-specific. However, some genotype-based imbalance is maintained across tissues and is associated with greater genetic variation, especially in 5′ and 3′ termini of transcripts. We further identify novel random monoallelic and imprinted genes and find that genotype can modify penetrance of parental origin even in the setting of large imprinted regions. Examination of nascent transcripts in single cells from inbred parental strains reveals that genes showing genotype-based imbalance in hybrids can also exhibit monoallelic expression in isogenic backgrounds. This surprising observation may suggest a competition between alleles and/or reflect the combined impact of cis- and trans-acting variation on expression of a given gene. Our findings provide novel insights into gene regulation and may be relevant to human genetic variation and disease. PMID:25858912

  8. Genomic Features That Predict Allelic Imbalance in Humans Suggest Patterns of Constraint on Gene Expression Variation

    Science.gov (United States)

    Fédrigo, Olivier; Haygood, Ralph; Mukherjee, Sayan; Wray, Gregory A.

    2009-01-01

    Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In particular, measurements of gene expression usually do not reveal whether the genetic basis for any observed variation lies in cis or in trans to the gene, a distinction that has direct relevance to the physical location of the underlying genetic variant, and which may also impact its evolutionary trajectory. Allelic imbalance measurements identify cis-acting genetic effects by assaying the relative contribution of the two alleles of a cis-regulatory region to gene expression within individuals. Identification of patterns that predict commonly imbalanced genes could therefore serve as a useful tool and also shed light on the evolution of cis-regulatory variation itself. Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set. Reduction of this feature set to four factors revealed that only one factor significantly differentiated between commonly imbalanced and nonimbalanced genes. We demonstrate that these results are consistent between the original data set and a second published data set in humans obtained using different technical and statistical methods. Finally, we show that variation in the single allelic imbalance-associated factor is partially explained by the density of genes in the region of a target gene (allelic imbalance is less probable for genes in gene-dense regions), and, to a lesser extent, the evenness of expression of the gene across tissues and the magnitude of negative selection on putative regulatory regions of the gene. These results suggest that the genomic distribution of functional cis-regulatory variants in the human genome is nonrandom, perhaps due to local differences in evolutionary

  9. Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents

    DEFF Research Database (Denmark)

    Birkbak, Nicolai J.; Wang, Zhigang C.; Kim, Ji-Young

    2012-01-01

    with triple-negative breast cancer (TNBC). In serous ovarian cancer treated with platinum-based chemotherapy, higher levels of NtAI forecast a better initial response. We found an inverse relationship between BRCA1 expression and NtAI in sporadic TNBC and serous ovarian cancers without BRCA1 or BRCA2 mutation...... of defective DNA repair in cell lines and tumors and correlated these signatures to platinum sensitivity. The number of subchromosomal regions with allelic imbalance extending to the telomere (NtAI) predicted cisplatin sensitivity in vitro and pathologic response to preoperative cisplatin treatment in patients...... also benefit from these agents. NtAI, a genomic measure of unfaithfully repaired DNA, may identify cancer patients likely to benefit from treatments targeting defective DNA repair. Cancer Discov; 2(4); 366–75. ©2012 AACR. This article is highlighted in the In This Issue feature, p. 288...

  10. Allelic imbalance on chromosome 1 in human breast cancer. I. Minisatellite and RFLP analysis.

    Science.gov (United States)

    Loupart, M L; Armour, J; Walker, R; Adams, S; Brammar, W; Varley, J

    1995-01-01

    In order to characterise the role of chromosome 1 more fully in breast cancer, polymorphic markers mapping along the length of the whole chromosome were used to assess a panel of 71 tumour-lymphocyte pairs for allelic imbalance. Complex patterns of alterations were established that are consistent with cytogenetic data in the literature. Deletion mapping of individuals with loss of heterozygosity identified five independent smallest common regions of deletion, two of which are novel. There are also three discrete regions showing a gain in copy number of one homologue. The two arms of the chromosome may be subject to different events; the short arm primarily undergoes interstitial deletions, whereas the long arm is subject to whole arm events (as both gains and losses) as well as regional deletions.

  11. 8q24 allelic imbalance and MYC gene copy number in primary prostate cancer.

    Science.gov (United States)

    Chen, H; Liu, W; Roberts, W; Hooker, S; Fedor, H; DeMarzo, A; Isaacs, W; Kittles, R A

    2010-09-01

    Four independent regions within 8q24 near the MYC gene are associated with risk for prostate cancer (Pca). Here, we investigated allelic imbalance (AI) at 8q24 risk variants and MYC gene DNA copy number (CN) in 27 primary Pcas. Heterozygotes were observed in 24 of 27 patients at one or more 8q24 markers and 27% of the loci exhibited AI in tumor DNA. The 8q24 risk alleles were preferentially favored in the tumors. Increased MYC gene CN was observed in 33% of tumors, and the co-existence of increased MYC gene CN with AI at risk loci was observed in 86% (P<0.004 exact binomial test) of the informative tumors. No AI was observed in tumors, which did not reveal increased MYC gene CN. Higher Gleason score was associated with tumors exhibiting AI (P=0.04) and also with increased MYC gene CN (P=0.02). Our results suggest that AI at 8q24 and increased MYC gene CN may both be related to high Gleason score in Pca. Our findings also suggest that these two somatic alterations may be due to the same preferential chromosomal duplication event during prostate tumorigenesis.

  12. Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

    Directory of Open Access Journals (Sweden)

    Dahlgren Andreas

    2004-10-01

    Full Text Available Abstract Background Each of the human genes or transcriptional units is likely to contain single nucleotide polymorphisms that may give rise to sequence variation between individuals and tissues on the level of RNA. Based on recent studies, differential expression of the two alleles of heterozygous coding single nucleotide polymorphisms (SNPs may be frequent for human genes. Methods with high accuracy to be used in a high throughput setting are needed for systematic surveys of expressed sequence variation. In this study we evaluated two formats of multiplexed, microarray based minisequencing for quantitative detection of imbalanced expression of SNP alleles. We used a panel of ten SNPs located in five genes known to be expressed in two endothelial cell lines as our model system. Results The accuracy and sensitivity of quantitative detection of allelic imbalance was assessed for each SNP by constructing regression lines using a dilution series of mixed samples from individuals of different genotype. Accurate quantification of SNP alleles by both assay formats was evidenced for by R2 values > 0.95 for the majority of the regression lines. According to a two sample t-test, we were able to distinguish 1–9% of a minority SNP allele from a homozygous genotype, with larger variation between SNPs than between assay formats. Six of the SNPs, heterozygous in either of the two cell lines, were genotyped in RNA extracted from the endothelial cells. The coefficient of variation between the fluorescent signals from five parallel reactions was similar for cDNA and genomic DNA. The fluorescence signal intensity ratios measured in the cDNA samples were compared to those in genomic DNA to determine the relative expression levels of the two alleles of each SNP. Four of the six SNPs tested displayed a higher than 1.4-fold difference in allelic ratios between cDNA and genomic DNA. The results were verified by allele-specific oligonucleotide hybridisation and

  13. Allelic imbalance and fine mapping of the 17p13.3 subregion in sporadic breast carcinomas

    DEFF Research Database (Denmark)

    Hoff, C; Mollenhauer, J; Waldau, B

    2001-01-01

    Chromosome arm 17p is frequently altered in a variety of human cancers, especially in breast cancer, and allelic imbalances (AIs) in the region 17p13.1 do not always coincide with mutations in the TP53 gene. A second interval that frequently shows AIs at 17p is the chromosomal band 17p13.3. This ......Chromosome arm 17p is frequently altered in a variety of human cancers, especially in breast cancer, and allelic imbalances (AIs) in the region 17p13.1 do not always coincide with mutations in the TP53 gene. A second interval that frequently shows AIs at 17p is the chromosomal band 17p13...

  14. Analysis of APC allelic imbalance/loss of heterozygosity and APC protein expression in cutaneous squamous cell carcinomas.

    LENUS (Irish Health Repository)

    Gray, Sarah E

    2012-02-01

    BACKGROUND: The adenomatous polyposis coli (APC) gene is a tumor suppressor gene which is mutated in the hereditary disease, familial adenomatous polyposis (FAP). Somatic mutations of the APC gene have also been identified in the majority of sporadic colorectal carcinomas, and mutation of the APC gene appears to be an early step in the initiation of colon cancer. Loss of heterozygosity (LOH) of APC has been described in a variety of other cancer types, including renal cell carcinoma, gastric cancer, non-small cell lung cancer, endometrial cancer and oral squamous cell carcinomas (SCC). AIM: To determine the role played by APC gene in the genesis of cutaneous SCC. MATERIALS AND METHODS: Allelic imbalance\\/loss of heterozygosity (AI\\/LOH) was examined in twenty-two histologically confirmed cutaneous squamous cell carcinomas (SCC) using microsatellite markers, proximal to the APC gene. Immunohistochemical analysis of APC protein expression was also examined in the cutaneous SCC. RESULTS: AI\\/LOH was detected in 60% of the SCC samples using D5S346 marker (proximal to the APC gene). Ninty-five percent of the SCC samples showed positive reduced APC expression, however the localization of the APC protein was abnormal. CONCLUSION: The abnormal expression of APC suggests that APC gene may play a role in cutaneous SCC development.

  15. Allelic imbalance modulates surface expression of the tolerance-inducing HLA-G molecule on primary trophoblast cells.

    Science.gov (United States)

    Djurisic, S; Teiblum, S; Tolstrup, C K; Christiansen, O B; Hviid, T V F

    2015-03-01

    The HLA-G molecule is expressed on trophoblast cells at the feto-maternal interface, where it interacts with local immune cells, and upholds tolerance against the semi-allogeneic fetus. Aberrant HLA-G expression in the placenta and reduced soluble HLA-G levels are observed in pregnancy complications, partly explained by HLA-G polymorphisms which are associated with differences in the alternative splicing pattern and of the stability of HLA-G mRNA. Of special importance is a 14 bp insertion/deletion polymorphism located in the 3'-untranslated region of the HLA-G gene. In the current study, we present novel evidence for allelic imbalance of the 14 bp insertion/deletion polymorphism, using a very accurate and sensitive Digital droplet PCR technique. Allelic imbalance in heterozygous samples was observed as differential expression levels of 14 bp insertion/deletion allele-specific mRNA transcripts, which was further associated with low levels of HLA-G surface expression on primary trophoblast cells. Full gene sequencing of HLA-G allowed us to study correlations between HLA-G extended haplotypes and single-nucleotide polymorphisms and HLA-G surface expression. We found that a 1:1 expression (allelic balance) of the 14 bp insertion/deletion mRNA alleles was associated with high surface expression of HLA-G and with a specific HLA-G extended haplotype. The 14 bp del/del genotype was associated with a significantly lower abundance of the G1 mRNA isoform, and a higher abundance of the G3 mRNA isoform. Overall, the present study provides original evidence for allelic imbalance of the 14 bp insertion/deletion polymorphism, which influences HLA-G surface expression on primary trophoblast cells, considered to be important in the pathogenesis of pre-eclampsia and other pregnancy complications. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Lynch syndrome associated with two MLH1 promoter variants and allelic imbalance of MLH1 expression.

    Science.gov (United States)

    Hesson, Luke B; Packham, Deborah; Kwok, Chau-To; Nunez, Andrea C; Ng, Benedict; Schmidt, Christa; Fields, Michael; Wong, Jason W H; Sloane, Mathew A; Ward, Robyn L

    2015-06-01

    Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5'untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5'UTR in the pathogenesis of Lynch syndrome. © 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

  17. Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analysis analyses of pooled RNA-Seq samples in rainbow trout

    Science.gov (United States)

    Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, mus...

  18. Human minisatellite alleles detectable only after PCR amplification.

    Science.gov (United States)

    Armour, J A; Crosier, M; Jeffreys, A J

    1992-01-01

    We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

  19. Imbalance aware lithography hotspot detection: a deep learning approach

    Science.gov (United States)

    Yang, Haoyu; Luo, Luyang; Su, Jing; Lin, Chenxi; Yu, Bei

    2017-07-01

    With the advancement of very large scale integrated circuits (VLSI) technology nodes, lithographic hotspots become a serious problem that affects manufacture yield. Lithography hotspot detection at the post-OPC stage is imperative to check potential circuit failures when transferring designed patterns onto silicon wafers. Although conventional lithography hotspot detection methods, such as machine learning, have gained satisfactory performance, with the extreme scaling of transistor feature size and layout patterns growing in complexity, conventional methodologies may suffer from performance degradation. For example, manual or ad hoc feature extraction in a machine learning framework may lose important information when predicting potential errors in ultra-large-scale integrated circuit masks. We present a deep convolutional neural network (CNN) that targets representative feature learning in lithography hotspot detection. We carefully analyze the impact and effectiveness of different CNN hyperparameters, through which a hotspot-detection-oriented neural network model is established. Because hotspot patterns are always in the minority in VLSI mask design, the training dataset is highly imbalanced. In this situation, a neural network is no longer reliable, because a trained model with high classification accuracy may still suffer from a high number of false negative results (missing hotspots), which is fatal in hotspot detection problems. To address the imbalance problem, we further apply hotspot upsampling and random-mirror flipping before training the network. Experimental results show that our proposed neural network model achieves comparable or better performance on the ICCAD 2012 contest benchmark compared to state-of-the-art hotspot detectors based on deep or representative machine leaning.

  20. Genome-Wide analysis of allelic imbalance in laser microdissected prostate cancer tissue using the Affymetrix 50K Mapping array identifies genomic patterns associated with metastasis and differentiation

    DEFF Research Database (Denmark)

    Tørring, Niels; Borre, Michael; Sørensen, Karina

    2007-01-01

    , patterns of allelic imbalance were discovered in PCa, consisting allelic loss as an early event in tumour development, and distinct patterns of allelic amplification related to tumour progression and poor differentiation.British Journal of Cancer advance online publication, 23 January 2007; doi:10.1038/sj...

  1. Allele-Specific DNA Methylation Detection by Pyrosequencing®

    DEFF Research Database (Denmark)

    Kristensen, Lasse Sommer; Johansen, Jens Vilstrup; Grønbæk, Kirsten

    2015-01-01

    DNA methylation is an epigenetic modification that plays important roles in healthy as well as diseased cells, by influencing the transcription of genes. In spite the fact that human somatic cells are diploid, most of the currently available methods for the study of DNA methylation do not provide......-effective protocol for allele-specific DNA methylation detection based on Pyrosequencing(®) of methylation-specific PCR (MSP) products including a single nucleotide polymorphism (SNP) within the amplicon....

  2. Charge imbalance

    International Nuclear Information System (INIS)

    Clarke, J.

    1981-01-01

    This article provides a long theoretical development of the main ideas of charge imbalance in superconductors. Concepts of charge imbalance and quasiparticle charge are introduced, especially in regards to the use of tunnel injection in producing and detecting charge imbalance. Various mechanisms of charge relaxation are discussed, including inelastic scattering processes, elastic scattering in the presence of energy-gap anisotropy, and various pair-breaking mechanisms. In each case, present theories are reviewed in comparison with experimental data

  3. CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Ishikawa Shumpei

    2006-02-01

    Full Text Available Abstract Background DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell. Results We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods. Conclusion Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.

  4. An imbalance fault detection method based on data normalization and EMD for marine current turbines.

    Science.gov (United States)

    Zhang, Milu; Wang, Tianzhen; Tang, Tianhao; Benbouzid, Mohamed; Diallo, Demba

    2017-05-01

    This paper proposes an imbalance fault detection method based on data normalization and Empirical Mode Decomposition (EMD) for variable speed direct-drive Marine Current Turbine (MCT) system. The method is based on the MCT stator current under the condition of wave and turbulence. The goal of this method is to extract blade imbalance fault feature, which is concealed by the supply frequency and the environment noise. First, a Generalized Likelihood Ratio Test (GLRT) detector is developed and the monitoring variable is selected by analyzing the relationship between the variables. Then, the selected monitoring variable is converted into a time series through data normalization, which makes the imbalance fault characteristic frequency into a constant. At the end, the monitoring variable is filtered out by EMD method to eliminate the effect of turbulence. The experiments show that the proposed method is robust against turbulence through comparing the different fault severities and the different turbulence intensities. Comparison with other methods, the experimental results indicate the feasibility and efficacy of the proposed method. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  5. Class imbalance in unsupervised change detection - A diagnostic analysis from urban remote sensing

    Science.gov (United States)

    Leichtle, Tobias; Geiß, Christian; Lakes, Tobia; Taubenböck, Hannes

    2017-08-01

    Automatic monitoring of changes on the Earth's surface is an intrinsic capability and simultaneously a persistent methodological challenge in remote sensing, especially regarding imagery with very-high spatial resolution (VHR) and complex urban environments. In order to enable a high level of automatization, the change detection problem is solved in an unsupervised way to alleviate efforts associated with collection of properly encoded prior knowledge. In this context, this paper systematically investigates the nature and effects of class distribution and class imbalance in an unsupervised binary change detection application based on VHR imagery over urban areas. For this purpose, a diagnostic framework for sensitivity analysis of a large range of possible degrees of class imbalance is presented, which is of particular importance with respect to unsupervised approaches where the content of images and thus the occurrence and the distribution of classes are generally unknown a priori. Furthermore, this framework can serve as a general technique to evaluate model transferability in any two-class classification problem. The applied change detection approach is based on object-based difference features calculated from VHR imagery and subsequent unsupervised two-class clustering using k-means, genetic k-means and self-organizing map (SOM) clustering. The results from two test sites with different structural characteristics of the built environment demonstrated that classification performance is generally worse in imbalanced class distribution settings while best results were reached in balanced or close to balanced situations. Regarding suitable accuracy measures for evaluating model performance in imbalanced settings, this study revealed that the Kappa statistics show significant response to class distribution while the true skill statistic was widely insensitive to imbalanced classes. In general, the genetic k-means clustering algorithm achieved the most robust results

  6. Regions of micro-calcifications clusters detection based on new features from imbalance data in mammograms

    Science.gov (United States)

    Wang, Keju; Dong, Min; Yang, Zhen; Guo, Yanan; Ma, Yide

    2017-02-01

    Breast cancer is the most common cancer among women. Micro-calcification cluster on X-ray mammogram is one of the most important abnormalities, and it is effective for early cancer detection. Surrounding Region Dependence Method (SRDM), a statistical texture analysis method is applied for detecting Regions of Interest (ROIs) containing microcalcifications. Inspired by the SRDM, we present a method that extract gray and other features which are effective to predict the positive and negative regions of micro-calcifications clusters in mammogram. By constructing a set of artificial images only containing micro-calcifications, we locate the suspicious pixels of calcifications of a SRDM matrix in original image map. Features are extracted based on these pixels for imbalance date and then the repeated random subsampling method and Random Forest (RF) classifier are used for classification. True Positive (TP) rate and False Positive (FP) can reflect how the result will be. The TP rate is 90% and FP rate is 88.8% when the threshold q is 10. We draw the Receiver Operating Characteristic (ROC) curve and the Area Under the ROC Curve (AUC) value reaches 0.9224. The experiment indicates that our method is effective. A novel regions of micro-calcifications clusters detection method is developed, which is based on new features for imbalance data in mammography, and it can be considered to help improving the accuracy of computer aided diagnosis breast cancer.

  7. Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea

    OpenAIRE

    Zhang, Xin; Xie, Fei; Lv, Baobei; Zhao, Pengxiang; Ma, Xuemei

    2016-01-01

    A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea. Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension (ASPE) assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene (BenA), H272 and 272Y of the Succinate dehydrogenase iron–sulfur...

  8. Retinal Microaneurysms Detection Using Gradient Vector Analysis and Class Imbalance Classification.

    Science.gov (United States)

    Dai, Baisheng; Wu, Xiangqian; Bu, Wei

    2016-01-01

    Retinal microaneurysms (MAs) are the earliest clinically observable lesions of diabetic retinopathy. Reliable automated MAs detection is thus critical for early diagnosis of diabetic retinopathy. This paper proposes a novel method for the automated MAs detection in color fundus images based on gradient vector analysis and class imbalance classification, which is composed of two stages, i.e. candidate MAs extraction and classification. In the first stage, a candidate MAs extraction algorithm is devised by analyzing the gradient field of the image, in which a multi-scale log condition number map is computed based on the gradient vectors for vessel removal, and then the candidate MAs are localized according to the second order directional derivatives computed in different directions. Due to the complexity of fundus image, besides a small number of true MAs, there are also a large amount of non-MAs in the extracted candidates. Classifying the true MAs and the non-MAs is an extremely class imbalanced classification problem. Therefore, in the second stage, several types of features including geometry, contrast, intensity, edge, texture, region descriptors and other features are extracted from the candidate MAs and a class imbalance classifier, i.e., RUSBoost, is trained for the MAs classification. With the Retinopathy Online Challenge (ROC) criterion, the proposed method achieves an average sensitivity of 0.433 at 1/8, 1/4, 1/2, 1, 2, 4 and 8 false positives per image on the ROC database, which is comparable with the state-of-the-art approaches, and 0.321 on the DiaRetDB1 V2.1 database, which outperforms the state-of-the-art approaches.

  9. Propensity score to detect baseline imbalance in cluster randomized trials: the role of the c-statistic.

    Science.gov (United States)

    Leyrat, Clémence; Caille, Agnès; Foucher, Yohann; Giraudeau, Bruno

    2016-01-22

    Despite randomization, baseline imbalance and confounding bias may occur in cluster randomized trials (CRTs). Covariate imbalance may jeopardize the validity of statistical inferences if they occur on prognostic factors. Thus, the diagnosis of a such imbalance is essential to adjust statistical analysis if required. We developed a tool based on the c-statistic of the propensity score (PS) model to detect global baseline covariate imbalance in CRTs and assess the risk of confounding bias. We performed a simulation study to assess the performance of the proposed tool and applied this method to analyze the data from 2 published CRTs. The proposed method had good performance for large sample sizes (n =500 per arm) and when the number of unbalanced covariates was not too small as compared with the total number of baseline covariates (≥40% of unbalanced covariates). We also provide a strategy for pre selection of the covariates needed to be included in the PS model to enhance imbalance detection. The proposed tool could be useful in deciding whether covariate adjustment is required before performing statistical analyses of CRTs.

  10. Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

    Directory of Open Access Journals (Sweden)

    Sinilnikova Olga

    2011-05-01

    Full Text Available Abstract Background The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether CHEK2 was subject to DAE in lymphoblastoid cell lines (LCLs from high-risk breast cancer patients for whom no mutation in BRCA1 or BRCA2 had been identified. Methods We implemented an assay based on high-resolution melting (HRM curve analysis and developed an analysis tool for DAE assessment. Results We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of CHEK2 that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs. Conclusions Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms.

  11. Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection

    International Nuclear Information System (INIS)

    Zapparoli, Giada V; Jorissen, Robert N; Hewitt, Chelsee A; McBean, Michelle; Westerman, David A; Dobrovic, Alexander

    2013-01-01

    The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10 -4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a

  12. Detection of MPL mutations by a novel allele-specific PCR-based strategy.

    Science.gov (United States)

    Furtado, Larissa V; Weigelin, Helmut C; Elenitoba-Johnson, Kojo S J; Betz, Bryan L

    2013-11-01

    MPL mutation testing is recommended in patients with suspected primary myelofibrosis or essential thrombocythemia who lack the JAK2 V617F mutation. MPL mutations can occur at allelic levels below 15%, which may escape detection by commonly used mutation screening methods such as Sanger sequencing. We developed a novel multiplexed allele-specific PCR assay capable of detecting most recurrent MPL exon 10 mutations associated with primary myelofibrosis and essential thrombocythemia (W515L, W515K, W515A, and S505N) down to a sensitivity of 2.5% mutant allele. Test results were reviewed from 15 reference cases and 1380 consecutive specimens referred to our laboratory for testing. Assay performance was compared to Sanger sequencing across a series of 58 specimens with MPL mutations. Positive cases consisted of 45 with W515L, 6 with S505N, 5 with W515K, 1 with W515A, and 1 with both W515L and S505N. Seven cases had mutations below 5% that were undetected by Sanger sequencing. Ten additional cases had mutation levels between 5% and 15% that were not consistently detected by sequencing. All results were easily interpreted in the allele-specific test. This assay offers a sensitive and reliable solution for MPL mutation testing. Sanger sequencing appears insufficiently sensitive for robust MPL mutation detection. Our data also suggest the relative frequency of S505N mutations may be underestimated, highlighting the necessity for inclusion of this mutation in MPL test platforms. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  13. QTL detection and elite alleles mining for stigma traits in Oryza sativa by association mapping

    Directory of Open Access Journals (Sweden)

    Xiaojing Dang

    2016-08-01

    Full Text Available Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across two years and assessed their genotypic variation with 249 simple sequence repeat (SSR markers. By combining phenotypic and genotypic data, a genome-wide association (GWA map was generated. Large phenotypic variations in stigma length (STL, stigma brush-shaped part length (SBPL and stigma non-brush-shaped part length (SNBPL were found. Significant positive correlations were identified among stigma traits. In total, 2,072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.

  14. Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    Xin Zhang

    2016-09-01

    Full Text Available A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea. Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension (ASPE assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene (BenA, H272 and 272Y of the Succinate dehydrogenase iron–sulfur subunit gene (SdhB, I365 and 365S of the putative osmosensor histidine kinase gene (BcOS1, and F412 and 412S of the 3-ketoreductase gene (erg27. This assay was first established and optimized with eight plasmid templates containing the DNA sequence variants BenA-E198, BenA-198A, SdhB-H272, SdhB-272Y, BcOS1-I365, BcOS1-365S, erg27-F412, and erg27-412S. Results indicated that none of the probes showed cross-reactivity with one another. The minimum limit of detection for these genotypes was one copy per test. Four mutant plasmids were mixed with 10 ng/μL wild-type genomic DNA in different ratios. Detection sensitivity of mutant loci was 0.45% for BenA-E198A, BcOS1-I365S, and erg27-F412S, and was 4.5% for SdhB-H272Y. A minimum quantity of 0.1 ng of genomic DNA was necessary to obtain reliable results. This is the first reported assay that can simultaneously detect mutations in BenA, SdhB, BcOS1, and erg27.

  15. Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea.

    Science.gov (United States)

    Zhang, Xin; Xie, Fei; Lv, Baobei; Zhao, Pengxiang; Ma, Xuemei

    2016-01-01

    A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea . Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene ( BenA ), H272 and 272Y of the Succinate dehydrogenase iron-sulfur subunit gene ( SdhB) , I365 and 365S of the putative osmosensor histidine kinase gene ( BcOS1 ), and F412 and 412S of the 3-ketoreductase gene ( erg27 ). This assay was first established and optimized with eight plasmid templates containing the DNA sequence variants BenA- E198, BenA- 198A, SdhB- H272, SdhB- 272Y, BcOS1- I365, BcOS1- 365S, erg27 -F412, and erg27 -412S. Results indicated that none of the probes showed cross-reactivity with one another. The minimum limit of detection for these genotypes was one copy per test. Four mutant plasmids were mixed with 10 ng/μL wild-type genomic DNA in different ratios. Detection sensitivity of mutant loci was 0.45% for BenA- E198A, BcOS1- I365S, and erg27 -F412S, and was 4.5% for SdhB- H272Y. A minimum quantity of 0.1 ng of genomic DNA was necessary to obtain reliable results. This is the first reported assay that can simultaneously detect mutations in BenA , SdhB , BcOS1 , and erg27 .

  16. Method and system for detecting, in real time, the imbalance of the head in a high-precision rotary mechanism

    OpenAIRE

    Toro Matamoros, Raúl Mario del; Schmittdiel, Michael Charles; Haber Guerra, Rodolfo E.

    2008-01-01

    [EN] The invention relates to a method for detecting, in real time, an imbalance of the head in a high-precision rotary mechanism, and to the system for carrying out said method. The method comprises the following steps: a) the signal X(t) corresponding to the acceleration of the vibrations of the head is acquired by means of an acquisition means at a sampling rate FS; and b) it is determined, from the signal X(t) obtained, whether the head is imbalanced.

  17. Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing® technology

    Directory of Open Access Journals (Sweden)

    Gallagher Margaret L

    2009-08-01

    Full Text Available Abstract Background Identification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology. Methods A single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow. Results Pyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics. Conclusion This Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies.

  18. Detecting slow introgression of invasive alleles in an extensively restocked game bird

    Directory of Open Access Journals (Sweden)

    Ines eSanchez-Donoso

    2014-04-01

    Full Text Available Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail (Coturnix coturnix populations in Europe have been restocked extensively with farm quails of hybrid origin (crosses with Japanese quails, C. japonica. We genetically monitored a common quail population over 15 years to investigate whether genetic introgression is occurring and used simulations to investigate our power to detect it. Our results revealed that some introgression has occurred, but we did not observe a significant increase over time in the proportion of admixed individuals. However, simulations showed that the degree of admixture may be larger than anticipated due to the limited power of analyses over a short time span, and that observed data was compatible with a low rate of introgression, probably resulting from reduced fitness of admixed individuals. Simulations predicted this could result in extensive admixture in the near future.

  19. Detection of Redox Imbalance in Normal Lymphocytes with Induced Mitochondrial Dysfunction - EPR Study.

    Science.gov (United States)

    Georgieva, Ekaterina; Zhelev, Zhivko; Aoki, Ichio; Bakalova, Rumiana; Higashi, Tatsuya

    2016-10-01

    The present study describes a new approach for direct imaging of redox status in live cells using paramagnetic spin-probes, which allows evaluation of the level of oxidative stress due to overproduction of superoxide. The method is based on redox cycling of cell/mitochondria-penetrating nitroxide radicals (e.g. mito-TEMPO) and their electron-paramagnetic resonance (EPR) contrast, which makes them useful molecular sensors for analysis of redox status and oxidative stress in cells and tissues. Oxidative stress was induced in normal human lymphocytes by treatment with 2-methoxyestradiol and rotenone (ME/Rot) at different concentrations. This combination provokes mitochondrial dysfunction, which is accompanied by overproduction of superoxide. The EPR measurements were performed in dynamics on X-Band spectrometer after addition of mito-TEMPO to cell suspensions. The intensity of the EPR signal in untreated cells decreased significantly, which indicates a conversion of paramagnetic mito-TEMPO to its non-contrast diamagnetic form (hydroxylamine - mito-TEMPOH) due to reduction. In ME/Rot-treated cells, the signal decreased more slowly and to a lower level with increasing the concentration of ME/Rot. These data indicate an induction of oxidative stress in the cells in a concentration-dependent manner. A very good positive correlation between the intensity of EPR signal of mito-TEMPO and the intracellular level of superoxide was found, analyzed by conventional dihydroethidium test (R=0.9143, pEPR imaging of the superoxide level in live cells, as well as for EPR imaging of mitochondrial dysfunction and metabolic activity, accompanied by superoxide imbalance. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  20. Detection of MPLW515L/K mutations and determination of allele frequencies with a single-tube PCR assay.

    Science.gov (United States)

    Takei, Hiraku; Morishita, Soji; Araki, Marito; Edahiro, Yoko; Sunami, Yoshitaka; Hironaka, Yumi; Noda, Naohiro; Sekiguchi, Yuji; Tsuneda, Satoshi; Ohsaka, Akimichi; Komatsu, Norio

    2014-01-01

    A gain-of-function mutation in the myeloproliferative leukemia virus (MPL) gene, which encodes the thrombopoietin receptor, has been identified in patients with essential thrombocythemia and primary myelofibrosis, subgroups of classic myeloproliferative neoplasms (MPNs). The presence of MPL gene mutations is a critical diagnostic criterion for these diseases. Here, we developed a rapid, simple, and cost-effective method of detecting two major MPL mutations, MPLW515L/K, in a single PCR assay; we termed this method DARMS (dual amplification refractory mutation system)-PCR. DARMS-PCR is designed to produce three different PCR products corresponding to MPLW515L, MPLW515K, and all MPL alleles. The amplicons are later detected and quantified using a capillary sequencer to determine the relative frequencies of the mutant and wild-type alleles. Applying DARMS-PCR to human specimens, we successfully identified MPL mutations in MPN patients, with the exception of patients bearing mutant allele frequencies below the detection limit (5%) of this method. The MPL mutant allele frequencies determined using DARMS-PCR correlated strongly with the values determined using deep sequencing. Thus, we demonstrated the potential of DARMS-PCR to detect MPL mutations and determine the allele frequencies in a timely and cost-effective manner.

  1. Detection of MPLW515L/K mutations and determination of allele frequencies with a single-tube PCR assay.

    Directory of Open Access Journals (Sweden)

    Hiraku Takei

    Full Text Available A gain-of-function mutation in the myeloproliferative leukemia virus (MPL gene, which encodes the thrombopoietin receptor, has been identified in patients with essential thrombocythemia and primary myelofibrosis, subgroups of classic myeloproliferative neoplasms (MPNs. The presence of MPL gene mutations is a critical diagnostic criterion for these diseases. Here, we developed a rapid, simple, and cost-effective method of detecting two major MPL mutations, MPLW515L/K, in a single PCR assay; we termed this method DARMS (dual amplification refractory mutation system-PCR. DARMS-PCR is designed to produce three different PCR products corresponding to MPLW515L, MPLW515K, and all MPL alleles. The amplicons are later detected and quantified using a capillary sequencer to determine the relative frequencies of the mutant and wild-type alleles. Applying DARMS-PCR to human specimens, we successfully identified MPL mutations in MPN patients, with the exception of patients bearing mutant allele frequencies below the detection limit (5% of this method. The MPL mutant allele frequencies determined using DARMS-PCR correlated strongly with the values determined using deep sequencing. Thus, we demonstrated the potential of DARMS-PCR to detect MPL mutations and determine the allele frequencies in a timely and cost-effective manner.

  2. Sensitive and reliable detection of genomic imbalances in human neuroblastomas using comparative genomic hybridisation analysis

    NARCIS (Netherlands)

    van Gele, M.; van Roy, N.; Jauch, A.; Laureys, G.; Benoit, Y.; Schelfhout, V.; de Potter, C. R.; Brock, P.; Uyttebroeck, A.; Sciot, R.; Schuuring, E.; Versteeg, R.; Speleman, F.

    1997-01-01

    Deletions of the short arm of chromosome 1, extra copies of chromosome 17q and MYCN amplification are the most frequently encountered genetic changes in neuroblastomas. Standard techniques for detection of one or more of these genetic changes are karyotyping, FISH analysis and LOH analysis by

  3. Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

    Directory of Open Access Journals (Sweden)

    Trognitz Friederike

    2007-02-01

    Full Text Available Abstract Background The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs. This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge. Results We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles

  4. High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

    Science.gov (United States)

    Preston, Jessica L; Royall, Ariel E; Randel, Melissa A; Sikkink, Kristin L; Phillips, Patrick C; Johnson, Eric A

    2016-06-14

    Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.

  5. HLA-DQBl*0402 alleles polymorphisms detected in Javanese HIV patients with positive anti-Toxoplasma gondii IgM

    Science.gov (United States)

    Sari, Yulia; Haryati, Sri; Prasetyo, Afiono Agung; Hartono, Adnan, Zainal Arifin

    2017-02-01

    The human leukocyte antigen (HLA)-DQB1 gene polymorphisms may associated with the infection risk of Toxoplasma gondii in HIV patients. The HLA-DQB1*0402 in HIV-1-positive patients could be considered risk factors for developing neurological opportunistic infections, mainly Toxoplasma encephalitis. However, the HLA-DQB1*0402 gene polymorphisms status in the Javanese HIV patients is unknown. This study evaluated the prevalence of HLA-DQB*0402 alleles polymorphisms in Javanese HIV patients with positive anti-Toxoplasma gondii IgM status. Since 2009 our research group performing a molecular epidemiology of blood borne viruses in Central Java Indonesia, by collecting the epidemiological and clinical data from the high risk communities. All blood samples were screened for blood borne pathogens by serological and molecular assays including for HIV and Toxoplasma gondii. The genomic DNA was isolated from the whole blood samples. Genetic polymorphisms of HLA-DQB1*0402 alleles were detected with polymerase chain reaction-sequence-specific primers (PCR-SSPs) technique. The genotypes were defined according to generated fragment patterns in the agarose gel electrophoresis analysis of PCR products. All of the samples were tested at least in duplicate. HLA-DQB1*0402 alleles were detected in 20.8% (16/77) patients and not detected in all HIV positive samples with negative anti-Toxoplasma gondii IgM status (n= 200). The HLA-DQB1*0402 alleles polymorphisms were detected in Javanese HIV patients with positive anti-Toxoplasma gondii IgM. The polymorphisms found may have association with the infection risk of Toxoplasma gondii in HIV patients.

  6. Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.

    Science.gov (United States)

    Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

    2013-01-01

    The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.

  7. Chimerism representing both paternal alleles detected by HLA typing before kidney transplantation

    DEFF Research Database (Denmark)

    Christiansen, Mette; Petersen, Mikkel Steen; Møller, Bjarne Kuno

    2014-01-01

    trisomy 6p or by chimerism. Flow cytometric analysis, employing antibodies specific for the two paternal HLA-A alleles, clearly showed two distinct populations of cells: 83% expressing HLA-A11 and 12% expressing HLA-A2, suggesting a paternal chimerism. We are studying these cell populations to possibly...... identify the mechanism behind this rather unusual paternally derived chimerism. This exceptional case illustrates that careful scrutiny of HLA-typing results may produce atypical conclusions. Clinically, the father is considered the best donor based on immunogenetics....

  8. Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

    Science.gov (United States)

    Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

    2017-01-03

    Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

  9. Technical aspects of typing for HLA-DP alleles using allele-specific DNA in vitro amplification and sequence-specific oligonucleotide probes. Detection of single base mismatches

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P

    1990-01-01

    The polymerase chain reaction (PCR) is an effective method for in vitro DNA amplification which combined with probing with synthetic oligonucleotides can be used for, e.g., HLA-typing. We have studied the technical aspects of HLA-DP typing with the technique. DNA from mononuclear nucleated cells...... was extracted with either a simple salting out method or phenol/chloroform. Both DNAs could be readily used for PCR. The MgC2 concentration of the PCR buffer and the annealing temperature of the thermal cycle of the PCR were the two most important variables. The MgCl2 concentration and the temperature must...... be carefully titrated for each primer pair in the PCR. The influence of mismatches between the primer and the DNA template were studied and we found that, by using primers differing only from each other at the 3' end, cross-amplification of closely homologous alleles could be avoided. Thus, single base...

  10. Blind I/Q imbalance and nonlinear ISI mitigation in Nyquist-SCM direct detection system with cascaded widely linear and Volterra equalizer

    Science.gov (United States)

    Liu, Na; Ju, Cheng

    2018-02-01

    Nyquist-SCM signal after fiber transmission, direct detection (DD), and analog down-conversion suffers from linear ISI, nonlinear ISI, and I/Q imbalance, simultaneously. Theoretical analysis based on widely linear (WL) and Volterra series is given to explain the relationship and interaction of these three interferences. A blind equalization algorithm, cascaded WL and Volterra equalizer, is designed to mitigate these three interferences. Furthermore, the feasibility of the proposed cascaded algorithm is experimentally demonstrated based on a 40-Gbps data rate 16-quadrature amplitude modulation (QAM) virtual single sideband (VSSB) Nyquist-SCM DD system over 100-km standard single mode fiber (SSMF) transmission. In addition, the performances of conventional strictly linear equalizer, WL equalizer, Volterra equalizer, and cascaded WL and Volterra equalizer are experimentally evaluated, respectively.

  11. An SSP-PCR method for the rapid detection of disease-associated alleles HLA-A*29 and HLA-B*51.

    Science.gov (United States)

    Amstutz, U; Schaerer, D; Andrey, G; Wirthmueller, U; Largiadèr, C R

    2018-05-15

    HLA-A*29 and HLA-B*51 are associated with birdshot uveitis and Behçet's disease, respectively, and are used as a diagnostic criterion in patients with suspected disease, requiring their detection in diagnostic laboratories. While commercial tests for individual HLA alleles are available for other disease-associated HLA variants, no similar allele-specific assays are available for HLA-A*29 and -B*51. Here, we report SSP-PCR methods for the detection of HLA-A*29 and -B*51 using a single PCR reaction per allele. The assays were tested in 30 and 32 previously HLA-typed samples, respectively, representing >97% of HLA-A alleles and >93% of HLA-B alleles in a European population. A concordance of 100% was observed with previous typing results, validating these methods for use in a diagnostic or research context. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  12. The Impact of Collisions on the Ability to Detect Rare Mutant Alleles Using Barcode-Type Next-Generation Sequencing Techniques

    Directory of Open Access Journals (Sweden)

    Jenna VanLiere Canzoniero

    2017-07-01

    Full Text Available Barcoding techniques are used to reduce error from next-generation sequencing, with applications ranging from understanding tumor subclone populations to detecting circulating tumor DNA. Collisions occur when more than one sample molecule is tagged by the same unique identifier (UID and can result in failure to detect very-low-frequency mutations and error in estimating mutation frequency. Here, we created computer models of barcoding technique, with and without amplification bias introduced by the UID, and analyzed the effect of collisions for a range of mutant allele frequencies (1e−6 to 0.2, number of sample molecules (10 000 to 1e7, and number of UIDs (4 10 -4 14 . Inability to detect rare mutant alleles occurred in 0% to 100% of simulations, depending on collisions and number of mutant molecules. Collisions also introduced error in estimating mutant allele frequency resulting in underestimation of minor allele frequency. Incorporating an understanding of the effect of collisions into experimental design can allow for optimization of the number of sample molecules and number of UIDs to minimize the negative impact on rare mutant detection and mutant frequency estimation.

  13. Detection of CALR and MPL Mutations in Low Allelic Burden JAK2 V617F Essential Thrombocythemia.

    Science.gov (United States)

    Usseglio, Fabrice; Beaufils, Nathalie; Calleja, Anne; Raynaud, Sophie; Gabert, Jean

    2017-01-01

    Myeloproliferative neoplasms are clonal hematopoietic stem cell disorders characterized by aberrant proliferation and an increased tendency toward leukemic transformation. The genes JAK2, MPL, and CALR are frequently altered in these syndromes, and their mutations are often a strong argument for diagnosis. We analyzed the mutational profiles of these three genes in a cohort of 164 suspected myeloproliferative neoplasms. JAK2 V617F mutation was detected by real-time PCR, whereas high-resolution melting analysis followed by Sanger sequencing were used for searching for mutations in JAK2 exon 12, CALR, and MPL. JAK2 V617F mutation was associated with CALR (n = 4) and MPL (n = 4) mutations in 8 of 103 essential thrombocytosis patients. These cases were harboring a JAK2 V617F allelic burden of MPL genes in myeloproliferative neoplasms and suggest that CALR and MPL should be analyzed not only in JAK2-negative patients but also in low V617F mutation patients. Follow-up of these double-mutation cases will be important for determining whether this group of patients presents particular evolution or complications. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  14. Melting curve analysis after T allele enrichment (MelcaTle as a highly sensitive and reliable method for detecting the JAK2V617F mutation.

    Directory of Open Access Journals (Sweden)

    Soji Morishita

    Full Text Available Detection of the JAK2V617F mutation is essential for diagnosing patients with classical myeloproliferative neoplasms (MPNs. However, detection of the low-frequency JAK2V617F mutation is a challenging task due to the necessity of discriminating between true-positive and false-positive results. Here, we have developed a highly sensitive and accurate assay for the detection of JAK2V617F and named it melting curve analysis after T allele enrichment (MelcaTle. MelcaTle comprises three steps: 1 two cycles of JAK2V617F allele enrichment by PCR amplification followed by BsaXI digestion, 2 selective amplification of the JAK2V617F allele in the presence of a bridged nucleic acid (BNA probe, and 3 a melting curve assay using a BODIPY-FL-labeled oligonucleotide. Using this assay, we successfully detected nearly a single copy of the JAK2V617F allele, without false-positive signals, using 10 ng of genomic DNA standard. Furthermore, MelcaTle showed no positive signals in 90 assays screening healthy individuals for JAK2V617F. When applying MelcaTle to 27 patients who were initially classified as JAK2V617F-positive on the basis of allele-specific PCR analysis and were thus suspected as having MPNs, we found that two of the patients were actually JAK2V617F-negative. A more careful clinical data analysis revealed that these two patients had developed transient erythrocytosis of unknown etiology but not polycythemia vera, a subtype of MPNs. These findings indicate that the newly developed MelcaTle assay should markedly improve the diagnosis of JAK2V617F-positive MPNs.

  15. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3.

    Directory of Open Access Journals (Sweden)

    Célia Dechavanne

    Full Text Available Mass spectrometry (MS analysis for detection of immunoglobulins (IG of the human IgG3 subclass is described that relies on polymorphic amino acids of the heavy gamma3 chains. IgG3 is the most polymorphic human IgG subclass with thirteen G3m allotypes located on the constant CH2 and CH3 domains of the gamma3 chain, the combination of which leads to six major G3m alleles. Amino acid changes resulting of extensive sequencing previously led to the definition of 19 IGHG3 alleles that have been correlated to the G3m alleles. As a proof of concept, MS proteotypic peptides were defined which encompass discriminatory amino acids for the identification of the G3m and IGHG3 alleles. Plasma samples originating from ten individuals either homozygous or heterozygous for different G3m alleles, and including one mother and her baby (drawn sequentially from birth to 9 months of age, were analyzed. Total IgG3 were purified using affinity chromatography and then digested by a combination of AspN and trypsin proteases, and peptides of interest were detected by mass spectrometry. The sensitivity of the method was assessed by mixing variable amounts of two plasma samples bearing distinct G3m allotypes. A label-free approach using the high-performance liquid chromatography (HPLC retention time of peptides and their MS mass analyzer peak intensity gave semi-quantitative information. Quantification was realized by selected reaction monitoring (SRM using synthetic peptides as internal standards. The possibility offered by this new methodology to detect and quantify neo-synthesized IgG in newborns will improve knowledge on the first acquisition of antibodies in infants and constitutes a promising diagnostic tool for vertically-transmitted diseases.

  16. Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Marcelo Razera Baruffi

    2003-01-01

    Full Text Available We applied a combination of comparative genomic hybridization (CGH and fluorescence in situ hybridization (FISH, to characterize the genetic aberrations in three osteosarcomas (OS and one Ewing's sarcoma. CGH identified recurrent chromosomal losses at 10p14-pter and gains at 8q22.3-24.1 in OS. Interphase FISH allowed to confirm 8q gain in two cases. A high amplification level of 11q12-qter was detected in one OS. The Ewing's sarcoma showed gain at 1p32-36.1 as the sole chromosome alteration. These studies demonstrate the value of molecular cytogenetic methods in the characterization of recurrent genomic alterations in bone tumor tissue.

  17. Applicability of major histocompatibility complex DRB1 alleles as markers to detect vertebrate hybridization: a case study from Iberian ibex × domestic goat in southern Spain

    Directory of Open Access Journals (Sweden)

    Alasaad Samer

    2012-09-01

    Full Text Available Abstract Background Hybridization between closely related wild and domestic species is of great concern because it can alter the evolutionary integrity of the affected populations. The high allelic variability of Major Histocompatibility Complex (MHC loci usually excludes them from being used in studies to detect hybridization events. However, if a the parental species don’t share alleles, and b one of the parental species possesses an exceptionally low number of alleles (to facilitate analysis, then even MHC loci have the potential to detect hybrids. Results By genotyping the exon2 of the MHC class II DRB1 locus, we were able to detect hybridization between domestic goats (Capra hircus and free-ranging Iberian ibex (Capra pyrenaica hispanica by molecular means. Conclusions This is the first documentation of a Capra pyrenaica × Capra hircus hybridization, which presented us the opportunity to test the applicability of MHC loci as new, simple, cost-effective, and time-saving approach to detect hybridization between wild species and their domesticated relatives, thus adding value to MHC genes role in animal conservation and management.

  18. Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.

    Science.gov (United States)

    Zhang, Qi; Zeng, Xin; Younkin, Sam; Kawli, Trupti; Snyder, Michael P; Keleş, Sündüz

    2016-02-24

    Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.

  19. Options on capacity imbalance

    International Nuclear Information System (INIS)

    Roggen, M.

    2002-01-01

    Since the start of this year, the Dutch energy company Nuon has been using a computer system to formulate real-time responses to national capacity imbalances in the electricity supply market. The work earns Nuon a fixed fee from TenneT (Dutch Transmission System Operator) and ensures a more stable imbalance price for everyone. The key to success has been the decision to start the project from scratch [nl

  20. Infrequent detection of germline allele-specific expression of TGFBR1 in lymphoblasts and tissues of colon cancer patients.

    LENUS (Irish Health Repository)

    Guda, Kishore

    2009-06-15

    Recently, germline allele-specific expression (ASE) of the gene encoding for transforming growth factor-beta type I receptor (TGFBR1) has been proposed to be a major risk factor for cancer predisposition in the colon. Germline ASE results in a lowered expression of one of the TGFBR1 alleles (>1.5-fold), and was shown to occur in approximately 20% of informative familial and sporadic colorectal cancer (CRC) cases. In the present study, using the highly quantitative pyrosequencing technique, we estimated the frequency of ASE in TGFBR1 in a cohort of affected individuals from familial clusters of advanced colon neoplasias (cancers and adenomas with high-grade dysplasia), and also from a cohort of individuals with sporadic CRCs. Cases were considered positive for the presence of ASE if demonstrating an allelic expression ratio <0.67 or >1.5. Using RNA derived from lymphoblastoid cell lines, we find that of 46 informative Caucasian advanced colon neoplasia cases with a family history, only 2 individuals display a modest ASE, with allelic ratios of 1.65 and 1.73, respectively. Given that ASE of TGFBR1, if present, would likely be more pronounced in the colon compared with other tissues, we additionally determined the allele ratios of TGFBR1 in the RNA derived from normal-appearing colonic mucosa of sporadic CRC cases. We, however, found no evidence of ASE in any of 44 informative sporadic cases analyzed. Taken together, we find that germline ASE of TGFBR1, as assayed in lymphoblastoid and colon epithelial cells of colon cancer patients, is a relatively rare event.

  1. Three Phase Power Imbalance Decomposition into Systematic Imbalance and Random Imbalance

    DEFF Research Database (Denmark)

    Kong, Wangwei; Ma, Kang; Wu, Qiuwei

    2017-01-01

    Uneven load allocations and random load behaviors are two major causes for three-phase power imbalance. The former mainly cause systematic imbalance, which can be addressed by low-cost phase swapping; the latter contribute to random imbalance, which requires relatively costly demand...... minimum phase, or both. Then, this paper proposes a new method to decompose three-phase power series into a systematic imbalance component and a random imbalance component as the closed-form solutions of quadratic optimization models that minimize random imbalance. A degree of power imbalance...... is calculated based on the systematic imbalance component to guide phase swapping. Case studies demonstrate that 72.8% of 782 low voltage substations have systematic imbalance components. The degree of power imbalance results reveal the maximum need for phase swapping and the random imbalance components reveal...

  2. Toward fully automated genotyping: Allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Burks, M.B. [Carnegie Mellon Univ., Pittsburgh, PA (United States); Hoop, R.C.; Hoffman, E.P. [Univ. of Pittsburgh School of Medicine, PA (United States)

    1994-10-01

    Human genetic maps have made quantum leaps in the past few years, because of the characterization of >2,000 CA dinucleotide repeat loci: these PCR-based markers offer extraordinarily high PIC, and within the next year their density is expected to reach intervals of a few centimorgans per marker. These new genetic maps open new avenues for disease gene research, including large-scale genotyping for both simple and complex disease loci. However, the allele patterns of many dinucleotide repeat loci can be complex and difficult to interpret, with genotyping errors a recognized problem. Furthermore, the possibility of genotyping individuals at hundreds or thousands of polymorphic loci requires improvements in data handling and analysis. The automation of genotyping and analysis of computer-derived haplotypes would remove many of the barriers preventing optimal use of dense and informative dinucleotide genetic maps. Toward this end, we have automated the allele identification, genotyping, phase determinations, and inheritance consistency checks generated by four CA repeats within the 2.5-Mbp, 10-cM X-linked dystrophin gene, using fluorescein-labeled multiplexed PCR products analyzed on automated sequencers. The described algorithms can deconvolute and resolve closely spaced alleles, despite interfering stutter noise; set phase in females; propagate the phase through the family; and identify recombination events. We show the implementation of these algorithms for the completely automated interpretation of allele data and risk assessment for five Duchenne/Becker muscular dystrophy families. The described approach can be scaled up to perform genome-based analyses with hundreds or thousands of CA-repeat loci, using multiple fluorophors on automated sequencers. 16 refs., 5 figs., 1 tab.

  3. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    Directory of Open Access Journals (Sweden)

    Carol A Soderlund

    Full Text Available Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor, where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense, and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available

  4. On gradiometer imbalance

    NARCIS (Netherlands)

    Uzunbajakau, S.A.; Rijpma, A.P.; Brake, ter H.J.M.; Peters, M.J.

    2006-01-01

    We present methods to compute the imbalance in a gradiometer of arbitrary shape due to imperfections in its geometry, eddy currents induced in the radio-frequency interference shield, and screening currents induced in the modules of the superconducting quantum interference devices (SQUIDs). As an

  5. Where Is the Imbalance?

    Science.gov (United States)

    Chan, John H. F.

    2009-01-01

    For many researchers, the concept of a power imbalance is central to the understanding of bullying, and its presence in the bully-victim relationship is a prerequisite condition that needs to be fulfilled before bullying is deemed to have taken place. Despite the concept's central importance in many definitions of bullying, the nature of the power…

  6. Evaluation of efficiency of nested multiplex allele-specific PCR assay for detection of multidrug resistant tuberculosis directly from sputum samples.

    Science.gov (United States)

    Mistri, S K; Sultana, M; Kamal, S M M; Alam, M M; Irin, F; Nessa, J; Ahsan, C R; Yasmin, M

    2016-05-01

    For an effective control of tuberculosis, rapid detection of multidrug resistant tuberculosis (MDR-TB) is necessary. Therefore, we developed a modified nested multiplex allele-specific polymerase chain reaction (MAS-PCR) method that enables rapid MDR-TB detection directly from sputum samples. The efficacy of this method was evaluated using 79 sputum samples collected from suspected tuberculosis patients. The performance of nested MAS-PCR method was compared with other MDR-TB detection methods like drug susceptibility testing (DST) and DNA sequencing. As rifampicin (RIF) resistance conforms to MDR-TB in greater than 90% cases, only the presence of RIF-associated mutations in rpoB gene was determined by DNA sequencing and nested MAS-PCR to detect MDR-TB. The concordance between nested MAS-PCR and DNA sequencing results was found to be 96·3%. When compared with DST, the sensitivity and specificity of nested MAS-PCR for RIF-resistance detection were determined to be 92·9 and 100% respectively. For developing- and high-TB burden countries, molecular-based tests have been recommended by the World Health Organization for rapid detection of MDR-TB. The results of this study indicate that, nested MAS-PCR assay might be a practical and relatively cost effective molecular method for rapid detection of MDR-TB from suspected sputum samples in developing countries with resource poor settings. © 2016 The Society for Applied Microbiology.

  7. Development of a TaqMan Allelic Discrimination Assay for detection of Single Nucleotides Polymorphisms associated with anti-malarial drug resistance

    Directory of Open Access Journals (Sweden)

    Kamau Edwin

    2012-01-01

    Full Text Available Abstract Background Anti-malarial drug resistance poses a threat to current global efforts towards control and elimination of malaria. Several methods are used in monitoring anti-malarial drug resistance. Molecular markers such as single nucleotide polymorphism (SNP for example are increasingly being used to identify genetic mutations related to anti-malarial drug resistance. Several methods are currently being used in analysis of SNP associated with anti-malarial drug resistance and although each one of these methods has unique strengths and shortcoming, there is still need to improve and/or develop new methods that will close the gap found in the current methods. Methods TaqMan Allelic Discrimination assays for detection of SNPs associated with anti-malarial drug resistance were designed for analysis on Applied Biosystems PCR platform. These assays were designed by submitting SNP sequences associated with anti-malarial drug resistance to Applied Biosystems website. Eleven SNPs associated with resistance to anti-malarial drugs were selected and tested. The performance of each SNP assay was tested by creating plasmid DNAs carrying codons of interests and analysing them for analysis. To test the sensitivity and specificity of each SNP assay, 12 clinical samples were sequenced at codons of interest and used in the analysis. Plasmid DNAs were used to establish the Limit of Detection (LoD for each assay. Results Data from genetic profiles of the Plasmodium falciparum laboratory strains and sequence data from 12 clinical samples was used as the reference method with which the performance of the SNP assays were compared to. The sensitivity and specificity of each SNP assay was establish at 100%. LoD for each assay was established at 2 GE, equivalent to less than 1 parasite/μL. SNP assays performed well in detecting mixed infection and analysis of clinical samples. Conclusion TaqMan Allelic Discrimination assay provides a good alternative tool in

  8. Operating a redox flow battery with a negative electrolyte imbalance

    Science.gov (United States)

    Pham, Quoc; Chang, On; Durairaj, Sumitha

    2015-03-31

    Loss of flow battery electrode catalyst layers during self-discharge or charge reversal may be prevented by establishing and maintaining a negative electrolyte imbalance during at least parts of a flow battery's operation. Negative imbalance may be established and/or maintained actively, passively or both. Actively establishing a negative imbalance may involve detecting an imbalance that is less negative than a desired threshold, and processing one or both electrolytes until the imbalance reaches a desired negative level. Negative imbalance may be effectively established and maintained passively within a cell by constructing a cell with a negative electrode chamber that is larger than the cell's positive electrode chamber, thereby providing a larger quantity of negative electrolyte for reaction with positive electrolyte.

  9. Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation.

    Science.gov (United States)

    Buchman, Vladimir L; Cooper-Knock, Johnathan; Connor-Robson, Natalie; Higginbottom, Adrian; Kirby, Janine; Razinskaya, Olga D; Ninkina, Natalia; Shaw, Pamela J

    2013-04-08

    Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which account for approximately 10% of all amyotrophic lateral sclerosis (ALS) cases, is urgently required to answer fundamental questions about mechanisms of pathogenesis in this important genetic variant. Currently employed PCR protocols are limited to discrimination between the presence and absence of a modified allele with more than 30 copies of the repeat, while Southern hybridisation-based methods are confounded by the somatic heterogeneity commonly present in blood samples, which might cause false-negative or ambiguous results. We describe an optimised Southern hybridisation-based protocol that allows confident detection of the presence of a C9ORF72 repeat expansion alongside independent assessment of its heterogeneity and the number of repeat units. The protocol can be used with either a radiolabeled or non-radiolabeled probe. Using this method we have successfully sized the C9ORF72 repeat expansion in lymphoblastoid cells, peripheral blood, and post-mortem central nervous system (CNS) tissue from ALS patients. It was also possible to confidently demonstrate the presence of repeat expansion, although of different magnitude, in both C9ORF72 alleles of the genome of one patient. The suggested protocol has sufficient advantages to warrant adoption as a standard for Southern blot hybridisation analysis of GGGGCC repeat expansions in the C9ORF72 locus.

  10. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards.

    Science.gov (United States)

    Masny, Aleksander; Jagiełło, Agata; Płucienniczak, Grażyna; Golab, Elzbieta

    2012-09-01

    Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Parental genome dosage imbalance deregulates imprinting in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Pauline E Jullien

    2010-03-01

    Full Text Available In mammals and in plants, parental genome dosage imbalance deregulates embryo growth and might be involved in reproductive isolation between emerging new species. Increased dosage of maternal genomes represses growth while an increased dosage of paternal genomes has the opposite effect. These observations led to the discovery of imprinted genes, which are expressed by a single parental allele. It was further proposed in the frame of the parental conflict theory that parental genome imbalances are directly mirrored by antagonistic regulations of imprinted genes encoding maternal growth inhibitors and paternal growth enhancers. However these hypotheses were never tested directly. Here, we investigated the effect of parental genome imbalance on the expression of Arabidopsis imprinted genes FERTILIZATION INDEPENDENT SEED2 (FIS2 and FLOWERING WAGENINGEN (FWA controlled by DNA methylation, and MEDEA (MEA and PHERES1 (PHE1 controlled by histone methylation. Genome dosage imbalance deregulated the expression of FIS2 and PHE1 in an antagonistic manner. In addition increased dosage of inactive alleles caused a loss of imprinting of FIS2 and MEA. Although FIS2 controls histone methylation, which represses MEA and PHE1 expression, the changes of PHE1 and MEA expression could not be fully accounted for by the corresponding fluctuations of FIS2 expression. Our results show that parental genome dosage imbalance deregulates imprinting using mechanisms, which are independent from known regulators of imprinting. The complexity of the network of regulations between expressed and silenced alleles of imprinted genes activated in response to parental dosage imbalance does not support simple models derived from the parental conflict hypothesis.

  12. QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.

    Science.gov (United States)

    Kalita, Cynthia A; Moyerbrailean, Gregory A; Brown, Christopher; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2018-03-01

    The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets. We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays. http://github.com/piquelab/QuASAR/tree/master/mpra. fluca@wayne.edu or rpique@wayne.edu. Supplementary data are available online at Bioinformatics. © The Author (2017). Published by

  13. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

    Directory of Open Access Journals (Sweden)

    Assawamakin Anunchai

    2007-08-01

    Full Text Available Abstract Background Allele-specific (AS Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number

  14. Detection of EGFR mutations in plasma and biopsies from non-small cell lung cancer patients by allele-specific PCR assays

    DEFF Research Database (Denmark)

    Weber, Britta; Meldgaard, Peter; Hager, Henrik

    2014-01-01

    samples with allele-specific PCR assays. METHODS: Pairs of the diagnostic biopsy and plasma obtained just prior to start of erlotinib treatment were collected from 199 patients with adenocarcinoma of non-small-cell lung cancer. DNA from both sample types was isolated and examined for the presence...... of mutations in exons 18-21 of the EGFR gene, employing the cobas(®) EGFR Tissue Test and cobas(®) EGFR Blood Test (in development, Roche Molecular Systems, Inc., CA, USA). RESULTS: Test results were obtained in all 199 (100%) plasma samples and 196/199 (98%) of the biopsies. EGFR-activating mutations were...... identified in 24/199 (12%) plasma samples and 28/196 (14%) biopsy samples, and 17/196 (9%) matched pairs contained the same mutation. Six EGFR mutations were present only in plasma samples but not in the biopsy samples. The overall concordance of the EGFR gene mutations detected in plasma and biopsy tissue...

  15. Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P

    1989-01-01

    DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for the HLA-DPB locus. Typing for the individual DPB alleles was exclusively dependent on the hybridizations of the probe...

  16. Comparison of allelic discrimination by dHPLC, HRM, and TaqMan in the detection of BRAF mutation V600E.

    Science.gov (United States)

    Carbonell, Pablo; Turpin, María C; Torres-Moreno, Daniel; Molina-Martínez, Irene; García-Solano, José; Perez-Guillermo, Miguel; Conesa-Zamora, Pablo

    2011-09-01

    The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study was to compare the performance characteristics in V600E detection of denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM) with TaqMan allelic discrimination as well as direct-sequencing methods in a series of 195 colorectal paraffin-embedded specimens up to the age of 15 years. The effectiveness for obtaining results on mutation status was best using TaqMan (96.9%), followed by dHPLC (93.3%), HRM (88.7%), and sequencing (88.2%). In general, TaqMan was best for analyzing older tissues, whereas sequencing was the least efficient. Heterozygotic V600E was detected in 11.6%, 9.9%, 11.6%, and 9.9% of tissues using TaqMan, dHPLC, HRM, and sequencing, respectively. Result concordances between dHPLC and TaqMan or sequencing were excellent (κ = 0.9411 and κ = 0.8988, respectively); for HRM, the concordances were good (κ = 0.7973 and κ = 0.7488, respectively). By using DNA dilutions from tumor tissue, a minimum of 10% of V600E harboring cancer content was required for the analysis by dHPLC and HRM. dHPLC could detect four non-V600E mutations, whereas HRM detected one. Our results indicate that dHPLC and HRM are techniques that can be reliably used for the detection of the BRAFV600E mutation in archival paraffin-embedded tissues. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  17. Competition for biomass. Regional imbalances

    International Nuclear Information System (INIS)

    Wiklund, S.E.; Bohlin, B.; Remes, M.; Aakesson, H.; Warnqvist, B.; Norrstroem, H.; Jonsson, Tomas

    1997-04-01

    The main aim of this study has been to investigate if a substantial increase in biofuel utilization may lead to pronounced regional differences in supply and demand, and what effects such imbalances could lead to. In the study the country has been split up into ten regions, from north to south, and it is confirmed that there would be an imbalance effect. confirmed that there would be an imbalance effect

  18. Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of genetic marker alleles associated with a trait indicative of fertility of the bovine subject and/or off-spring

    DEFF Research Database (Denmark)

    2009-01-01

    NOVELTY - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles that are associated with a trait indicative of fertility of the bovine subject and/or off-spring. USE - The methods are useful...... for determining fertility in a bovine subject; and selecting bovine subjects for breeding purposes (all claimed). DETAILED DESCRIPTION - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles...... that are associated with a trait indicative of fertility of the bovine subject and/or off-spring, where the two or more genetic marker alleles are single nucleotide polymorphisms selected from Hapmap60827-rs29019866, ARS-BFGL-NGS-40979, Hapmap47854-BTA-119090, ARS-BFGL-NGS-114679, Hapmap43841-BTA-34601, Hapmap43407...

  19. Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns.

    Science.gov (United States)

    Hedell, Ronny; Dufva, Charlotte; Ansell, Ricky; Mostad, Petter; Hedman, Johannes

    2015-01-01

    Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84 pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84 pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17 pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those

  20. Minority drug-resistant HIV-1 variants in treatment naïve East-African and Caucasian patients detected by allele-specific real-time PCR.

    Directory of Open Access Journals (Sweden)

    Halime Ekici

    Full Text Available To assess the presence of two major non-nucleoside reverse transcriptase inhibitors (NNRTI drug resistance mutations (DRMs, Y181C and K103N, in minor viral quasispecies of treatment naïve HIV-1 infected East-African and Swedish patients by allele-specific polymerase chain reaction (AS-PCR.Treatment naïve adults (n=191 with three epidemiological backgrounds were included: 92 Ethiopians living in Ethiopia; 55 East-Africans who had migrated to Sweden; and 44 Caucasians living in Sweden. The pol gene was analysed by standard population sequencing and by AS-PCR for the detection of Y181C and K103N.The Y181C was detected in the minority quasispecies of six Ethiopians (6.5%, in two Caucasians (4.5%, and in one East-African (1.8%. The K103N was detected in one East- African (1.8%, by both methods. The proportion of mutants ranged from 0.25% to 17.5%. Additional DRMs were found in all three treatment naïve patient groups by population sequencing.Major NNRTI mutations can be found by AS-PCR in minor quasispecies of treatment naïve HIV-1 infected Ethiopians living in Ethiopia, in East-African and Caucasian patients living in Sweden in whom population sequencing reveal wild-type virus only. Surveys with standard sequencing are likely to underestimate transmitted drug resistance and the presence of resistant minor quasispecies in treatment naïve patients should be topic for future large scale studies.

  1. Fine-mapping the HOXB region detects common variants tagging a rare coding allele: evidence for synthetic association in prostate cancer.

    Directory of Open Access Journals (Sweden)

    Edward J Saunders

    2014-02-01

    Full Text Available The HOXB13 gene has been implicated in prostate cancer (PrCa susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs using a custom Illumina iSelect array (iCOGS followed by imputation of 3195 SNPs in 20,440 PrCa cases and 21,469 controls in The PRACTICAL consortium. We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk, described by rs117576373 (OR 1.30, P = 2.62×10(-14. Additional genotyping, conditional regression and haplotype analyses indicated that the newly identified common variants tag a rare, partially correlated coding variant in the HOXB13 gene (G84E, rs138213197, which has been identified recently as a moderate penetrance PrCa susceptibility allele. The potential for GWAS associations detected through common SNPs to be driven by rare causal variants with higher relative risks has long been proposed; however, to our knowledge this is the first experimental evidence for this phenomenon of synthetic association contributing to cancer susceptibility.

  2. Self-(in)compatibility of the almonds P. dulcis and P. webbii: detection and cloning of 'wild-type Sf ' and new self-compatibility alleles encoding inactive S-RNases.

    Science.gov (United States)

    Bosković, Radovan I; Tobutt, Kenneth R; Ortega, Encarnación; Sutherland, Bruce G; Godini, Angelo

    2007-12-01

    Prunus dulcis, the almond, is a predominantly self-incompatible (SI) species with a gametophytic self-incompatibility system mediated by S-RNases. The economically important allele Sf, which results in self-compatibility in P. dulcis, is said to have arisen by introgression from Prunus webbii in the Italian region of Apulia. We investigated the range of self-(in)compatibility alleles in Apulian material of the two species. About 23 cultivars of P. dulcis (14 self-compatible (SC) and nine SI) and 33 accessions of P. webbii (16 SC, two SI and 15 initially of unknown status), all from Apulia, were analysed using PCR of genomic DNA to amplify S-RNase alleles and, in most cases, IEF and staining of stylar protein extracts to detect S-RNase activity. Some amplification products were cloned and sequenced. The allele Sf was present in nearly all the SC cultivars of P. dulcis but, surprisingly, was absent from nearly all SC accessions of P. webbii. And of particular interest was the presence in many SI cultivars of P. dulcis of a new active allele, labelled S30, the sequence of which showed it to be the wild-type of Sf so that Sf can be regarded as a stylar part mutant S30 degrees . These findings indicate Sf may have arisen within P. dulcis, by mutation. One SC cultivar of P. dulcis, 'Patalina', had a new self-compatibility allele lacking RNase activity, Sn5, which could be useful in breeding programmes. In the accessions of P. webbii, some of which were known to be SC, three new alleles were found which lacked RNase activity but had normal DNA sequences.

  3. Establishment of real time allele specific locked nucleic acid quantitative PCR for detection of HBV YIDD (ATT mutation and evaluation of its application.

    Directory of Open Access Journals (Sweden)

    Yongbin Zeng

    Full Text Available BACKGROUND: Long-term use of nucleos(tide analogues can increase risk of HBV drug-resistance mutations. The rtM204I (ATT coding for isoleucine is one of the most important resistance mutation sites. Establishing a simple, rapid, reliable and highly sensitive assay to detect the resistant mutants as early as possible is of great clinical significance. METHODS: Recombinant plasmids for HBV YMDD (tyrosine-methionine-aspartate-aspartate and YIDD (tyrosine-isoleucine-aspartate-aspartate were constructed by TA cloning. Real time allele specific locked nucleic acid quantitative PCR (RT-AS-LNA-qPCR with SYBR Green I was established by LNA-modified primers and evaluated with standard recombinant plasmids, clinical templates (the clinical wild type and mutant HBV DNA mixture and 102 serum samples from nucleos(tide analogues-experienced patients. The serum samples from a chronic hepatitis B (CHB patient firstly received LMV mono therapy and then switched to LMV + ADV combined therapy were also dynamically analyzed for 10 times. RESULTS: The linear range of the assay was between 1×10(9 copies/μl and 1 × 10(2 copies/μl. The low detection limit was 1 × 10(1 copies/μl. Sensitivity of the assay were 10(-6, 10(-4 and 10(-2 in the wild-type background of 1 × 10(9 copies/μl, 1 × 10(7 copies/μl and 1 × 10(5 copies/μl, respectively. The sensitivity of the assay in detection of clinical samples was 0.03%. The complete coincidence rate between RT-AS-LNA-qPCR and direct sequencing was 91.2% (93/102, partial coincidence rate was 8.8% (9/102, and no complete discordance was observed. The two assays showed a high concordance (Kappa = 0.676, P = 0.000. Minor variants can be detected 18 weeks earlier than the rebound of HBV DNA load and alanine aminotransferase level. CONCLUSIONS: A rapid, cost-effective, high sensitive, specific and reliable method of RT-AS-LNA-qPCR with SYBR Green I for early and absolute quantification of HBV YIDD (ATT coding for isoleucine

  4. Abnormal segregation of alleles in CEPH pedigree DNAs arising from allele loss in lymphoblastoid DNA.

    Science.gov (United States)

    Royle, N J; Armour, J A; Crosier, M; Jeffreys, A J

    1993-01-01

    Somatic events that result in the reduction to hemi- or homozygosity at all loci affected by the event have been identified in lymphoblastoid DNA from mothers of two CEPH families. Using suitably informative probes, the allele deficiencies were detected by the abnormal transmission of alleles from grandparents to grandchildren, with the apparent absence of the alleles from the parent. Undetected somatic deficiencies in family DNAs could result in misscoring of recombination events and consequently introduce errors into linkage analysis.

  5. Automatic voltage imbalance detector

    Science.gov (United States)

    Bobbett, Ronald E.; McCormick, J. Byron; Kerwin, William J.

    1984-01-01

    A device for indicating and preventing damage to voltage cells such as galvanic cells and fuel cells connected in series by detecting sequential voltages and comparing these voltages to adjacent voltage cells. The device is implemented by using operational amplifiers and switching circuitry is provided by transistors. The device can be utilized in battery powered electric vehicles to prevent galvanic cell damage and also in series connected fuel cells to prevent fuel cell damage.

  6. A new allelic discrimination assay using locked nucleic acid-modified nucleotides (LNA) probes for detection of JAK2 V617F mutation

    Czech Academy of Sciences Publication Activity Database

    Marková, J.; Průková, Dana; Volková, Z.; Schwarz, J.

    2007-01-01

    Roč. 48, č. 3 (2007), s. 638-641 ISSN 1042-8194 Institutional research plan: CEZ:AV0Z50520514 Keywords : Ph1-negative myeloproliferative disorders * JAK2V617F mutation * allelic discrimination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.512, year: 2007

  7. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

    Directory of Open Access Journals (Sweden)

    Neuvial Pierre

    2010-05-01

    Full Text Available Abstract Background High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses. Results We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances. Conclusions TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific CRMA v2 for Affymetrix or BeadStudio's (proprietary XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package aroma.cn, which is part of the Aroma Project (http://www.aroma-project.org/.

  8. Drivers of imbalance cost of wind power

    DEFF Research Database (Denmark)

    Obersteiner, C.; Siewierski, T.; Andersen, Anders

    2010-01-01

    In Europe an increasing share of wind power is sold on the power market. Therefore more and more wind power generators become balancing responsible and face imbalance cost that reduce revenues from selling wind power. A comparison of literature illustrates that the imbalance cost of wind power...... varies in a wide range. To explain differences we indentify parameters influencing imbalance cost and compare them for case studies in Austria, Denmark and Poland. Besides the wind power forecast error also the correlation between imbalance and imbalance price influences imbalance cost significantly...... of imperfect forecast is better suited to reflect real cost incurred due to inaccurate wind power forecasts....

  9. HPV has left the building – the absence of detectable HPV DNA and the presence of r allele/s for the P72R polymorphism in the TP53 gene may call for more aggressive therapeutic approach in HPV-associated tumours

    International Nuclear Information System (INIS)

    Petkova, Rumena; Chelenkova, Pavlina; Yemendzhiev, Husein; Tsekov, Iliya; Kalvatchev, Zlatko; Chakarov, Stoyan

    2013-01-01

    HPV infection is a major pathogenetic factor in cervical carcinoma as well as in many of the squamous cancers of head and neck and other epithelial cancers. Persistence of HPV DNA detectable by routine methods is considered to be a risk factor for advanced CIN and, in patients treated by surgery or non-surgical treatment modalities (radiotherapy, chemotherapy), HPV persistence is believed to be associated with increased risk for local recurrence. In terms of survival, however, it has been repeatedly proven that patients with cervical cancer and other HPV-associated cancers with detectable HPV DNA tend to have better outcomes than patients with HPV-negative tumours. The P72R polymorphism in the human TP53 gene has been contemplated as an independent phenotype modifier in cancers, especially the R allele which has been shown to confer higher pro-apoptotic properties to the resultant p53 protein. It has been demonstrated, however, that RR homozygotes were much more common in study groups with HPV-associated tumours than the other two genotypes and that the P allele in P/R heterozygotes was preferentially lost while the R allele was preferentially retained and mutated. It is possible that HPV-dependent carcinogenesis strictly relies on the presence of HPV and the expression of the E6 and E7 onco proteins only in the initial phases of transformation of infected cells (e.g. CIN). It may be associated with activation of latent HPV that would create a background of decreased control over the integrity of the genome of the host cell. The process can develop further by mechanisms independent of the presence of HPV and if the virus clears at some later point, that would not halt the already ongoing neoplastic transformation. Absence of HPV DNA in cervical tumours, whether before or after treatment, is not a reason to decrease vigilant monitoring and rule out the need for further treatment, as it may be quite possible that the TP53 gene of the infected cells has already been

  10. Dijet imbalance in hadronic collisions

    International Nuclear Information System (INIS)

    Boer, Danieel; Mulders, Piet J.; Pisano, Cristian

    2009-01-01

    The imbalance of dijets produced in hadronic collisions has been used to extract the average transverse momentum of partons inside the hadrons. In this paper we discuss new contributions to the dijet imbalance that could complicate or even hamper this extraction. They are due to polarization of initial state partons inside unpolarized hadrons that can arise in the presence of nonzero parton transverse momentum. Transversely polarized quarks and linearly polarized gluons produce specific azimuthal dependences of the two jets that in principle are not suppressed. Their effects cannot be isolated just by looking at the angular deviation from the back-to-back situation; rather they enter jet broadening observables. In this way they directly affect the extraction of the average transverse momentum of unpolarized partons that is thought to be extracted. We discuss appropriately weighted cross sections to isolate the additional contributions.

  11. TARGET Imbalances at Record Levels

    DEFF Research Database (Denmark)

    Hallett, Andrew Hughes

    quantitative easing, but are not driven by it. The main threats are the divergence that interrupts further economic integration; and the increasing liabilities taken on by the ECB since 2015. That said, self-correcting mechanisms are weak which makes symmetric adjustments by both creditor and debtor countries...... essential (because of the adding up constraint); and the difficulty that the imbalances cannot always be eliminated simply by balancing current accounts around the system....

  12. Nutrient imbalance in Norway spruce

    International Nuclear Information System (INIS)

    Thelin, Gunnar

    2000-11-01

    The studies presented in my thesis indicate that growing Norway spruce in monoculture does not constitute sustainable forest management in a high N and S deposition environment, such as in southern Sweden. The combination of N-induced high growth rates and leaching due to soil acidification causes soil reserves of nutrients to decrease. This will increase the risk of nutrient imbalance within the trees when nutrient demands are not met. The development of nutrient imbalance in Scania, southern Sweden, was shown as negative trends in needle and soil nutrient status from the mid-80s to the present in Norway spruce and Scots pine stands. This imbalance appears to be connected to high levels of N and S deposition. Clear negative effects on tree vitality were found when using a new branch development method. Today, growth and vitality seems to be limited by K, rather than N, in spruce stands older than 40 years. However, younger stands appear to be able to absorb the deposited N without negative effects on growth and vitality. When investigating effects of nutrient stress on tree vitality, indicators such as branch length and shoot multiplication rate, which include effects accumulated over several years, are suitable. Countermeasures are needed in order to maintain the forest production at a high level. Positive effects on tree nutrient status after vitality fertilization (N-free fertilization) was shown in two micronutrient deficient stands in south-central Sweden. In addition, tree vitality was positively affected after the application of a site-adapted fertilizer to the canopy. Site-adaption of fertilizers will most likely improve the possibilities of a positive response on tree growth and vitality in declining stands. In a survey of Norway spruce in mixtures with beech, birch, or oak compared to monocultures it was shown that spruce nutrient status was higher in mixtures with deciduous species than in monocultures. By using mixed-species stands the need for

  13. Nutrient imbalance in Norway spruce

    Energy Technology Data Exchange (ETDEWEB)

    Thelin, Gunnar

    2000-11-01

    The studies presented in my thesis indicate that growing Norway spruce in monoculture does not constitute sustainable forest management in a high N and S deposition environment, such as in southern Sweden. The combination of N-induced high growth rates and leaching due to soil acidification causes soil reserves of nutrients to decrease. This will increase the risk of nutrient imbalance within the trees when nutrient demands are not met. The development of nutrient imbalance in Scania, southern Sweden, was shown as negative trends in needle and soil nutrient status from the mid-80s to the present in Norway spruce and Scots pine stands. This imbalance appears to be connected to high levels of N and S deposition. Clear negative effects on tree vitality were found when using a new branch development method. Today, growth and vitality seems to be limited by K, rather than N, in spruce stands older than 40 years. However, younger stands appear to be able to absorb the deposited N without negative effects on growth and vitality. When investigating effects of nutrient stress on tree vitality, indicators such as branch length and shoot multiplication rate, which include effects accumulated over several years, are suitable. Countermeasures are needed in order to maintain the forest production at a high level. Positive effects on tree nutrient status after vitality fertilization (N-free fertilization) was shown in two micronutrient deficient stands in south-central Sweden. In addition, tree vitality was positively affected after the application of a site-adapted fertilizer to the canopy. Site-adaption of fertilizers will most likely improve the possibilities of a positive response on tree growth and vitality in declining stands. In a survey of Norway spruce in mixtures with beech, birch, or oak compared to monocultures it was shown that spruce nutrient status was higher in mixtures with deciduous species than in monocultures. By using mixed-species stands the need for

  14. Validation of a Multiplex Allele-Specific Polymerase Chain Reaction Assay for Detection of KRAS Gene Mutations in Formalin-Fixed, Paraffin-Embedded Tissues from Colorectal Cancer Patients.

    Directory of Open Access Journals (Sweden)

    Sirirat Seekhuntod

    Full Text Available Patients with KRAS mutations do not respond to epidermal growth factor receptor (EGFR inhibitors and fail to benefit from adjuvant chemotherapy. Mutation analysis of KRAS is needed before starting treatment with monoclonal anti-EGFR antibodies in patients with metastatic colorectal cancer (mCRC. The objective of this study is to develop a multiplex allele-specific PCR (MAS-PCR assay to detect KRAS mutations.We developed a single-tube MAS-PCR assay for the detection of seven KRAS mutations (G12D, G12A, G12R, G12C, G12S, G12V, and G13D. We performed MAS-PCR assay analysis for KRAS on DNA isolated from 270 formalin-fixed paraffin-embedded (FFPE colorectal cancer tissues. Sequences of all 270 samples were determined by pyrosequencing. Seven known point-mutation DNA samples diluted with wild-type DNA were assayed to determine the limitation of detection and reproducibility of the MAS-PCR assay.Overall, the results of MAS-PCR assay were in good concordance with pyrosequencing, and only seven discordant samples were found. The MAS-PCR assay reproducibly detected 1 to 2% mutant alleles. The most common mutations were G13D in codon 13 (49.17%, G12D (25.83% and G12V (12.50% in codon 12.The MAS-PCR assay provides a rapid, cost-effective, and reliable diagnostic tool for accurate detection of KRAS mutations in routine FFPE colorectal cancer tissues.

  15. Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification.

    Science.gov (United States)

    de Miguel, Marina; Cabezas, José-Antonio; de María, Nuria; Sánchez-Gómez, David; Guevara, María-Ángeles; Vélez, María-Dolores; Sáez-Laguna, Enrique; Díaz, Luis-Manuel; Mancha, Jose-Antonio; Barbero, María-Carmen; Collada, Carmen; Díaz-Sala, Carmen; Aranda, Ismael; Cervera, María-Teresa

    2014-06-12

    Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

  16. Charge imbalance: its relaxation, diffusion and oscillation

    International Nuclear Information System (INIS)

    Pethick, C.J.

    1981-01-01

    In this article, the authors use a model for charge density based on two charge components: the normal quasiparticle component and the superfluid/condensate component. Based on the quasiparticle Boltzmann equation, this two-component model, when used in nonequilibrium contexts, is fruitful in describing a variety of charge-imbalance phenomena in superconductors. The authors discuss various methods of generating charge-imbalances, charge-imbalance relaxation processes (such as phonons, impurity scattering and magnetic impurities) and applications of the two-component model of charge imbalance to spatially inhomogeneous conditions

  17. Neurovascular conflict in oculomotor imbalance

    Directory of Open Access Journals (Sweden)

    Natalya Agafonovna Totolyan

    2015-12-01

    Full Text Available This article, based on the data of Russian and foreign literature, considers modern approaches to the understanding of neurovascular conflict (NVC term, different causes of its development and realization mechanisms; statistical data are presented on its occurrence in different medical specialties; modern approaches to early diagnosis of neurovascular conflicts are covered. Special attention is drawn to oculomotor imbalances being one of neurovascular conflict manifestations. Based on global experience, approaches to most exact and early diagnosis are described, differences in notion terminology of neurovascular contact and neurovascular conflict are shown. As most effective method for NVC diagnosis, the use of neurovisualization method, that is high-resolution magnetic resonance imaging (MRI (high field MRI, is positioned.

  18. Global imbalances: a gathering storm

    Directory of Open Access Journals (Sweden)

    Ugo Sacchetti

    2010-01-01

    Full Text Available This article provides a detailed analysis of the many factors that, over a period of several years, have contributed to the international financial crisis and highlights the global imbalances, both financial and economic, that continue to pose significant threats to the stability of the world economy. The examination goes beyond looking strictly at the case of the USA to include the positions of other relevant countries, and underscores the shifting relations between the USA and the rest of the world. The pertinent geopolitical aspects are covered, followed by a discussion on possible institutional changes in international financial agencies, prospective financial problems of the USA and their implications, monetary developments, external balances, and international economic problems.

  19. Identification of TCT, a novel knockdown resistance allele mutation and analysis of resistance detection methods in the voltage-gated Na⁺ channel of Culex pipiens pallens from Shandong Province, China.

    Science.gov (United States)

    Liu, Hong-Mei; Cheng, Peng; Huang, Xiaodan; Dai, Yu-Hua; Wang, Hai-Fang; Liu, Li-Juan; Zhao, Yu-Qiang; Wang, Huai-Wei; Gong, Mao-Qing

    2013-02-01

    The present study aimed to investigate deltamethrin resistance in Culex pipiens pallens (C. pipiens pallens) mosquitoes and its correlation with knockdown resistance (kdr) mutations. In addition, mosquito‑resistance testing methods were analyzed. Using specific primers in polymerase chain reaction (PCR) and allele-specific (AS)-PCR, kdr gene sequences isolated from wild C. pipiens pallens mosquitoes were sequenced. Linear regression analysis was used to determine the correlation between the mutations and deltamethrin resistance. A kdr allelic gene was cloned and sequenced. Analysis of the DNA sequences revealed the presence of two point mutations at the L1014 residue in the IIS6 transmembrane segment of the voltage‑gated sodium channel (VGSC): L1014F, TTA→TTT, replacing a leucine (L) with a phenylalanine (F); L1014S, TTA→TCA, replacing leucine (L) with serine (S). Two alternative kdr-like mutations, L1014F and L1014S, were identified to be positively correlated with the deltamethrin-resistant phenotype. In addition a novel mutation, TCT, was identified in the VGSC of C. pipiens pallens. PCR and AS-PCR yielded consistent results with respect to mosquito resistance. However, the detection rate of PCR was higher than that of AS-PCR. Further studies are required to determine the specific resistance mechanism. PCR and AS-PCR demonstrated suitability for mosquito resistance field tests, however, the former method may be superior to the latter.

  20. HRAS mutations in Costello syndrome: detection of constitutional activating mutations in codon 12 and 13 and loss of wild-type allele in malignancy.

    Science.gov (United States)

    Estep, Anne L; Tidyman, William E; Teitell, Michael A; Cotter, Philip D; Rauen, Katherine A

    2006-01-01

    Costello syndrome (CS) is a complex developmental disorder involving characteristic craniofacial features, failure to thrive, developmental delay, cardiac and skeletal anomalies, and a predisposition to develop neoplasia. Based on similarities with other cancer syndromes, we previously hypothesized that CS is likely due to activation of signal transduction through the Ras/MAPK pathway [Tartaglia et al., 2003]. In this study, the HRAS coding region was sequenced for mutations in a large, well-characterized cohort of 36 CS patients. Heterogeneous missense point mutations predicting an amino acid substitution were identified in 33/36 (92%) patients. The majority (91%) had a 34G --> A transition in codon 12. Less frequent mutations included 35G --> C (codon 12) and 37G --> T (codon 13). Parental samples did not have an HRAS mutation supporting the hypothesis of de novo heterogeneous mutations. There is phenotypic variability among patients with a 34G --> A transition. The most consistent features included characteristic facies and skin, failure to thrive, developmental delay, musculoskeletal abnormalities, visual impairment, cardiac abnormalities, and generalized hyperpigmentation. The two patients with 35G --> C had cardiac arrhythmias whereas one patient with a 37G --> T transversion had an enlarged aortic root. Of the patients with a clinical diagnosis of CS, neoplasia was the most consistent phenotypic feature for predicating an HRAS mutation. To gain an understanding of the relationship between constitutional HRAS mutations and malignancy, HRAS was sequenced in an advanced biphasic rhabdomyosarcoma/fibrosarcoma from an individual with a 34G --> A mutation. Loss of the wild-type HRAS allele was observed, suggesting tumorigenesis in CS patients is accompanied by additional somatic changes affecting HRAS. Finally, due to phenotypic overlap between CS and cardio-facio-cutaneous (CFC) syndromes, the HRAS coding region was sequenced in a well-characterized CFC cohort

  1. Reflections on the surface energy imbalance problem

    Science.gov (United States)

    Ray Leuning; Eva van Gorsela; William J. Massman; Peter R. Isaac

    2012-01-01

    The 'energy imbalance problem' in micrometeorology arises because at most flux measurement sites the sum of eddy fluxes of sensible and latent heat (H + λE) is less than the available energy (A). Either eddy fluxes are underestimated or A is overestimated. Reasons for the imbalance are: (1) a failure to satisfy the fundamental assumption of one-...

  2. Computing Thermal Imbalance Forces On Satellites

    Science.gov (United States)

    Vigue, Yvonne; Schutz, Robert E.; Sewell, Granville; Abusali, Pothai A. M.

    1994-01-01

    HEAT.PRO computer program calculates imbalance force caused by heating of surfaces of satellite. Calculates thermal imbalance force and determines its effect on orbit of satellite, especially where shadow cast by Earth Causes periodic changes in thermal environment around satellite. Written in FORTRAN 77.

  3. Gender Imbalance and Terrorism in Developing Countries

    Science.gov (United States)

    Younas, Javed

    2016-01-01

    This article investigates whether gender imbalance may be conducive to domestic terrorism in developing countries. A female-dominated society may not provide sufficient administration, law, or order to limit domestic terrorism, especially since societies in developing countries primarily turn to males for administration, policing, and paramilitary forces. Other economic considerations support female imbalance resulting in grievance-generated terrorism. Because male dominance may also be linked to terrorism, empirical tests are ultimately needed to support our prediction. Based on panel data for 128 developing countries for 1975 to 2011, we find that female gender imbalance results in more total and domestic terrorist attacks. This female gender imbalance does not affect transnational terrorism in developing countries or domestic and transnational terrorism in developed countries. Further tests show that gender imbalance affects terrorism only when bureaucratic institutions are weak. Many robustness tests support our results. PMID:28232755

  4. Gender Imbalance and Terrorism in Developing Countries.

    Science.gov (United States)

    Younas, Javed; Sandler, Todd

    2017-03-01

    This article investigates whether gender imbalance may be conducive to domestic terrorism in developing countries. A female-dominated society may not provide sufficient administration, law, or order to limit domestic terrorism, especially since societies in developing countries primarily turn to males for administration, policing, and paramilitary forces. Other economic considerations support female imbalance resulting in grievance-generated terrorism. Because male dominance may also be linked to terrorism, empirical tests are ultimately needed to support our prediction. Based on panel data for 128 developing countries for 1975 to 2011, we find that female gender imbalance results in more total and domestic terrorist attacks. This female gender imbalance does not affect transnational terrorism in developing countries or domestic and transnational terrorism in developed countries. Further tests show that gender imbalance affects terrorism only when bureaucratic institutions are weak. Many robustness tests support our results.

  5. A high-throughput method for genotyping S-RNase alleles in apple

    DEFF Research Database (Denmark)

    Larsen, Bjarne; Ørgaard, Marian; Toldam-Andersen, Torben Bo

    2016-01-01

    We present a new efficient screening tool for detection of S-alleles in apple. The protocol using general and multiplexed primers for PCR reaction and fragment detection on an automatized capillary DNA sequencer exposed a higher number of alleles than any previous studies. Analysis of alleles...

  6. Development of an allele-specific, loop-mediated, isothermal amplification method (AS-LAMP to detect the L1014F kdr-w mutation in Anopheles gambiae s. l.

    Directory of Open Access Journals (Sweden)

    Badolo Athanase

    2012-07-01

    Full Text Available Abstract Background Malaria control relies heavily on treated bed nets and indoor residual spraying with pyrethroid insecticides. Unfortunately, the resistance to pyrethroid insecticides, mainly due to the kdr mutation, is spreading in the main malaria vector Anopheles gambiae s.l., decreasing the insecticides’ efficacy. To manage the insecticide resistance rapidly and flexibly, simple and effective tools for the early detection of resistant mosquitoes are needed. This study aimed to develop an allele-specific, loop-mediated, isothermal amplification (AS-LAMP method to detect the West African-type kdr mutation (kdr-w; L1014F in field-collected mosquitoes. Methods DNA fragments of the wild-type and the mutated kdr gene were used to select the primers and develop the method. The primers were designed with the mutation at the 5’ end of the backward inner primer (BIP. The AS-LAMP method was compared to the AS-PCR method using the genomic DNA of 120 field-collected mosquitoes. Results The AS-LAMP method could discriminate between the wild-type homozygote, the heterozygote, and the kdr-w homozygote within 75 min. The AS-LAMP method has the advantage of being faster and at least as sensitive and specific as the AS-PCR method. Conclusions The AS-LAMP method can be used to detect the kdr mutation for quick decision-making, even in less well-equipped laboratories.

  7. RHD alleles in the Tunisian population

    Science.gov (United States)

    Ouchari, Mouna; Jemni-Yaacoub, Saloua; Chakroun, Taher; Abdelkefi, Saida; Houissa, Batoul; Hmida, Slama

    2013-01-01

    Background: A comprehensive survey of RHD alleles in Tunisia population was lacking. The aim of this study was to use a multiplex RHD typing assay for simultaneous detection of partial D especially with RHD/RHCE deoxyribonucleic acid (DNA) sequence exchange mechanism and some weak D alleles. Materials and Methods: Six RHD specific primer sets were designed to amplify RHD exons 3, 4, 5, 6, 7 and 9. DNA from 2000 blood donors (1777 D+ and 223 D-) from several regions was selected for RHD genotyping using a PCR multiplex assay. Further molecular investigations were done to characterize the RHD variants that were identified by the PCR multiplex assay. Results: In the 1777 D+ samples, only 10 individuals showed the absence of amplification of exons 4 and 5 that were subsequently identified by PCR-SSP as weak D type 4 variants. No hybrid allele was detected. In the 223 D-, RHD amplification of some exons was observed only in 5 samples: 4 individuals expressed only RHD exon 9, and one subject lacking exons 4 and 5. These samples were then screened by PCR-SSPs on d(C) ces and weak D type 4, respectively. Conclusion: The weak D type 4 appears to be the most common D variant allele. We have not found any partial D variant. Findings also indicated that RHD gene deletion is the most prevalent cause of the D- phenotype in the Tunisian population. PMID:24014941

  8. Charge-imbalance fluctuations in superconductors

    International Nuclear Information System (INIS)

    Lemberger, T.R.

    1981-01-01

    We calculate that the mean-square amplitude of the fluctuations of the condensate chemical potential μ/sub s/ due to charge-imbalance fluctuations in the limit Δ/k/sub B/T 2 > = 2(k/sub B/T) 2 /πdeltaΩN(0) in a volume Ω of superconductor. We relate these fluctuations via Nyquist's theorem to measured values of the contribution of self-injected charge imbalance to the dc resistance of SIN tunnel junctions. In this relation the dynamic charge-imbalance relaxation rate is 1/tau/sub E/, the electron-phonon scattering rate

  9. Poor man’s 1000 genome project: Recent human population expansion confounds the detection of disease alleles in 7,098 complete mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Hie Lim eKim

    2013-02-01

    Full Text Available Rapid growth of the human population has caused the accumulation of rare genetic variants that may play a role in the origin of genetic diseases. However, it is challenging to identify those rare variants responsible for specific diseases without genetic data from an extraordinarily large population sample. Here we focused on the accumulated data from the human mitochondrial (mt genome sequences because this data provided 7,098 whole genomes for analysis. In this dataset we identified 6,110 single nucleotide variants (SNVs and their frequency and determined that the best-fit demographic model for the 7,098 genomes included severe population bottlenecks and exponential expansions of the non-African population. Using this model, we simulated the evolution of mt genomes in order to ascertain the behavior of deleterious mutations. We found that such deleterious mutations barely survived during population expansion. We derived the threshold frequency of a deleterious mutation in separate African, Asian, and European populations and used it to identify pathogenic mutations in our dataset. Although threshold frequency was very low, the proportion of variants showing a lower frequency than that threshold was 82%, 83%, and 91% of the total variants for the African, Asian, and European populations, respectively. Within these variants, only 18 known pathogenic mutations were detected in the 7,098 genomes. This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study.

  10. High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

    Directory of Open Access Journals (Sweden)

    Clark Taane G

    2010-04-01

    Full Text Available Abstract Background Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. Results Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%. Conclusions Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes

  11. Genomic imbalances in syndromic congenital heart disease.

    Science.gov (United States)

    Molck, Miriam Coelho; Simioni, Milena; Paiva Vieira, Társis; Sgardioli, Ilária Cristina; Paoli Monteiro, Fabíola; Souza, Josiane; Fett-Conte, Agnes Cristina; Félix, Têmis Maria; Lopes Monlléo, Isabella; Gil-da-Silva-Lopes, Vera Lúcia

    To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). Clinically significant copy number variations (CNVs ≥300kb) were identified in 10% (8/78) of cases. In addition, potentially relevant CNVs were detected in two cases (993kb duplication in 15q21.1 and 706kb duplication in 2p22.3). Genes inside the CNV regions found in this study, such as IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1, and LTPB1 are known to participate in cardiac development and could be candidate genes for CHD. These data showed that patients presenting CHD with extra cardiac anomalies and exclusion of 22q11.2 DS should be investigated by CMA. The present study emphasizes the possible role of CNVs in CHD. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  12. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  13. The charge imbalance in ultracold plasmas

    International Nuclear Information System (INIS)

    Chen, Tianxing; Lu, Ronghua; Guo, Li; Han, Shensheng

    2016-01-01

    Ultracold plasmas are regarded as quasineutral but not strictly neutral. The results of charge imbalance in the expansion of ultracold plasmas are reported. The calculations are performed by a full molecular-dynamics simulation. The details of the electron velocity distributions are calculated without the assumption of electron global thermal equilibrium and Boltzmann distribution. Spontaneous evolutions of the charge imbalance from the initial states with perfect neutrality are given in the simulations. The expansion of outer plasma slows down with the charge imbalance. The influences of plasma size and parameters on the charge imbalance are discussed. The radial profiles of electron temperature are given for the first time, and the self-similar expansion can still occur even if there is no global thermal equilibrium. The electron disorder induced heating is also found in the simulation.

  14. The charge imbalance in ultracold plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Tianxing; Lu, Ronghua, E-mail: lurh@siom.ac.cn; Guo, Li; Han, Shensheng [Key Laboratory for Quantum Optics and Center for Cold Atom Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China)

    2016-09-15

    Ultracold plasmas are regarded as quasineutral but not strictly neutral. The results of charge imbalance in the expansion of ultracold plasmas are reported. The calculations are performed by a full molecular-dynamics simulation. The details of the electron velocity distributions are calculated without the assumption of electron global thermal equilibrium and Boltzmann distribution. Spontaneous evolutions of the charge imbalance from the initial states with perfect neutrality are given in the simulations. The expansion of outer plasma slows down with the charge imbalance. The influences of plasma size and parameters on the charge imbalance are discussed. The radial profiles of electron temperature are given for the first time, and the self-similar expansion can still occur even if there is no global thermal equilibrium. The electron disorder induced heating is also found in the simulation.

  15. Trunk imbalance in adolescent idiopathic scoliosis.

    Science.gov (United States)

    Fortin, Carole; Grunstein, Erin; Labelle, Hubert; Parent, Stefan; Ehrmann Feldman, Debbie

    2016-06-01

    Trunk imbalance (ie, frontal trunk shift measured with a plumb line from C7 to S1) is part of the clinical evaluation in adolescent idiopathic scoliosis (AIS), but its prevalence and relationship with scoliosis, back pain, and health-related factors are not well documented. The principal objectives are to document trunk imbalance prevalence and to explore the association between trunk imbalance and the following factors: Cobb angle, type of scoliosis, back pain, function, mental health, and self-image. The secondary objective is to determine back pain prevalence and the relationship between back pain and each of the following: Cobb angle, function, mental health, and self-image. This is a cross-sectional study in a scoliosis clinic of a tertiary university hospital center. The sample includes youth with AIS (N=55). The outcome measures were trunk imbalance prevalence and magnitude, and back pain prevalence and intensity using the Numeric Pain Rating Scale (NPRS) and the Scoliosis Research Society-22 (SRS-22) pain score, and the function, self-image, and mental health domains of the SRS-22. Trunk imbalance and back pain were assessed in 55 patients with AIS (Cobb angle: 10-60°). Patients completed the SRS-22 questionnaire and the NPRS. Correlations were done between trunk imbalance and scoliosis (Cobb angle, type of scoliosis), back pain (NPRS and SRS-22 pain score), and health-related factors using Pearson correlation coefficients (r) and logistic regression models. Trunk imbalance prevalence is 85% and back pain prevalence is 73%. We found fair to moderate significant positive correlation between trunk imbalance and Cobb angle (r=0.32-0.66, pself-image, or type of scoliosis. Lower self-reported pain significantly correlated with lower Cobb angles (r=0.29, p=.03), higher function (r=0.55, p=.000), higher self-image (r=0.44, p=.001), and better mental health (r=0.48, p=.000). There was a trend for trunk imbalance to be related with lower pain in logistic regression

  16. Probing Lipid Bilayers under Ionic Imbalance.

    Science.gov (United States)

    Lin, Jiaqi; Alexander-Katz, Alfredo

    2016-12-06

    Biological membranes are normally under a resting transmembrane potential (TMP), which originates from the ionic imbalance between extracellular fluids and cytosols, and serves as electric power storage for cells. In cell electroporation, the ionic imbalance builds up a high TMP, resulting in the poration of cell membranes. However, the relationship between ionic imbalance and TMP is not clearly understood, and little is known about the effect of ionic imbalance on the structure and dynamics of biological membranes. In this study, we used coarse-grained molecular dynamics to characterize a dipalmitoylphosphatidylcholine bilayer system under ionic imbalances ranging from 0 to ∼0.06 e charges per lipid (e/Lip). We found that the TMP displayed three distinct regimes: 1) a linear regime between 0 and 0.045 e/Lip, where the TMP increased linearly with ionic imbalance; 2) a yielding regime between ∼0.045 and 0.060 e/Lip, where the TMP displayed a plateau; and 3) a poration regime above ∼0.060 e/Lip, where we observed pore formation within the sampling time (80 ns). We found no structural changes in the linear regime, apart from a nonlinear increase in the area per lipid, whereas in the yielding regime the bilayer exhibited substantial thinning, leading to an excess of water and Na + within the bilayer, as well as significant misalignment of the lipid tails. In the poration regime, lipid molecules diffused slightly faster. We also found that the fluid-to-gel phase transition temperature of the bilayer dropped below the normal value with increased ionic imbalances. Our results show that a high ionic imbalance can substantially alter the essential properties of the bilayer, making the bilayer more fluid like, or conversely, depolarization of a cell could in principle lead to membrane stiffening. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Thermoelectric charge imbalance in superconducting aluminum

    International Nuclear Information System (INIS)

    Heidel, D.F.; Garland, J.C.

    1981-01-01

    The charge imbalance voltage produced in superconducting aluminum by the presence of a temperature gradient and an electric current has been studied over the temperature range 0.5-1.2 K. Measurements were obtained of the magnitude and temperature dependence of the charge imbalance voltage of seven samples, two of which contained magnetic impurities. The data are compared with recent theoretical models of the effect

  18. Dynamic Imbalance Would Counter Offcenter Thrust

    Science.gov (United States)

    Mccanna, Jason

    1994-01-01

    Dynamic imbalance generated by offcenter thrust on rotating body eliminated by shifting some of mass of body to generate opposing dynamic imbalance. Technique proposed originally for spacecraft including massive crew module connected via long, lightweight intermediate structure to massive engine module, such that artificial gravitation in crew module generated by rotating spacecraft around axis parallel to thrust generated by engine. Also applicable to dynamic balancing of rotating terrestrial equipment to which offcenter forces applied.

  19. Interaction of ACTN3 gene polymorphism and muscle imbalance effects on kinematic efficiency in combat sports athletes.

    Science.gov (United States)

    Jung, Hansang; Lee, Namju; Park, Sok

    2016-06-01

    The purpose of this study was to determine the interaction of ACTN3 gene polymorphism and muscle imbalance effects on kinematic efficiency changes in combat sports athletes. Six types of combat sports athletes (Judo, Taekwondo, boxing, kendo, wrestling, and Korean Ssi-reum) participated in the study. ATCN3 gene polymorphism and muscle imbalance in lower extremity were evaluated followed by analysis of differences of moment in hip, knee, and ankle joint during V-cut jumping and stop. To examine the moment difference due to an interaction of ATCN3 polymorphism and muscle imbalance, all participants were divided into 4 groups (R+MB, R+MIB, X+MB, and X+MIB). There was no significant difference of hip, knee, and ankle joint moment in R allele and X allele during V-cut jumping and stop based on ACTN3 gene polymorphism. Otherwise, muscle imbalance of knee moment in X-axis and ground reaction force of knee in Z-axis showed a higher significance in muscle imbalance during V-cut jumping and stop compared to muscle balance (pimbalance in X allele group had significantly higher knee moment of V-cut ground reaction force in X-axis and higher ankle moment of jumping ground reaction force in X and Z-axis compared to muscle balance with R and/or X group (p imbalance in lower extremity of combat athletes might induce higher risk factors of sports injury incidence than genetic factor and training might reduce the ratio of sports injury risk incidence.

  20. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call...

  1. Analysis and compensation of I/Q imbalance in amplify-and-forward cooperative systems

    KAUST Repository

    Qi, Jian; Aissa, Sonia; Alouini, Mohamed-Slim

    2012-01-01

    In this paper, dual-hop amplify-and-forward (AF) cooperative systems in the presence of in-phase and quadrature-phase (I/Q) imbalance, which refers to the mismatch between components in I and Q branches, are investigated. First, we analyze the performance of the considered AF cooperative protocol without compensation for I/Q imbalance as the benchmark. Furthermore, a compensation algorithm for I/Q imbalance is proposed, which makes use of the received signals at the destination, from the source and relay nodes, together with their conjugations to detect the transmitted signal. The performance of the AF cooperative system under study is evaluated in terms of average symbol error probability (SEP), which is derived considering transmission over Rayleigh fading channels. Numerical results are provided and show that the proposed compensation algorithm can efficiently mitigate the effect of I/Q imbalance. © 2012 IEEE.

  2. Analysis and compensation of I/Q imbalance in amplify-and-forward cooperative systems

    KAUST Repository

    Qi, Jian

    2012-04-01

    In this paper, dual-hop amplify-and-forward (AF) cooperative systems in the presence of in-phase and quadrature-phase (I/Q) imbalance, which refers to the mismatch between components in I and Q branches, are investigated. First, we analyze the performance of the considered AF cooperative protocol without compensation for I/Q imbalance as the benchmark. Furthermore, a compensation algorithm for I/Q imbalance is proposed, which makes use of the received signals at the destination, from the source and relay nodes, together with their conjugations to detect the transmitted signal. The performance of the AF cooperative system under study is evaluated in terms of average symbol error probability (SEP), which is derived considering transmission over Rayleigh fading channels. Numerical results are provided and show that the proposed compensation algorithm can efficiently mitigate the effect of I/Q imbalance. © 2012 IEEE.

  3. Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission.

    Directory of Open Access Journals (Sweden)

    Andrea Hauser

    Full Text Available Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS and allele-specific real-time PCR (ASPCR for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT.Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F. In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System.Drug-resistant HIV-variants were identified in 69% (20/29 of women by UDS and in 45% (13/29 by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24. By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41. The proportions of variants quantified by UDS were approximately 2-3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml, resulting in missing or insufficient sequence coverage.Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in the HIV-1 quasispecies.

  4. Allele frequency distribution for 21 autosomal STR loci in Nepal.

    Science.gov (United States)

    Kraaijenbrink, T; van Driem, G L; Opgenort, J R M L; Tuladhar, N M; de Knijff, P

    2007-05-24

    The allele frequency distributions of 21 autosomal loci contained in the AmpFlSTR Identifiler, the Powerplex 16 and the FFFL multiplex PCR kits, was studied in 953 unrelated individuals from Nepal. Several new alleles (i.e. not yet reported in the NIST Short Tandem Repeat DNA Internet DataBase [http://www.cstl.nist.gov/biotech/strbase/]) have been detected in the process.

  5. Identification of a common single nucleotide polymorphism at the primer binding site of D2S1360 that causes heterozygote peak imbalance when using the Investigator HDplex Kit.

    Science.gov (United States)

    Inokuchi, Shota; Yamashita, Yasuhiro; Nishimura, Kazuma; Nakanishi, Hiroaki; Saito, Kazuyuki

    2017-11-01

    Phenomena known as null alleles and peak imbalance can occur because of mutations in the primer binding sites used for DNA typing. In these cases, an accurate statistical evaluation of DNA typing is difficult. The estimated likelihood ratio is incorrectly calculated because of the null allele and allele dropout caused by mutation-induced peak imbalance. Although a number of studies have attempted to uncover examples of these phenomena, few reports are available on the human identification kit manufactured by Qiagen. In this study, 196 Japanese individuals who were heterozygous at D2S1360 were genotyped using an Investigator HDplex Kit with optimal amounts of DNA. A peak imbalance was frequently observed at the D2S1360 locus. We performed a sequencing analysis of the area surrounding the D2S1360 repeat motif to identify the cause for peak imbalance. A point mutation (G>A transition) 136 nucleotides upstream from the D2S1360 repeat motif was discovered in a number of samples. The allele frequency of the mutation was 0.0566 in the Japanese population. Therefore, human identification or kinship testing using the Investigator HDplex Kit requires caution because of the higher frequency of single nucleotide polymorphisms at the primer binding site of D2S1360 locus in the Japanese population.

  6. Double-adjustment in propensity score matching analysis: choosing a threshold for considering residual imbalance.

    Science.gov (United States)

    Nguyen, Tri-Long; Collins, Gary S; Spence, Jessica; Daurès, Jean-Pierre; Devereaux, P J; Landais, Paul; Le Manach, Yannick

    2017-04-28

    Double-adjustment can be used to remove confounding if imbalance exists after propensity score (PS) matching. However, it is not always possible to include all covariates in adjustment. We aimed to find the optimal imbalance threshold for entering covariates into regression. We conducted a series of Monte Carlo simulations on virtual populations of 5,000 subjects. We performed PS 1:1 nearest-neighbor matching on each sample. We calculated standardized mean differences across groups to detect any remaining imbalance in the matched samples. We examined 25 thresholds (from 0.01 to 0.25, stepwise 0.01) for considering residual imbalance. The treatment effect was estimated using logistic regression that contained only those covariates considered to be unbalanced by these thresholds. We showed that regression adjustment could dramatically remove residual confounding bias when it included all of the covariates with a standardized difference greater than 0.10. The additional benefit was negligible when we also adjusted for covariates with less imbalance. We found that the mean squared error of the estimates was minimized under the same conditions. If covariate balance is not achieved, we recommend reiterating PS modeling until standardized differences below 0.10 are achieved on most covariates. In case of remaining imbalance, a double adjustment might be worth considering.

  7. Ocean heat content and Earth's radiation imbalance

    International Nuclear Information System (INIS)

    Douglass, David H.; Knox, Robert S.

    2009-01-01

    Earth's radiation imbalance is determined from ocean heat content data and compared with results of direct measurements. Distinct time intervals of alternating positive and negative values are found: 1960-mid-1970s (-0.15), mid-1970s-2000 (+0.15), 2001-present (-0.2 W/m 2 ), and are consistent with prior reports. These climate shifts limit climate predictability.

  8. Flywheels Would Compensate for Rotor Imbalance

    Science.gov (United States)

    Hrastar, J. A. S.

    1982-01-01

    Spinning flywheels within rotor can null imbalance forces in rotor. Flywheels axes are perpendicular to each other and to rotor axis. Feedback signals from accelerometers or strain gages in platform control flywheel speeds and rotation directions. Concept should be useful for compensating rotating bodies on Earth. For example, may be applied to large industrial centrifuge, particularly if balance changes during operation.

  9. Evaluation of electrolyte imbalance among tuberculosis patients ...

    African Journals Online (AJOL)

    Adebimpe Wasiu Olalekan

    2015-02-24

    Feb 24, 2015 ... a Department of Community Medicine, College of Health Sciences, Osun State University Osogbo, ... trolyte imbalance among TB patients receiving treatments. ... mental organizations whose presence could be felt in the areas ... anti tuberculous drugs with 11 males and 09 females. ... workers in the facility.

  10. Allele Age Under Non-Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach.

    Science.gov (United States)

    De Sanctis, Bianca; Krukov, Ivan; de Koning, A P Jason

    2017-09-19

    Determination of the age of an allele based on its population frequency is a well-studied problem in population genetics, for which a variety of approximations have been proposed. We present a new result that, surprisingly, allows the expectation and variance of allele age to be computed exactly (within machine precision) for any finite absorbing Markov chain model in a matter of seconds. This approach makes none of the classical assumptions (e.g., weak selection, reversibility, infinite sites), exploits modern sparse linear algebra techniques, integrates over all sample paths, and is rapidly computable for Wright-Fisher populations up to N e  = 100,000. With this approach, we study the joint effect of recurrent mutation, dominance, and selection, and demonstrate new examples of "selective strolls" where the classical symmetry of allele age with respect to selection is violated by weakly selected alleles that are older than neutral alleles at the same frequency. We also show evidence for a strong age imbalance, where rare deleterious alleles are expected to be substantially older than advantageous alleles observed at the same frequency when population-scaled mutation rates are large. These results highlight the under-appreciated utility of computational methods for the direct analysis of Markov chain models in population genetics.

  11. Allele frequency analysis of Chinese chestnut ( Castanea mollissima ...

    African Journals Online (AJOL)

    The aim of this study was to establish a method for allele frequency detection in bulk samples. The abundance of polymerase chain reaction (PCR) products in bulk leaf samples was detected using fluorescent labeled Simple sequence repeat (SSR) primers and an Applied biosystems (AB) automatic DNA analyzer.

  12. Education in the imbalance of Nature

    Science.gov (United States)

    Shlafman, L. M.; Kontar, V. A.

    2013-12-01

    There are two concepts understanding of the real Nature: balanced and imbalanced. The traditional balanced concept understanding of Nature was originated in prehistoric times to calm the frightened souls of prehistoric man and manage groups of people. The balanced concept presupposes that Nature is isotropic, balanced, etc. The balanced concept of understanding of Nature gradually has moved to science and technology. The balanced concept of understanding of Nature is dominating from the prehistoric time up to today. But always parallel and opposite was exists the concept imbalanced understanding of Nature, which presupposes that Nature is anisotropy, imbalanced, etc. The balanced concept is much simpler than Imbalanced. The balanced concept has given mankind a lot of rough description of Nature which helped to solve a lot of practical problems but with sufficient accuracy, i.e. approximately, but not with an absolute precision. While people were few, and a lot of resources, person could take from Nature only what Nature gave willingly. During this period, people feared and respected Nature and Nature was able easily compensate the activity of people. The high accuracy of the description of Nature was not needed when resources were plentiful and people were few. But now the situation is completely different. The population has become a very large and growing. Traditional resources are almost run out and the lack of resources escalates. People are not afraid of Nature and bravely try to take by force what Nature does not give voluntarily. People invaded into imbalance Nature, and Nature can no longer compensate activity of people. The era of global change is started, including those that man provokes. In the conditions of global changes is insufficiently of the approximate solutions of the traditional balanced concept. The balanced concept is exhausted, and increasingly misleads people. The balanced concept cannot solve the problems that arise in the global change

  13. Noninvasive Optoelectronic Assessment of Induced Sagittal Imbalance Using the Vicon System.

    Science.gov (United States)

    Ould-Slimane, Mourad; Latrobe, Charles; Michelin, Paul; Chastan, Nathalie; Dujardin, Franck; Roussignol, Xavier; Gauthé, Rémi

    2017-06-01

    Spinal diseases often induce gait disorders with multifactorial origins such as lumbar pain, radicular pain, neurologic complications, or spinal deformities. However, radiography does not permit an analysis of spinal dynamics; therefore, sagittal balance dynamics during gait remain largely unexplored. This prospective and controlled pilot study assessed the Vicon system for detecting sagittal spinopelvic imbalance, to determine the correlations between optoelectronic and radiographic parameters. Reversible anterior sagittal imbalance was induced in 24 healthy men using a thoracolumbar corset. Radiographic, optoelectronic, and comparative analyses were conducted. Corset wearing induced significant variations in radiographic parameters indicative of imbalance; the mean C7-tilt and d/D ratio increased by 15° ± 7.4° and 359%, respectively, whereas the mean spinosacral angle decreased by 16.8° ± 8° (all P imbalance; the mean spinal angle increased by 15.4° ± 5.6° (P imbalance detected using the Vicon system. Optoelectronic C7'S1' correlated with radiographic C7-tilt and d/D ratio. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Muscular Imbalance Correction in the Power Fitness Training

    OpenAIRE

    Olga E. Aftimichuk; Alexander V. Varvarich

    2013-01-01

    Muscular imbalance is one of the manifestations of pathological-biomechanical changes in muscular-skeletal system. It is the result of tonus-power imbalance of short and relaxed muscles. Muscle shortening is the most striking sign of muscular imbalance. Hypodynamia and passive lifestyle can cause such results. The paper justifies the experimental technique of women muscular imbalances correction by means of power training. Selection of exercises, weights and machines was made, taking into acc...

  15. Bomb radiocarbon: imbalance in the budget

    International Nuclear Information System (INIS)

    Joos, Fortunat

    1994-01-01

    An improved understanding of the global carbon cycle is crucial to global climate change research. The uncertainties surrounding the level of oceanic carbon uptake are discussed. A revision downwards of 25% in the currently accepted figure is suggested by authors who base their estimates on a new analysis of the oceanic uptake of radiocarbon released in the atomic bomb tests of the late 1950s and early 1960s. The reduction in uptake level is required to take account of a global imbalance in the bomb-radiocarbon budget in the post test-ban period which emerges from recent carbon-cycle models. Large uncertainties exist in the estimate of the imbalance, however, and bomb-radiocarbon and anthropogenic CO 2 do not behave identically. Any revision of CO 2 uptake estimates may be substantially smaller than the 25% put forward for the bomb-radiocarbon inventory. (UK)

  16. Imbalance in the Local Galactic halo?

    International Nuclear Information System (INIS)

    Croswell, K.; Latham, D.W.; Carney, B.W.; North Carolina Univ., Chapel Hill)

    1987-01-01

    In a kinematically biased sample of 119 single halo stars, 65 percent of the stars are traveling away from the plane of the Galaxy. Halo spectroscopic binaries do not show this imbalance. Other kinematically biased halo surveys exhibit the same effect. Combining these samples with those of the authors' results in 223 halo stars, 63 percent of which are heading away from the plane of the Galaxy. The probability that the first result could be obtained from a symmetric w velocity distribution is 0.2 percent; the probability that the second result could be so obtained is 0.02 percent. Single halo stars traveling away from the disk appear to have a larger w velocity dispersion than those traveling toward it. Selection effects are analyzed and rejected as the cause of the observed asymmetry. Possible mechanisms for producing the imbalance are discussed, but each has serious difficulties accounting for the observations. 28 references

  17. Fiscal Imbalances, Poverty and Inequality in Pakistan

    OpenAIRE

    Irfan Ullah - Naimatullah Baber

    2014-01-01

    This paper has analyzed the fiscal imbalances, poverty and inequality with relevance to Pakistan. We use time series data from 1981 to 2010 and employ Autoregressive Distributed Lag Model (ARDL) to cointegration for estimation. The empirical findings suggest that fiscal deficits increase the poverty level and provide biases for inequality. Since deficit is financed through money supply, government debt and indirect taxes which threaten the purchasing power of the poor and drag them towards po...

  18. Detection of the V1016G mutation in the voltage-gated sodium channel gene of Aedes aegypti (Diptera: Culicidae) by allele-specific PCR assay, and its distribution and effect on deltamethrin resistance in Thailand.

    Science.gov (United States)

    Stenhouse, Steven A; Plernsub, Suriya; Yanola, Jintana; Lumjuan, Nongkran; Dantrakool, Anchalee; Choochote, Wej; Somboon, Pradya

    2013-08-30

    Resistance to pyrethroid insecticides is widespread among populations of Aedes aegypti, the main vector for the dengue virus. Several different point mutations within the voltage-gated sodium channel (VGSC) gene contribute to such resistance. A mutation at position 1016 in domain II, segment 6 of the VGSC gene in Ae. aegypti leads to a valine to glycine substitution (V1016G) that confers resistance to deltamethrin. This study developed and utilized an allele-specific PCR (AS-PCR) assay that could be used to detect the V1016G mutation. The assay was validated against a number of sequenced DNA samples of known genotype and was determined to be in complete agreement. Larvae and pupae were collected from various localities throughout Thailand. Samples were reared to adulthood and their resistance status against deltamethrin was determined by standard WHO susceptibility bioassays. Deltamethrin-resistant and susceptible insects were then genotyped for the V1016G mutation. Additionally, some samples were genotyped for a second mutation at position 1534 in domain III (F1534C) which is also known to confer pyrethroid resistance. The bioassay results revealed an overall mortality of 77.6%. Homozygous 1016G individuals survived at higher rates than either heterozygous or wild-type (1016 V) mosquitoes. The 1016G mutation was significantly and positively associated with deltamethrin resistance and was widely distributed throughout Thailand. Interestingly, wild-type 1016 V mosquitoes tested were homozygous for the 1534C mutation, and all heterozygous mosquitoes were also heterozygous for 1534C. Mutant homozygous (G/G) mosquitoes expressed the wild-type (F/F) at position 1534. However, the presence of the 1534C mutation was not associated with deltamethrin resistance. Our bioassay results indicate that all populations sampled display some degree of resistance to deltamethrin. Homozygous 1016G mosquitoes were far likelier to survive such exposure. However, resistance in some

  19. Diagnostic yield by supplementing prenatal metaphase karyotyping with MLPA for microdeletion syndromes and subtelomere imbalances

    DEFF Research Database (Denmark)

    Kjaergaard, S; Sundberg, K; Jørgensen, F S

    2010-01-01

    The aim of the study was to retrospectively assess the relevance of using multiplex ligation-dependent probe amplification (MLPA) for detection of selected microdeletion syndromes (22q11, Prader-Willi/Angelman, Miller-Dieker, Smith-Magenis, 1p-, Williams), the reciprocal microduplication syndrome...... and imbalance at the subtelomere regions of chromosomes in a routine prenatal setting....

  20. Analysis of genomic imbalances and gene expression changes in transformed follicular lymphoma (FL)

    DEFF Research Database (Denmark)

    Obel, G.; Farinha, P.; Lam, W.

    2005-01-01

    American patients with transformed FL. Methods: High-resolution BAC-array comparative genomic hybridisation (CGH) was used to detect genomic imbalances. Gene expression profiling was performed using cDNA microarrays (Affymetrix). Results: Of 9 biopsy pairs identified so far, analysis results of the first 4...

  1. Population imbalance as a vortex catalyst in Fermi superfluids

    International Nuclear Information System (INIS)

    Tempere, J.; Devreese, J.T.

    2008-01-01

    Pairing leads to superfluidity in ultracold atomic gases, but this pairing can be frustrated when a population imbalance is present between the pairing partners. Here we investigate how vortices in the fermionic superfluid are affected by imbalance. We show that the vortex core radius is increased by imbalance, accommodating excess component atoms. This has two intriguing consequences. Firstly, a small imbalance acts as a catalyst for vortex formation, decreasing the critical rotation frequency. Secondly, imbalanced gases near critical imbalance can exhibit rotationally induced superfluidity

  2. Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples.

    Science.gov (United States)

    Westen, Antoinette A; Matai, Anuska S; Laros, Jeroen F J; Meiland, Hugo C; Jasper, Mandy; de Leeuw, Wiljo J F; de Knijff, Peter; Sijen, Titia

    2009-09-01

    For the analysis of degraded DNA in disaster victim identification (DVI) and criminal investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising markers mainly because they can be analyzed in short sized amplicons. Most SNPs are bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic) SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15 SNPs residing on 14 different chromosomes. Multiplex SNaPshot assays were developed, and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore, we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately 500-year-old bone and molar samples. In both types of degraded DNA samples, the larger sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample.

  3. Allelic prevalence of intron 3 insertion/deletion genetic ...

    African Journals Online (AJOL)

    Leila Fallahzadeh-Abarghooei

    2015-03-18

    Mar 18, 2015 ... Tabriz (East Azerbaijan province; belong to Azaris), and Yasuj (Kohgiluyeh va Boyer-Ahmad pro- vince; belong to Lurs), respectively. Genotypic analysis of the Ins/Del XRCC4 polymorphism was detected by the PCR method. Results: The prevalence of the Del allele in Shiraz, Abarku, Tabriz, and Yasuj was ...

  4. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    Energy Technology Data Exchange (ETDEWEB)

    Tomczak, J.; Grebner, E.E. (Thomas Jefferson Univ., Philadelphia, PA (United States)); Boogen, C. (Univ. of Essen Medical School (Germany))

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

  5. Impact of I/Q imbalance on the performance of two-way CSI-assisted AF relaying

    KAUST Repository

    Qi, Jian; Aï ssa, Sonia; Alouini, Mohamed-Slim

    2013-01-01

    In this paper, we investigate half-duplex two-way dual-hop channel state information (CSI)-assisted amplify-and-forward (AF) relaying in the presence of in-phase and quadrature-phase (I/Q) imbalance. A compensation approach for the I/Q imbalance is proposed, which employs the received signals together with their conjugations to detect the desired signal. We also derive the average symbol error probability of the considered half-duplex two-way dual-hop CSI-assisted AF relaying networks with and without compensation for I/Q imbalance in Rayleigh fading channels. Numerical results are provided and show that the proposed compensation method mitigates the impact of I/Q imbalance to a certain extent. © 2013 IEEE.

  6. Impact of I/Q imbalance on the performance of two-way CSI-assisted AF relaying

    KAUST Repository

    Qi, Jian

    2013-04-01

    In this paper, we investigate half-duplex two-way dual-hop channel state information (CSI)-assisted amplify-and-forward (AF) relaying in the presence of in-phase and quadrature-phase (I/Q) imbalance. A compensation approach for the I/Q imbalance is proposed, which employs the received signals together with their conjugations to detect the desired signal. We also derive the average symbol error probability of the considered half-duplex two-way dual-hop CSI-assisted AF relaying networks with and without compensation for I/Q imbalance in Rayleigh fading channels. Numerical results are provided and show that the proposed compensation method mitigates the impact of I/Q imbalance to a certain extent. © 2013 IEEE.

  7. Assessment of the myostatin Q204X allele using an allelic discrimination assay

    OpenAIRE

    Sifuentes-Rincón,Ana M.; Puentes-Montiel,Herlinda E.; Moreno-Medina,Víctor R.; Rosa-Reyna,Xóchitl F. de la

    2006-01-01

    An allelic discrimination assay was designed and used to determine the genotypic and allelic frequencies of the myostatin (MSTN) gene Q204X allele from two Mexican Full-French herds. The assay is a simple high throughput genotyping method that could be applied to investigate the effect of the Q204X allele on the Charolais breed.

  8. Notch1 Signaling Regulates the Th17/Treg Immune Imbalance in Patients with Psoriasis Vulgaris.

    Science.gov (United States)

    Ma, Lei; Xue, HaiBo; Gao, Tianqin; Gao, MeiLan; Zhang, YuJie

    2018-01-01

    To evaluate the regulating effect of Notch1 signaling on Th17/Treg immune imbalance in psoriasis vulgaris (PV). Notch1, Hes-1, ROR γ t, Foxp3, IL-17, and IL-10 mRNA expression, as well as Th17 and Treg cell percentages in peripheral CD4 + T cells, were detected by real-time quantitative RT-PCR and flow cytometry, and serum concentrations of IL-17 and IL-10 were detected by ELISA in 36 PV patients and 32 healthy controls. Additionally, CD4 + T cells from 12 PV patients were treated with γ -secretase inhibitor DAPT, and the above indexes were measured. PV patients presented distinct Th17/Treg immune imbalance and highly expressed Notch1 and Hes-1 mRNA levels, which were positively correlated with psoriasis area and severity index (PASI) and the ratios of Th17/Treg and ROR γ t/Foxp3. DAPT treatment resulted in the obvious downregulation of Th17 cell percentage in cocultured CD4 + T cells, ROR γ t and IL-17 mRNA levels, and IL-17 concentration in cell-free supernatant from cocultured CD4 + T cells of PV patients in a dose-dependent manner, while there was no significant influence on Treg cell percentage, Foxp3, and IL-10 expression, therefore leading to the recovery of Th17/Treg immune imbalance. Notch1 signaling may contribute to the pathogenesis of PV by regulating Th17/Treg immune imbalance.

  9. Common breast cancer risk alleles and risk assessment

    DEFF Research Database (Denmark)

    Näslund-Koch, C; Nordestgaard, B G; Bojesen, S E

    2017-01-01

    general population were followed in Danish health registries for up to 21 years after blood sampling. After genotyping 72 breast cancer risk loci, each with 0-2 alleles, the sum for each individual was calculated. We used the simple allele sum instead of the conventional polygenic risk score......, as it is likely more sensitive in detecting associations with risks of other endpoints than breast cancer. RESULTS: Breast cancer incidence in the 19,010 women was increased across allele sum quintiles (log-rank trend test; p=1*10(-12)), but not incidence of other cancers (p=0.41). Age- and study-adjusted hazard...... ratio for the 5(th) vs. 1(st) allele sum quintile was 1.82(95% confidence interval;1.53-2.18). Corresponding hazard ratios per allele were 1.04(1.03-1.05) and 1.05(1.02-1.08) for breast cancer incidence and mortality, similar across risk factors. In 50-year old women, the starting age for screening...

  10. Mechanism for Corrective Action on Budget Imbalances

    Directory of Open Access Journals (Sweden)

    Ion Lucian CATRINA

    2014-02-01

    Full Text Available The European Fiscal Compact sets the obligation for the signatory states to establish an automatic mechanism for taking corrective action on budget imbalances. Nevertheless, the European Treaty says nothing about the tools that should be used in order to reach the desired equilibrium of budgets, but only that it should aim at correcting deviations from the medium-term objective or the adjustment path, including their cumulated impact on government debt dynamics. This paper is aiming at showing that each member state has to build the correction mechanism according to the impact of the chosen tools on economic growth and on general government revenues. We will also emphasize that the correction mechanism should be built not only exacerbating the corrective action through spending/ tax based adjustments, but on a high quality package of economic policies as well.

  11. Array-CGH detection of three cryptic submicroscopic imbalances in ...

    Indian Academy of Sciences (India)

    2The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Guangdong Province. 518020, People's Republic of China ... Here, we describe a phenotypically normal prenatal case who was found to carry an apparently balanced .... Precise definitions of CCRs and their real complexity can only be ...

  12. Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility.

    Directory of Open Access Journals (Sweden)

    Jesus Perez-Losada

    Full Text Available Genome-wide association studies (GWAS have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5-10%. There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001, but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility.

  13. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST)

    International Nuclear Information System (INIS)

    Morgenthaler, Stephan; Thilly, William G.

    2007-01-01

    A method is described to discover if a gene carries one or more allelic mutations that confer risk for any specified common disease. The method does not depend upon genetic linkage of risk-conferring mutations to high frequency genetic markers such as single nucleotide polymorphisms. Instead, the sums of allelic mutation frequencies in case and control cohorts are determined and a statistical test is applied to discover if the difference in these sums is greater than would be expected by chance. A statistical model is presented that defines the ability of such tests to detect significant gene-disease relationships as a function of case and control cohort sizes and key confounding variables: zygosity and genicity, environmental risk factors, errors in diagnosis, limits to mutant detection, linkage of neutral and risk-conferring mutations, ethnic diversity in the general population and the expectation that among all exonic mutants in the human genome greater than 90% will be neutral with regard to any effect on disease risk. Means to test the null hypothesis for, and determine the statistical power of, each test are provided. For this 'cohort allelic sums test' or 'CAST', the statistical model and test are provided as an Excel (TM) program, CASTAT (C) at http://epidemiology.mit.edu. Based on genetics, technology and statistics, a strategy of enumerating the mutant alleles carried in the exons and splice sites of the estimated ∼25,000 human genes in case cohort samples of 10,000 persons for each of 100 common diseases is proposed and evaluated: A wide range of possible conditions of multi-allelic or mono-allelic and monogenic, multigenic or polygenic (including epistatic) risk are found to be detectable using the statistical criteria of 1 or 10 ''false positive'' gene associations per 25,000 gene-disease pair-wise trials and a statistical power of >0.8. Using estimates of the distribution of both neutral and gene-inactivating nondeleterious mutations in humans and

  14. Love and fear of heights: the pathophysiology and psychology of height imbalance.

    Science.gov (United States)

    Salassa, John R; Zapala, David A

    2009-01-01

    Individual psychological responses to heights vary on a continuum from acrophobia to height intolerance, height tolerance, and height enjoyment. This paper reviews the English literature and summarizes the physiologic and psychological factors that generate different responses to heights while standing still in a static or motionless environment. Perceptual cues to height arise from vision. Normal postural sway of 2 cm for peripheral objects within 3 m increases as eye-object distance increases. Postural sway >10 cm can result in a fall. A minimum of 20 minutes of peripheral retinal arc is required to detect motion. Trigonometry dictates that a 20-minute peripheral retinal arch can no longer be achieved in a standing position at an eye-object distance of >20 m. At this distance, visual cues conflict with somatosensory and vestibular inputs, resulting in variable degrees of imbalance. Co-occurring deficits in the visual, vestibular, and somatosensory systems can significantly increase height imbalance. An individual's psychological makeup, influenced by learned and genetic factors, can influence reactions to height imbalance. Enhancing peripheral vision and vestibular, proprioceptive, and haptic functions may improve height imbalance. Psychotherapy may improve the troubling subjective sensations to heights.

  15. THE ROLE OF IONORGANIC ION IMBALANCE IN AQUATIC TOXICITY TESTING

    Science.gov (United States)

    This paper assessess the issue of ion imbalance, provides summary of applicable data, presents several successful technical tools to address toxicity resulting from salinity and ion imbalances, and discusses regulatory/compliance options to manage discharges with salinity/ion imb...

  16. Covariate Imbalance and Precision in Measuring Treatment Effects

    Science.gov (United States)

    Liu, Xiaofeng Steven

    2011-01-01

    Covariate adjustment can increase the precision of estimates by removing unexplained variance from the error in randomized experiments, although chance covariate imbalance tends to counteract the improvement in precision. The author develops an easy measure to examine chance covariate imbalance in randomization by standardizing the average…

  17. Effort reward imbalance, and salivary cortisol in the morning

    DEFF Research Database (Denmark)

    Eller, Nanna Hurwitz; Nielsen, Søren Feodor; Blønd, Morten

    2012-01-01

    Effort reward imbalance (ERI) is suggested to increase risk for stress and is hypothesized to increase cortisol levels, especially the awakening cortisol response, ACR.......Effort reward imbalance (ERI) is suggested to increase risk for stress and is hypothesized to increase cortisol levels, especially the awakening cortisol response, ACR....

  18. Population differentiation in allele frequencies of obesity-associated SNPs.

    Science.gov (United States)

    Mao, Linyong; Fang, Yayin; Campbell, Michael; Southerland, William M

    2017-11-10

    Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms). We collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R 2 = 0.35, P = 0.0060) with obesity prevalence. We have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population

  19. Current account imbalances in the euro area

    Directory of Open Access Journals (Sweden)

    Klára Plecitá

    2013-01-01

    Full Text Available While the current account balance for the euro area as a whole has been in balance, divergences in current account positions among the euro-area members have widened since the introduction of the common currency euro. During the last 13 years Portugal, Greece and Spain have run large and persistent current account deficits, whereas Luxembourg, the Netherlands, Finland or Germany have displayed during the same period large and persistent surpluses. However, there is no unambiguous agreement among economists, whether this divergence of current account positions of the euro-area countries mirrors growing intra-euro-area imbalances (Gros, 2012 or just reflects proper functioning of the European integration process (Schmitz and von Hagen, 2009. Therefore, the aim of this paper is to estimate equilibrium current account position for each of the original 12 euro area countries so that it is possible to assess whether the divergence of intra-euro current account balances could be explained on the basis of economic fundamentals or it just reflects misallocation of resources and thus macroeconomic imbalances. The equilibrium current account balance is estimated using a panel-econometric technique for a sample of 30 industrial countries, which represent euro-area member states and their main business partners, over the period 1993–2011. Economic fundamentals affecting the equilibrium current account position are selected on the basis of the saving-investment balance, the trade balance and the net income balance, to ensure that we take into an account all theoretically important explanatory variables. We find that the main determinants of current account norms in our sample are fiscal balance, a country’s net international investment position, oil balance and a country’s stage of economic development. The major part of the euro-area countries exhibits current account positions close to their equilibrium levels with the exception of the Netherlands and

  20. [Analysis of allele dropout at TH01 locus in paternity testing].

    Science.gov (United States)

    Lai, Li; Shen, Xiao-li; Xue, Shi-jie; Hu, Jie

    2013-10-01

    To analyze allele dropout at TH01 locus in paternity testing in order to determine the accurate genotype. To use a two STR loci genotyping system to verify an abnormal genotype for the TH01 locus with PCR using specific primers, cloning and DNA sequencing. A rare allele at TH01 locus named 5.2, which was undetectable with PowerPlex 21 system, was detected with an Identifiler system. Genetic variations may result in rare alleles and loci loss. To avoid misjudgment, laboratories should have a variety of methods for detecting loci loss.

  1. QuASAR: quantitative allele-specific analysis of reads.

    Science.gov (United States)

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Cardiac angiogenic imbalance leads to peripartum cardiomyopathy.

    Science.gov (United States)

    Patten, Ian S; Rana, Sarosh; Shahul, Sajid; Rowe, Glenn C; Jang, Cholsoon; Liu, Laura; Hacker, Michele R; Rhee, Julie S; Mitchell, John; Mahmood, Feroze; Hess, Philip; Farrell, Caitlin; Koulisis, Nicole; Khankin, Eliyahu V; Burke, Suzanne D; Tudorache, Igor; Bauersachs, Johann; del Monte, Federica; Hilfiker-Kleiner, Denise; Karumanchi, S Ananth; Arany, Zoltan

    2012-05-09

    Peripartum cardiomyopathy (PPCM) is an often fatal disease that affects pregnant women who are near delivery, and it occurs more frequently in women with pre-eclampsia and/or multiple gestation. The aetiology of PPCM, and why it is associated with pre-eclampsia, remain unknown. Here we show that PPCM is associated with a systemic angiogenic imbalance, accentuated by pre-eclampsia. Mice that lack cardiac PGC-1α, a powerful regulator of angiogenesis, develop profound PPCM. Importantly, the PPCM is entirely rescued by pro-angiogenic therapies. In humans, the placenta in late gestation secretes VEGF inhibitors like soluble FLT1 (sFLT1), and this is accentuated by multiple gestation and pre-eclampsia. This anti-angiogenic environment is accompanied by subclinical cardiac dysfunction, the extent of which correlates with circulating levels of sFLT1. Exogenous sFLT1 alone caused diastolic dysfunction in wild-type mice, and profound systolic dysfunction in mice lacking cardiac PGC-1α. Finally, plasma samples from women with PPCM contained abnormally high levels of sFLT1. These data indicate that PPCM is mainly a vascular disease, caused by excess anti-angiogenic signalling in the peripartum period. The data also explain how late pregnancy poses a threat to cardiac homeostasis, and why pre-eclampsia and multiple gestation are important risk factors for the development of PPCM.

  3. Golden Jubilee Photos: A Universal Imbalance

    CERN Multimedia

    2004-01-01

    http://www.cern.ch/cern50/ View along the NA48 beamline with the detector in the distance. No one is sure why the Universe wound up the way it has: all matter and no antimatter. According to prevailing theories, the early universe had equal amounts of matter and antimatter. However, whenever such opposites meet, they annihilate and become a burst of energy. This would seem to leave the Universe with neither matter nor antimatter - and thus no stars, planets, or physicists. If nature shows a bias for matter over antimatter, this could explain why the Universe is all matter. To see what might be missing from the theories, physicists search for the rare cases in which matter and antimatter behave differently. One such imbalance, called direct CP violation, showed up in the NA 31 experiment at CERN. The results from this experiment, first presented in 1993, showed that when K mesons and their antimatter cousins decay, they show a slight preference for matter over antimatter. Later experiments with neutral K mes...

  4. Procoagulant imbalance in patients with non-alcoholic fatty liver disease.

    Science.gov (United States)

    Tripodi, Armando; Fracanzani, Anna L; Primignani, Massimo; Chantarangkul, Veena; Clerici, Marigrazia; Mannucci, Pier Mannuccio; Peyvandi, Flora; Bertelli, Cristina; Valenti, Luca; Fargion, Silvia

    2014-07-01

    Non-alcoholic fatty liver disease (NAFLD) is characterized by increased risk of cardiovascular events and liver-fibrosis. Both could be explained by a procoagulant-imbalance that was surmised but never directly demonstrated. We investigated 113 patients with varying histological liver damage [steatosis (n=32), steatohepatitis (n=51), metabolic-cirrhosis (n=30)], 54 with alcoholic/viral-cirrhosis and 179 controls. Plasma was evaluated for levels of pro- and anti-coagulants, and for thrombin-generation assessed as endogenous-thrombin-potential (ETP) with and without thrombomodulin or Protac® as protein C activators. The procoagulant-imbalance was defined as ETP-ratio (with-to-without thrombomodulin) or as Protac®-induced-coagulation-inhibition (PICI%). High ETP-ratios or low PICI% indicate resistance to thrombomodulin or Protac® and hence a procoagulant-imbalance. ETP-ratio increased from controls [0.57 (0.11-0.89)] to steatosis [0.72 (0.33-0.86)] and metabolic-cirrhosis [0.80 (0.57-0.95)], (pimbalance detected as ETP-ratio greater or PICI% lower than the median value of controls tended to have a higher risk of metabolic-syndrome, higher intima-media thickness, fibrosis, steatosis or lobular inflammation, all considered clinical manifestations of NAFLD. NAFLD is characterized by a procoagulant-imbalance progressing from the less severe (steatosis) to the most severe form of the disease (metabolic-cirrhosis). This imbalance appears to result from increased factor VIII and reduced protein C and might play a role in the risk of cardiovascular events and liver-fibrosis commonly observed in NAFLD. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  5. Allelic imbalance modulates surface expression of the tolerance-inducing HLA-G molecule on primary trophoblast cells

    DEFF Research Database (Denmark)

    Djurisic, S; Teiblum, S; Tolstrup, C K

    2015-01-01

    The HLA-G molecule is expressed on trophoblast cells at the feto-maternal interface, where it interacts with local immune cells, and upholds tolerance against the semi-allogeneic fetus. Aberrant HLA-G expression in the placenta and reduced soluble HLA-G levels are observed in pregnancy complicati...

  6. Analysis of APC allelic imbalance/loss of heterozygosity and APC protein expression in cutaneous squamous cell carcinomas.

    LENUS (Irish Health Repository)

    Gray, Sarah E

    2011-05-01

    The adenomatous polyposis coli (APC) gene is a tumor suppressor gene which is mutated in the hereditary disease, familial adenomatous polyposis (FAP). Somatic mutations of the APC gene have also been identified in the majority of sporadic colorectal carcinomas, and mutation of the APC gene appears to be an early step in the initiation of colon cancer. Loss of heterozygosity (LOH) of APC has been described in a variety of other cancer types, including renal cell carcinoma, gastric cancer, non-small cell lung cancer, endometrial cancer and oral squamous cell carcinomas (SCC).

  7. Spatial-frequency dependent binocular imbalance in amblyopia.

    Science.gov (United States)

    Kwon, MiYoung; Wiecek, Emily; Dakin, Steven C; Bex, Peter J

    2015-11-25

    While amblyopia involves both binocular imbalance and deficits in processing high spatial frequency information, little is known about the spatial-frequency dependence of binocular imbalance. Here we examined binocular imbalance as a function of spatial frequency in amblyopia using a novel computer-based method. Binocular imbalance at four spatial frequencies was measured with a novel dichoptic letter chart in individuals with amblyopia, or normal vision. Our dichoptic letter chart was composed of band-pass filtered letters arranged in a layout similar to the ETDRS acuity chart. A different chart was presented to each eye of the observer via stereo-shutter glasses. The relative contrast of the corresponding letter in each eye was adjusted by a computer staircase to determine a binocular Balance Point at which the observer reports the letter presented to either eye with equal probability. Amblyopes showed pronounced binocular imbalance across all spatial frequencies, with greater imbalance at high compared to low spatial frequencies (an average increase of 19%, p imbalance may be useful for diagnosing amblyopia and as an outcome measure for recovery of binocular vision following therapy.

  8. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project.

    Science.gov (United States)

    Cross, Deanna S; Ivacic, Lynn C; Stefanski, Elisha L; McCarty, Catherine A

    2010-06-17

    There is a lack of knowledge regarding the frequency of disease associated polymorphisms in populations and population attributable risk for many populations remains unknown. Factors that could affect the association of the allele with disease, either positively or negatively, such as race, ethnicity, and gender, may not be possible to determine without population based allele frequencies.Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined. There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German.41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders. This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are important for the design and

  9. Monoclonal B-cell hyperplasia and leukocyte imbalance precede development of B-cell malignancies in uracil-DNA glycosylase deficient mice

    DEFF Research Database (Denmark)

    Andersen, Sonja; Ericsson, Madelene; Dai, Hong Yan

    2005-01-01

    causes a significant reduction of T-helper cells, and 50% of the young Ung(-/-) mice investigated have no detectable NK/NKT-cell population in their spleen. The immunological imbalance is confirmed in experiments with spleen cells where the production of the cytokines interferon gamma, interleukin 6....... The immunological imbalances shown here in the Ung-deficient mice may be central in the development of lymphomas in a background of generalised lymphoid hyperplasia....

  10. Hamstrings strength imbalance in professional football (soccer) players in Australia.

    Science.gov (United States)

    Ardern, Clare L; Pizzari, Tania; Wollin, Martin R; Webster, Kate E

    2015-04-01

    The aim of this study was to describe the isokinetic thigh muscle strength profile of professional male football players in Australia. Concentric (60° and 240°·s(-1)) and eccentric (30° and 120°·s(-1)) hamstrings and quadriceps isokinetic strength was measured with a HUMAC NORM dynamometer. The primary variables were bilateral concentric and eccentric hamstring and quadriceps peak torque ratios, concentric hamstring-quadriceps peak torque ratios, and mixed ratios (eccentric hamstring 30°·s(-1) ÷ concentric quadriceps 240°·s(-1)). Hamstring strength imbalance was defined as deficits in any 2 of: bilateral concentric hamstring peak torque ratio imbalance. Athletes with strength imbalance had significantly reduced concentric and eccentric bilateral hamstring peak torque ratios at all angular velocities tested; and reduced eccentric quadriceps peak torque (30°·s(-1)) in their stance leg, compared with those without strength imbalance. Approximately, 1 in 4 players had preseason hamstring strength imbalance; and all strength deficits were observed in the stance leg. Concentric and eccentric hamstrings strength imbalance may impact in-season football performance and could have implications for the future risk of injury.

  11. External Sector Rebalancing and Endogenous Trade Imbalance Models

    Directory of Open Access Journals (Sweden)

    John Whalley

    2012-12-01

    Full Text Available I discuss the need for trade models to incorporate endogenous trade imbalances both to more adequately capture the reality of a global economy with large imbalances and pressures from the financial crisis for countries to reduce imbalances. Conventional general equilibrium trade models implicitly incorporate monetary neutrality and either have zero trade balance as a property of equilibrium, or have a fixed and exogenous trade imbalance. Models which are discussed here have a variety of forms. In one, central banks fix exchange rates and operate a non accommodative monetary policy and accumulate reserves. Changes in both trade and monetary policies change reserve accumulative and with the external sector imbalances. This is a reflection of China’s current policy regime. In another intertemporal preferences allow for simultaneous inter commodity and intertemporal trade across countries, and with changed intertemporal trade changed external sector imbalances within the period. These formulations are each applied to potential tax initiatives to aid in rebalancing.

  12. Microangiopathic complications related to different alleles of ...

    African Journals Online (AJOL)

    Egyptian Journal of Biochemistry and Molecular Biology. Journal Home ... Microangiopathic complications related to different alleles of manganese superoxide dismutase gene in diabetes mellitus type 1. TM EL Masry ... 23(2) 2005: 155-167 ...

  13. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  14. Analysis of FBN1 allele expression by dermal fibroblasts from Marfan syndrome patients

    Energy Technology Data Exchange (ETDEWEB)

    Putman, E.A.; Cao, S.N.; Milewicz, D.M. [Univ. of Texas Medical School, Houston, TX (United States)

    1994-09-01

    Screening for mutations in the FBN1 cDNA from Marfan patient cell strains has detected mutations in only 10-15% of patients. In an attempt to explain this poor detection rate, we examined FBN1 allele expression and fibrillin synthesis by 26 cell strains from Marfan patients. DNA from the patients and 10 controls was assessed for the presence of a polymorphic Rsa I restriction site in the 3{prime} untranslated region of the FBN1 gene. Twelve of 26 patient and 5 of 10 control DNAs were heterozygous. Fibroblast RNA from the heterozygous cell strains was reverse-transcribed and subsequently PCR amplified using a [{sup 32}P]-labelled primer, digested with Rsa I and analyzed. Although 3 samples showed no transcript from one allele by ethidium bromide staining, a Betagen scanner detected low levels (10-15%) of that allele. In addition, there was unequal expression of the two alleles in three other patients; for example, only 30% expression from one allele. The remaining patients and the controls had equal expression of each allele. Fibrillin protein synthesis by fibroblasts from these heterozygous patients was also examined. After a 30 minute pulse with [{sup 35}S]-cysteine, cell lysates were collected and proteins analyzed by SDS-PAGE. The amount of fibrillin produced relative to a reference protein was determined using a Betagen scanner. Fibrillin protein synthesis was reduced in 2 of the 3 patients with very low RNA production from one of the FBN1 alleles. All other Marfan and control cell strains showed normal amounts of fibrillin synthesized. The low expression levels from one allele may contribute to, but not fully account for, the low detection rate of FBN1 mutations. Interestingly, protein synthesis levels were not affected in 4 of 6 cell strains demonstrating low levels of RNA expression.

  15. Mineral imbalances in farm animals and their study and diagnosis with isotopic tracers

    International Nuclear Information System (INIS)

    Underwood, E.J.

    1976-01-01

    Twenty-two mineral elements are known to be essential for animal life. These are calcium, phosphorus, sulphur, potassium, sodium, chlorine, magnesium, iron, iodine, copper, manganese, zinc, cobalt, molybdenum, selenium, chromium, tin, vanadium, fluorine, silicon, nickel and arsenic. Naturally occurring and man-made dietary imbalances of many of these elements and their interactions with other minerals are described and their functions and requirements by farm animals are outlined. The nature and importance of metabolic interactions among the mineral elements are discussed and the important concept stressed that there is no single minimum requirement or safe tolerance of a particular mineral, but a series of such minimum requirements and safe tolerances depending on the extent to which other minerals with which it interacts is present or absent from the diet. Radioactive tracer elements are shown to be of great value in the determination of mineral nutrient availability to the animal and for following mineral metabolic movements in the body. They are also shown to have considerable potential for the diagnosis of mineral imbalances. Various in vivo and in vitro techniques involving both radioactive and stable tracers developed for the early diagnosis of mineral deficiencies are described and the strengths and weaknesses of such techniques, in comparison with standard biochemical tests, are discussed. The need for further critical studies with isotopic tracers in the detection and diagnosis of mineral imbalances is emphasized. The main types of biochemical criteria used in the diagnosis of mineral deficiencies and excesses are given, with appropriate examples of their use. (author)

  16. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data

    International Nuclear Information System (INIS)

    Baudis, Michael

    2007-01-01

    Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed. With large variation in overall genomic instability, recurring genomic gains and losses were prominent. Most entities showed frequent gains involving 8q2, while gains on 20q, 1q, 3q, 5p, 7q and 17q were frequent in different entities. Loss 'hot spots' included 3p, 4q, 13q, 17p and 18q among others. Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca.) and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites). Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. Focus on the respective regions should aid in target gene detection and pathway deduction

  17. Acid base imbalances in ill neonatal foals and their association with survival.

    Science.gov (United States)

    Viu, J; Armengou, L; Ríos, J; Cesarini, C; Jose-Cunilleras, E

    2017-01-01

    Acid-base imbalances observed in human paediatric patients are associated with outcome. Likewise, neonatal foals may have different acid-base imbalances associated with diagnosis or prognosis. To determine acid-base imbalances by the quantitative method in ill neonatal foals and assess their association with diagnosis and prognosis. Observational prospective clinical study. This study included 65 ill neonatal foals (32 septic, 33 nonseptic) admitted to an equine referral hospital from 2005 to 2011with acid-base parameters determined on admission and a control group of 33 healthy neonatal foals. Blood pH, pCO 2 , sodium, potassium, chloride, L-lactate, albumin and phosphate concentrations were determined. Bicarbonate, globulin, measured strong ion difference (SID m ), nonvolatile weak buffer concentrations (A tot ), base excess and its components were calculated. Analysis of covariance (ANCOVA) and multiple linear regression statistical analyses were performed. Results are summarised as mean ± s.d. for normally distributed variables and median [25-75th percentiles] for non-normally distributed ones. A total of 63% of ill foals had respiratory alkalosis and 58.5% had SID m acidosis. The combination of both alterations was detected in 21 of 65 ill foals and abnormal pH was found in 24 of 65. Compared with healthy foals, ill foals had significantly lower SID m (nonseptic 31.6 ± 6.3 [Pacid-base imbalances observed in ill foals were respiratory alkalosis, SID m acidosis or mixed respiratory alkalosis with strong ion acidosis. Increased venous pCO 2 and blood L-lactate concentration were associated with poor outcome. © 2015 EVJ Ltd.

  18. Molecular analyses of the agouti allele in the Japanese house mouse identify a novel variant of the agouti gene.

    Science.gov (United States)

    Iwasa, Masahiro A; Kawamura, Sayaka; Myoshu, Hikari; Suzuki, Taichi A

    2018-03-01

    It has been thought that the Japanese house mouse carries the A w allele at the agouti locus causing light-colored bellies, but they do not always show this coloration. Thus, the presence of the A w allele seems to be doubtful in them. To ascertain whether the A w allele is present, a two-pronged approach was used. First, we compared lengths of DNA fragments obtained from three PCRs conducted on them to the known fragment sizes generated from mouse strains exhibiting homozygosities of either a/a, A/A, or A w /A w . PCR I, PCR II, and PCR III amplify only in the A and A w alleles, the a and A w alleles, and the a allele, respectively, and we detected amplifications in strains with A/A and A w /A w by PCR I, in those with a/a and the Japanese house mouse by PCR II, and in those with a/a by PCR III. Second, we sequenced the exon 1A region of the agouti gene and obtained sequences corresponding to the above strains and the Japanese house mouse, but their sequences were similar to those of the a allele. We concluded that their agouti allele is not identical to the A w allele and seems to be a novel type similar to the a allele.

  19. Imbalance between sympathetic and sensory innervation in peritoneal endometriosis.

    Science.gov (United States)

    Arnold, Julia; Barcena de Arellano, Maria L; Rüster, Carola; Vercellino, Giuseppe F; Chiantera, Vito; Schneider, Achim; Mechsner, Sylvia

    2012-01-01

    To investigate possible mechanisms of pain pathophysiology in patients with peritoneal endometriosis, a clinical study on sensory and sympathetic nerve fibre sprouting in endometriosis was performed. Peritoneal lesions (n=40) and healthy peritoneum (n=12) were immunostained and analysed with anti-protein gene product 9.5 (PGP 9.5), anti-substance P (SP) and anti-tyrosine hydroxylase (TH), specific markers for intact nerve fibres, sensory nerve fibres and sympathetic nerve fibres, respectively, to identify the ratio of sympathetic and sensory nerve fibres. In addition, immune cell infiltrates in peritoneal endometriotic lesions were analysed and the nerve growth factor (NGF) and interleukin (IL)-1β expression was correlate with the nerve fibre density. Peritoneal fluids from patients with endometriosis (n=40) and without endometriosis (n=20) were used for the in vitro neuronal growth assay. Cultured chicken dorsal root ganglia (DRG) and sympathetic ganglia were stained with anti-growth associated protein 43 (anti-GAP 43), anti-SP and anti-TH. We could detect an increased sensory and decreased sympathetic nerve fibres density in peritoneal lesions compared to healthy peritoneum. Peritoneal fluids of patients with endometriosis compared to patients without endometriosis induced an increased sprouting of sensory neurites from DRG and decreased neurite outgrowth from sympathetic ganglia. In conclusion, this study demonstrates an imbalance between sympathetic and sensory nerve fibres in peritoneal endometriosis, as well as an altered modulation of peritoneal fluids from patients with endometriosis on sympathetic and sensory innervation which might directly be involved in the maintenance of inflammation and pain. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

    Science.gov (United States)

    Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

    2016-01-01

    Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

  1. Neoliberalism, trade imbalances, and economic policy in the Eurozone crisis

    Directory of Open Access Journals (Sweden)

    Engelbert Stockhammer

    2016-12-01

    Full Text Available This paper analyzes the causes of the Eurozone crisis. In doing so, it carefully surveys authors from different economic schools of thought. The paper discusses competing explanations for European current account imbalances. Remarkably, opposing views on the relative importance of cost developments and demand developments in explaining current account imbalances can be found in both heterodox and orthodox economics. Regarding the assessment of fiscal and monetary policy there is a clearer polarisation, with heterodox analysis regarding austerity as unhelpful and most of orthodox economics endorsing it. We advocate a post-Keynesian view, which holds that current account imbalances are not a fundamental cause of the sovereign debt crisis. Rather, the economic policy architecture of the Eurozone, which aims at restricting the role of fiscal and monetary policy, is the key to understanding the crisis in Europe.

  2. Charge imbalance induced by a temperature gradient in superconducting aluminum

    International Nuclear Information System (INIS)

    Mamin, H.J.; Clarke, J.; Van Harlingen, D.J.

    1984-01-01

    The quasiparticle transport current induced in a superconducting aluminum film by a temperature gradient has been measured by means of the spatially decaying charge imbalance generated near the end of the sample where the current is divergent. The magnitude and decay length of the charge imbalance are in good agreement with the predictions of a simple model that takes into account the nonuniformity of the temperature gradient. The inferred value of the thermopower in the superconducting state agrees reasonably well with the value measured in the normal state. Measurements of the decay length of charge imbalance induced by current injection yield a value of the inelastic relaxation time tau/sub E/ of about 2 ns. This value is substantially smaller than that obtained from other measurements for reasons that are not known

  3. Total hip arthroplasty in patients with neuromuscular imbalance.

    Science.gov (United States)

    Konan, S; Duncan, C P

    2018-01-01

    Patients with neuromuscular imbalance who require total hip arthroplasty (THA) present particular technical problems due to altered anatomy, abnormal bone stock, muscular imbalance and problems of rehabilitation. In this systematic review, we studied articles dealing with THA in patients with neuromuscular imbalance, published before April 2017. We recorded the demographics of the patients and the type of neuromuscular pathology, the indication for surgery, surgical approach, concomitant soft-tissue releases, the type of implant and bearing, pain and functional outcome as well as complications and survival. Recent advances in THA technology allow for successful outcomes in these patients. Our review suggests excellent benefits for pain relief and good functional outcome might be expected with a modest risk of complication. Cite this article: Bone Joint J 2018;100-B(1 Supple A):17-21. ©2018 The British Editorial Society of Bone & Joint Surgery.

  4. Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts

    NARCIS (Netherlands)

    Bouwman, Aniek C.; Hayes, Ben J.; Calus, Mario P.L.

    2017-01-01

    Background: Genomic evaluation is used to predict direct genomic values (DGV) for selection candidates in breeding programs, but also to estimate allele substitution effects (ASE) of single nucleotide polymorphisms (SNPs). Scaling of allele counts influences the estimated ASE, because scaling of

  5. Chromosomal imbalances in four new uterine cervix carcinoma derived cell lines

    International Nuclear Information System (INIS)

    Hidalgo, Alfredo; Monroy, Alberto; Arana, Rosa Ma; Taja, Lucía; Vázquez, Guelaguetza; Salcedo, Mauricio

    2003-01-01

    Uterine cervix carcinoma is the second most common female malignancy worldwide and a major health problem in Mexico, representing the primary cause of death among the Mexican female population. High risk human papillomavirus (HPV) infection is considered to be the most important risk factor for the development of this tumor and cervical carcinoma derived cell lines are very useful models for the study of viral carcinogenesis. Comparative Genomic Hybridization (CGH) experiments have detected a specific pattern of chromosomal imbalances during cervical cancer progression, indicating chromosomal regions that might contain genes that are important for cervical transformation. We performed HPV detection and CGH analysis in order to initiate the genomic characterization of four recently established cervical carcinoma derived cell lines from Mexican patients. All the cell lines were HPV18 positive. The most prevalent imbalances in the cell lines were gains in chromosomes 1q23-q32, 3q11.2-q13.1, 3q22-q26.1, 5p15.1-p11.2, this alteration present as a high copy number amplification in three of the cell lines, 7p15-p13, 7q21, 7q31, 11q21, and 12q12, and losses in 2q35-qter, 4p16, 6q26-qter, 9q34 and 19q13.2-qter. Analysis of our present findings and previously reported data suggest that gains at 1q31-q32 and 7p13-p14, as well as losses at 6q26-q27 are alterations that might be unique for HPV18 positive cases. These chromosomal regions, as well as regions with high copy number amplifications, coincide with known fragile sites and known HPV integration sites. The general pattern of chromosomal imbalances detected in the cells resembled that found in invasive cervical tumors, suggesting that the cells represent good models for the study of cervical carcinoma

  6. Managing external imbalances in Montenegro - will faciliate integration to EU

    Directory of Open Access Journals (Sweden)

    Jacimović Danijela

    2017-01-01

    Full Text Available Montenegro as a new state has had similar approach to the development models as other European transition economies. High openness to foreign investments andeuroisation have influenced high liquidity, fiscal and financial expansion. With the current crisis, Montenegro is experiencing significant slowdown of economic activity, external imbalances, shortage of foreign capital, low credit activity, fiscal tightening and increase of public debt. This article aims to investigate the main effects to balance of payment imbalances in Montenegro. It compares economic indicators with the Eurozone countries, especially with the countries of the Eurozone periphery, trying to find similiraties and differences and possible policy recommendations, based on the experience in the Eurozone.

  7. In-phase and quadrature imbalance modeling, estimation, and compensation

    CERN Document Server

    Li, Yabo

    2013-01-01

    This book provides a unified IQ imbalance model and systematically reviews the existing estimation and compensation schemes. It covers the different assumptions and approaches that lead to many models of IQ imbalance. In wireless communication systems, the In-phase and Quadrature (IQ) modulator and demodulator are usually used as transmitter (TX) and receiver (RX), respectively. For Digital-to-Analog Converter (DAC) and Analog-to-Digital Converter (ADC) limited systems, such as multi-giga-hertz bandwidth millimeter-wave systems, using analog modulator and demodulator is still a low power and l

  8. The Great Moderation and the U.S. External Imbalance

    OpenAIRE

    Alessandra Fogli; Fabrizio Perri

    2006-01-01

    The early 1980s marked the onset of two striking features of the current world macroeconomy: the fall in U.S. business cycle volatility (the ggreat moderation h) and the large and persistent U.S. external imbalance. In this paper, we argue that an external imbalance is a natural consequence of the great moderation. If a country experiences a fall in volatility greater than that of its partners, its incentives to accumulate precautionary savings fall and this results in a permanent deteriorati...

  9. Different nutritional states and autonomic imbalance in childhood.

    Science.gov (United States)

    Dippacher, S; Willaschek, C; Buchhorn, R

    2014-11-01

    Autonomic imbalance, measured as heart rate variability (HRV), and an increased cardiovascular risk are described for overweight children, as well as for patients with anorexia nervosa. We investigate whether body mass index or actual caloric intake influences HRV. In our cross-sectional study, we compared HRV parameters for a healthy control group (n=52), anorexia nervosa patients (n=17), thin (n=18) and overweight children (n=19). Anorexia nervosa patients showed significantly lower heart rates at night (Pchildren showed an opposing pattern. SDNN and heart rate at night are highly correlated (r=0.89, R(2)=0.79, Panorexia nervosa are characterized by a specific pattern of autonomic imbalance.

  10. Allelic genealogies in sporophytic self-incompatibility systems in plants

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Vekemans, Xavier; Christiansen, Freddy Bugge

    1998-01-01

    , alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self...

  11. Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

    Science.gov (United States)

    Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

    2018-01-01

    Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Expression and loss of alleles in cultured mouse embryonic fibroblasts and stem cells carrying allelic fluorescent protein genes

    Directory of Open Access Journals (Sweden)

    Stringer Saundra L

    2006-10-01

    Full Text Available Abstract Background Loss of heterozygosity (LOH contributes to many cancers, but the rate at which these events occur in normal cells of the body is not clear. LOH would be detectable in diverse cell types in the body if this event were to confer an obvious cellular phenotype. Mice that carry two different fluorescent protein genes as alleles of a locus would seem to be a useful tool for addressing this issue because LOH would change a cell's phenotype from dichromatic to monochromatic. In addition, LOH caused by mitotic crossing over might be discernable in tissues because this event produces a pair of neighboring monochromatic cells that are different colors. Results As a step in assessing the utility of this approach, we derived primary embryonic fibroblast populations and embryonic stem cell lines from mice that carried two different fluorescent protein genes as alleles at the chromosome 6 locus, ROSA26. Fluorescence activated cell sorting (FACS showed that the vast majority of cells in each line expressed the two marker proteins at similar levels, and that populations exhibited expression noise similar to that seen in bacteria and yeast. Cells with a monochromatic phenotype were present at frequencies on the order of 10-4 and appeared to be produced at a rate of approximately 10-5 variant cells per mitosis. 45 of 45 stably monochromatic ES cell clones exhibited loss of the expected allele at the ROSA26 locus. More than half of these clones retained heterozygosity at a locus between ROSA26 and the centromere. Other clones exhibited LOH near the centromere, but were disomic for chromosome 6. Conclusion Allelic fluorescent markers allowed LOH at the ROSA26 locus to be detected by FACS. LOH at this locus was usually not accompanied by LOH near the centromere, suggesting that mitotic recombination was the major cause of ROSA26 LOH. Dichromatic mouse embryonic cells provide a novel system for studying genetic/karyotypic stability and factors

  13. Spontaneous correction of coronal imbalance after selective thoracolumbar-lumbar fusion in patients with Lenke-5C adolescent idiopathic scoliosis.

    Science.gov (United States)

    Hwang, Chang Ju; Lee, Choon Sung; Kim, Hyojune; Lee, Dong-Ho; Cho, Jae Hwan

    2018-03-22

    Coronal imbalance is a complication of corrective surgeries in adolescent idiopathic scoliosis (AIS). However, few studies about immediate coronal decompensation in Lenke-5C curves have reported its incidence, prognosis, and related factors. To evaluate the development of coronal imbalance after selective thoracolumbar-lumbar (TL/L) fusion (SLF) in Lenke-5C AIS, and to reveal related factors. Retrospective comparative study. This study included 50 consecutive patients with Lenke-5C AIS who underwent SLF at a single center. Whole-spine anteroposterior and lateral radiographs were used to measure radiological parameters. Patients were divided into two groups according to the presence or absence of coronal imbalance (distance between C7 plumb line and central sacral vertical line >2 cm) in the early (1 month) postoperative period. Various radiological parameters were statistically compared between groups. Of the patients, 28% (14 of 50) showed coronal imbalance in the early postoperative period; however, most of them (13 of 14) showed spontaneous correction during follow-up. The development of coronal imbalance was related to less flexibility of the TL/L curve (51.3% vs. 52.6%, p=.040), greater T10-L2 kyphosis (11.7° vs. 6.4°, p=.034), and greater distal junctional angle (6.0° vs. 3.7°, p=.025) in preoperative radiographs. Lowermost instrumented vertebra (LIV) tilt was greater in the decompensation [+] group in the early postoperative period (8.8° vs. 4.4°, p=.009). However, this difference disappeared in final follow-up with the decrease of LIV tilt in the decompensation [+] group. Less flexibility of the TL/L curve, greater TL kyphosis, and greater distal junctional angle preoperatively were predictive factors for immediate coronal imbalance in Lenke-5C curves. Although coronal imbalance was frequently detected in the early postoperative period after SLF, it was mostly corrected spontaneously with a decrease of LIV tilt. Thus, SLF for Lenke-5C curves can be

  14. Diversity of Lactase Persistence Alleles in Ethiopia

    DEFF Research Database (Denmark)

    Jones, BL; Raga, TO; Liebert, Anke

    2013-01-01

    The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (−13910∗T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene ...

  15. On cuff imbalance and tripolar ENG amplifier configurations.

    Science.gov (United States)

    Triantis, Iasonas F; Demosthenous, Andreas; Donaldson, Nick

    2005-02-01

    Electroneurogram (ENG) recording techniques benefit from the use of tripolar cuffs because they assist in reducing interference from sources outside the cuff. However, in practice the performance of ENG amplifier configurations, such as the quasi-tripole and the true-tripole, has been widely reported to be degraded due to the departure of the tripolar cuff from ideal behavior. This paper establishes the presence of cuff imbalance and investigates its relationship to cuff asymmetry, cuff end-effects and interference source proximity. The paper also presents a comparison of the aforementioned amplifier configurations with a new alternative, termed the adaptive-tripole, developed to automatically compensate for cuff imbalance. The output signal-to-interference ratio of the three amplifier configurations were compared in vivo for two interference signals (stimulus artifact and M-wave) superimposed on compound action potentials. The experiments showed (for the first time) that the two interference signals result in different cuff imbalance values. Nevertheless, even with two distinct cuff imbalances present, the adaptive-tripole performed better than the other two systems in 61.9% of the trials.

  16. Interaction between current imbalance and magnetization in LHC cables

    NARCIS (Netherlands)

    Haverkamp, M.; Kuijper, A.; Kuijper, A.; den Ouden, A.; ten Haken, Bernard; Bottura, L.; ten Kate, Herman H.J.

    2001-01-01

    The quality of the magnetic field in superconducting accelerator magnets is associated with the properties of the superconducting cable. Current imbalances due to coupling currents ¿I, as large as 100 A, are induced by spatial variations of the field sweep rate and contact resistances. During

  17. THE ROLE OF INORGANIC ION IMBALANCE IN AQUATIC TOXICITY TESTING

    Science.gov (United States)

    Effluent toxicity testing methods have been well defined, but to a large part have not attempted to segregate the effects of active ionic concentrations and ion imbalances upon test and species performances. The role that various total dissolved solids in effluents have on regula...

  18. Heat split imbalance study for annular fuel rod

    International Nuclear Information System (INIS)

    He Xiaojun; Ji Songtao; Zhang Yingchao

    2014-01-01

    Annular fuel rod has two gaps at inner and outer side. Under irradiation condition, the dimensional change of pellets is always larger than claddings' due to thermal expansion, swelling and densification, and this tends to enlarge the inner gap and reduce the outer gap. The gap size asymmetry must induce heat split imbalance problem that the heat flux will be larger at outer side of the rod. In this work, computer code AFPAC l.0 is used to simulate this heat split imbalance phenomena. The effect of initial gap size, rod inner pressure, roughness of pellets and cladding is studied, the results reveal that: l) Adjusting initial size of both gaps, reducing inner gap and enlarging outer gap could effectively alleviate heat split imbalance problem; 2) Adjusting the initial roughness of pellets and cladding is another effective approach to reducing heat split imbalance; 3) It seems that changing the rod inner pressure has a little effect on solving the heat flux asymmetry problem. (authors)

  19. Private consumption-savings behavior and macroeconomic imbalances

    NARCIS (Netherlands)

    de Castro Campos, M.

    2016-01-01

    Between the signing of the Maastricht Treaty in 1991 and 2007 many of the existing macroeconomic theories were applied to support the claim that the euro area was an optimal currency union and to argue that increasing macroeconomic imbalances were a logical part of the financial integration process.

  20. Labor Markets in Imbalance: Review of Qualitative Evidence.

    Science.gov (United States)

    Medoff, James L.; Wiener, Jonathan B.

    Recent statistical investigations indicate that labor market imbalance has increased during the past decade and has had important deleterious effects on the nation's inflation and productivity growth records. A growing difficulty in filling skilled jobs at a given unemployment rate is reflected. Business community analysts attribute the growing…

  1. Prism adaptation improves postural imbalance in neglect patients

    NARCIS (Netherlands)

    Nijboer, Tanja C W; Olthoff, Liselot; Van der Stigchel, Stefan; Visser-Meily, Johanna M a

    2014-01-01

    Several studies have found a negative relation between neglect and postural imbalance. The aim of the current study was to investigate the influence of a single session of prism adaptation on balance [i.e. mediolateral and anteroposterior center of pressure (CoP)] and postural sway (i.e. mean

  2. Acute proximal junctional failure in patients with preoperative sagittal imbalance.

    Science.gov (United States)

    Smith, Micah W; Annis, Prokopis; Lawrence, Brandon D; Daubs, Michael D; Brodke, Darrel S

    2015-10-01

    Proximal junctional failure (PJF) is a recognized complication of spinal deformity surgery. Acute PJF (APJF) has recently been demonstrated to be 5.6% in the adult spinal deformity (ASD) population. The incidence and rate of return to the operating room for APJF have not been specifically investigated in individuals with sagittal imbalance. The purpose of this study was to report the incidence of APJF in patients with preoperative sagittal imbalance and the rate of return to the operating room for APJF. This study is based on a retrospective review of prospectively collected database of ASD patients. One hundred seventy-three consecutive patients were included with preoperative sagittal imbalance according to one of the following common parameters: sagittal vertical axis (SVA) greater than 50 mm, global sagittal alignment greater than 45°, or pelvic incidence minus lumbar lordosis greater than 10°. Outcome measure was presence and/or absence of APJF defined as fracture at the upper instrumented vertebra (UIV) or UIV+1, failure of UIV fixation, 15° or more proximal junctional kyphosis, or need for extension of instrumentation within 6 months of surgery. We performed radiographic measurements on X-rays at preoperative, immediate postoperative, and 6-month follow-up visits. The APJF rate was reported for the entire patient population with preoperative sagittal imbalance. Acute PJF incidence was calculated postoperatively for each of the accepted sagittal balance parameters and/or formulas. Patients with persistent postoperative sagittal imbalance were compared with the sagittally balanced group. We also assessed for threshold values. Acute PJF was observed in 60 of 173 patients (35%) and was least common in fusions with the UIV in the upper thoracic (UT) spine (p=.035). Of those who developed APJF, 21.7% required surgery. Proximal junctional kyphosis 15° or more was the most common form of APJF in fusions to the UT spine but least likely to need revision (p=.014

  3. Estimating the probability of allelic drop-out of STR alleles in forensic genetics

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2009-01-01

    In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop......-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework....

  4. Redox imbalance and mitochondrial abnormalities in the diabetic lung.

    Science.gov (United States)

    Wu, Jinzi; Jin, Zhen; Yan, Liang-Jun

    2017-04-01

    Although the lung is one of the least studied organs in diabetes, increasing evidence indicates that it is an inevitable target of diabetic complications. Nevertheless, the underlying biochemical mechanisms of lung injury in diabetes remain largely unexplored. Given that redox imbalance, oxidative stress, and mitochondrial dysfunction have been implicated in diabetic tissue injury, we set out to investigate mechanisms of lung injury in diabetes. The objective of this study was to evaluate NADH/NAD + redox status, oxidative stress, and mitochondrial abnormalities in the diabetic lung. Using STZ induced diabetes in rat as a model, we measured redox-imbalance related parameters including aldose reductase activity, level of poly ADP ribose polymerase (PAPR-1), NAD + content, NADPH content, reduced form of glutathione (GSH), and glucose 6-phophate dehydrogenase (G6PD) activity. For assessment of mitochondrial abnormalities in the diabetic lung, we measured the activities of mitochondrial electron transport chain complexes I to IV and complex V as well as dihydrolipoamide dehydrogenase (DLDH) content and activity. We also measured the protein content of NAD + dependent enzymes such as sirtuin3 (sirt3) and NAD(P)H: quinone oxidoreductase 1 (NQO1). Our results demonstrate that NADH/NAD + redox imbalance occurs in the diabetic lung. This redox imbalance upregulates the activities of complexes I to IV, but not complex V; and this upregulation is likely the source of increased mitochondrial ROS production, oxidative stress, and cell death in the diabetic lung. These results, together with the findings that the protein contents of DLDH, sirt3, and NQO1 all are decreased in the diabetic lung, demonstrate that redox imbalance, mitochondrial abnormality, and oxidative stress contribute to lung injury in diabetes. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Allelic Variation of Cytochrome P450s Drives Resistance to Bednet Insecticides in a Major Malaria Vector.

    Science.gov (United States)

    Ibrahim, Sulaiman S; Riveron, Jacob M; Bibby, Jaclyn; Irving, Helen; Yunta, Cristina; Paine, Mark J I; Wondji, Charles S

    2015-10-01

    Scale up of Long Lasting Insecticide Nets (LLINs) has massively contributed to reduce malaria mortality across Africa. However, resistance to pyrethroid insecticides in malaria vectors threatens its continued effectiveness. Deciphering the detailed molecular basis of such resistance and designing diagnostic tools is critical to implement suitable resistance management strategies. Here, we demonstrated that allelic variation in two cytochrome P450 genes is the most important driver of pyrethroid resistance in the major African malaria vector Anopheles funestus and detected key mutations controlling this resistance. An Africa-wide polymorphism analysis of the duplicated genes CYP6P9a and CYP6P9b revealed that both genes are directionally selected with alleles segregating according to resistance phenotypes. Modelling and docking simulations predicted that resistant alleles were better metabolizers of pyrethroids than susceptible alleles. Metabolism assays performed with recombinant enzymes of various alleles confirmed that alleles from resistant mosquitoes had significantly higher activities toward pyrethroids. Additionally, transgenic expression in Drosophila showed that flies expressing resistant alleles of both genes were significantly more resistant to pyrethroids compared with those expressing the susceptible alleles, indicating that allelic variation is the key resistance mechanism. Furthermore, site-directed mutagenesis and functional analyses demonstrated that three amino acid changes (Val109Ile, Asp335Glu and Asn384Ser) from the resistant allele of CYP6P9b were key pyrethroid resistance mutations inducing high metabolic efficiency. The detection of these first DNA markers of metabolic resistance to pyrethroids allows the design of DNA-based diagnostic tools to detect and track resistance associated with bednets scale up, which will improve the design of evidence-based resistance management strategies.

  6. Maintaining access to safe abortion and reducing sex ratio imbalances in Asia.

    Science.gov (United States)

    Ganatra, Bela

    2008-05-01

    High sex ratios at birth (108 boys to 100 girls or higher) are seen in China, Taiwan, South Korea and parts of India and Viet Nam. The imbalance is the result of son preference, accentuated by declining fertility. Prenatal sex detection with ultrasound followed by second trimester abortion is one of the ways sex selection manifests itself, but it is not the causative factor. Advocates and governments seeking to reverse this imbalance have largely prohibited sex detection tests and/or sex selective abortion, assuming these measures would reverse the trend. Such policies have been difficult to enforce and have met with only limited success. At the same time, such policies are starting to have adverse effects on the already limited access to safe and legal second trimester abortion for reasons other than sex selection. Moreover, the sex selection issue is being used as a platform for anti-abortion rhetoric by certain groups. Maintaining access to safe abortion and achieving a decline in high sex ratios are both important goals. Both are possible if the focus shifts to addressing the conditions that drive son preference.

  7. Human leukocyte antigen class II susceptibility conferring alleles among non-insulin dependent diabetes mellitus patients

    International Nuclear Information System (INIS)

    Tipu, H.N.; Ahmed, T.A.; Bashir, M.M.

    2010-01-01

    To determine the frequency of Human Leukocyte Antigen (HLA) class II susceptibility conferring alleles among type 2 Diabetes mellitus patients, in comparison with healthy controls. Cross-sectional comparative study. Patients with non-insulin dependent Diabetes mellitus meeting World Health Organization criteria were studied. These were compared with age and gender matched healthy control subjects. For each subject (patients as well as controls), DNA was extracted from ethylene diamine tetra-acetate sample and HLA class II DRB1 typing was carried out at allele group level (DRB1*01-DRB1*16) by sequence specific primers. Human leukocyte antigen DRB1 type was determined by agarose gel electrophoresis and results were recorded. Frequencies were determined as number of an allele divided by total number of alleles per group; p-value was computed using Pearson's chi-square test. Among the 100 patients, there were 63 males and 37 females with 68 controls. A total of 13 different HLA DRB1 alleles were detected, with DRB1*15 being the commonest in both the groups. The allele DRB1*13 had statistically significant higher frequency in patient group as compared to controls (p 0.005). HLA DRB1*13 was found with a significantly increased frequency in non-insulin dependent Diabetes mellitus. (author)

  8. Interlaboratory comparison of fig (Ficus carica L. microsatellite genotyping data and determination of reference alleles

    Directory of Open Access Journals (Sweden)

    Matjaž HLADNIK

    2018-04-01

    Full Text Available Microsatellites have been identified as the marker of choice in plant genotyping projects. However, due to length discrepancies obtained between different laboratories for the same allele, interlaboratory comparison of fingerprinting results is often a difficult task. The objectives of this study were to compare genotyping results of two laboratories, to evaluate genetic parameters of microsatellite markers and to determine reference allele sizes for fig cultivars from the Istrian peninsula.Genotyping results of ninety fig (Ficus carica L. accessions were comparable between the laboratories despite differences observed when comparing electropherograms of different capillary electrophoresis systems. Differences in lengths of the same alleles were detected due to different PCR methods and laboratory equipment, but the distances between alleles of the same locus were preserved. However, locus FSYC01 exhibited one allele dropout which led to misidentification of 28 heterozygotes as homozygote individuals suggesting this locus as unreliable. Allele dropout was assigned to the tail PCR technology or to a touchdown PCR protocol.Genotypes of twenty-four reference cultivars from the Istrian peninsula were confirmed by both laboratories. These results will contribute to the usage of markers with greater reliability, discrimination power and consequently, to more reliable standardization with other fig genotyping projects.

  9. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

    Directory of Open Access Journals (Sweden)

    Elissa J. Chesler

    2016-12-01

    Full Text Available Multi-parent populations (MPPs capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.

  10. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

    Science.gov (United States)

    Majumdar, Arunabha; Witte, John S; Ghosh, Saurabh

    2015-12-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors and genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g., MultiPhen (O'Reilly et al. []), have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. In this article, we explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (Binomial regression-based Association of Multivariate Phenotypes [BAMP]), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a single-nucleotide polymorphism (Distance-based Association of Multivariate Phenotypes [DAMP]). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association is compared with the genotype-level test MultiPhen's. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found to be substantially more powerful. All three tests are applied to two different real data and the results offer some support for the simulation study. We propose a hybrid approach for testing multivariate association that implements MultiPhen when Hardy-Weinberg Equilibrium (HWE) is violated and BAMP otherwise, because the allelic approaches assume HWE

  11. BRAF Gene Copy Number and Mutant Allele Frequency Correlate with Time to Progression in Metastatic Melanoma Patients Treated with MAPK Inhibitors.

    Science.gov (United States)

    Stagni, Camilla; Zamuner, Carolina; Elefanti, Lisa; Zanin, Tiziana; Bianco, Paola Del; Sommariva, Antonio; Fabozzi, Alessio; Pigozzo, Jacopo; Mocellin, Simone; Montesco, Maria Cristina; Chiarion-Sileni, Vanna; De Nicolo, Arcangela; Menin, Chiara

    2018-06-01

    Metastatic melanoma is characterized by complex genomic alterations, including a high rate of mutations in driver genes and widespread deletions and amplifications encompassing various chromosome regions. Among them, chromosome 7 is frequently gained in BRAF -mutant melanoma, inducing a mutant allele-specific imbalance. Although BRAF amplification is a known mechanism of acquired resistance to therapy with MAPK inhibitors, it is still unclear if BRAF copy-number variation and BRAF mutant allele imbalance at baseline can be associated with response to treatment. In this study, we used a multimodal approach to assess BRAF copy number and mutant allele frequency in pretreatment melanoma samples from 46 patients who received MAPK inhibitor-based therapy, and we analyzed the association with progression-free survival. We found that 65% patients displayed BRAF gains, often supported by chromosome 7 polysomy. In addition, we observed that 64% patients had a balanced BRAF -mutant/wild-type allele ratio, whereas 14% and 23% patients had low and high BRAF mutant allele frequency, respectively. Notably, a significantly higher risk of progression was observed in patients with a diploid BRAF status versus those with BRAF gains [HR, 2.86; 95% confidence interval (CI), 1.29-6.35; P = 0.01] and in patients with low percentage versus those with a balanced BRAF mutant allele percentage (HR, 4.54; 95% CI, 1.33-15.53; P = 0.016). Our data suggest that quantitative analysis of the BRAF gene could be useful to select the melanoma patients who are most likely to benefit from therapy with MAPK inhibitors. Mol Cancer Ther; 17(6); 1332-40. ©2018 AACR . ©2018 American Association for Cancer Research.

  12. Exploring new alleles for frost tolerance in winter rye.

    Science.gov (United States)

    Erath, Wiltrud; Bauer, Eva; Fowler, D Brian; Gordillo, Andres; Korzun, Viktor; Ponomareva, Mira; Schmidt, Malthe; Schmiedchen, Brigitta; Wilde, Peer; Schön, Chris-Carolin

    2017-10-01

    Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

  13. Lung ventilation-perfusion imbalance in pulmonary emphysema. Assessment with automated V/Q quotient SPECT

    International Nuclear Information System (INIS)

    Suga, Kazuyoshi; Kawakami, Yasuhiko; Koike, Hiroaki; Iwanaga, Hideyuki; Tokuda, Osamu; Okada, Munemasa; Matsunaga, Naofumi

    2010-01-01

    Tc-99m-Technegas-macro-aggregated albumin (MAA) single photon emission computed tomography (SPECT)-derived ventilation (V)/perfusion (Q) quotient SPECT was used to assess lung V-Q imbalance in patients with pulmonary emphysema. V/Q quotient SPECT and V/Q profile were automatically built in 38 patients with pulmonary emphysema and 12 controls, and V/Q distribution and V/Q profile parameters were compared. V/Q distribution on V/Q quotient SPECT was correlated with low attenuation areas (LAA) on density-mask computed tomography (CT). Parameters of V/Q profile such as the median, standard deviation (SD), kurtosis and skewness were proposed to objectively evaluate the severity of lung V-Q imbalance. In contrast to uniform V/Q distribution on V/Q quotient SPECT and a sharp peak with symmetrical V/Q distribution on V/Q profile in controls, lung areas showing heterogeneously high or low V/Q and flattened peaks with broadened V/Q distribution were frequently seen in patients with emphysema, including lung areas with only slight LAA. V/Q distribution was also often asymmetric regardless of symmetric LAA. All the proposed parameters of V/Q profile in entire lungs of patients with emphysema showed large variations compared with controls; SD and kurtosis were significantly different from controls (P<0.0001 and P<0.001, respectively), and a significant correlation was found between SD and A-aDO2 (P<0.0001). V/Q quotient SPECT appears to be more sensitive to detect emphysematous lungs compared with morphologic CT in patients with emphysema. SD and kurtosis of V/Q profile can be adequate parameters to assess the severity of lung V-Q imbalance causing gas-exchange impairment in patients with emphysema. (author)

  14. A comparison of traditional and quantitative analysis of acid-base imbalances in hypoalbuminemic dogs.

    Science.gov (United States)

    Torrente, Carlos; Manzanilla, Edgar G; de Gopegui, Rafael Ruiz

    2014-01-01

    To compare the traditional (HH) and quantitative approaches used for the evaluation of the acid-base balance in hypoalbuminemic dogs. Prospective observational study. ICU of a veterinary teaching hospital. One hundred and five client-owned dogs. Jugular venous blood samples were collected from each patient on admission to determine: total plasma protein (TP), albumin (Alb), blood urea nitrogen (BUN), glucose (Glu), hematocrit (HCT), Na(+) , Cl(-) , K(+) , phosphate (Pi ), pH, PvCO2, bicarbonate (HCO3 (-) ), anion gap (AG), adjusted anion gap for albumin (AGalb ) or phosphate (AGalb-phos ), standardized base excess (SBE), strong ion difference (SID), concentration of nonvolatile weak buffers (Atot ), and strong ion gap (SIG). Patients were divided in 2 groups according to the severity of the hypoalbuminemia: mild (Alb = 21-25 g/L) and severe (Alb ≤20 g/L). All parameters were compared among groups. Patients with severe hypoalbuminemia showed significant decrease in TP (P = 0.011), Atot (P = 0.050), and a significant increase in adjusted AG (P = 0.048) and the magnitude of SIG (P = 0.011) compared to animals with mild hypoalbuminemia. According to the HH approach, the most frequent imbalances were simple disorders (51.4%), primarily metabolic acidosis (84.7%) associated with a high AG acidosis. However, when using the quantitative method, 58.1% of patients had complex disorders, with SIG acidosis (74.3%) and Atot alkalosis (33.3%) as the most frequent acid-base imbalances. Agreement between methods only matched in 32 cases (kappa acid-base balance was poor and many imbalances detected using the quantitative approach were missed using the HH approach. Further studies are necessary to confirm the clinical utility of using the quantitative approach in the decision-making process of the severely ill hypoalbuminemic patients. © Veterinary Emergency and Critical Care Society 2014.

  15. Modified Mahalanobis Taguchi System for Imbalance Data Classification

    Directory of Open Access Journals (Sweden)

    Mahmoud El-Banna

    2017-01-01

    Full Text Available The Mahalanobis Taguchi System (MTS is considered one of the most promising binary classification algorithms to handle imbalance data. Unfortunately, MTS lacks a method for determining an efficient threshold for the binary classification. In this paper, a nonlinear optimization model is formulated based on minimizing the distance between MTS Receiver Operating Characteristics (ROC curve and the theoretical optimal point named Modified Mahalanobis Taguchi System (MMTS. To validate the MMTS classification efficacy, it has been benchmarked with Support Vector Machines (SVMs, Naive Bayes (NB, Probabilistic Mahalanobis Taguchi Systems (PTM, Synthetic Minority Oversampling Technique (SMOTE, Adaptive Conformal Transformation (ACT, Kernel Boundary Alignment (KBA, Hidden Naive Bayes (HNB, and other improved Naive Bayes algorithms. MMTS outperforms the benchmarked algorithms especially when the imbalance ratio is greater than 400. A real life case study on manufacturing sector is used to demonstrate the applicability of the proposed model and to compare its performance with Mahalanobis Genetic Algorithm (MGA.

  16. Metabolic disorders in adipocytokine imbalance and gestational complications

    Directory of Open Access Journals (Sweden)

    Natalya B. Chabanova

    2017-06-01

    Full Text Available Adipose tissue as an endocrine organ synthesizes a large number of biologically active substances, adipocytokines, which have both local and systemic effects influencing the vascular wall, tissue sensitivity to insulin, glucose metabolism, and systemic inflammation. The data obtained from clinical and experimental studies demonstrate the close relationship between the imbalance of adipocytokines and pregnancy complications such as insulin resistance, gestational diabetes, and preeclampsia. In this connection, close attention of obstetrician-gynecologists and endocrinologists is focused on etiopathogenic aspects of the formation of gestational complications with metabolic disorders caused by an imbalance of adipocytokines with maternal obesity and to the search for markers of these disorders. The review presents the current literature data on adipose tissue hormones and their influence on the course of a gestational process.

  17. Spinal pedicle subtraction osteotomy for fixed sagittal imbalance patients

    Science.gov (United States)

    Hyun, Seung-Jae; Kim, Yongjung J; Rhim, Seung-Chul

    2013-01-01

    In addressing spinal sagittal imbalance through a posterior approach, the surgeon now may choose from among a variety of osteotomy techniques. Posterior column osteotomies such as the facetectomy or Ponte or Smith-Petersen osteotomy provide the least correction, but can be used at multiple levels with minimal blood loss and a lower operative risk. Pedicle subtraction osteotomies provide nearly 3 times the per-level correction of Ponte/Smith-Petersen osteotomies; however, they carry increased technical demands, longer operative time, and greater blood loss and associated significant morbidity, including neurological injury. The literature focusing on pedicle subtraction osteotomy for fixed sagittal imbalance patients is reviewed. The long-term overall outcomes, surgical tips to reduce the complications and suggestions for their proper application are also provided. PMID:24340276

  18. Modified Mahalanobis Taguchi System for Imbalance Data Classification

    Science.gov (United States)

    2017-01-01

    The Mahalanobis Taguchi System (MTS) is considered one of the most promising binary classification algorithms to handle imbalance data. Unfortunately, MTS lacks a method for determining an efficient threshold for the binary classification. In this paper, a nonlinear optimization model is formulated based on minimizing the distance between MTS Receiver Operating Characteristics (ROC) curve and the theoretical optimal point named Modified Mahalanobis Taguchi System (MMTS). To validate the MMTS classification efficacy, it has been benchmarked with Support Vector Machines (SVMs), Naive Bayes (NB), Probabilistic Mahalanobis Taguchi Systems (PTM), Synthetic Minority Oversampling Technique (SMOTE), Adaptive Conformal Transformation (ACT), Kernel Boundary Alignment (KBA), Hidden Naive Bayes (HNB), and other improved Naive Bayes algorithms. MMTS outperforms the benchmarked algorithms especially when the imbalance ratio is greater than 400. A real life case study on manufacturing sector is used to demonstrate the applicability of the proposed model and to compare its performance with Mahalanobis Genetic Algorithm (MGA). PMID:28811820

  19. Vorticity imbalance and stability in relation to convection

    Science.gov (United States)

    Read, W. L.; Scoggins, J. R.

    1977-01-01

    A complete synoptic-scale vorticity budget was related to convection storm development in the eastern two-thirds of the United States. The 3-h sounding interval permitted a study of time changes of the vorticity budget in areas of convective storms. Results of analyses revealed significant changes in values of terms in the vorticity equation at different stages of squall line development. Average budgets for all areas of convection indicate systematic imbalance in the terms in the vorticity equation. This imbalance resulted primarily from sub-grid scale processes. Potential instability in the lower troposphere was analyzed in relation to the development of convective activity. Instability was related to areas of convection; however, instability alone was inadequate for forecast purposes. Combinations of stability and terms in the vorticity equation in the form of indices succeeded in depicting areas of convection better than any one item separately.

  20. Spin imbalance effect on the Larkin-Ovchinnikov-Fulde-Ferrel state

    International Nuclear Information System (INIS)

    Yoshii, Ryosuke; Tsuchiya, Shunji; Marmorini, Giacomo; Nitta, Muneto

    2011-01-01

    We study spin imbalance effects on the Larkin-Ovchinnikov-Fulde-Ferrel (LOFF) state relevant for superconductors under a strong magnetic field and spin polarized ultracold Fermi gas. We obtain the exact solution for the condensates with arbitrary spin imbalance and the fermion spectrum perturbatively in the presence of small spin imbalance. We also obtain fermion zero mode exactly without perturbation theory.

  1. Prevalence and distribution of muscle-imbalance in the human body ...

    African Journals Online (AJOL)

    The phenomenon of muscle imbalance is pandemic, and may contribute to problems such as poor posture, low back pain. Significant is the fact that muscle imbalance may influence the motor patterning process. Key words: Muscle imbalance, low back pain, posture, malposture, withdrawal response. (Af. J. Physical, Health ...

  2. KNEE ISOKINETIC TORQUE IMBALANCE IN FEMALE FUTSAL PLAYERS

    Directory of Open Access Journals (Sweden)

    Ana Carolina de Mello Alves Rodrigues

    Full Text Available ABSTRACT Introduction: The specificity of sports training can lead to muscle specialization with a possible change in the natural hamstring/quadriceps torque ratio (HQ ratio, constituting a risk factor for muscle injury at the joint angles in which muscle imbalance may impair dynamic stability. Objective: The aim was to evaluate the torque distribution of the hamstrings and quadriceps and the HQ ratio throughout the range of motion in order to identify possible muscle imbalances at the knee of female futsal athletes. Methods: Nineteen amateur female futsal athletes had their dominant limb HQ ratio evaluated in a series of five maximum repetitions of flexion/extension of the knee at 180°/second in the total joint range of motion (30° to 80°. The peak flexor and extensor torque and the HQ ratio (% were compared each 5° of knee motion using one-way repeated measures ANOVA and Tukey’s post hoc test (p<0.05 to determine the joint angles that present muscular imbalance. Results: Quadriceps torque was higher than 50° to 60° of knee flexion, while hamstrings torque was higher than 55° to 65°. The HQ ratio presented lower values than 30° to 45° of knee flexion and four athletes presented values lower than 60%, which may represent a risk of injury. However, the HQ ratio calculated by the peak torque showed only one athlete with less than 60%. Conclusion: The HQ ratio analyzed throughout the knee range of motion allowed identifying muscle imbalance at specific joint angles in female futsal players.

  3. Geographical Labor Market Imbalances by Chiara Mussida and Francesco Pastore

    Directory of Open Access Journals (Sweden)

    Daniela PASNICU

    2016-04-01

    Full Text Available The book, entitled Geographical Labor Market Imbalances represents a collective volume of outstanding scientific papers concerning regional issues, which were presented at the XXVII National Conference of Labour Economics organized by AIEL (Italian Association of Labor Economics, the Department of Law of SecundaUniversità di Napoli and the Departments of Economic and Social Sciences of the UniversitàCattolica del SacroCuore (Piacenza, 27-28 September 2012.

  4. Decentralisation of GST Services and Vertical Imbalances in Pakistan

    OpenAIRE

    Iffat Ara; Muhammad Sabir

    2010-01-01

    In Pakistan, provincial finances largely hinge on federal transfers from the divisible pool via the National Finance Commission (NFC) Award. While provincial share in tax revenue is less than 5 percent, provincial share in expenditure is over 25 percent, indicating dependence on federal transfers and the extent of vertical fiscal imbalance. The sustainability of public services provided by the provinces requires enough “own” revenues rather than reliance on federal transfers and grants. The 7...

  5. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... the normal cellular process of replication of DNA molecules. ... probability of a certain genetic variant (alleles) occuring in ... have preservatives that hinder spoilage and are easily packaged .... Allele distribution at Nine STR.

  6. A new electrophoresis technique to separate microsatellite alleles ...

    African Journals Online (AJOL)

    A new electrophoresis technique to separate microsatellite alleles* ... African Journal of Biotechnology ... with the CEQTM 8000 Genetic Analysis System and ABI 3130xl DNA Sequencer easily separated products and determined allelic size, ...

  7. Allele specific expression and methylation in the bumblebee, Bombus terrestris

    Directory of Open Access Journals (Sweden)

    Zoë Lonsdale

    2017-09-01

    Full Text Available The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression.

  8. Comparative frequency and allelic distribution of ABO and Rh (D ...

    African Journals Online (AJOL)

    Gourab Dewan

    2015-02-18

    Feb 18, 2015 ... desh and having borders with India and Myanmar (Fig. 1). It is a hilly area with ..... calculated allelic frequencies for ABO/Rh systems previously. Therefore, allelic .... in backward caste population of Uttar Pradesh, India. Not Sci.

  9. Association mapping and favourable QTL alleles for fibre quality ...

    Indian Academy of Sciences (India)

    Cheng-Guang Dong

    A total of 201 markers were polymorphic and generated 394 allele loci, and 403 ... identified as containing favourable allele loci related to fibre quality traits. The identified .... environment. Field management followed respective local practices.

  10. Relative frequencies of DRB1*11 alleles and their DRB3 associations in five major population groups in a United States bone marrow registry.

    Science.gov (United States)

    Tang, T F; Huang, A Y; Pappas, A; Slack, R; Ng, J; Hartzman, R J; Hurley, C K

    2000-08-01

    One hundred sixty-one individuals from each of five US population groups, Caucasians (CAU), African Americans (AFA), Asians/Pacific Islanders (API), Hispanics (HIS), and Native Americans (NAT), were randomly selected from a volunteer bone marrow registry database consisting of 14,452 HLA-DRB1*11 positive individuals. This sampling provided at least an 80% probability of detecting a rare allele that occurred at 1% in the DRB1*11 positive population. Samples were typed for DRB1*11 alleles by polymerase chain reaction-sequence specific oligonucleotide probe typing (PCR-SSOP). A total of 10 DRB1*11 alleles out of 27 possible alleles were detected. The distribution and diversity of DRB1*11 alleles varied among populations although DRB1*1101 was the predominant DRB1*11 allele in all populations. Caucasians were the least diversified; only four common alleles (DRB1*1101-*1104) were observed. As well as the four common alleles, other groups also carried one or two other less frequent alleles including DRB1*1105 (API), *1106 (API), *1110 (AFA), *1114 (HIS), *1115 (NAT), and *1117 (AFA). A subset (418) of these individuals were also typed for DRB3 alleles. Most (97.6%) showed a strong association of DRB1*11 with DRB3*0202.

  11. Mass imbalances in EPANET water-quality simulations

    Science.gov (United States)

    Davis, Michael J.; Janke, Robert; Taxon, Thomas N.

    2018-04-01

    EPANET is widely employed to simulate water quality in water distribution systems. However, in general, the time-driven simulation approach used to determine concentrations of water-quality constituents provides accurate results only for short water-quality time steps. Overly long time steps can yield errors in concentration estimates and can result in situations in which constituent mass is not conserved. The use of a time step that is sufficiently short to avoid these problems may not always be feasible. The absence of EPANET errors or warnings does not ensure conservation of mass. This paper provides examples illustrating mass imbalances and explains how such imbalances can occur because of fundamental limitations in the water-quality routing algorithm used in EPANET. In general, these limitations cannot be overcome by the use of improved water-quality modeling practices. This paper also presents a preliminary event-driven approach that conserves mass with a water-quality time step that is as long as the hydraulic time step. Results obtained using the current approach converge, or tend to converge, toward those obtained using the preliminary event-driven approach as the water-quality time step decreases. Improving the water-quality routing algorithm used in EPANET could eliminate mass imbalances and related errors in estimated concentrations. The results presented in this paper should be of value to those who perform water-quality simulations using EPANET or use the results of such simulations, including utility managers and engineers.

  12. Systemic Redox Imbalance in Chronic Kidney Disease: A Systematic Review

    Science.gov (United States)

    Kaltsatou, Antonia; Jamurtas, Athanasios Z.; Koutedakis, Yiannis; Stefanidis, Ioannis; Sakkas, Giorgos K.

    2016-01-01

    Patients with chronic kidney disease (CKD) experience imbalance between oxygen reactive species (ROS) production and antioxidant defenses leading to cell and tissue damage. However, it remains unclear at which stage of renal insufficiency the redox imbalance becomes more profound. The aim of this systematic review was to provide an update on recent advances in our understanding of how the redox status changes in the progression of renal disease from predialysis stages 1 to 4 to end stage 5 and whether the various treatments and dialysis modalities influence the redox balance. A systematic review was conducted searching PubMed and Scopus by using the Cochrane and PRISMA guidelines. In total, thirty-nine studies met the inclusion criteria and were reviewed. Even from an early stage, imbalance in redox status is evident and as the kidney function worsens it becomes more profound. Hemodialysis therapy per se seems to negatively influence the redox status by the elevation of lipid peroxidation markers, protein carbonylation, and impairing erythrocyte antioxidant defense. However, other dialysis modalities do not so far appear to confer advantages. Supplementation with antioxidants might assist and should be considered as an early intervention to halt premature atherogenesis development at an early stage of CKD. PMID:27563376

  13. Systemic Redox Imbalance in Chronic Kidney Disease: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Konstantina P. Poulianiti

    2016-01-01

    Full Text Available Patients with chronic kidney disease (CKD experience imbalance between oxygen reactive species (ROS production and antioxidant defenses leading to cell and tissue damage. However, it remains unclear at which stage of renal insufficiency the redox imbalance becomes more profound. The aim of this systematic review was to provide an update on recent advances in our understanding of how the redox status changes in the progression of renal disease from predialysis stages 1 to 4 to end stage 5 and whether the various treatments and dialysis modalities influence the redox balance. A systematic review was conducted searching PubMed and Scopus by using the Cochrane and PRISMA guidelines. In total, thirty-nine studies met the inclusion criteria and were reviewed. Even from an early stage, imbalance in redox status is evident and as the kidney function worsens it becomes more profound. Hemodialysis therapy per se seems to negatively influence the redox status by the elevation of lipid peroxidation markers, protein carbonylation, and impairing erythrocyte antioxidant defense. However, other dialysis modalities do not so far appear to confer advantages. Supplementation with antioxidants might assist and should be considered as an early intervention to halt premature atherogenesis development at an early stage of CKD.

  14. Imbalance between abstract and concrete repetitive thinking modes in schizophrenia.

    Science.gov (United States)

    Maurage, Pierre; Philippot, Pierre; Grynberg, Delphine; Leleux, Dominique; Delatte, Benoît; Mangelinckx, Camille; Belge, Jan-Baptist; Constant, Eric

    2017-10-01

    Repetitive thoughts can be divided in two modes: abstract/analytic (decontextualized and dysfunctional) and concrete/experiential (problem-focused and adaptive). They constitute a transdiagnostic process involved in many psychopathological states but have received little attention in schizophrenia, as earlier studies only indexed increased ruminations (related to dysfunctional repetitive thoughts) without jointly exploring both modes. This study explored the two repetitive thinking modes, beyond ruminations, to determine their imbalance in schizophrenia. Thirty stabilized patients with schizophrenia and 30 matched controls completed the Repetitive Response Scale and the Mini Cambridge-Exeter Repetitive Thought Scale, both measuring repetitive thinking modes. Complementary measures related to schizophrenic symptomatology, depression and anxiety were also conducted. Compared to controls, patients with schizophrenia presented an imbalance between repetitive thinking modes, with increased abstract/analytic and reduced concrete/experiential thoughts, even after controlling for comorbidities. Schizophrenia is associated with stronger dysfunctional repetitive thoughts (i.e. abstract thinking) and impaired ability to efficiently use repetitive thinking for current problem-solving (i.e. concrete thinking). This imbalance confirms the double-faced nature of repetitive thinking modes, whose influence on schizophrenia's symptomatology should be further investigated. The present results also claim for evaluating these processes in clinical settings and for rehabilitating the balance between opposite repetitive thinking modes. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Transfer Learning for Class Imbalance Problems with Inadequate Data.

    Science.gov (United States)

    Al-Stouhi, Samir; Reddy, Chandan K

    2016-07-01

    A fundamental problem in data mining is to effectively build robust classifiers in the presence of skewed data distributions. Class imbalance classifiers are trained specifically for skewed distribution datasets. Existing methods assume an ample supply of training examples as a fundamental prerequisite for constructing an effective classifier. However, when sufficient data is not readily available, the development of a representative classification algorithm becomes even more difficult due to the unequal distribution between classes. We provide a unified framework that will potentially take advantage of auxiliary data using a transfer learning mechanism and simultaneously build a robust classifier to tackle this imbalance issue in the presence of few training samples in a particular target domain of interest. Transfer learning methods use auxiliary data to augment learning when training examples are not sufficient and in this paper we will develop a method that is optimized to simultaneously augment the training data and induce balance into skewed datasets. We propose a novel boosting based instance-transfer classifier with a label-dependent update mechanism that simultaneously compensates for class imbalance and incorporates samples from an auxiliary domain to improve classification. We provide theoretical and empirical validation of our method and apply to healthcare and text classification applications.

  16. Money and age in schools: Bullying and power imbalances.

    Science.gov (United States)

    Chaux, Enrique; Castellanos, Melisa

    2015-05-01

    School bullying continues to be a serious problem around the world. Thus, it seems crucial to clearly identify the risk factors associated with being a victim or a bully. The current study focused in particular on the role that age and socio-economic differences between classmates could play on bullying. Logistic and multilevel analyses were conducted using data from 53,316 5th and 9th grade students from a representative sample of public and private Colombian schools. Higher age and better family socio-economic conditions than classmates were risk factors associated with being a bully, while younger age and poorer socio-economic conditions than classmates were associated with being a victim of bullying. Coming from authoritarian families or violent neighborhoods, and supporting beliefs legitimizing aggression, were also associated with bullying and victimization. Empathy was negatively associated with being a bully, and in some cases positively associated with being a victim. The results highlight the need to take into account possible sources of power imbalances, such as age and socio-economic differences among classmates, when seeking to prevent bullying. In particular, interventions focused on peer group dynamics might contribute to avoid power imbalances or to prevent power imbalances from becoming power abuse. Aggr. Behav. 41:280-293, 2015. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

  17. On broadened definitions of instability for stars in thermal imbalance

    International Nuclear Information System (INIS)

    Simon, N.R.

    1977-01-01

    The classical theory of stability of dynamical systems is employed to demonstrate that traditional definitions of pulsational instability cannot be directly applied to stars in thermal imbalance. In particular, it is shown that, for the case of thermal imbalance, pulsational displacements and pulsational velocities have separate and distinct e-folding times. This being true, a broadened set of definitions becomes necessary, and such a set is formulated again with reference to the classical theory. In accordance with the new definitions, it is argued that the development of observable pulsations requires as a necessary condition infinitesimal instability of both absolute displacement and velocity. If either one is unstable without the other, this constitutes a class of (probably) non-pulsational instability, not previously treated in the astrophysical literature. Finally, it is shown that the stability of stars in thermal imbalance may be evaluated according to the present definitions by employing either of two existing theories - the energy approach due to Demaret (1974; 1975; 1976) or the small perturbation technique of Cox et al. (1973). (Auth.)

  18. Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Gowda Cholenahalli LL

    2008-10-01

    Full Text Available Abstract Background Plant genetic resources (PGR are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA, 117 in South and South East Asia (SSEA, and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53% than kabuli (46%, while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78% of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents

  19. An allele of the crm gene blocks cyanobacterial circadian rhythms.

    Science.gov (United States)

    Boyd, Joseph S; Bordowitz, Juliana R; Bree, Anna C; Golden, Susan S

    2013-08-20

    The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (rpaA) is the only gene other than kaiA, kaiB, and kaiC, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of rpaA in Synechococcus elongatus PCC 7942 termed crm (for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The crm ORF complements the defect when expressed in trans, but only if it can be translated, suggesting that crm encodes a small protein. The crm1 insertion allele phenotypes are distinct from those of an rpaA null; crm1 mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the crm1 mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA.

  20. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

    NARCIS (Netherlands)

    Geest, van Geert; Bourke, Peter M.; Voorrips, Roeland E.; Marasek-Ciolakowska, Agnieszka; Liao, Yanlin; Post, Aike; Meeteren, van Uulke; Visser, Richard G.F.; Maliepaard, Chris; Arens, Paul

    2017-01-01

    Key message: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL.Abstract: Construction and use of linkage maps are challenging in hexaploids with polysomic

  1. Study on the association of BoLA-DRB3.2 alleles with clinical ...

    African Journals Online (AJOL)

    USER

    2010-04-12

    Apr 12, 2010 ... analysis (HA) in a non-denaturing gel, successfully detected the resistant genotype to ... PHS, polish heath sheep; PLS polish lowland sheep; SCC, ... of the MHC genes and their possible role in disease ... alleles with clinical mastitis in Sarabi and Iranian Holstein cattle, ..... Nomenclature for factors of the.

  2. How large are the consequences of covariate imbalance in cluster randomized trials: a simulation study with a continuous outcome and a binary covariate at the cluster level.

    Science.gov (United States)

    Moerbeek, Mirjam; van Schie, Sander

    2016-07-11

    The number of clusters in a cluster randomized trial is often low. It is therefore likely random assignment of clusters to treatment conditions results in covariate imbalance. There are no studies that quantify the consequences of covariate imbalance in cluster randomized trials on parameter and standard error bias and on power to detect treatment effects. The consequences of covariance imbalance in unadjusted and adjusted linear mixed models are investigated by means of a simulation study. The factors in this study are the degree of imbalance, the covariate effect size, the cluster size and the intraclass correlation coefficient. The covariate is binary and measured at the cluster level; the outcome is continuous and measured at the individual level. The results show covariate imbalance results in negligible parameter bias and small standard error bias in adjusted linear mixed models. Ignoring the possibility of covariate imbalance while calculating the sample size at the cluster level may result in a loss in power of at most 25 % in the adjusted linear mixed model. The results are more severe for the unadjusted linear mixed model: parameter biases up to 100 % and standard error biases up to 200 % may be observed. Power levels based on the unadjusted linear mixed model are often too low. The consequences are most severe for large clusters and/or small intraclass correlation coefficients since then the required number of clusters to achieve a desired power level is smallest. The possibility of covariate imbalance should be taken into account while calculating the sample size of a cluster randomized trial. Otherwise more sophisticated methods to randomize clusters to treatments should be used, such as stratification or balance algorithms. All relevant covariates should be carefully identified, be actually measured and included in the statistical model to avoid severe levels of parameter and standard error bias and insufficient power levels.

  3. Allele and genotype frequencies of -β lactoglobulin gene in Iranian ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... Blood samples were supplied from 80 Najdi cattle and 80 buffalo from different cities of Khouzestan province. ... The allele B of β-Lactoglobulin occurred at a higher frequency than the allele A in both. Najdi cattle and buffalo. .... that of the B allele in both groups of animals studied. Expected heterozygosity ...

  4. Directional Positive Selection on an Allele of Arbitrary Dominance

    OpenAIRE

    Teshima, Kosuke M.; Przeworski, Molly

    2006-01-01

    Most models of positive directional selection assume codominance of the beneficial allele. We examine the importance of this assumption by implementing a coalescent model of positive directional selection with arbitrary dominance. We find that, for a given mean fixation time, a beneficial allele has a much weaker effect on diversity at linked neutral sites when the allele is recessive.

  5. Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple.

    Science.gov (United States)

    Ma, X; Cai, Z; Liu, W; Ge, S; Tang, L

    2017-09-01

    The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

  6. Dual-hop amplify-and-forward cooperative relaying in the presence of Tx and Rx in-phase and quadrature-phase imbalance

    KAUST Repository

    Qi, Jian

    2014-02-13

    In this study, dual-hop channel state information-assisted amplify-and-forward (AF) cooperative systems in the presence of in-phase and quadrature-phase (I/Q) imbalance, which refers to the mismatch between components in the I and Q branches, are investigated. First, the authors analyse the performance of the considered AF cooperative protocol without compensation for the I/Q imbalance as the benchmark. Then, a compensation algorithm for the I/Q imbalance is proposed, which makes use of the received signals at the destination, from the source and the relay nodes, together with their conjugations to detect the transmitted signal. Moreover, the authors study the considered AF cooperative system implemented with the opportunistic relay selection and the proposed compensation mechanism for the I/Q imbalance. The performance of the AF cooperative system under study is evaluated in terms of average symbol error probability, which is derived by considering transmission in a Rayleigh fading environment. Numerical results are provided and show that the proposed compensation algorithm can efficiently mitigate the effect of the I/Q imbalance. On the other hand, it is observed that the AF cooperative system with opportunistic relay selection acquires a performance gain beyond that without relay selection.

  7. Identification and distribution of three serologically undetected alleles of HLA-DR by oligonucleotide x DNA typing analysis

    International Nuclear Information System (INIS)

    Tiercy, J.M.; Gorski, J.; Jeannet, M.; Mach, B.

    1988-01-01

    Recent progress in the molecular biology of human major histocompatibility complex class II genes (HLA-DP, -DQ, -DR) have shown that the genetic complexity and allelic polymorphism are greater than expected. In the case of HLA-DR, three DR β-chain loci have been identified and linked, two of which (DR βI and DR βIII, now assigned names HLA-DR1B and HLA-DR3B) are functional. The authors have shown that the HLA micropolymorphism detected at the DNA sequence level can easily be analyzed by hybridization with allele-specific oligonucleotides (HLA oligotyping). In the case of the HLA DRw52 supertypic specificity, which includes the DR3, DR5, DRw6, and DRw8 haplotypes, three alleles, referred to as DRw52a, DRw52b, and DRw52c, have recently been identified at the HLA-DR3B locus by DNA sequencing. Hybridization with locus- and allele-specific oligonucleotide probes (designated 52a, 52b, and 52c) has been performed on DNA from normal individuals forming a panel of 82 haplotypes to establish the distribution of these three alleles. Individuals of the DR3 haplotype had either the DRw52a or DRw52b allele, and individuals of extended haplotype HLA-A1,B8,DR3 had only the DRw52a allele. DR5 individuals all had the DRw52b allele, while individuals of DRw6 haplotype had the DRw52a, -52b, or -52c allele. None of these three alleles are found in DRw8 individuals. Analysis of this micropolymorphism, undetectable by common typing procedures, is therefore now operational for more accurate HLA matching for transplantation and for improving correlations between HLA and disease susceptibility

  8. Plasminogen alleles influence susceptibility to invasive aspergillosis.

    Directory of Open Access Journals (Sweden)

    Aimee K Zaas

    2008-06-01

    Full Text Available Invasive aspergillosis (IA is a common and life-threatening infection in immunocompromised individuals. A number of environmental and epidemiologic risk factors for developing IA have been identified. However, genetic factors that affect risk for developing IA have not been clearly identified. We report that host genetic differences influence outcome following establishment of pulmonary aspergillosis in an exogenously immune suppressed mouse model. Computational haplotype-based genetic analysis indicated that genetic variation within the biologically plausible positional candidate gene plasminogen (Plg; Gene ID 18855 correlated with murine outcome. There was a single nonsynonymous coding change (Gly110Ser where the minor allele was found in all of the susceptible strains, but not in the resistant strains. A nonsynonymous single nucleotide polymorphism (Asp472Asn was also identified in the human homolog (PLG; Gene ID 5340. An association study within a cohort of 236 allogeneic hematopoietic stem cell transplant (HSCT recipients revealed that alleles at this SNP significantly affected the risk of developing IA after HSCT. Furthermore, we demonstrated that plasminogen directly binds to Aspergillus fumigatus. We propose that genetic variation within the plasminogen pathway influences the pathogenesis of this invasive fungal infection.

  9. Sputum-Based Molecular Biomarkers for the Early Detection of Lung Cancer: Limitations and Promise

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Connie E. [Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016 (United States); Tchou-Wong, Kam-Meng; Rom, William N., E-mail: william.rom@nyumc.org [Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016 (United States); Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987 (United States)

    2011-07-19

    Lung cancer is the leading cause of cancer deaths, with an overall survival of 15% at five years. Biomarkers that can sensitively and specifically detect lung cancer at early stage are crucial for improving this poor survival rate. Sputum has been the target for the discovery of non-invasive biomarkers for lung cancer because it contains airway epithelial cells, and molecular alterations identified in sputum are most likely to reflect tumor-associated changes or field cancerization caused by smoking in the lung. Sputum-based molecular biomarkers include morphology, allelic imbalance, promoter hypermethylation, gene mutations and, recently, differential miRNA expression. To improve the sensitivity and reproducibility of sputum-based biomarkers, we recommend standardization of processing protocols, bronchial epithelial cell enrichment, and identification of field cancerization biomarkers.

  10. The Imbalance of Water in Nature as System

    Science.gov (United States)

    Kontar, V. A.; Imbalance of Water in Nature

    2011-12-01

    Consider some of the water-containing area. Choose some the factors which we consider important to the system. The system contains a system factors, and the external environment these factors doesn't contain. Between the system and the external environment must be some flows into the system, out of the system and along the border. If the flows into and out of the system are not equal, that means within the system exactly something is happening. But the equality of the flows into and out of the system does not mean that within the system nothing happens. It is extremely important to determine the time factor. Everything has a beginning and an end. Each factor has its own life from 0 to 1, as well as their watches. Thus that within the system and the environment at the same time are going a lot of the watches and each watch is going by their own pace. System-wide time is needed to describe the system as a whole and to be able to re-measure the individual time of each factor. It is also very important to identify each factor of the system, environment and border. Definition of each particular factor depends on the level of our knowledge. There are many examples where one factor was divided into several, and vice versa, several factors have combined in one or even disappear as a non-existent. Each factor is determined by specific people for reasons of convenience, the specific of tasks, the possible accuracy of measurement, available resources, etc. The development of the science and applications are going to the direction of the clearer separation of factors and the precision of their measurements. Now is extremely important to more clearly define the boundaries of systems, factors and the allowed accuracy of their measurements. With such a revision, many previously balanced situations become to the imbalance. There are many specific details for each case, but they do not change the basic approach described above. If not clearly resolved the questions listed above so

  11. Policy and organizational implications of gender imbalance in the NHS.

    Science.gov (United States)

    Miller, Karen

    2007-01-01

    The purpose of the paper is to examine the policy and organizational implications of gender imbalance in management, which research suggests exists in the NHS. The research in this paper involved a qualitative approach with an analysis of elite interviews conducted with a non-random sample of officials involved in health policy and interviews with a random sample of senior managers in NHS Scotland. The research formed part of a larger study, which explored the enablers and inhibitors to female career progression in various Scottish sectors. The paper finds that gender imbalance in management exists in the NHS. This is manifested in a masculine organizational context, leadership and policy decision-making process, which have implications for female career advancement opportunities and subsequently access to macro policy decisions. The paper involved a sample (30 percent) of senior managers and examined policy processes in NHS Scotland. To improve the external validity of the findings further research should be conducted in NHS organizations in England and Wales. The findings in the paper suggest that gender imbalance in management and a masculine organizational context and leadership style within the NHS create a less than conducive environment for female employees. This has practical implications in terms of levels of part-time employment, career progression and attrition rates. The paper adds to the debate of gender and organizational studies by examining the health sector, which has high levels of female employment but low levels of female representation at senior management levels. The paper therefore adds to an often-neglected area of study, women in leadership and senior managerial positions. The paper is original in its approach by examining the micro and meso organizational dimensions which impact on women's ability to influence macro health policy.

  12. DQB1*06:02 allele-specific expression varies by allelic dosage, not narcolepsy status

    DEFF Research Database (Denmark)

    Weiner Lachmi, Karin; Lin, Ling; Kornum, Birgitte Rahbek

    2012-01-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single-allele human leukocyte antigen (HLA) associations. In this study, we explored genome-wide expression...

  13. Redox imbalance due to the loss of mitochondrial NAD(P)-transhydrogenase markedly aggravates high fat diet-induced fatty liver disease in mice.

    Science.gov (United States)

    Navarro, Claudia D C; Figueira, Tiago R; Francisco, Annelise; Dal'Bó, Genoefa A; Ronchi, Juliana A; Rovani, Juliana C; Escanhoela, Cecilia A F; Oliveira, Helena C F; Castilho, Roger F; Vercesi, Anibal E

    2017-12-01

    The mechanisms by which a high fat diet (HFD) promotes non-alcoholic fatty liver disease (NAFLD) appear to involve liver mitochondrial dysfunctions and redox imbalance. We hypothesized that a HFD would increase mitochondrial reliance on NAD(P)-transhydrogenase (NNT) as the source of NADPH for antioxidant systems that counteract NAFLD development. Therefore, we studied HFD-induced liver mitochondrial dysfunctions and NAFLD in C57Unib.B6 congenic mice with (Nnt +/+ ) or without (Nnt -/- ) NNT activity; the spontaneously mutated allele (Nnt -/- ) was inherited from the C57BL/6J mouse substrain. After 20 weeks on a HFD, Nnt -/- mice exhibited a higher prevalence of steatohepatitis and content of liver triglycerides compared to Nnt +/+ mice on an identical diet. Under a HFD, the aggravated NAFLD phenotype in the Nnt -/- mice was accompanied by an increased H 2 O 2 release rate from mitochondria, decreased aconitase activity (a redox-sensitive mitochondrial enzyme) and higher susceptibility to Ca 2+ -induced mitochondrial permeability transition. In addition, HFD led to the phosphorylation (inhibition) of pyruvate dehydrogenase (PDH) and markedly reduced the ability of liver mitochondria to remove peroxide in Nnt -/- mice. Bypass or pharmacological reactivation of PDH by dichloroacetate restored the peroxide removal capability of mitochondria from Nnt -/- mice on a HFD. Noteworthy, compared to mice that were chow-fed, the HFD did not impair peroxide removal nor elicit redox imbalance in mitochondria from Nnt +/+ mice. Therefore, HFD interacted with Nnt mutation to generate PDH inhibition and further suppression of peroxide removal. We conclude that NNT plays a critical role in counteracting mitochondrial redox imbalance, PDH inhibition and advancement of NAFLD in mice fed a HFD. The present study provide seminal experimental evidence that redox imbalance in liver mitochondria potentiates the progression from simple steatosis to steatohepatitis following a HFD. Copyright

  14. Full-duplex relaying under I/Q imbalance using improper Gaussian signaling

    KAUST Repository

    Javed, Sidrah; Amin, Osama; Alouini, Mohamed-Slim

    2017-01-01

    In this paper, we study the benefits of employing improper Gaussian signaling (IGS) in full duplex relaying (FDR) suffering from in-phase and quadrature imbalance (IQI). Different from the traditional symmetric signaling scheme, proper Gaussian signaling (PGS), that is parametrized by its variance, IGS needs additional statistical-quantity called the pseudo-variance to be fully described. The cooperative system under consideration suffers from two types of interferences, the residual self-interference (RSI) and IQI. To evaluate the system performance gain using IGS, first we express the end-to-end achievable rate for different IQI. Then, we optimize the pseudo-variance to compensate the interferences impact and improve the end-to-end achievable rate. Interestingly, IGS-based scheme outperforms its counterpart PGS-based scheme, especially at higher interference-to-noise ratio. Our findings reveal that using single-user detection with asymmetric signaling can compensate both RSI and IQI and improve the system performance.

  15. Sex steroid imbalances in the muricid Stramonita haemastoma from TBT contaminated sites.

    Science.gov (United States)

    Rossato, M; Castro, I B; Paganini, C L; Colares, E P; Fillmann, G; Pinho, G L L

    2016-04-01

    Imposex incidence, organotin tissue levels, and sex steroid (free and esterified testosterone and estradiol) levels were assessed in Stramonita haemastoma from Babitonga Bay (Santa Catarina State, Southern Brazil). The imposex levels showed a reduction when compared to a previous evaluation performed in the same area. In spite of that, the detected imposex incidence indicated the occurrence of tributyltin (TBT) inputs that were still able to produce endocrine disruption in local gastropods. In addition, a high level of organotins was observed in tissues of imposexed females. These females also showed a hormonal imbalance, especially in the total testosterone/total estradiol ratio. These findings obtained under realistic field conditions suggest that the steroid pathway could be responsible by the imposex induction after exposure to TBT. In this case, measurements of sex steroid levels can be an additional evidence for monitoring sites and impose affected gastropod populations.

  16. Full-duplex relaying under I/Q imbalance using improper Gaussian signaling

    KAUST Repository

    Javed, Sidrah

    2017-06-20

    In this paper, we study the benefits of employing improper Gaussian signaling (IGS) in full duplex relaying (FDR) suffering from in-phase and quadrature imbalance (IQI). Different from the traditional symmetric signaling scheme, proper Gaussian signaling (PGS), that is parametrized by its variance, IGS needs additional statistical-quantity called the pseudo-variance to be fully described. The cooperative system under consideration suffers from two types of interferences, the residual self-interference (RSI) and IQI. To evaluate the system performance gain using IGS, first we express the end-to-end achievable rate for different IQI. Then, we optimize the pseudo-variance to compensate the interferences impact and improve the end-to-end achievable rate. Interestingly, IGS-based scheme outperforms its counterpart PGS-based scheme, especially at higher interference-to-noise ratio. Our findings reveal that using single-user detection with asymmetric signaling can compensate both RSI and IQI and improve the system performance.

  17. Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.).

    Science.gov (United States)

    Witsenboer, H; Michelmore, R W; Vogel, J

    1997-12-01

    Selectively amplified microsatellite polymorphic locus (SAMPL) analysis is a method of amplifying microsatellite loci using generic PCR primers. SAMPL analysis uses one AFLP primer in combination with a primer complementary to microsatellite sequences. SAMPL primers based on compound microsatellite sequences provided the clearest amplification patterns. We explored the potential of SAMPL analysis in lettuce to detect PCR-based codominant microsatellite markers. Fifty-eight SAMPLs were identified and placed on the genetic map. Seventeen were codominant. SAMPLs were dispersed with RFLP markers on 11 of the 12 main linkage groups in lettuce, indicating that they have a similar genomic distribution. Some but not all fragments amplified by SAMPL analysis were confirmed to contain microsatellite sequences by Southern hybridization. Forty-five cultivars of lettuce and five wild species of Lactuca were analyzed to determine the allelic diversity for codominant SAMPLs. From 3 to 11 putative alleles were found for each SAMPL; 2-6 alleles were found within Lactuca sativa and 1-3 alleles were found among the crisphead genotypes, the most genetically homogeneous plant type of L. sativa. This allelic diversity is greater than that found for RFLP markers. Numerous new alleles were observed in the wild species; however, there were frequent null alleles. Therefore, SAMPL analysis is more applicable to intraspecific than to interspecific comparisons. A phenetic analysis based on SAMPLs resulted in a dendrogram similar to those based on RFLP and AFLP markers.

  18. Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences

    Energy Technology Data Exchange (ETDEWEB)

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I. [Humboldt Univ., Berlin (Germany)

    1997-02-01

    Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

  19. TEMPOL increases NAD+ and improves redox imbalance in obese mice

    Directory of Open Access Journals (Sweden)

    Mayumi Yamato

    2016-08-01

    Full Text Available Continuous energy conversion is controlled by reduction–oxidation (redox processes. NAD+ and NADH represent an important redox couple in energy metabolism. 4-Hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPOL is a redox-cycling nitroxide that promotes the scavenging of several reactive oxygen species (ROS and is reduced to hydroxylamine by NADH. TEMPOL is also involved in NAD+ production in the ascorbic acid–glutathione redox cycle. We utilized the chemical properties of TEMPOL to investigate the effects of antioxidants and NAD+/NADH modulators on the metabolic imbalance in obese mice. Increases in the NAD+/NADH ratio by TEMPOL ameliorated the metabolic imbalance when combined with a dietary intervention, changing from a high-fat diet to a normal diet. Plasma levels of the superoxide marker dihydroethidium were higher in mice receiving the dietary intervention compared with a control diet, but were normalized with TEMPOL consumption. These findings provide novel insights into redox regulation in obesity.

  20. Gender equity imbalance in electrocardiology: A call to action.

    Science.gov (United States)

    Clarke Whalen, E; Xu, G; Cygankiewicz, I; Bacharova, L; Zareba, W; Steinberg, J S; Tereshchenko, L G; Baranchuk, A

    Despite the increasing number of women entering the medical profession, senior positions and academic productivity in many fields of medicine remain to be men dominated. We explored gender equity in electrocardiology as perceived by recent academic productivity and also active participation (presidencies and board constituents) in both the International Society of Electrocardiology (ISE) and the International Society for Holter and Noninvasive Electrocardiology (ISHNE). Academic productivity was measured by authorship (first and senior) in the Journal of Electrocardiology (JECG) and the Annals of Noninvasive Electrocardiology (ANE) in 2015. The percentage of women ISE and ISHNE Presidents was 5.6% and 0%, respectively. Current women board constituents for each society was 12.1% for ISE, and 9.4% for ISHNE. JECG articles published in 2015 had considerably less women compared to men for both senior (16.3%) and first (25.3%) authorship. ANE articles published in 2015 followed the same trends in gender, having less women compared to men for both senior (9.4%) and first (19.3%) authorship. There is a gender equity imbalance in the field of Electrocardiology. Identifying a gender imbalance is important for understanding reasons behind these trends, and may also help improve gender equity in Electrocardiology. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Wikipedia Culture Gap: Quantifying Content Imbalances Across 40 Language Editions

    Directory of Open Access Journals (Sweden)

    Marc Miquel-Ribé

    2018-06-01

    Full Text Available The online encyclopedia Wikipedia is the largest general information repository created through collaborative efforts from all over the globe. Despite the project's goal being to achieve the sum of human knowledge, there are strong content imbalances across the language editions. In order to quantify and investigate these imbalances, we study the impact of cultural context in 40 language editions. To this purpose, we developed a computational method to identify articles that can be related to the editors' cultural context associated to each Wikipedia language edition. We employed a combination of strategies taking into account geolocated articles, specific keywords and categories, as well as links between articles. We verified the method's quality with manual assessment and found an average precision of 0.92 and an average recall of 0.95. The results show that about a quarter of each Wikipedia language edition is dedicated to represent the corresponding cultural context. Although a considerable part of this content was created during the first years of the project, its creation is sustained over time. An analysis of cross-language coverage of this content shows that most of it is unique in its original language, and reveals special links between cultural contexts; at the same time, it highlights gaps where the encyclopedia could extend its content. The approach and findings presented in this study can help to foster participation and inter-cultural enrichment of Wikipedias. The datasets produced are made available for further research.

  2. Hypobaric Hypoxia Imbalances Mitochondrial Dynamics in Rat Brain Hippocampus

    Directory of Open Access Journals (Sweden)

    Khushbu Jain

    2015-01-01

    Full Text Available Brain is predominantly susceptible to oxidative stress and mitochondrial dysfunction during hypobaric hypoxia, and therefore undergoes neurodegeneration due to energy crisis. Evidences illustrate a high degree of association for mitochondrial fusion/fission imbalance and mitochondrial dysfunction. Mitochondrial fusion/fission is a recently reported dynamic mechanism which frequently occurs among cellular mitochondrial network. Hence, the study investigated the temporal alteration and involvement of abnormal mitochondrial dynamics (fusion/fission along with disturbed mitochondrial functionality during chronic exposure to hypobaric hypoxia (HH. The Sprague-Dawley rats were exposed to simulated high altitude equivalent to 25000 ft for 3, 7, 14, 21, and 28 days. Mitochondrial morphology, distribution within neurons, enzyme activity of respiratory complexes, Δψm, ADP: ATP, and expression of fission/fusion key proteins were determined. Results demonstrated HH induced alteration in mitochondrial morphology by damaged, small mitochondria observed in neurons with disturbance of mitochondrial functionality and reduced mitochondrial density in neuronal processes manifested by excessive mitochondrial fragmentation (fission and decreased mitochondrial fusion as compared to unexposed rat brain hippocampus. The study suggested that imbalance in mitochondrial dynamics is one of the noteworthy mechanisms occurring in hippocampal neurons during HH insult.

  3. The effect of spinal manipulation on imbalances in leg strength.

    Science.gov (United States)

    Chilibeck, Philip D; Cornish, Stephen M; Schulte, Al; Jantz, Nathan; Magnus, Charlene R A; Schwanbeck, Shane; Juurlink, Bernhard H J

    2011-09-01

    We hypothesized that spinal manipulation (SM) would reduce strength imbalances between legs. Using an un-blinded randomized design, 28 males and 21 females (54 ± 19y) with at least a 15% difference in isometric strength between legs for hip flexion, extension, abduction, or knee flexion were randomized to treatment or placebo (mock spinal manipulation). Strength of the stronger and weaker legs for hip flexion, extension, abduction, and/or knee flexion was assessed before and after the intervention. SM reduced the relative strength difference between legs for knee flexion (mean ± SD 57 ± 53 to 5 ± 14%) and hip flexion (24 ± 12 to 11 ± 15%) compared to placebo (34 ± 29 to 24 ± 36%, and 20 ± 18 to 22 ± 26%, respectively) (p = 0.05). SM also improved strength in the weak leg for hip abduction (104 ± 43 to 116 ± 43 Nm) compared to placebo (84 ± 24 to 85 ± 31 Nm) (p = 0.03). This study suggests that spinal manipulation may reduce imbalances in strength between legs for knee and hip flexion.

  4. Mass imbalances in EPANET water-quality simulations

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Michael J.; Janke, Robert; Taxon, Thomas N.

    2018-04-06

    EPANET is widely employed to simulate water quality in water distribution systems. However, the time-driven simulation approach used to determine concentrations of water-quality constituents provides accurate results, in general, only for small water-quality time steps; use of an adequately short time step may not be feasible. Overly long time steps can yield errors in concentrations and result in situations in which constituent mass is not conserved. Mass may not be conserved even when EPANET gives no errors or warnings. This paper explains how such imbalances can occur and provides examples of such cases; it also presents a preliminary event-driven approach that conserves mass with a water-quality time step that is as long as the hydraulic time step. Results obtained using the current approach converge, or tend to converge, to those obtained using the new approach as the water-quality time step decreases. Improving the water-quality routing algorithm used in EPANET could eliminate mass imbalances and related errors in estimated concentrations.

  5. Nitric oxide synthase gene G298 allele

    International Nuclear Information System (INIS)

    Nagib El-Kilany, Galal E.; Nayel, Ehab; Hazzaa, Sahar

    2004-01-01

    Background: Nitric oxide (NO) has an important effect on blood pressure, arterial wall, and the basal release of endothelial NO in hypertension (HPN) may be reduced. Until now, there is no solid data revealing the potential role of the polymorphism of the nitric oxide synthase gene (NOS) in patients with HPN and microvascular angina. Aim: The aim of the present study is to investigate the gene of endothelial nitric oxide synthase (eNOS), as the polymorphism of this gene may be a putative candidate for HPN and initiate the process of atherosclerosis. Methods: Sixty participants were recruited for this study; 50 were hypertensive patients complaining of chest pain [30 of them have electrocardiogram (EKG) changes of ischemia], 20 had isolated HPN, and 10 healthy volunteers served as control. All patients underwent stress myocardial perfusion imaging (MPI) and coronary angiography. Genotyping of eNOS for all patients and controls was performed. The linkages between HPN, microvascular angina and eNOS gene polymorphism were investigated. Results: MPI and coronary angiography revealed that 15 patients had chest pain with true ischemia and reversible myocardial perfusion defects (multiple and mild) but normal epicardial coronary arteries (microvascular angina), while 15 patients had significant coronary artery disease (CAD), and 20 hypertensive patients showed normal perfusion scan and coronary angiography. The prevalence of the NOS G 298 allele was higher in the hypertensive group with microvascular angina (documented by MPI) than it was among the control participants (P<.005). The eNOS allele was significantly higher in the hypertensive group than in the control participants, but there was no significant difference in homozygote mutants among hypertensive participants, x-syndrome and patients with CAD. Conclusion: eNOS gene polymorphism is proved to be an important etiology in microvascular angina (x-syndrome) among hypertensive patients. In addition, the eNOS mutant

  6. Composition and functional analysis of low-molecular-weight glutenin alleles with Aroona near-isogenic lines of bread wheat

    Directory of Open Access Journals (Sweden)

    Zhang Xiaofei

    2012-12-01

    Full Text Available Abstract Background Low-molecular-weight glutenin subunits (LMW-GS strongly influence the bread-making quality of bread wheat. These proteins are encoded by a multi-gene family located at the Glu-A3, Glu-B3 and Glu-D3 loci on the short arms of homoeologous group 1 chromosomes, and show high allelic variation. To characterize the genetic and protein compositions of LMW-GS alleles, we investigated 16 Aroona near-isogenic lines (NILs using SDS-PAGE, 2D-PAGE and the LMW-GS gene marker system. Moreover, the composition of glutenin macro-polymers, dough properties and pan bread quality parameters were determined for functional analysis of LMW-GS alleles in the NILs. Results Using the LMW-GS gene marker system, 14–20 LMW-GS genes were identified in individual NILs. At the Glu-A3 locus, two m-type and 2–4 i-type genes were identified and their allelic variants showed high polymorphisms in length and nucleotide sequences. The Glu-A3d allele possessed three active genes, the highest number among Glu-A3 alleles. At the Glu-B3 locus, 2–3 m-type and 1–3 s-type genes were identified from individual NILs. Based on the different compositions of s-type genes, Glu-B3 alleles were divided into two groups, one containing Glu-B3a, B3b, B3f and B3g, and the other comprising Glu-B3c, B3d, B3h and B3i. Eight conserved genes were identified among Glu-D3 alleles, except for Glu-D3f. The protein products of the unique active genes in each NIL were detected using protein electrophoresis. Among Glu-3 alleles, the Glu-A3e genotype without i-type LMW-GS performed worst in almost all quality properties. Glu-B3b, B3g and B3i showed better quality parameters than the other Glu-B3 alleles, whereas the Glu-B3c allele containing s-type genes with low expression levels had an inferior effect on bread-making quality. Due to the conserved genes at Glu-D3 locus, Glu-D3 alleles showed no significant differences in effects on all quality parameters. Conclusions This work

  7. Botulinum toxin for the treatment of motor imbalance in obstetrical brachial plexus palsy.

    Science.gov (United States)

    Arad, Ehud; Stephens, Derek; Curtis, Christine G; Clarke, Howard M

    2013-06-01

    Residual muscle imbalance is a common problem affecting obstetrical brachial plexus palsy patients. The goal of this study was to examine the efficacy of botulinum toxin type A (Botox) in improving this muscle imbalance. The authors retrospectively reviewed obstetrical brachial plexus palsy patients treated with Botox for muscle imbalance as an isolated procedure. Outcomes were the change in Active Movement Scale scores from pre-Botox scores to scores at 1 month after Botox and 1 year after Botox. Twenty-seven patients were included, 19 treated for shoulder imbalance and eight treated for elbow imbalance. Active Movement Scale scores (mean±SD) for shoulder external rotation improved from 0.6±1.0 before Botox to 2.6±2.14 (pimbalance produces improvement in external rotation that is not sufficiently sustained over time to be of clinical benefit. However, Botox for elbow movement imbalance produces a sustained and clinically useful improvement. Therapeutic, IV.

  8. Allele Frequency - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nd 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively. Derived from Flat f... assay (JBIC-allele and RIKEN_japanese_*), TaqMan assay (RIKEN-allele) or direct sequencing / allelic discri...unteers under informed consent RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteer...s ( body mass index RIKEN_japanese_obese - 796 unrelated japanese obese patients

  9. Itinerant ferromagnetism in an atomic Fermi gas: Influence of population imbalance

    International Nuclear Information System (INIS)

    Conduit, G. J.; Simons, B. D.

    2009-01-01

    We investigate ferromagnetic ordering in an itinerant ultracold atomic Fermi gas with repulsive interactions and population imbalance. In a spatially uniform system, we show that at zero temperature the transition to the itinerant magnetic phase transforms from first to second order with increasing population imbalance. Drawing on these results, we elucidate the phases present in a trapped geometry, finding three characteristic types of behavior with changing population imbalance. Finally, we outline the potential experimental implications of the findings.

  10. Database for the ampC alleles in Acinetobacter baumannii.

    Directory of Open Access Journals (Sweden)

    Nabil Karah

    Full Text Available Acinetobacter baumannii is a troublesome opportunistic pathogen with a high capacity for clonal dissemination. We announce the establishment of a database for the ampC locus in A. baumannii, in which novel ampC alleles are differentiated based on the occurrence of ≥ 1 nucleotide change, regardless of whether it is silent or missense. The database is openly accessible at the pubmlst platform for A. baumannii (http://pubmlst.org/abaumannii/. Forty-eight distinctive alleles of the ampC locus have so far been identified and deposited in the database. Isolates from clonal complex 1 (CC1, according to the Pasteur multilocus sequence typing scheme, had a variety of the ampC locus alleles, including alleles 1, 3, 4, 5, 6, 7, 8, 13, 14, 17, and 18. On the other hand, isolates from CC2 had the ampC alleles 2, 3, 19, 20, 21, 22, 23, 24, 26, 27, 28, and 46. Allele 3 was characteristic for sequence types ST3 or ST32. The ampC alleles 10, 16, and 25 were characteristic for CC10, ST16, and CC25, respectively. Our study points out that novel gene databases, in which alleles are numbered based on differences in their nucleotide identities, should replace traditional records that use amino acid substitutions to define new alleles.

  11. Allele frequencies of AVPR1A and MAOA in the Afrikaner population

    Directory of Open Access Journals (Sweden)

    J. Christoff Erasmus

    2015-07-01

    Full Text Available The Afrikaner population was founded mainly by European immigrants that arrived in South Africa from 1652. However, female slaves from Asia and Africa and local KhoeSan women may have contributed as much as 7% to this population’s genes. We quantified variation at two tandem repeats to see if this historical founder effect and/or admixture could be detected. The two loci were chosen because they are in the promoters of genes of neurotransmitters that are known to be correlated with social behaviour. Specifically, arginine vasopressin receptor 1A’s (AVPR1A RS3 locus has been shown to correlate with age of sexual onset and happiness in monogamous relationships while the tandem repeat in the promoter of the monoamine oxidase A (MAOA gene correlates with reactive aggression. The Afrikaner population contained more AVPR1A RS3 alleles than other Caucasoid populations, potentially reflecting a history of admixture. Even though Afrikaners have one of the lowest recorded non-paternity rates in the world, the population did not differ at AVPR1A RS3 locus form other European populations, suggesting a non-genetic explanation, presumably religion, for the low non-paternity rate. By comparing population allele-frequency spectra it was found that different studies have confused AVPR1A RS3 alleles and we make some suggestions to rectify these mistakes in future studies. While MAOA allele frequencies differed between racial groups, the Afrikaner population showed no evidence of admixture. In fact, Afrikaners had more 4-repeat alleles than other populations of European origin, not fewer. The 4-repeat allele may have been selected for during colonisation.

  12. Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta

    Directory of Open Access Journals (Sweden)

    van Straalen Nico M

    2007-06-01

    Full Text Available Abstract Background Metallothionein (mt transcription is elevated in heavy metal tolerant field populations of Orchesella cincta (Collembola. This suggests that natural selection acts on transcriptional regulation of mt in springtails at sites where cadmium (Cd levels in soil reach toxic values This study investigates the nature and the evolutionary origin of polymorphisms in the metallothionein promoter (pmt and their functional significance for mt expression. Results We sequenced approximately 1600 bp upstream the mt coding region by genome walking. Nine pmt alleles were discovered in NW-European populations. They differ in the number of some indels, consensus transcription factor binding sites and core promoter elements. Extensive recombination events between some of the alleles can be inferred from the alignment. A deviation from neutral expectations was detected in a cadmium tolerant population, pointing towards balancing selection on some promoter stretches. Luciferase constructs were made from the most abundant alleles, and responses to Cd, paraquat (oxidative stress inducer and moulting hormone were studied in cell lines. By using paraquat we were able to dissect the effect of oxidative stress from the Cd specific effect, and extensive differences in mt induction levels between these two stressors were observed. Conclusion The pmt alleles evolved by a number of recombination events, and exhibited differential inducibilities by Cd, paraquat and molting hormone. In a tolerant population from a metal contaminated site, promoter allele frequencies differed significantly from a reference site and nucleotide polymorphisms in some promoter stretches deviated from neutral expectations, revealing a signature of balancing selection. Our results suggest that the structural differences in the Orchesella cincta metallothionein promoter alleles contribute to the metallothionein -over-expresser phenotype in cadmium tolerant populations.

  13. Genetic exchange of fimbrial alleles exemplifies the adaptive virulence strategy of Porphyromonas gingivalis.

    Directory of Open Access Journals (Sweden)

    Jennifer E Kerr

    Full Text Available Porphyromonas gingivalis is a gram-negative anaerobic bacterium, a member of the human oral microbiome, and a proposed "keystone" pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions.

  14. Genetic exchange of fimbrial alleles exemplifies the adaptive virulence strategy of Porphyromonas gingivalis.

    Science.gov (United States)

    Kerr, Jennifer E; Abramian, Jared R; Dao, Doan-Hieu V; Rigney, Todd W; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D

    2014-01-01

    Porphyromonas gingivalis is a gram-negative anaerobic bacterium, a member of the human oral microbiome, and a proposed "keystone" pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions.

  15. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation

    Directory of Open Access Journals (Sweden)

    Brockmann Knut

    2009-03-01

    Full Text Available Abstract Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR. The aim of the study was to evaluate a quantitative PCR (qPCR protocol established by Boehm et al. (2004 in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8% with 20 subtelomeric imbalances were identified. Six of the aberrations (2% were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases or the aberration were be detected in the patient and an equally affected parent (1 case. The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%. Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.

  16. Pedicle subtraction osteotomy in elderly patients with degenerative sagittal imbalance.

    Science.gov (United States)

    Cho, Kyu-Jung; Kim, Ki-Tack; Kim, Whoan-Jeang; Lee, Sang-Hoon; Jung, Jae-Hoon; Kim, Young-Tae; Park, Hae-Bong

    2013-11-15

    Retrospective, radiographical analysis. To evaluate pedicle subtraction osteotomy (PSO) as a means of correcting severe degenerative sagittal imbalance in elderly patients. PSO in patients with degenerative sagittal imbalance is likely to cause more complications than in patients with iatrogenic flatback deformity. This study analyzed 34 patients who underwent fusion to the sacrum, with a minimum 2-year follow-up. Age of the patients were in the range from 58 to 73 with the mean at 65.5 years. PSO was performed at one segment in all cases, consisting of L3 (n = 26), L4 (n = 4), L2 (n = 3), and L1 (n = 1). The average number of levels fused was 8.15. Ten patients had structural interbody fusion at the lumbosacral junction. Applying PSO at one segment, the mean correction of the lordotic angle at the osteotomy site was 33.3°, of which the loss of correction (LOC) was 4.0° at the last visit. The correction of lumbar lordosis was 33.7° and the LOC was 8.5°. The sagittal C7 plumb was 215.9 mm before surgery, corrected to 35.1 mm after surgery, and changed to 95.9 mm by the last visit. The correction of the sagittal C7 plumb was 119.9 mm and the LOC was 60.9 mm. There was substantial LOC in lumbar lordosis and sagittal C7 plumb. In 10 patients with addition of posterior lumbar interbody fusion, the LOC of lumbar lordosis was 7.4°, which was less than 9° in those without it. PSO for the correction of degenerative sagittal imbalance in elderly patients resulted in correction of sagittal alignment with a significant LOC of lumbar lordosis and sagittal C7 plumb. The LOC of lumbar lordosis occurred at both the osteotomy and non-osteotomy site. The addition of anterior column support is helpful to maintain correction and reduce complications. N/A.

  17. Postural Consequences of Cervical Sagittal Imbalance: A Novel Laboratory Model.

    Science.gov (United States)

    Patwardhan, Avinash G; Havey, Robert M; Khayatzadeh, Saeed; Muriuki, Muturi G; Voronov, Leonard I; Carandang, Gerard; Nguyen, Ngoc-Lam; Ghanayem, Alexander J; Schuit, Dale; Patel, Alpesh A; Smith, Zachary A; Sears, William

    2015-06-01

    A biomechanical study using human spine specimens. To study postural compensations in lordosis angles that are necessary to maintain horizontal gaze in the presence of forward head posture and increasing T1 sagittal tilt. Forward head posture relative to the shoulders, assessed radiographically using the horizontal offset distance between the C2 and C7 vertebral bodies (C2-C7 [sagittal vertical alignment] SVA), is a measure of global cervical imbalance. This may result from kyphotic alignment of cervical segments, muscle imbalance, as well as malalignment of thoracolumbar spine. Ten cadaveric cervical spines (occiput-T1) were tested. The T1 vertebra was anchored to a tilting and translating base. The occiput was free to move vertically but its angular orientation was constrained to ensure horizontal gaze regardless of sagittal imbalance. A 5-kg mass was attached to the occiput to mimic head weight. Forward head posture magnitude and T1 tilt were varied and motions of individual vertebrae were measured to calculate C2-C7 SVA and lordosis across C0-C2 and C2-C7. Increasing C2-C7 SVA caused flexion of lower cervical (C2-C7) segments and hyperextension of suboccipital (C0-C1-C2) segments to maintain horizontal gaze. Increasing kyphotic T1 tilt primarily increased lordosis across the C2-C7 segments. Regression models were developed to predict the compensatory C0-C2 and C2-C7 angulation needed to maintain horizontal gaze given values of C2-C7 SVA and T1 tilt. This study established predictive relationships between radiographical measures of forward head posture, T1 tilt, and postural compensations in the cervical lordosis angles needed to maintain horizontal gaze. The laboratory model predicted that normalization of C2-C7 SVA will reduce suboccipital (C0-C2) hyperextension, whereas T1 tilt reduction will reduce the hyperextension in the C2-C7 segments. The predictive relationships may help in planning corrective strategy in patients experiencing neck pain, which may be

  18. Consensus-based Distributed Control for Accurate Reactive, Harmonic and Imbalance Power Sharing in Microgrids

    DEFF Research Database (Denmark)

    Zhou, Jianguo; Kim, Sunghyok; Zhang, Huaguang

    2018-01-01

    This paper investigates the issue of accurate reactive, harmonic and imbalance power sharing in a microgrid. Harmonic and imbalance droop controllers are developed to proportionally share the harmonic power and the imbalance power among distributed generation (DG) units and improve the voltage...... voltage. With the proposed methods, the microgrid system reliability and flexibility can be enhanced and the knowledge of the line impedance is not required. And the reactive, harmonic and imbalance power can be proportionally shared among the DG units. Moreover, the quality of the voltage at PCC can...

  19. Wet cupping therapy restores sympathovagal imbalances in cardiac rhythm.

    Science.gov (United States)

    Arslan, Müzeyyen; Yeşilçam, Nesibe; Aydin, Duygu; Yüksel, Ramazan; Dane, Senol

    2014-04-01

    A recent study showed that cupping had therapeutic effects in rats with myocardial infarction and cardiac arrhythmias. The current studyaimed to investigate the possible useful effects of cupping therapy on cardiac rhythm in terms of heart rate variability (HRV). Forty healthy participants were included. Classic wet cupping therapy was applied on five points of the back. Recording electrocardiography (to determine HRV) was applied 1 hour before and 1 hour after cupping therapy. All HRV parameters increased after cupping therapy compared with before cupping therapy in healthy persons. These results indicate for the first time in humans that cupping might be cardioprotective. In this study, cupping therapy restored sympathovagal imbalances by stimulating the peripheral nervous system.

  20. Redox Imbalance and Viral Infections in Neurodegenerative Diseases

    Directory of Open Access Journals (Sweden)

    Dolores Limongi

    2016-01-01

    Full Text Available Reactive oxygen species (ROS are essential molecules for many physiological functions and act as second messengers in a large variety of tissues. An imbalance in the production and elimination of ROS is associated with human diseases including neurodegenerative disorders. In the last years the notion that neurodegenerative diseases are accompanied by chronic viral infections, which may result in an increase of neurodegenerative diseases progression, emerged. It is known in literature that enhanced viral infection risk, observed during neurodegeneration, is partly due to the increase of ROS accumulation in brain cells. However, the molecular mechanisms of viral infection, occurring during the progression of neurodegeneration, remain unclear. In this review, we discuss the recent knowledge regarding the role of influenza, herpes simplex virus type-1, and retroviruses infection in ROS/RNS-mediated Parkinson’s disease (PD, Alzheimer’s disease (AD, and amyotrophic lateral sclerosis (ALS.

  1. Investigation of Global Imbalances Based on a Gravity Model

    Directory of Open Access Journals (Sweden)

    Hyun-Hoon Lee

    2011-06-01

    Full Text Available Using the US Treasury International Capital (TIC data, this paper attempts to analyze the size and trend of foreign investment in the U.S. in the form of equities, bonds and bank lending during the period of 2001-2007. In addition, this paper assesses the determinants of foreign investment in the U.S., using the financial gravity model which includes an East Asian dummy as an explanatory variable. The results show that most East Asian countries have invested more in the U.S. than the optimal level suggested by the gravity model. Such an over-investment is more evident in long-term bond investment than in equity investment or bank lending. Thus, the results confirm that global imbalance does exist between East Asian countries and the U.S.

  2. Evaluating imbalances of adverse events during biosimilar development

    Science.gov (United States)

    Vana, Alicia M.; Freyman, Amy W.; Reich, Steven D.; Yin, Donghua; Li, Ruifeng; Anderson, Scott; Jacobs, Ira A.; Zacharchuk, Charles M.; Ewesuedo, Reginald

    2016-01-01

    ABSTRACT Biosimilars are designed to be highly similar to approved or licensed (reference) biologics and are evaluated based on the totality of evidence from extensive analytical, nonclinical and clinical studies. As part of the stepwise approach recommended by regulatory agencies, the first step in the clinical evaluation of biosimilarity is to conduct a pharmacokinetics similarity study in which the potential biosimilar is compared with the reference product. In the context of biosimilar development, a pharmacokinetics similarity study is not necessarily designed for a comparative assessment of safety. Development of PF-05280014, a potential biosimilar to trastuzumab, illustrates how a numerical imbalance in an adverse event in a small pharmacokinetics study can raise questions on safety that may require additional clinical trials. PMID:27050730

  3. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    Science.gov (United States)

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

  4. Effort-reward imbalance and depression among private practice physicians.

    Science.gov (United States)

    Tsutsumi, Akizumi; Kawanami, Shoko; Horie, Seichi

    2012-02-01

    Current private practice physicians provide medical services in a harsh economic situation. The effort-reward imbalance (ERI) model puts its emphasis on an imbalance between high efforts spent and low rewards received in occupational life. ERI model includes three different reward factors from task to organizational levels. We examined whether ERI in terms of low organizational reward (poor prospective and job insecurity) could be the most relevant and strongly associated with depression among private practice physicians. This is a cross-sectional questionnaire study of 1,103 private practice physicians who were currently working in clinical settings and completed the data of exposure and outcome. The study questionnaire was mailed to all the physicians listed as members of a local branch of the Japan Medical Association (n = 3,441) between November and December 2008. Outcomes were prevalence of depression as measured by the Center for Epidemiologic Studies Depression Scale and adjusted odds ratios (OR) of depression with respect to ERI. Fifty-seven percent of physicians were exposed to ERI, and 18% of the physicians were depressed. Logistic regression analyses revealed that ERI was significantly associated with depression (OR and 95% confidence interval = 3.57; 2.43-5.26). ERI with regard to organizational reward was most prevalent (60%) and had the strongest association with depression (5.14; 3.36-7.92). Predominant prevalence of ERI in terms of organizational level low reward and strong associations between the ERI component and depression suggests that countermeasures from social perspective are crucial.

  5. Propensity to obesity impacts the neuronal response to energy imbalance

    Directory of Open Access Journals (Sweden)

    Marc-Andre eCornier

    2015-02-01

    Full Text Available The mechanisms responsible for the propensity to gain weight or remain normal weight are poorly understood. The objective of this study was to study the neuronal response to visual food cues during short-term energy imbalance in healthy adults recruited as obesity-resistant (OR or obesity-prone (OP based on self-identification, BMI, and personal/family weight history. 25 OR and 28 OP subjects were studied in underfed (UF and overfed (OF as compared to eucaloric (EU conditions in a randomized crossover design. Each study phase included a 3 day run-in diet, 1 day of controlled feeding (basal energy needs for EU, 40% above/below basal energy needs for OF/UF, and a test day. On the test day fMRI was performed in the acute fed stated (30 minutes after a test meal while subjects viewed images of foods of high hedonic value and neutral non-food objects. Measures of appetite and hormones were also performed before and every 30 minutes after the test meal. UF was associated with significantly increased activation of insula, somatosensory cortex, inferior and medial prefrontal cortex, parahippocampus, precuneus, cingulate and visual cortex in OR. However, UF had no impact in OP. As a result, UF was associated with significantly greater activation, specifically in the insula, inferior prefrontal cortex, and somatosensory cortex in OR as compared to OP. While OF was overall associated with reduced activation of inferior visual cortex, no group interaction was observed with OF. In summary, these findings suggest that individuals resistant to weight gain and obesity are more sensitive to short-term energy imbalance, particularly with UF, than those prone to weight gain. The inability to sense or adapt to changes in energy balance may represent an important mechanism contributing to excess energy intake and risk for obesity.

  6. Propensity to obesity impacts the neuronal response to energy imbalance.

    Science.gov (United States)

    Cornier, Marc-Andre; McFadden, Kristina L; Thomas, Elizabeth A; Bechtell, Jamie L; Bessesen, Daniel H; Tregellas, Jason R

    2015-01-01

    The mechanisms responsible for the propensity to gain weight or remain normal weight are poorly understood. The objective of this study was to study the neuronal response to visual food cues during short-term energy imbalance in healthy adults recruited as obesity-resistant (OR) or obesity-prone (OP) based on self-identification, body mass index, and personal/family weight history. Twenty-five OR and 28 OP subjects were studied in underfed (UF) and overfed (OF) as compared to eucaloric (EU) conditions in a randomized crossover design. Each study phase included a 3-day run-in diet, 1 day of controlled feeding (basal energy needs for EU, 40% above/below basal energy needs for OF/UF), and a test day. On the test day, fMRI was performed in the acute fed stated (30 min after a test meal) while subjects viewed images of foods of high hedonic value and neutral non-food objects. Measures of appetite and hormones were also performed before and every 30 min after the test meal. UF was associated with significantly increased activation of insula, somatosensory cortex, inferior and medial prefrontal cortex (PFC), parahippocampus, precuneus, cingulate, and visual cortex in OR. However, UF had no impact in OP. As a result, UF was associated with significantly greater activation, specifically in the insula, inferior PFC, and somatosensory cortex in OR as compared to OP. While OF was overall associated with reduced activation of inferior visual cortex, no group interaction was observed with OF. In summary, these findings suggest that individuals resistant to weight gain and obesity are more sensitive to short-term energy imbalance, particularly with UF, than those prone to weight gain. The inability to sense or adapt to changes in energy balance may represent an important mechanism contributing to excess energy intake and risk for obesity.

  7. Postural loads during walking after an imbalance of occlusion created with unilateral cotton rolls

    Directory of Open Access Journals (Sweden)

    Saccucci Matteo

    2010-05-01

    Full Text Available Abstract Background It was showed that stomatognathic functions correlate with alterations in locomotion, that are detectable through the analysis of loading during walking. For example, subjects with symptoms of Temporomandibular disorders (TMDs showed a significant higher load pressure on the two feet, respect to health subjects, when cotton rolls were inserted. This previous study appeared to suggest that the alteration of postural loads associated to a particular alteration of stomatognathic condition (in this case, the cotton rolls inserted between the two dental arches is detectable only in TMD's subjects, while it resulted not detectable in health subjects, because in that study, health subjects did not show any significant alteration of postural loads related to the different stomatognathic tested conditions. In other words, in that previous study, in the group of health subjects, no significant difference in postural loads was observed among the different test conditions; while TMD subjects showed a significant higher load pressure on the two feet when cotton rolls were inserted, respect to all the other tested conditions. Thus, the aim of this study was to better investigate these correlations in health subjects without TMD's symptoms, testing other different intra-oral conditions, and to verifywhether an experimentally induced imbalance of occlusion, obtained putting an unilateral cotton roll, could cause an alteration of postural loading on feet during walking. Findings In a sample of thirty Caucasian adult females (mean age 28.5 ± 4.5, asymptomatic for TMDs, when a cotton roll was positioned on the left or the right sides of dental arches, so causing a lateral shift of the mandible, the percentage of loading and the loading surface of the ipsi-lateral foot, left or right, were found to be significantly lower than in habitual occlusion (p Conclusions This study showed that in health subjects without TMD's symptoms, an experimentally

  8. HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand.

    Science.gov (United States)

    Kongmaroeng, C; Romphruk, A; Puapairoj, C; Leelayuwat, C; Kulski, J K; Inoko, H; Dunn, D S; Romphruk, A V

    2015-09-01

    This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations.

    Science.gov (United States)

    Duan, Qing; Xu, Zheng; Raffield, Laura M; Chang, Suhua; Wu, Di; Lange, Ethan M; Reiner, Alex P; Li, Yun

    2018-04-01

    Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA. © 2017 WILEY PERIODICALS, INC.

  10. Estimating and testing the effect of allelic recombination on the ...

    African Journals Online (AJOL)

    Jane

    2011-01-21

    Jan 21, 2011 ... The significance of the correlation coefficient as well as the fitted regression model was obtained using. Analysis of Variance method. Key words: Allele, genotype, regression, correlation, F-ratio, analysis of variance. INTRODUCTION .... while if the allelic replacement is being made on an Aa individual the ...

  11. Low Penetrance Alleles in Colorectal Cancer: the arachidonic acid pathway

    NARCIS (Netherlands)

    C.L.E. Siezen

    2006-01-01

    textabstractIn summary, we can conclude that we have successfully identified low penetrance alleles in the PPAR., PLA2G2A and ALOX15 genes, conferring differential colorectal adenoma risk, and two such alleles in the PTGS2 gene, one of which is also involved in colorectal cancer risk. These

  12. Comparison of bovine lymphocyte antigen DRB3.2 allele ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell ... alleles were more resistant to clinical mastitis. ... DRB3.2 allele pattern in two Iranian Holstein cow .... observed and the number of immune parameters with.

  13. Evolutionary dynamics of sporophytic self-incompatibility alleles in plants

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Vekemans, Xavier; Christiansen, Freddy Bugge

    1997-01-01

    codominantly in both pollen and style (SSIcod), in the second, alleles form a dominance hierarchy in pollen and style (SSIdom). In the third model, alleles interact codominantly in the style and form a dominance hierarchy in the pollen (SSIdomcod). The SSIcod model behaves similarly to the model...

  14. Comparative frequency and allelic distribution of ABO and Rh (D ...

    African Journals Online (AJOL)

    Background: Allelic distribution of major blood groups (ABO and rhesus) has not been defined in Bangladeshi population. Determinants of blood group frequency in this region have not been studied properly. Aim: To determine ABO and rhesus blood group frequency and allelic distribution in a multiethnic area of ...

  15. Apolipoprotein E4 allele does not influence serum triglyceride ...

    African Journals Online (AJOL)

    This study investigated how the APOε4 allele affects the serum triglyceride response after a fatmeal in apparently healthy black South African young adults. Sixty students were successfully screened for APOE genotype using Restriction Fragment Length Polymorphism (RFLP) and were divided into four groups; the ε2 allele ...

  16. Geostatistical analysis of allele presence patterns among American black bears in eastern North Carolina

    Science.gov (United States)

    Thompson, L.M.; Van Manen, F.T.; King, T.L.

    2005-01-01

    Highways are one of the leading causes of wildlife habitat fragmentation and may particularly affect wide-ranging species, such as American black bears (Ursus americanus). We initiated a research project in 2000 to determine potential effects of a 4-lane highway on black bear ecology in Washington County, North Carolina. The research design included a treatment area (highway construction) and a control area and a pre- and post-construction phase. We used data from the pre-construction phase to determine whether we could detect scale dependency or directionality among allele occurrence patterns using geostatistics. Detection of such patterns could provide a powerful tool to measure the effects of landscape fragmentation on gene flow. We sampled DNA from roots of black bear hair at 70 hair-sampling sites on each study area for 7 weeks during fall of 2000. We used microsatellite analysis based on 10 loci to determine unique multi-locus genotypes. We examined all alleles sampled at ???25 sites on each study area and mapped their presence or absence at each hair-sample site. We calculated semivariograms, which measure the strength of statistical correlation as a function of distance, and adjusted them for anisotropy to determine the maximum direction of spatial continuity. We then calculated the mean direction of spatial continuity for all examined alleles. The mean direction of allele frequency variation was 118.3?? (SE = 8.5) on the treatment area and 172.3?? (SE = 6.0) on the control area. Rayleigh's tests showed that these directions differed from random distributions (P = 0.028 and P < 0.001, respectively), indicating consistent directional patterns for the alleles we examined in each area. Despite the small spatial scale of our study (approximately 11,000 ha for each study area), we observed distinct and consistent patterns of allele occurrence, suggesting different directions of gene flow between the study areas. These directions seemed to coincide with the

  17. Segregation of Tay-Sachs and Sandhoff alleles in a non-Jewish family.

    OpenAIRE

    Lane, A B; Young, E; Jenkins, T

    1980-01-01

    A non-Jewish family is presented in which the genes for Tay-Sachs disease and Sandhoff disease are segregating. Individuals heterozygous for both alleles have low serum and white cell total hexosaminidase levels together with a proportion of heat-labile hexosaminidase A (HEX A) which falls in the normal range. The individuals would not be detected as carriers of Tay-Sachs disease or Sandhoff disease in a population screening program.

  18. Segregation of Tay-Sachs and Sandhoff alleles in a non-Jewish family.

    Science.gov (United States)

    Lane, A B; Young, E; Jenkins, T

    1980-01-01

    A non-Jewish family is presented in which the genes for Tay-Sachs disease and Sandhoff disease are segregating. Individuals heterozygous for both alleles have low serum and white cell total hexosaminidase levels together with a proportion of heat-labile hexosaminidase A (HEX A) which falls in the normal range. The individuals would not be detected as carriers of Tay-Sachs disease or Sandhoff disease in a population screening program. PMID:7446530

  19. Assigning breed origin to alleles in crossbred animals.

    Science.gov (United States)

    Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

    2016-08-22

    For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns

  20. Imbalance of Nature due to Anthropogenic Activities in the Bay of Bacorehuis, Sinaloa, Mexico

    Science.gov (United States)

    Torrecillas Nunez, C.; Cárdenas Cota, H.

    2013-05-01

    Pollution is further enhancing water scarcity by reducing water usability downstream, globally the most prevalent water quality problem is eutrophication, a result of high-nutrient loads, which substantially impairs beneficial uses of water. Projected food production needs and increasing wastewater effluents associated with an increasing population over the next three decades suggest a 10%-15% increase in the river input of nitrogen loads into coastal ecosystems (UNO, 2009). Our study in the Bay of Bacorehuis in the State of Sinaloa, which was carried out due to a request from local fishermen who wanted to find out the reason for fishing stocks depletion, confirmed this trend with the consequent imbalance of nature. Sinaloa depends heavily on intensive agricultural production to support its economy which in turn relies on water irrigation and the application of agro-chemicals. The research project included a desk top study of geophysical and environmental factors as well as sampling and testing of the water. In addition we carried out socio-economic research to find out the impact on the local community of the imbalance caused by anthropogenic activities in the watershed upstream from the Bay. Our research established that the Bay of Bacorehuis is contaminated by organic matter, bacteria coliforms, pesticides and mercury due to the discharge of surplus runoff generated by irrigation of farmlands into drainage networks as well as the discharge of untreated industrial and domestic wastewater form more than 24,000 inhabitants. The main contaminants detected in the water bodies were organic matter, faecal coliforms, mercury, dimethoate, endosulfan, heptachlor, DDE, DDT, organonitrogen, synthetic pyrethroid, chlorothalonil, ethion, endosulfan, diazinon, malathion and chlorpyrifos. Contaminants in sediments included the pesticides endosulfan, heptachlor, DDE, DDT, organophosphates, organonitrogen and synthetic pyrethroids. Natural water courses have been highly modified

  1. Wife Beating in South Africa: An Imbalance Theory of Resources and Power

    Science.gov (United States)

    Choi, Susanne Y. P.; Ting, Kwok-Fai

    2008-01-01

    This article develops an imbalance theory to explain physical violence against women in intimate relationships in South Africa. The theory proposes four typologies: dependence, compensation, submission, and transgression, through which imbalances in resource contribution and power distribution between spouses are hypothesized to contribute to…

  2. Effect of magnetic field on charge imbalance relaxation of non-equilibrium superconductivity

    International Nuclear Information System (INIS)

    Tsuboi, Kazuki; Yagi, Ryuta

    2010-01-01

    We have studied relaxation of charge imbalance of non-equilibrium superconductivity in magnetic field. We found that excess current due to charge imbalance showed striking dependence on magnitude of magnetic field and its orientation. We discussed origin of the relaxation.

  3. Excitatory/inhibitory imbalance in autism spectrum disorders: Implications for interventions and therapeutics.

    Science.gov (United States)

    Uzunova, Genoveva; Pallanti, Stefano; Hollander, Eric

    2016-04-01

    Imbalance between excitation and inhibition and increased excitatory-inhibitory (E-I) ratio is a common mechanism in autism spectrum disorders (ASD) that is responsible for the learning and memory, cognitive, sensory, motor deficits, and seizures occurring in these disorders. ASD are very heterogeneous and better understanding of E-I imbalance in brain will lead to better diagnosis and treatments. We perform a critical literature review of the causes and presentations of E-I imbalance in ASD. E-I imbalance in ASD is due primarily to abnormal glutamatergic and GABAergic neurotransmission in key brain regions such as neocortex, hippocampus, amygdala, and cerebellum. Other causes are due to dysfunction of neuropeptides (oxytocin), synaptic proteins (neuroligins), and immune system molecules (cytokines). At the neuropathological level E-I imbalance in ASD is presented as a "minicolumnopathy". E-I imbalance alters the manner by which the brain processes information and regulates behaviour. New developments for investigating E-I imbalance such as optogenetics and transcranial magnetic stimulation (TMS) are presented. Non-invasive brain stimulation methods such as TMS for treatment of the core symptoms of ASD are discussed. Understanding E-I imbalance has important implications for developing better pharmacological and behavioural treatments for ASD, including TMS, new drugs, biomarkers and patient stratification.

  4. A comparison of imbalance settlement designs and results of Germany and the Netherlands

    NARCIS (Netherlands)

    Van der Veen, R.A.C.; Abbasy, A.; Hakvoort, R.A.

    2010-01-01

    Imbalance settlement is a vital part of the balancing market, i.e. the institutional arrangement that establishes market-based balance management in liberalized electricity markets. We investigate the impact of the imbalance settlement design on the behaviour of Balance Responsible Parties and

  5. The effect of impurity scattering on the thermally induced charge imbalance in a clean superconductor

    International Nuclear Information System (INIS)

    Nielsen, J.B.; Smith, H.; Ono, Y.A.; Pethick, C.J.

    1980-01-01

    The charge imbalance generated in a current-carrying clean superconductor by a temperature gradient is calculated, assuming that non-magnetic or magnetic impurities are the only source of scattering. The charge imbalance is obtained from exact solutions of the quasiparticle Boltzmann equation, valid at any temperature and superfluid velocity. (author)

  6. A risk allele for nicotine dependence in CHRNA5 is a protective allele for cocaine dependence.

    Science.gov (United States)

    Grucza, Richard A; Wang, Jen C; Stitzel, Jerry A; Hinrichs, Anthony L; Saccone, Scott F; Saccone, Nancy L; Bucholz, Kathleen K; Cloninger, C Robert; Neuman, Rosalind J; Budde, John P; Fox, Louis; Bertelsen, Sarah; Kramer, John; Hesselbrock, Victor; Tischfield, Jay; Nurnberger, John I; Almasy, Laura; Porjesz, Bernice; Kuperman, Samuel; Schuckit, Marc A; Edenberg, Howard J; Rice, John P; Goate, Alison M; Bierut, Laura J

    2008-12-01

    A nonsynonymous coding polymorphism, rs16969968, of the CHRNA5 gene that encodes the alpha-5 subunit of the nicotinic acetylcholine receptor (nAChR) has been found to be associated with nicotine dependence. The goal of this study was to examine the association of this variant with cocaine dependence. Genetic association analysis was performed in two independent samples of unrelated case and control subjects: 1) 504 European Americans participating in the Family Study on Cocaine Dependence (FSCD) and 2) 814 European Americans participating in the Collaborative Study on the Genetics of Alcoholism (COGA). In the FSCD, there was a significant association between the CHRNA5 variant and cocaine dependence (odds ratio = .67 per allele, p = .0045, assuming an additive genetic model), but in the reverse direction compared with that previously observed for nicotine dependence. In multivariate analyses that controlled for the effects of nicotine dependence, both the protective effect for cocaine dependence and the previously documented risk effect for nicotine dependence were statistically significant. The protective effect for cocaine dependence was replicated in the COGA sample. In COGA, effect sizes for habitual smoking, a proxy phenotype for nicotine dependence, were consistent with those observed in FSCD. The minor (A) allele of rs16969968, relative to the major G allele, appears to be both a risk factor for nicotine dependence and a protective factor for cocaine dependence. The biological plausibility of such a bidirectional association stems from the involvement of nAChRs with both excitatory and inhibitory modulation of dopamine-mediated reward pathways.

  7. Detection of quorum-sensing pathway and construction of luxS gene allelic exchange plasmid of Streptococcus mutans%变形链球菌AI-2活性测定及luxS基因同源重组质粒的构建

    Institute of Scientific and Technical Information of China (English)

    于丹妮; 韩育植; 韩福胜; 陈杰

    2008-01-01

    Objective To detect the AI-2 quorum-sensing pathway and construct the luxS g-ene allelic exchange plasmid of Streptococcus mutans. Methods To dectect AI-2 pathway in Streptococcus mutans,the Vibrio harveyi BB170 was used as reporter strain. The PCR fragments of the upstream and downstream regions of luxS and the Erythromycin resistance gene were amplified with the primers respetively,and these fragments were ligated into pUC19 vector with double endonuclease reaction sequentially,the ligated DNAs were transformed into Escherichia coli DH5α,then the reconstructed plasmids were isolated and identified by restricted endonuclease digestions. Results Streptococcus mutans Ingbritt C could induce luminescene of BB170, suggesting the presense of AI-2 quorum sensing pathway in Streptococcus mutans,and such stimulatory activity was maximal at the mid-log growth phase.The recombinant plasmid pUCluxKO was digested by PstI-BamHI,and the digest product were 1000 bp and 5000 bp.When the pUCluxKO Was digested by BamHI-KpnI,the digest product were 1500 bp and 4500 bp.While it was digested by KpnI-ECORI,the digest product were 1000 bp and 5000 bp. All PCR product was in a single belt respectively.Conclusions The recombinant plasmid was cloned effectively and can be used in the construction of S. mutans luxS mutant.%目的 构建用于转化变形链球菌的luxS基因缺失的同源重组克隆载体.方法 利用哈氏弧菌(Vibrio harveyi)BB170作为报告菌株,对变形链球菌在不同生长时期诱导生物发光的能力进行测定,然后分别PCR扩增变链菌luxS基因上下游片段及质粒PJT10的红霉素抗性基因片段,采用分子克隆技术将基因片段依次双酶切后连接入载体pUC19,构建luxS基因缺失的重组质粒,转化到大肠杆菌DH5α感受态细胞经筛选后,抽提重组质粒,进行酶切鉴定.结果 变链菌国际标准株可诱导哈氏弧菌BB170的生物发光现象,提示变链菌中存在AI-2数量感应通路.构建的重

  8. Identification of the Rare, Four Repeat Allele of IL-4 Intron-3 VNTR Polymorphism in Indian Populations.

    Science.gov (United States)

    Verma, Henu Kumar; Jha, Aditya Nath; Khodiar, Prafulla Kumar; Patra, Pradeep Kumar; Bhaskar, Lakkakula Venkata Kameswara Subrahmanya

    2016-06-01

    Cytokines are cell signaling molecules which upon release by cells facilitate the recruitment of immune-modulatory cells towards the sites of inflammation. Genetic variations in cytokine genes are shown to regulate their production and affect the risk of infectious as well as autoimmune diseases. Intron-3 of interleukin-4 gene (IL-4) harbors 70-bp variable number of tandem repeats (VNTR) that may alter the expression level of IL-4 gene. To determine the distribution of IL-4 70-bp VNTR polymorphism in seven genetically heterogeneous populations of Chhattisgarh, India and their comparison with the finding of other Indian and world populations. A total of 371 healthy unrelated individuals from 5 caste and 2 tribal populations were included in the present study. The IL-4 70-bp VNTR genotyping was carried out using PCR and electrophoresis. Overall, 3 alleles of IL-4 70-bp VNTR (a2, a3 and a4) were detected. The results demonstrated the variability of the IL-4 70-bp VNTR polymorphism in Chhattisgarh populations. Allele a3 was the most common allele at the 70-bp VNTR locus in all populations followed by a2 allele. This study reports the presence four repeat allele a4 at a low frequency in the majority of the Chhattisgarh populations studied. Further, the frequency of the minor allele (a2) in Chhattisgarh populations showed similarity with the frequencies of European populations but not with the East Asian populations where the a2 allele is a major allele. Our study provides a baseline for future research into the role of the IL-4 locus in diseases linked to inflammation in Indian populations.

  9. Effects of a chemical imbalance causal explanation on individuals' perceptions of their depressive symptoms.

    Science.gov (United States)

    Kemp, Joshua J; Lickel, James J; Deacon, Brett J

    2014-05-01

    Although the chemical imbalance theory is the dominant causal explanation of depression in the United States, little is known about the effects of this explanation on depressed individuals. This experiment examined the impact of chemical imbalance test feedback on perceptions of stigma, prognosis, negative mood regulation expectancies, and treatment credibility and expectancy. Participants endorsing a past or current depressive episode received results of a bogus but credible biological test demonstrating their depressive symptoms to be caused, or not caused, by a chemical imbalance in the brain. Results showed that chemical imbalance test feedback failed to reduce self-blame, elicited worse prognostic pessimism and negative mood regulation expectancies, and led participants to view pharmacotherapy as more credible and effective than psychotherapy. The present findings add to a growing literature highlighting the unhelpful and potentially iatrogenic effects of attributing depressive symptoms to a chemical imbalance. Clinical and societal implications of these findings are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Diurnal Variations of the Flux Imbalance Over Homogeneous and Heterogeneous Landscapes

    Science.gov (United States)

    Zhou, Yanzhao; Li, Dan; Liu, Heping; Li, Xin

    2018-05-01

    It is well known that the sum of the turbulent sensible and latent heat fluxes as measured by the eddy-covariance method is systematically lower than the available energy (i.e., the net radiation minus the ground heat flux). We examine the separate and joint effects of diurnal and spatial variations of surface temperature on this flux imbalance in a dry convective boundary layer using the Weather Research and Forecasting model. Results show that, over homogeneous surfaces, the flux due to turbulent-organized structures is responsible for the imbalance, whereas over heterogeneous surfaces, the flux due to mesoscale or secondary circulations is the main contributor to the imbalance. Over homogeneous surfaces, the flux imbalance in free convective conditions exhibits a clear diurnal cycle, showing that the flux-imbalance magnitude slowly decreases during the morning period and rapidly increases during the afternoon period. However, in shear convective conditions, the flux-imbalance magnitude is much smaller, but slightly increases with time. The flux imbalance over heterogeneous surfaces exhibits a diurnal cycle under both free and shear convective conditions, which is similar to that over homogeneous surfaces in free convective conditions, and is also consistent with the general trend in the global observations. The rapid increase in the flux-imbalance magnitude during the afternoon period is mainly caused by the afternoon decay of the turbulent kinetic energy (TKE). Interestingly, over heterogeneous surfaces, the flux imbalance is linearly related to the TKE and the difference between the potential temperature and surface temperature, ΔT; the larger the TKE and ΔT values, the smaller the flux-imbalance magnitude.

  11. Hypomorphic temperature-sensitive alleles of NSDHL cause CK syndrome.

    Science.gov (United States)

    McLarren, Keith W; Severson, Tesa M; du Souich, Christèle; Stockton, David W; Kratz, Lisa E; Cunningham, David; Hendson, Glenda; Morin, Ryan D; Wu, Diane; Paul, Jessica E; An, Jianghong; Nelson, Tanya N; Chou, Athena; DeBarber, Andrea E; Merkens, Louise S; Michaud, Jacques L; Waters, Paula J; Yin, Jingyi; McGillivray, Barbara; Demos, Michelle; Rouleau, Guy A; Grzeschik, Karl-Heinz; Smith, Raffaella; Tarpey, Patrick S; Shears, Debbie; Schwartz, Charles E; Gecz, Jozef; Stratton, Michael R; Arbour, Laura; Hurlburt, Jane; Van Allen, Margot I; Herman, Gail E; Zhao, Yongjun; Moore, Richard; Kelley, Richard I; Jones, Steven J M; Steiner, Robert D; Raymond, F Lucy; Marra, Marco A; Boerkoel, Cornelius F

    2010-12-10

    CK syndrome (CKS) is an X-linked recessive intellectual disability syndrome characterized by dysmorphism, cortical brain malformations, and an asthenic build. Through an X chromosome single-nucleotide variant scan in the first reported family, we identified linkage to a 5 Mb region on Xq28. Sequencing of this region detected a segregating 3 bp deletion (c.696_698del [p.Lys232del]) in exon 7 of NAD(P) dependent steroid dehydrogenase-like (NSDHL), a gene that encodes an enzyme in the cholesterol biosynthesis pathway. We also found that males with intellectual disability in another reported family with an NSDHL mutation (c.1098 dup [p.Arg367SerfsX33]) have CKS. These two mutations, which alter protein folding, show temperature-sensitive protein stability and complementation in Erg26-deficient yeast. As described for the allelic disorder CHILD syndrome, cells and cerebrospinal fluid from CKS patients have increased methyl sterol levels. We hypothesize that methyl sterol accumulation, not only cholesterol deficiency, causes CKS, given that cerebrospinal fluid cholesterol, plasma cholesterol, and plasma 24S-hydroxycholesterol levels are normal in males with CKS. In summary, CKS expands the spectrum of cholesterol-related disorders and insight into the role of cholesterol in human development. Copyright © 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  12. Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

    Science.gov (United States)

    Just, Rebecca S; Irwin, Jodi A

    2018-05-01

    Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools

  13. The man-made creators of the imbalance of water in Nature

    Science.gov (United States)

    Shlafman, L. M.; Kontar, V. A.

    2013-12-01

    At 2011 we have described the imbalance of water in Nature as the system [1]. At 2012 we have described water and carbon and the glaciers [2], [3] as creators of the imbalance of Nature. Now we are describing some man-made creators of the imbalance of Nature. The photosynthesis is a powerful creator of the imbalance of Nature. The photosynthesis significantly increases the complexity of the structures and reduces the entropy. Earth's hydrosphere contains water less than it was flowed via photosynthesis. This is an example of the imbalance of involving when the return of water has delayed because water is involved into the processes of life and other processes. People widely use photosynthesis and create not only an additional man-made imbalance of water in Nature, but also the man-made changing the albedo, and a lot of other important parameters of the planet of Earth. All of these processes are significantly imbalanced. The fossil hydrocarbons have accumulated during millions of years, but now are burned. This is an example of the imbalance delay by time. The man-made burning of the hydrocarbons is creating the imbalances of impact or explosive type, because of the burning processes is in millions of times faster than the accumulation processes. Please pay attention to the imbalance of redeployment by places. For example, oil and gas are extracted in one places, and burned in others. During combustion is standing out not only water, but energy, and other components. The temperature in the centers of big cities is always higher and there is dominating the rising air. It pollutes the environment, changes circulations, create greenhouse effect, etc. Other examples of the imbalance of relocation are shown in the production and consumption of food. The irrigation systems transfer water from one place to another. This transfer of water creates a lot of imbalances in change climate, ecosystems, etc in places where water was took and where the water was brought. Usually

  14. Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

    Directory of Open Access Journals (Sweden)

    Mary Anna Carbone

    Full Text Available The statistical power of genome-wide association (GWA studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG. Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR upon overexpression of transgenic human glaucoma-associated myocilin (MYOC. We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

  15. Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen.

    Science.gov (United States)

    Lu, Xunli; Kracher, Barbara; Saur, Isabel M L; Bauer, Saskia; Ellwood, Simon R; Wise, Roger; Yaeno, Takashi; Maekawa, Takaki; Schulze-Lefert, Paul

    2016-10-18

    Disease-resistance genes encoding intracellular nucleotide-binding domain and leucine-rich repeat proteins (NLRs) are key components of the plant innate immune system and typically detect the presence of isolate-specific avirulence (AVR) effectors from pathogens. NLR genes define the fastest-evolving gene family of flowering plants and are often arranged in gene clusters containing multiple paralogs, contributing to copy number and allele-specific NLR variation within a host species. Barley mildew resistance locus a (Mla) has been subject to extensive functional diversification, resulting in allelic resistance specificities each recognizing a cognate, but largely unidentified, AVR a gene of the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). We applied a transcriptome-wide association study among 17 Bgh isolates containing different AVR a genes and identified AVR a1 and AVR a13 , encoding candidate-secreted effectors recognized by Mla1 and Mla13 alleles, respectively. Transient expression of the effector genes in barley leaves or protoplasts was sufficient to trigger Mla1 or Mla13 allele-specific cell death, a hallmark of NLR receptor-mediated immunity. AVR a1 and AVR a13 are phylogenetically unrelated, demonstrating that certain allelic MLA receptors evolved to recognize sequence-unrelated effectors. They are ancient effectors because corresponding loci are present in wheat powdery mildew. AVR A1 recognition by barley MLA1 is retained in transgenic Arabidopsis, indicating that AVR A1 directly binds MLA1 or that its recognition involves an evolutionarily conserved host target of AVR A1 Furthermore, analysis of transcriptome-wide sequence variation among the Bgh isolates provides evidence for Bgh population structure that is partially linked to geographic isolation.

  16. Association of gliadin antibodies, HLA alleles, and schizophrenia in Cuban population patients

    Directory of Open Access Journals (Sweden)

    José A. Galván

    2016-05-01

    Full Text Available Introduction: Several lines of evidence have suggested an interesting link between gluten ingestion and schizophrenia. For example, increased levels of gliadin and transglutaminase antibodies have been observed in patients with schizophrenia. Methods: To verify these observations we compared the prevalence of gliadin and transglutaminse antibodies, as well as the presence of the HLA alleles, HLA DQA1*0501-DQB1*02 (DQ2 and HLA-DQA1*0301-DQB1*0302 (DQ8, among patients with schizophrenia and healthy controls. A total of 108 patients with schizophrenia and 60 healthy controls were evaluated. Gliadin antibodies were determined by a visual semiquantitative assay and tissue transglutaminase antibodies were determined both by one-step immunochromatografic assay and ELISA. HLA typing was performed by PCR amplification using sequence-specific primers for each allele. Results: We found a strong association between the presence of gliadin antibodies and schizophrenia (OR 3.488; 95% CI, 1.43-8.44. However, tissue transglutaminase antibodies were not detected in either group neither by immunochromatograpic or ELISA. No significant association was found for the DQ2 or DQ8 heterodimer and the disease, but a significant positive association between schizophrenia and HLA alleles DQA1*0301 and DQB1*02 was present (OR = 2.80; 95% CI, 1.27-6.17, and OR = 2.37, 95% CI, 1.24-4.53, respectively. Conclusions: The present study showed that the presence of gliadin antibodies was not correlated with the presence of HLA DQA1*0301 or DQB1*02 alleles within the group of patients with schizophrenia. Our study replicates the findings that anti-gliadin antibodies are associated with schizophrenia but also suggests that the presence of these antibodies and the HLA alleles DQB1*02 and DQA1*0301 are independently associated with susceptibility to schizophrenia.

  17. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    Directory of Open Access Journals (Sweden)

    Grażyna Adler

    2014-08-01

    Full Text Available Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12% and lower in the regions of Southeast Mediterranean (about 5%. Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Hercegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy subjects from Bosnia and Herzegovina (DNA collected 2011-2013.  Mean age of the cohort being 58.8 (±10.7 years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. 

  18. Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

    Science.gov (United States)

    Carbone, Mary Anna; Chen, Yuhong; Hughes, Guy A; Weinreb, Robert N; Zabriskie, Norman A; Zhang, Kang; Anholt, Robert R H

    2011-01-01

    The statistical power of genome-wide association (GWA) studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG). Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG) remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR) upon overexpression of transgenic human glaucoma-associated myocilin (MYOC). We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

  19. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping.

    Science.gov (United States)

    Edzesi, Wisdom M; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.

  20. Pension system in Romania. Long term imbalances and inconsistent policies

    Directory of Open Access Journals (Sweden)

    Ph. D. Associate Professor Razvan Papuc

    2012-05-01

    Full Text Available Public policies on retirement, both in Romania and in other EU countries, have been and still are conditioned by numerous short-term budgetary constaints and by long term major sustainability problems. Alongside objective, demographic developments known in all European countries , support systems for the elderly are facing numerous constraints, both due to government policies marked by fiscal indiscipline and lack of consistency of decisions and, hence, credibility phenomena caused by the phenomenon "the captive politician of a redistributive policy model". Modeling support institutions for pensioners by political actors was most of the times the expression of elections marked by Weberian instrumental rationality and not by wertrationalitat, using the axiom- guide for the behaviour of decision markers to "meet social interests in order to come to power" and not by the concern for a more long term efficient trans-redistributive approach. This paper aims to pursue the most important imbalances that chartacterize the public pension system in Romania, expression of decisions determined by aggregating in group individual preferences and noy by both rational and ethical analysis without redistribution centres.

  1. Monocular Perceptual Deprivation from Interocular Suppression Temporarily Imbalances Ocular Dominance.

    Science.gov (United States)

    Kim, Hyun-Woong; Kim, Chai-Youn; Blake, Randolph

    2017-03-20

    Early visual experience sculpts neural mechanisms that regulate the balance of influence exerted by the two eyes on cortical mechanisms underlying binocular vision [1, 2], and experience's impact on this neural balancing act continues into adulthood [3-5]. One recently described, compelling example of adult neural plasticity is the effect of patching one eye for a relatively short period of time: contrary to intuition, monocular visual deprivation actually improves the deprived eye's competitive advantage during a subsequent period of binocular rivalry [6-8], the robust form of visual competition prompted by dissimilar stimulation of the two eyes [9, 10]. Neural concomitants of this improvement in monocular dominance are reflected in measurements of brain responsiveness following eye patching [11, 12]. Here we report that patching an eye is unnecessary for producing this paradoxical deprivation effect: interocular suppression of an ordinarily visible stimulus being viewed by one eye is sufficient to produce shifts in subsequent predominance of that eye to an extent comparable to that produced by patching the eye. Moreover, this imbalance in eye dominance can also be induced by prior, extended viewing of two monocular images differing only in contrast. Regardless of how shifts in eye dominance are induced, the effect decays once the two eyes view stimuli equal in strength. These novel findings implicate the operation of interocular neural gain control that dynamically adjusts the relative balance of activity between the two eyes [13, 14]. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. A Rare Chromosome 3 Imbalance and Its Clinical Implications

    Directory of Open Access Journals (Sweden)

    Karen Sims

    2012-01-01

    Full Text Available The duplication of chromosome 3q is a rare disorder with varying chromosomal breakpoints and consequently symptoms. Even rarer is the unbalanced outcome from a parental inv(3 resulting in duplicated 3q and a deletion of 3p. Molecular karyotyping should aid in precisely determining the length and breakpoints of the 3q+/3p− so as to better understand a child’s future development and needs. We report a case of an infant male with a 57.5 Mb duplication from 3q23-qter. This patient also has an accompanying 1.7 Mb deletion of 3p26.3. The duplicated segment in this patient encompasses the known critical region of 3q26.3-q27, which is implicated in the previously reported 3q dup syndrome; however, the accompanying 3p26.3 deletion is smaller than the previously reported cases. The clinical phenotype of this patient relates to previously reported cases of 3q+ that may suggest that the accompanying 1.7 Mb heterozygous deletion is not clinically relevant. Taken together, our data has refined the location and extent of the chromosome 3 imbalance, which will aid in better understanding the molecular underpinning of the 3q syndrome.

  3. The loss-of-allele assay for ES cell screening and mouse genotyping.

    Science.gov (United States)

    Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

    2010-01-01

    Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction

  4. Beta2-adrenergic receptor allele frequencies in the Quechua, a high altitude native population.

    Science.gov (United States)

    Rupert, J L; Monsalve, M V; Devine, D V; Hochachka, P W

    2000-03-01

    The beta2-adrenergic receptor is involved in the control of numerous physiological processes and, as the primary catecholamine receptor in the lungs, is of particular importance in the regulation of pulmonary function. There are several polymorphic loci in the beta2-adrenergic receptor gene that have alleles that alter receptor function, including two (A/G46, G/C79) that increase agonist sensitivity. As such a phenotype may increase vaso and bronchial dilation, thereby facilitating air and blood flow through the lungs, we hypothesized that selection may have favoured these alleles in high altitude populations as part of an adaptive strategy to deal with the hypoxic conditions characteristic of such environments. We tested this hypothesis by determining the allele frequencies for these two polymorphisms, as well one additional missense mutation (C/T491) and two silent mutations (G/A252 and C/A523) in 63 Quechua speaking natives from communities located between 3200 and 4200 m on the Peruvian altiplano. These frequencies were compared with those of two lowland populations, one native American (Na-Dene from the west coast of Canada) and one Caucasian of Western European descent. The Quechua manifest many of the pulmonary characteristics of high altitude populations and differences in allele frequencies between the Quechua and lowlanders could be indicative of a selective advantage conferred by certain genotypes in high altitude environments. Allele frequencies varied between populations at some loci and patterns of linkage disequilibrium differed between the old-world and new-world samples; however, as these populations are not closely related, significant variation would be expected due to stochastic effects alone. Neither of the alleles associated with increased receptor sensitivity (A46, G79) was significantly over-represented in the Quechua compared with either lowland group. The Quechua were monomorphic for the C allele at base 79. This variant has been

  5. Constraints on oceanic N balance/imbalance from sedimentary 15N records

    Directory of Open Access Journals (Sweden)

    M. A. Altabet

    2007-01-01

    Full Text Available According to current best estimates, the modern ocean's N cycle is in severe deficit. N isotope budgeting provides an independent geochemical constraint in this regard as well as the only means for past reconstruction. Overall, it is the relative proportion of N2 fixation consumed by water column denitrification that sets average oceanic δ15N under steady-state conditions. Several factors (conversion of organic N to N2, Rayleigh closed and open system effects likely reduce the effective fractionation factor (ε for water column denitrification to about half the inherent microbial value for εden. If so, the average oceanic δ15N of ~5‰ is consistent with a canonical contribution from water column denitrification of 50% of the source flux from N2 fixation. If an imbalance in oceanic N sources and sinks changes this proportion then a transient in average oceanic δ15N would occur. Using a simple model, changing water column denitrification by ±30% or N2 fixation by ±15% produces detectable (>1‰ changes in average oceanic δ15N over one residence time period or more with corresponding changes in oceanic N inventory. Changing sedimentary denitrification produces no change in δ15N but does change N inventory. Sediment δ15N records from sites thought to be sensitive to oceanic average δ15N all show no detectible change over the last 3 kyr or so implying a balanced marine N budget over the latest Holocene. A mismatch in time scales is the most likely meaningful interpretation of the apparent conflict with modern flux estimates. Decadal to centennial scale oscillations between net N deficit and net surplus may occur but on the N residence timescale of several thousand years, net balance is achieved in sum. However, sediment δ15N records from the literature covering the period since the last glacial maximum show excursions of up to several ‰ that are consistent with sustained N deficit during the deglaciation followed by readjustment

  6. The Analysis of A Frequent TMPRSS3 Allele Containing P.V116M and P.V291L in A Cis Configuration among Deaf Koreans

    Directory of Open Access Journals (Sweden)

    Ah Reum Kim

    2017-10-01

    Full Text Available We performed targeted re-sequencing to identify the genetic etiology of early-onset postlingual deafness and encountered a frequent TMPRSS3 allele harboring two variants in a cis configuration. We aimed to evaluate the pathogenicity of the allele. Among 88 cochlear implantees with autosomal recessive non-syndromic hearing loss, subjects with GJB2 and SLC26A4 mutations were excluded. Thirty-one probands manifesting early-onset postlingual deafness were sorted. Through targeted re-sequencing, we detected two families with a TMPRSS3 mutant allele containing p.V116M and p.V291L in a cis configuration, p.[p.V116M; p.V291L]. A minor allele frequency was calculated and proteolytic activity was measured. A p.[p.V116M; p.V291L] allele demonstrated a significantly higher frequency compared to normal controls and merited attention due to its high frequency (4.84%, 3/62. The first family showed a novel deleterious splice site variant—c.783-1G>A—in a trans allele, while the other showed homozygosity. The progression to deafness was noted within the first decade, suggesting DFNB10. The proteolytic activity was significantly reduced, confirming the severe pathogenicity. This frequent mutant allele significantly contributes to early-onset postlingual deafness in Koreans. For clinical implication and proper auditory rehabilitation, it is important to pay attention to this allele with a severe pathogenic potential.

  7. Mannose-binding lectin variant alleles and HLA-DR4 alleles are associated with giant cell arteritis

    DEFF Research Database (Denmark)

    Jacobsen, Soren; Baslund, Bo; Madsen, Hans O.

    2002-01-01

    /GCA, MBL variant alleles were associated with signs of increased inflammatory activity and clinical signs of arteritic manifestations. This was not found for HLA-DR4 alleles. These findings indicate that HLA-DR4 and MBL are contributing to the pathophysiology of GCA at different levels in the disease...... alleles in controls, patients with PMR only, and patients with GCA was 37, 32, and 53% (p = 0.01), respectively. HLA-DRB1*04 was found in 47% of patients with PMR only and in 54% of patients with GCA, which differed significantly from the 35% found in controls (p = 0.01). HLA-DR4 alleles were...... not associated with any clinical phenotypes of PMR/GCA, whereas MBL variant alleles were associated with cranial arteritis, high erythrocyte sedimentation rate, and low B-hemoglobin. CONCLUSION: We found MBL variant alleles and HLA-DR4 alleles to be weak susceptibility markers for GCA. In patients with PMR...

  8. Human hypervariable sequences in risk assessment: rare Ha-ras alleles in cancer patients

    International Nuclear Information System (INIS)

    Krontiris, T.G.; DiMartino, N.A.; Mitcheson, H.D.; Lonergan, J.A.; Begg, C.; Parkinson, D.R.

    1987-01-01

    A variable tandem repeat (VTR) is responsible for the hyperallelism one kilobase 3' to the human c-Ha-ras-1 (Ha-ras) gene. Thirty-two distinct restriction fragments, comprising 3 allelic classes by frequency of occurrence, have thus far been detected in a sample size of approximately 800 caucasians. Rare Ha-ras alleles, 21 in all, are almost exclusively confined to the genomes of cancer patients. From their data the authors have computed the relative cancer risk associated with possession of a rare Ha-ras allele to be 27. To understand the molecular basis for this phenomenon, they have begun to clone Ha-ras fragments from nontumor DNA of cancer patients. They report here the weak activation, as detected by transfection and transformation of NIH 3T3 mouse cells, of two Ha-ras genes which were obtained from lymphocyte DNA of a melanoma patient. They have mapped the regions that confer this transforming activity to the fragment containing the VTR in one Ha-ras clone and the fragment containing gene coding sequences in the other

  9. allelic variation of hmw glutenin subunits of ethiopian bread wheat

    African Journals Online (AJOL)

    journal

    High molecular weight glutenins are often effective in identifying wheat (Triticum ... There were highly significant differences between genotypes and banding ... was without deliberate selection pressure towards high Glu-1 scoring alleles ...

  10. Association mapping and favorable QTL alleles for fiber quality traits ...

    Indian Academy of Sciences (India)

    A total of 201 markers were polymorphic and generated 394 ... identified favorable QTL alleles and typical accessions for fiber quality are excellent genetic resources for future cotton .... Field management followed respective local practices.

  11. Apolipoprotein e4 allele and cognitive decline in elderly men

    NARCIS (Netherlands)

    Feskens, E.J.M.; Havekes, L.M.; Kalmijn, S.; Knijff, P. de; Launer, L.J.; Kromhout, D.

    1994-01-01

    Objectives - To determine whether polymorphism of apolipoprotein E - notably, the e4 allele - predicts cognitive deterioration in the general population. Design - Population based cohort investigated in 1990 and in 1993. Setting - Zutphen, the Netherlands. Subjects - Representative cohort of 538

  12. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

    Science.gov (United States)

    Reinius, Björn; Mold, Jeff E; Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

    2016-11-01

    Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8 + T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

  13. DRD4 dopamine receptor allelic diversity in various primate species

    Energy Technology Data Exchange (ETDEWEB)

    Adamson, M.; Higley, D. [NIAAA, Rockville, MD (United States); O`Brien, S. [NCI, Frederick, MD (United States)] [and others

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  14. Tunnel injection and tunnel stimulation of superconductivity: the role of branch imbalance

    International Nuclear Information System (INIS)

    Gal'perin, Y.M.; Kozub, V.I.; Spivak, B.A.

    1983-01-01

    The tunnel injection and the tunnel extraction of quasiparticles in a superconductor are considered, taking into account the branch population imbalance. The stability of nonequilibrium states with branch imbalance is discussed. It is shown that if this imbalance is large enough, the nonequilibrim state becomes unstable with respect to spatially homogeneous fluctuations of the order parameter, the characteristic increment being of the order of that for the Cooper instability of the normal state at T>T/sub c/. As a result, states with oscillating order parameter can exist in a superconductor under injection or extraction. The relation of the results obtained to experimental results is discussed

  15. ALEA: a toolbox for allele-specific epigenomics analysis.

    Science.gov (United States)

    Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

    2014-04-15

    The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Allele-specific MMP-3 transcription under in vivo conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chaoyong, Zhu [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Odeberg, Jacob [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm (Sweden); Hamsten, Anders [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Eriksson, Per [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden)

    2006-09-29

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

  17. SSR allelic variation in almond (Prunus dulcis Mill.).

    Science.gov (United States)

    Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

    2006-01-01

    Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

  18. Origin of allelic diversity in antirrhinum S locus RNases.

    Science.gov (United States)

    Xue, Y; Carpenter, R; Dickinson, H G; Coen, E S

    1996-01-01

    In many plant species, self-incompatibility (SI) is genetically controlled by a single multiallelic S locus. Previous analysis of S alleles in the Solanaceae, in which S locus ribonucleases (S RNases) are responsible for stylar expression of SI, has demonstrated that allelic diversity predated speciation within this family. To understand how allelic diversity has evolved, we investigated the molecular basis of gametophytic SI in Antirrhinum, a member of the Scrophulariaceae, which is closely related to the Solanaceae. We have characterized three Antirrhinum cDNAs encoding polypeptides homologous to S RNases and shown that they are encoded by genes at the S locus. RNA in situ hybridization revealed that the Antirrhinum S RNase are primarily expressed in the stylar transmitting tissue. This expression is consistent with their proposed role in arresting the growth of self-pollen tubes. S alleles from the Scrophulariaceae form a separate group from those of the Solanaceae, indicating that new S alleles have been generated since these families separated (approximately 40 million years). We propose that the recruitment of an ancestral RNase gene into SI occurred during an early stage of angiosperm evolution and that, since that time, new alleles subsequently have arisen at a low rate. PMID:8672882

  19. Similar nature of ionic imbalances in cardiovascular and renal disorders

    International Nuclear Information System (INIS)

    Shahid, S.M.; Jawed, M.; Akram, H.; Mahboob, T.

    2004-01-01

    Background: Several studies have reported improper ionic environment in cardiovascular and renal patients but how the diseases are associated on ionic basis is still not clear. Objective: The present study was aimed to investigate sodium and potassium concentrations and their transport abnormalities in cardiovascular and renal patients. Patients and Methods: Thirty patients of various cardiovascular and thirty patients of various renal disorders (53.33% males, 46.67% females) were selected. Erythrocytes were isolated from freshly drawn blood samples, washed and used for the estimation of sodium and potassium levels using flame photometer (Corning 410). Serum sodium and potassium were measured by flame photometer. RBC membranes were prepared for the estimation of Na/sup +/-K/sup +/-ATPase activity in terms of inorganic phosphate released/mg protein/hour. Results: Intra-erythrocyte and serum sodium and potassium concentrations and Na/sup +/-K/sup +/-ATPase activity were different in cardiovascular and renal patients from controls. Intra-erythrocyte sodium level was increased significantly (P<0.01) in cardiovascular patients and non-significantly in renal patients as compared to controls. Na/sup +/-K/sup +/-ATPase activity and serum sodium level were decreased significantly (P<0.01) in both the groups as compared to controls. Serum potassium was found to be decreased significantly (P<0.01) in cardiovascular patients whereas it was raised significantly (P<0.01) in renal patients as compared to control subjects. Conclusion: The results indicated similar nature of ionic and electrolyte imbalances in cardiovascular and renal disorders resulting from impaired Na/sup +/-K/sup +/-ATPase system. Further investigations in the same area, may be of help to establish an understanding of the progression of diseases, associated complications and the preventive steps that should-be taken to arrest the progression of these disorders. (author)

  20. Work ability, effort-reward imbalance and disability pension claims.

    Science.gov (United States)

    Wienert, J; Spanier, K; Radoschewski, F M; Bethge, M

    2017-12-30

    Effort-reward imbalance (ERI) and self-rated work ability are known independent correlates and predictors of intended disability pension claims. However, little research has focused on the interrelationship between the three and whether self-rated work ability mediates the relationship between ERI and intended disability pension claims. To investigate whether self-rated work ability mediates the association between ERI and intended disability pension claims. Baseline data from participants of the Third German Sociomedical Panel of Employees, a 5-year cohort study that investigates determinants of work ability, rehabilitation utilization and disability pensions in employees who have previously received sickness benefits, were analysed. We tested direct associations between ERI with intended disability pension claims (Model 1) and self-rated work ability (Model 2). Additionally, we tested whether work ability mediates the association between ERI and intended disability pension claims (Model 3). There were 2585 participants. Model 1 indicated a significant association between ERI and intended disability pension claims. Model 2 showed a significant association between ERI and self-rated work ability. The mediation in Model 3 revealed a significant indirect association between ERI and intended disability pension claims via self-rated work ability. There was no significant direct association between ERI and intended disability pension claims. Our results support the adverse health-related impact of ERI on self-rated work ability and intended disability pension claims. © The Author 2017. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  1. Diagnosis of nutrient imbalances with vector analysis in agroforestry systems.

    Science.gov (United States)

    Isaac, Marney E; Kimaro, Anthony A

    2011-01-01

    Agricultural intensification has had unintended environmental consequences, including increased nutrient leaching and surface runoff and other agrarian-derived pollutants. Improved diagnosis of on-farm nutrient dynamics will have the advantage of increasing yields and will diminish financial and environmental costs. To achieve this, a management support system that allows for site-specific rapid evaluation of nutrient production imbalances and subsequent management prescriptions is needed for agroecological design. Vector diagnosis, a bivariate model to depict changes in yield and nutritional response simultaneously in a single graph, facilitates identification of nutritional status such as growth dilution, deficiency, sufficiency, luxury uptake, and toxicity. Quantitative data from cocoa agroforestry systems and pigeonpea intercropping trials in Ghana and Tanzania, respectively, were re-evaluated with vector analysis. Relative to monoculture, biomass increase in cocoa ( L.) under shade (35-80%) was accompanied by a 17 to 25% decline in P concentration, the most limiting nutrient on this site. Similarly, increasing biomass with declining P concentrations was noted for pigeonpea [ (L). Millsp.] in response to soil moisture availability under intercropping. Although vector analysis depicted nutrient responses, the current vector model does not consider non-nutrient resource effects on growth, such as ameliorated light and soil moisture, which were particularly active in these systems. We revisit and develop vector analysis into a framework for diagnosing nutrient and non-nutrient interactions in agroforestry systems. Such a diagnostic technique advances management decision-making by increasing nutrient precision and reducing environmental issues associated with agrarian-derived soil contamination. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

  2. Oxidative stress markers imbalance in late-life depression.

    Science.gov (United States)

    Diniz, Breno S; Mendes-Silva, Ana Paula; Silva, Lucelia Barroso; Bertola, Laiss; Vieira, Monica Costa; Ferreira, Jessica Diniz; Nicolau, Mariana; Bristot, Giovana; da Rosa, Eduarda Dias; Teixeira, Antonio L; Kapczinski, Flavio

    2018-03-20

    Oxidative stress has been implicated in the pathophysiology of mood disorders in young adults. However, there is few data to support its role in the elderly. The primary aim of this study was to evaluate whether subjects with late-life depression (LLD) presented with changes in oxidative stress response in comparison with the non-depressed control group. We then explored how oxidative stress markers associated with specific features of LLD, in particular cognitive performance and age of onset of major depressive disorder in these individuals. We included a convenience sample of 124 individuals, 77 with LLD and 47 non-depressed subjects (Controls). We measure the plasma levels of 6 oxidative stress markers: thiobarbituric acid reactive substances (TBARS), protein carbonil content (PCC), free 8-isoprostane, glutathione peroxidase (GPx) activity, glutathione reductase (GR) activity, and glutathione S-transferase (GST) activity. We found that participants with LLD had significantly higher free 8-isoprostane levels (p = 0.003) and lower glutathione peroxidase activity (p = 0.006) compared to controls. Free 8-isoprostane levels were also significantly correlated with worse scores in the initiation/perseverance (r = -0.24, p = 0.01), conceptualization (r = -0.22, p = 0.02) sub-scores, and the total scores (r = -0.21, p = 0.04) on the DRS. Our study provides robust evidence of the imbalance between oxidative stress damage, in particular lipid peroxidation, and anti-oxidative defenses as a mechanism related to LLD, and cognitive impairment in this population. Interventions aiming to reduce oxidative stress damage can have a potential neuroprotective effect for LLD subjects. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Copper imbalances in ruminants and humans: unexpected common ground.

    Science.gov (United States)

    Suttle, Neville F

    2012-09-01

    Ruminants are more vulnerable to copper deficiency than humans because rumen sulfide generation lowers copper availability from forage, increasing the risk of conditions such as swayback in lambs. Molybdenum-rich pastures promote thiomolybdate (TM) synthesis and formation of unabsorbable Cu-TM complexes, turning risk to clinical reality (hypocuprosis). Selection pressures created ruminant species with tolerance of deficiency but vulnerability to copper toxicity in alien environments, such as specific pathogen-free units. By contrast, cases of copper imbalance in humans seemed confined to rare genetic aberrations of copper metabolism. Recent descriptions of human swayback and the exploratory use of TM for the treatment of Wilson's disease, tumor growth, inflammatory diseases, and Alzheimer's disease have created unexpected common ground. The incidence of pre-hemolytic copper poisoning in specific pathogen-free lambs was reduced by an infection with Mycobacterium avium that left them more responsive to treatment with TM but vulnerable to long-term copper depletion. Copper requirements in ruminants and humans may need an extra allowance for the "copper cost" of immunity to infection. Residual cuproenzyme inhibition in TM-treated lambs and anomalies in plasma copper composition that appeared to depend on liver copper status raise this question "can chelating capacity be harnessed without inducing copper-deficiency in ruminants or humans?" A model of equilibria between exogenous (TM) and endogenous chelators (e.g., albumin, metallothionein) is used to predict risk of exposure and hypocuprosis; although risk of natural exposure in humans is remote, vulnerability to TM-induced copper deficiency may be high. Biomarkers of TM impact are needed, and copper chaperones for inhibited cuproenzymes are prime candidates.

  4. Power Imbalances, Food Insecurity, and Children's Rights in Canada.

    Science.gov (United States)

    Blay-Palmer, Alison

    2016-01-01

    Increasingly, food is provided through an industrial food system that separates people from the source of their food and results in high rates of food insecurity, particularly for the most vulnerable in society. A lack of food is a symptom of a lack of power in a system that privileges free market principles over social justice and the protection of human rights. In Canada, the high rates of food insecurity among Canadian children is a reflection of their lack of power and the disregard of their human rights, despite the adoption of the United Nations (UN) Convention on the Rights of the Child in 1991 and ratification of the International Covenant on Social, Economic and Cultural Rights in 1976, which established the right to food for all Canadians. Dueling tensions between human rights and market forces underpin this unacceptable state of affairs in Canada. Gaventa's "power cube" that describes different facets of power - including spaces, levels, and forms - is used to help understand the power imbalances that underlie this injustice. The analysis considers the impact of neoliberal free market principles on the realization of human rights, and the negative impacts this can have on health and well-being for the most vulnerable in society. Canadian case studies from both community organizations provide examples of how power can be shifted to achieve more inclusive, rights-based policy and action. Given increased global pressures toward more open trade markets and national austerity measures that hollow out social supports, Canada provides a cautionary tale for countries in the EU and the US, and for overall approaches to protect the most vulnerable in society.

  5. Carbon and nutrient use efficiencies optimally balance stoichiometric imbalances

    Science.gov (United States)

    Manzoni, Stefano; Čapek, Petr; Lindahl, Björn; Mooshammer, Maria; Richter, Andreas; Šantrůčková, Hana

    2016-04-01

    Decomposer organisms face large stoichiometric imbalances because their food is generally poor in nutrients compared to the decomposer cellular composition. The presence of excess carbon (C) requires adaptations to utilize nutrients effectively while disposing of or investing excess C. As food composition changes, these adaptations lead to variable C- and nutrient-use efficiencies (defined as the ratios of C and nutrients used for growth over the amounts consumed). For organisms to be ecologically competitive, these changes in efficiencies with resource stoichiometry have to balance advantages and disadvantages in an optimal way. We hypothesize that efficiencies are varied so that community growth rate is optimized along stoichiometric gradients of their resources. Building from previous theories, we predict that maximum growth is achieved when C and nutrients are co-limiting, so that the maximum C-use efficiency is reached, and nutrient release is minimized. This optimality principle is expected to be applicable across terrestrial-aquatic borders, to various elements, and at different trophic levels. While the growth rate maximization hypothesis has been evaluated for consumers and predators, in this contribution we test it for terrestrial and aquatic decomposers degrading resources across wide stoichiometry gradients. The optimality hypothesis predicts constant efficiencies at low substrate C:N and C:P, whereas above a stoichiometric threshold, C-use efficiency declines and nitrogen- and phosphorus-use efficiencies increase up to one. Thus, high resource C:N and C:P lead to low C-use efficiency, but effective retention of nitrogen and phosphorus. Predictions are broadly consistent with efficiency trends in decomposer communities across terrestrial and aquatic ecosystems.

  6. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    Directory of Open Access Journals (Sweden)

    Senthilkumar Pitchalu Kasthurinaidu

    Full Text Available Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME. Among the XMEs, glutathione-S-transferases (GST gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs. Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs. The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

  7. Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek’s disease virus infection via analysis of allele-specific expression

    Directory of Open Access Journals (Sweden)

    Sean eMaceachern

    2012-01-01

    Full Text Available Marek’s disease (MD is a commercially important neoplastic disease of chickens caused by Marek’s disease virus (MDV, an oncogenic alphaherpesvirus. Selecting for increased genetic resistance to MD is a control strategy that can augment vaccinal control measures. To identify high-confidence candidate MD resistance genes, we conducted a genome-wide screen for allele-specific expression (ASE amongst F1 progeny of two inbred chicken lines that differ in MD resistance. High throughput sequencing was used to profile transcriptomes from pools of uninfected and infected individuals at 4 days post-infection to identify any genes showing ASE in response to MDV infection. RNA sequencing identified 22,655 single nucleotide polymorphisms (SNPs of which 5,360 in 3,773 genes exhibited significant allelic imbalance. Illumina GoldenGate assays were subsequently used to quantify regulatory variation controlled at the gene (cis and elsewhere in the genome (trans by examining differences in expression between F1 individuals and artificial F1 RNA pools over 6 time periods in 1,536 of the most significant SNPs identified by RNA sequencing. Allelic imbalance as a result of cis-regulatory changes was confirmed in 861 of the 1,233 GoldenGate assays successfully examined. Furthermore we have identified 7 genes that display trans-regulation only in infected animals and approximately 500 SNP that show a complex interaction between cis- and trans-regulatory changes. Our results indicate ASE analyses are a powerful approach to identify regulatory variation responsible for differences in transcript abundance in genes underlying complex traits. And the genes with SNPs exhibiting ASE provide a strong foundation to further investigate the causative polymorphisms and genetic mechanisms for MD resistance. Finally, the methods used here for identifying specific genes and SNPs may have practical implications for applying marker-assisted selection to complex traits that are

  8. Magnetic field and contact resistance dependence of non-local charge imbalance

    International Nuclear Information System (INIS)

    Kleine, A; Baumgartner, A; Trbovic, J; Schoenenberger, C; Golubev, D S; Zaikin, A D

    2010-01-01

    Crossed Andreev reflection (CAR) in metallic nanostructures, a possible basis for solid-state electron entangler devices, is usually investigated by detecting non-local voltages in multi-terminal superconductor/normal metal devices. This task is difficult because other subgap processes may mask the effects of CAR. One of these processes is the generation of charge imbalance (CI) and the diffusion of non-equilibrium quasi-particles in the superconductor. Here we demonstrate a characteristic dependence of non-local CI on a magnetic field applied parallel to the superconducting wire, which can be understood by a generalization of the standard description of CI to non-local experiments. These results can be used to distinguish CAR and CI and to extract CI relaxation times in superconducting nanostructures. In addition, we investigate the dependence of non-local CI on the resistance of the injector and detector contacts and demonstrate a quantitative agreement with a recent theory using only material and junction characteristics extracted from separate direct measurements.

  9. Procedures for identifying S-allele genotypes of Brassica.

    Science.gov (United States)

    Wallace, D H

    1979-11-01

    Procedures are described for efficient selection of: (1) homozygous and heterozygous S-allele genotypes; (2) homozygous inbreds with the strong self- and sib-incompatibility required for effective seed production of single-cross F1 hybrids; (3) heterozygous genotypes with the high self- and sib-incompatibility required for effective seed production of 3- and 4-way hybrids.From reciprocal crosses between two first generation inbred (I1) plants there are three potential results: both crosses are incompatible; one is incompatible and the other compatible; and both are compatible. Incompatibility of both crosses is useful information only when combined with data from other reciprocal crosses. Each compatible cross, depending on whether its reciprocal is incompatible or compatible, dictates alternative reasoning and additional reciprocal crosses for efficiently and simultaneously identifying: (A) the S-allele genotype of all individual I1 plants, and (B) the expressions of dominance or codominance in pollen and stigma (sexual organs) of an S-allele heterozygous genotype. Reciprocal crosses provide the only efficient means of identifying S-allele genotypes and also the sexual-organ x S-allele-interaction types.Fluorescent microscope assay of pollen tube penetration into the style facilitates quantitation within 24-48 hours of incompatibility and compatibility of the reciprocal crosses. A procedure for quantitating the reciprocal difference is described that maximizes informational content of the data about interactions between S alleles in pollen and stigma of the S-allele-heterozygous genotype.Use of the non-inbred Io generation parent as a 'known' heterozygous S-allele genotype in crosses with its first generation selfed (I1) progeny usually reduces at least 7 fold the effort required for achieving objectives 1, 2, and 3, compared to the method of making reciprocal crosses only among I1 plants.Identifying the heterozygous and both homozygous S-allele genotypes during

  10. Cost-Effective Class-Imbalance Aware CNN for Vehicle Localization and Categorization in High Resolution Aerial Images

    Directory of Open Access Journals (Sweden)

    Feimo Li

    2017-05-01

    Full Text Available Joint vehicle localization and categorization in high resolution aerial images can provide useful information for applications such as traffic flow structure analysis. To maintain sufficient features to recognize small-scaled vehicles, a regions with convolutional neural network features (R-CNN -like detection structure is employed. In this setting, cascaded localization error can be averted by equally treating the negatives and differently typed positives as a multi-class classification task, but the problem of class-imbalance remains. To address this issue, a cost-effective network extension scheme is proposed. In it, the correlated convolution and connection costs during extension are reduced by feature map selection and bi-partite main-side network construction, which are realized with the assistance of a novel feature map class-importance measurement and a new class-imbalance sensitive main-side loss function. By using an image classification dataset established from a set of traditional real-colored aerial images with 0.13 m ground sampling distance which are taken from the height of 1000 m by an imaging system composed of non-metric cameras, the effectiveness of the proposed network extension is verified by comparing with its similarly shaped strong counter-parts. Experiments show an equivalent or better performance, while requiring the least parameter and memory overheads are required.

  11. Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides

    Directory of Open Access Journals (Sweden)

    Matos Isa

    2011-12-01

    Full Text Available Abstract Background Squalius alburnoides is an Iberian cyprinid fish resulting from an interspecific hybridisation between Squalius pyrenaicus females (P genome and males of an unknown Anaecypris hispanica-like species (A genome. S. alburnoides is an allopolyploid hybridogenetic complex, which makes it a likely candidate for ploidy mosaicism occurrence, and is also an interesting model to address questions about gene expression regulation and genomic interactions. Indeed, it was previously suggested that in S. alburnoides triploids (PAA composition silencing of one of the three alleles (mainly of the P allele occurs. However, not a whole haplome is inactivated but a more or less random inactivation of alleles varying between individuals and even between organs of the same fish was seen. In this work we intended to correlate expression differences between individuals and/or between organs to the occurrence of mosaicism, evaluating if mosaics could explain previous observations and its impact on the assessment of gene expression patterns. Results To achieve our goal, we developed flow cytometry and cell sorting protocols for this system generating more homogenous cellular and transcriptional samples. With this set-up we detected 10% ploidy mosaicism within the S. alburnoides complex, and determined the allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of mosaic and non-mosaic individuals coming from different rivers over a wide geographic range. Conclusions Ploidy mosaicism occurs sporadically within the S. alburnoides complex, but in a frequency significantly higher than reported for other organisms. Moreover, we could exclude the influence of this phenomenon on the detection of variable allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of triploid individuals. Finally, we determined that the expression patterns

  12. IQ imbalance tolerable parallel-channel DMT transmission for coherent optical OFDMA access network

    Science.gov (United States)

    Jung, Sang-Min; Mun, Kyoung-Hak; Jung, Sun-Young; Han, Sang-Kook

    2016-12-01

    Phase diversity of coherent optical communication provides spectrally efficient higher-order modulation for optical communications. However, in-phase/quadrature (IQ) imbalance in coherent optical communication degrades transmission performance by introducing unwanted signal distortions. In a coherent optical orthogonal frequency division multiple access (OFDMA) passive optical network (PON), IQ imbalance-induced signal distortions degrade transmission performance by interferences of mirror subcarriers, inter-symbol interference (ISI), and inter-channel interference (ICI). We propose parallel-channel discrete multitone (DMT) transmission to mitigate transceiver IQ imbalance-induced signal distortions in coherent orthogonal frequency division multiplexing (OFDM) transmissions. We experimentally demonstrate the effectiveness of parallel-channel DMT transmission compared with that of OFDM transmission in the presence of IQ imbalance.

  13. An Analysis of Economic Growth, Competitiveness and Macroeconomic Imbalances in the European Union

    Directory of Open Access Journals (Sweden)

    Gheorghe Hurduzeu

    2015-09-01

    Full Text Available Taking into consideration the determinants of the economic crisis and of the sovereign debt crisis, we aim to analyze the dynamics of the European economies and discuss changes related to macroeconomic imbalances, as highlighted by the recent crises as an important factor of the unfavorable dynamics registered during the last years. In this respect we considered both internal and external imbalances, as specified in the macroeconomic imbalance procedure that was implemented for the European Union member states since 2012, as a response to the crises that affected all open economies of the world. The purpose of this article is to provide a comprehensive analysis of economic imbalances in the European Union and to determine their influence on economic growth.

  14. An Assessment of Luminance Imbalance with ANVIS at an Army Helicopter Training Airfield

    National Research Council Canada - National Science Library

    McLean, William

    1997-01-01

    One of the casual factors listed in a 1996 mid-air collision between two Australian Army helicopters in formation was a speculation of possible luminance imbalance between the right and left channels...

  15. Codigestion of manure and industrial organic waste at centralized biogas plants: process imbalances and limitations

    DEFF Research Database (Denmark)

    Bangsø Nielsen, Henrik; Angelidaki, Irini

    2008-01-01

    The present study focuses on process imbalances in Danish centralized biogas plants treating manure in combination with industrial waste. Collection of process data from various full-scale plants along with a number of interviews showed that imbalances occur frequently. High concentrations...... of ammonia or long chain fatty acids is in most cases expected to be the cause of microbial inhibitions/imbalances while foaming in the prestorage tanks and digesters is the most important practical process problem at the plants. A correlation between increased residual biogas production (suboptimal process...... conditions) and high fractions of industrial waste in the feedstock was also observed. The process imbalances and suboptimal conditions are mainly allowed to occur due to 1) inadequate knowledge about the waste composition, 2) inadequate knowledge about the waste degradation characteristics, 3) inadequate...

  16. A single-to-differential low-noise amplifier with low differential output imbalance

    International Nuclear Information System (INIS)

    Duan Lian; Ma Chengyan; He Xiaofeng; Ye Tianchun; Huang Wei; Jin Yuhua

    2012-01-01

    This paper presents a single-ended input differential output low-noise amplifier intended for GPS applications. We propose a method to reduce the gain/amplitude and phase imbalance of a differential output exploiting the inductive coupling of a transformer or center-tapped differential inductor. A detailed analysis of the theory of imbalance reduction, as well as a discussion on the principle of choosing the dimensions of a transformer, are given. An LNA has been implemented using TSMC 0.18 μm technology with ESD-protected. Measurement on board shows a voltage gain of 24.6 dB at 1.575 GHz and a noise figure of 3.2 dB. The gain imbalance is below 0.2 dB and phase imbalance is less than 2 degrees. The LNA consumes 5.2 mA from a 1.8 V supply. (semiconductor integrated circuits)

  17. SYSTEMIC IMBALANCE OF ESSENTIAL METALS AND CARDIAC GENE EXPRESSION IN RATS FOLLOWING ACUTE PULMONARY ZINC EXPOSURE

    Science.gov (United States)

    We have recently demonstrated that PM containing water-soluble zinc may cause cardiac injury following pulmonary exposure. To investigate if pulmonary zinc exposure causes systemic metal imbalance and direct cardiac effects, we intratracheally (IT) instilled male Wistar Kyoto (WK...

  18. Pulsational stabilities of a star in thermal imbalance: comparison between the methods

    International Nuclear Information System (INIS)

    Vemury, S.K.

    1978-01-01

    The stability coefficients for quasi-adiabatic pulsations for a model in thermal imbalance are evaluated using the dynamical energy (DE) approach, the total (kinetic plus potential) energy (TE) approach, and the small amplitude (SA) approaches. From a comparison among the methods, it is found that there can exist two distinct stability coefficients under conditions of thermal imbalance as pointed out by Demaret. It is shown that both the TE approaches lead to one stability coefficient, while both the SA approaches lead to another coefficient. The coefficient obtained through the energy approaches is identified as the one which determines the stability of the velocity amplitudes.For a prenova model with a thin hydrogen-burning shell in thermal imbalance, several radial modes are found to be unstable both for radial displacements and for velocity amplitudes. However, a new kind of pulsational instability also appears, viz., while the radial displacements are unstable, the velocity amplitudes may be stabilized through the thermal imbalance terms

  19. Continuous Covariate Imbalance and Conditional Power for Clinical Trial Interim Analyses

    Science.gov (United States)

    Ciolino, Jody D.; Martin, Renee' H.; Zhao, Wenle; Jauch, Edward C.; Hill, Michael D.; Palesch, Yuko Y.

    2014-01-01

    Oftentimes valid statistical analyses for clinical trials involve adjustment for known influential covariates, regardless of imbalance observed in these covariates at baseline across treatment groups. Thus, it must be the case that valid interim analyses also properly adjust for these covariates. There are situations, however, in which covariate adjustment is not possible, not planned, or simply carries less merit as it makes inferences less generalizable and less intuitive. In this case, covariate imbalance between treatment groups can have a substantial effect on both interim and final primary outcome analyses. This paper illustrates the effect of influential continuous baseline covariate imbalance on unadjusted conditional power (CP), and thus, on trial decisions based on futility stopping bounds. The robustness of the relationship is illustrated for normal, skewed, and bimodal continuous baseline covariates that are related to a normally distributed primary outcome. Results suggest that unadjusted CP calculations in the presence of influential covariate imbalance require careful interpretation and evaluation. PMID:24607294

  20. Improved path imbalance measurement of a fiber-optic interferometer based on frequency scanning interferometry

    International Nuclear Information System (INIS)

    Hou, C B; Wang, J G; Yang, J; Li, H Y; Peng, F; Yuan, L B; Yuan, Y G

    2017-01-01

    We developed a path imbalance measuring system using a reference interferometer with alterable optical path difference (OPD), aiming to eliminate the uncertainties due to synthetic wavelength measurement and remove the requirement of a known and stable reference OPD in frequency scanning interferometry. The path imbalance can be solved by using the phase ratios between the two interferometers produced before and after altering the OPD in the reference interferometer. The results have shown that the measurement uncertainty and the path imbalance are linearly related and a combined relative uncertainty of 4.9  ×  10 −6 (1 σ ) in path imbalance measurement over a range from 0.5 m to 50 m is achieved. Besides, we analyzed the contributions to the uncertainty that limit the performance of the system, and we discussed how to obtain a better measurement uncertainty. (paper)

  1. Short-term overt hypothyroidism induces sympathovagal imbalance in thyroidectomized differentiated thyroid carcinoma patients

    NARCIS (Netherlands)

    Heemstra, Karen A.; Burggraaf, Jacobus; van der Klaauw, Agatha A.; Romijn, Johannes A.; Smit, Johannes W. A.; Corssmit, Eleonora P. M.

    2010-01-01

    Thyroid hormone impacts on the cardiovascular system. (Subclinical) hyperthyroidism results in sympathovagal imbalance due to decreased vagal tone. However, conflicting data have been reported on the effects of hypothyroidism on the activity of the autonomic nervous system (ANS). In hypothyroidism,

  2. A comparative study of imbalance reduction strategies for virtual power plant operation

    International Nuclear Information System (INIS)

    Zapata, J.; Vandewalle, J.; D'haeseleer, W.

    2014-01-01

    The penetration of a large amount of distributed generation (DG) technologies with intermittent output, such as photovoltaic installations and wind turbines, yields an important challenge to the electric grid. It is believed that aggregating them with controllable technologies such as cogeneration devices (CHP) can help to balance fluctuations of renewable energy. This work evaluates the ability of a virtual power plant (VPP) to reduce the imbalance error of renewable generators. The study is undertaken in a VPP that consists of several cogeneration devices and photovoltaic (PV) installations. The virtual power plant operator bids electricity into the day-ahead market using the forecast for solar irradiation and for the thermal demand. During the actual day, the imbalance due to deviations between the forecasted electricity delivered and the real output has to be settled in the balancing market. Thus, in order to compensate these errors and possible economic drawbacks, the operation of the CHP is adjusted periodically in a so called reschedule. Two different rescheduling strategies are compared against a ‘reference scenario’ in which the imbalance error is settled in the market. The first one (‘forced strategy’) aims at reducing the imbalance error every time step regardless of the imbalance prices. The second (‘economic strategy’) considers the imbalance prices and takes only action if it is economically appropriate and thus intends to reduce the total operational cost. The results show that the rescheduling technique is able to reduce the imbalance error (up to 90% depending on the season and the strategy). Additionally, the total operational cost is estimated. However, the nowadays imbalance prices only lead to a minor financial advantage that is unlikely to motivate real life operators to perform a rescheduling strategy. - Highlights: • The VPP is dispatched by a day-ahead optimization followed by a rescheduling. • A forced rescheduling strategy

  3. Drug-target interaction prediction via class imbalance-aware ensemble learning.

    Science.gov (United States)

    Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2016-12-22

    Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was

  4. Comprehensive Investigation on Current Imbalance among Parallel Chips inside MW-Scale IGBT Power Modules

    DEFF Research Database (Denmark)

    Wu, Rui; Smirnova, Liudmila; Wang, Huai

    2015-01-01

    With the demands for increasing the power rating and improving reliability level of the high power IGBT modules, there are further needs of understanding how to achieve stable paralleling and identical current sharing between the chips. This paper investigates the stray parameters imbalance among...... parallel chips inside the 1.7 kV/1 kA high power IGBT modules at different frequencies by Ansys Q3D parastics extractor. The resulted current imbalance is further confirmed by experimental measurement....

  5. Effort–Reward Imbalance at Work and Incident Coronary Heart Disease

    Science.gov (United States)

    Siegrist, Johannes; Nyberg, Solja T.; Lunau, Thorsten; Fransson, Eleonor I.; Alfredsson, Lars; Bjorner, Jakob B.; Borritz, Marianne; Burr, Hermann; Erbel, Raimund; Fahlén, Göran; Goldberg, Marcel; Hamer, Mark; Heikkilä, Katriina; Jöckel, Karl-Heinz; Knutsson, Anders; Madsen, Ida E. H.; Nielsen, Martin L.; Nordin, Maria; Oksanen, Tuula; Pejtersen, Jan H.; Pentti, Jaana; Rugulies, Reiner; Salo, Paula; Schupp, Jürgen; Singh-Manoux, Archana; Steptoe, Andrew; Theorell, Töres; Vahtera, Jussi; Westerholm, Peter J. M.; Westerlund, Hugo; Virtanen, Marianna; Zins, Marie; Batty, G. David; Kivimäki, Mika

    2017-01-01

    Background: Epidemiologic evidence for work stress as a risk factor for coronary heart disease is mostly based on a single measure of stressful work known as job strain, a combination of high demands and low job control. We examined whether a complementary stress measure that assesses an imbalance between efforts spent at work and rewards received predicted coronary heart disease. Methods: This multicohort study (the “IPD-Work” consortium) was based on harmonized individual-level data from 11 European prospective cohort studies. Stressful work in 90,164 men and women without coronary heart disease at baseline was assessed by validated effort–reward imbalance and job strain questionnaires. We defined incident coronary heart disease as the first nonfatal myocardial infarction or coronary death. Study-specific estimates were pooled by random effects meta-analysis. Results: At baseline, 31.7% of study members reported effort–reward imbalance at work and 15.9% reported job strain. During a mean follow-up of 9.8 years, 1,078 coronary events were recorded. After adjustment for potential confounders, a hazard ratio of 1.16 (95% confidence interval, 1.00–1.35) was observed for effort–reward imbalance compared with no imbalance. The hazard ratio was 1.16 (1.01–1.34) for having either effort–reward imbalance or job strain and 1.41 (1.12–1.76) for having both these stressors compared to having neither effort–reward imbalance nor job strain. Conclusions: Individuals with effort–reward imbalance at work have an increased risk of coronary heart disease, and this appears to be independent of job strain experienced. These findings support expanding focus beyond just job strain in future research on work stress. PMID:28570388

  6. Examination of Potential Benefits of an Energy Imbalance Market in the Western Interconnection

    Energy Technology Data Exchange (ETDEWEB)

    Milligan, M.; Clark, K.; King, J.; Kirby, B.; Guo, T.; Liu, G.

    2013-03-01

    In the Western Interconnection, there is significant interest in improving approaches to wide-area coordinated operations of the bulk electric power system, in part because of the increasing penetration of variable generation. One proposed solution is an energy imbalance market. This study focused on that approach alone, with the goal of identifying the potential benefits of an energy imbalance market in the year 2020.

  7. Effort-Reward Imbalance and Burnout Among ICU Nursing Staff: A Cross-Sectional Study.

    Science.gov (United States)

    Padilla Fortunatti, Cristobal; Palmeiro-Silva, Yasna K

    Occupational stress is commonly observed among staff in intensive care units (ICUs). Sociodemographic, organizational, and job-related factors may lead to burnout among ICU health workers. In addition, these factors could modify the balance between efforts done and rewards perceived by workers; consequently, this imbalance could increase levels of emotional exhaustion and depersonalization and decrease a sense of personal accomplishment. The purpose of this study was to analyze the relationship between effort-reward imbalance and burnout dimensions (emotional exhaustion, depersonalization, and personal accomplishment) among ICU nursing staff in a university hospital in Santiago, Chile. A convenience sample of 36 registered nurses and 46 nurse aides answered the Maslach Burnout Inventory and Effort-Reward Imbalance Questionnaire and provided sociodemographic and work-related data. Age and effort-reward imbalance were significantly associated with emotional exhaustion in both registered nurses and nurse aides; age was negatively correlated with emotional exhaustion, whereas effort-reward imbalance was positively correlated. Age was negatively associated with depersonalization. None of the predictors were associated with personal accomplishment. This study adds valuable information about relationships of sociodemographic factors and effort-reward imbalance and their impact on dimensions of burnout, particularly on emotional exhaustion.

  8. Analysis of the imbalance price scheme in the Spanish electricity market: A wind power test case

    International Nuclear Information System (INIS)

    Bueno-Lorenzo, Miriam; Moreno, M. Ángeles; Usaola, Julio

    2013-01-01

    This work investigates the interaction between wind power and electricity markets. The paper is focused on balancing markets pricing policies. The proposal of a new imbalance price scheme is included and conveniently evaluated. This proposed scheme tries to minimise the use of ancillary services to compensate for deviations in searching for a more efficient market design. The effectiveness of imbalance prices as market signals is also examined, and policy recommendations regarding imbalance services are discussed. Two test cases are included that analyse the participation of a wind power producer in the Spanish electricity market using a stochastic optimisation strategy. For this purpose, the uncertainty of the variables is considered, i.e., wind power production and prediction, intraday and imbalance prices. Test cases were run with real data for 10 months, and realistic results are presented along with a hypothetical test case. The regulation of the imbalance prices may not be adequate for the Spanish electricity market because an error drop is not sufficiently encouraged. Therefore, we suggest the application of a new imbalance price scheme, which includes an additional constraint. The conclusions of this paper can be assumed to be general policy recommendations

  9. Investigation of Psychological Health and Migraine Headaches Among Personnel According to Effort-Reward Imbalance Model

    Directory of Open Access Journals (Sweden)

    Z. Darami

    2012-05-01

    Full Text Available Background and aims: The relationship between physical-mental health and Migraine headaches and stress, especially job stress, is known. Many factors can construct job stress in work settings. The factor that has gained much attention recently is inequality (imbalance of employees’ effort versus the reward they gain. The aim of the current attempt was to investigate the validity of effort-reward imbalance model and indicate the relation of this model with migraine headaches and psychological well-being among subjects in balance and imbalance groups. Methods: Participants were 180 personnel of Oil distribution company located in Isfahan city, and instruments used were General health questionnaire (Goldberg & Hilier, Social Re-adjustment Rating Scale (Holmes & Rahe, Ahvaz Migraine Questionnaire (Najariyan and Effort-reward imbalance scale (Van Vegchel & et al.   Results: The result of exploratory and confirmatory factor analysis for investigating the Construct validity of the effort-reward imbalance model showed that in both analyses, the two factor model was confirmed. Moreover, findings indicate that balance group was in better psychological (p<0/01 and physical (migraine (p<0/05 status comparing to the imbalance group. These findings indicate the significance of justice to present appropriate reward relative to personnel performance on their health.   Conclusion: Implication of these findings can improve Iranian industrial personnel health from both physical and psychological aspects.  

  10. Age-Dependent and Lineage-Dependent Speciation and Extinction in the Imbalance of Phylogenetic Trees.

    Science.gov (United States)

    Holman, Eric W

    2017-11-01

    It is known that phylogenetic trees are more imbalanced than expected from a birth-death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species. [Crump-Mode-Jagers process; diversification; macroevolution; taxon sampling; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Examining postconcussion symptoms of dizziness and imbalance on neurocognitive performance in collegiate football players.

    Science.gov (United States)

    Honaker, Julie A; Lester, Houston F; Patterson, Jessie N; Jones, Sherri M

    2014-07-01

    This study examined the effects of symptom reports of dizziness and imbalance on cognitive function in concussed collegiate football players. Retrospective, descriptive. University athletic medicine facility. Twenty-seven collegiate football players were included in the final analysis: 16 with symptoms of dizziness/imbalance resulting from concussion and 11 without dizziness/imbalance resulting from concussion. Participants completed the Immediate Postconcussion Assessment and Cognitive Testing (ImPACT) at baseline, at 1 to 2 days postconcussion and 5 to 7 days postconcussion. The ImPACT neurocognitive assessment consists of 6 modules, yielding 4 composite scores: verbal memory, visual memory, visual-motor processing speed, and reaction time. In addition, it includes a postconcussion symptom scale total score. Results revealed that participants with reports of dizziness and imbalance had significantly lower scores on the ImPACT composite scores; however, these individuals also had an overall higher symptom inventory. When accounting for the additional postconcussion symptoms, time was the only significant effect. Dizziness and imbalance are common symptoms postconcussion; however, these symptoms did not predict performance on acute ImPACT scores. Further research is needed to understand the mechanisms causing postconcussion symptoms, including symptoms of dizziness and imbalance, and influence on outcomes postconcussion.

  12. Wide brick tunnel randomization - an unequal allocation procedure that limits the imbalance in treatment totals.

    Science.gov (United States)

    Kuznetsova, Olga M; Tymofyeyev, Yevgen

    2014-04-30

    In open-label studies, partial predictability of permuted block randomization provides potential for selection bias. To lessen the selection bias in two-arm studies with equal allocation, a number of allocation procedures that limit the imbalance in treatment totals at a pre-specified level but do not require the exact balance at the ends of the blocks were developed. In studies with unequal allocation, however, the task of designing a randomization procedure that sets a pre-specified limit on imbalance in group totals is not resolved. Existing allocation procedures either do not preserve the allocation ratio at every allocation or do not include all allocation sequences that comply with the pre-specified imbalance threshold. Kuznetsova and Tymofyeyev described the brick tunnel randomization for studies with unequal allocation that preserves the allocation ratio at every step and, in the two-arm case, includes all sequences that satisfy the smallest possible imbalance threshold. This article introduces wide brick tunnel randomization for studies with unequal allocation that allows all allocation sequences with imbalance not exceeding any pre-specified threshold while preserving the allocation ratio at every step. In open-label studies, allowing a larger imbalance in treatment totals lowers selection bias because of the predictability of treatment assignments. The applications of the technique in two-arm and multi-arm open-label studies with unequal allocation are described. Copyright © 2013 John Wiley & Sons, Ltd.

  13. Allostatic Load and Effort-Reward Imbalance: Associations over the Working-Career.

    Science.gov (United States)

    Coronado, José Ignacio Cuitún; Chandola, Tarani; Steptoe, Andrew

    2018-01-24

    Although associations between work stressors and stress-related biomarkers have been reported in cross-sectional studies, the use of single time measurements of work stressors could be one of the reasons for inconsistent associations. This study examines whether repeated reports of work stress towards the end of the working career predicts allostatic load, a measure of chronic stress related physiological processes. Data from waves 2 to 6 of the English Longitudinal Study of Ageing (ELSA) were analysed, with a main analytical sample of 2663 older adults (aged 50+) who had at least one measurement of effort-reward imbalance between waves 2-6 and a measurement of allostatic load at wave 6. Cumulative work stress over waves 2-6 were measured by the effort-reward imbalance model. ELSA respondents who had reported two or more occasions of imbalance had a higher (0.3) estimate of the allostatic load index than those who did not report any imbalance, controlling for a range of health and socio-demographic factors, as well as allostatic load at baseline. More recent reports of imbalance were significantly associated with a higher allostatic load index, whereas reports of imbalance from earlier waves of ELSA were not. The accumulation of work related stressors could have adverse effects on chronic stress biological processes.

  14. Effects of specific muscle imbalance improvement training on the balance ability in elite fencers.

    Science.gov (United States)

    Kim, Taewhan; Kil, Sekee; Chung, Jinwook; Moon, Jeheon; Oh, Eunyoung

    2015-05-01

    [Purpose] The lunge Motion that occurs frequently in fencing training and matches results in imbalance of the upper and lower limbs muscles. This research focuses on the improvement of the imbalance that occurs in the national team fencers of the Republic of Korea through specific muscle imbalance improvement training. [Subjects] The subjects of this research were limited to right-handed male fencers. Nine male, right-handed national fencing athletes were selected for this study (4 epee, 5 sabre; age 28.2 ± 2.2 years; height 182.3 ± 4.0 cm; weight 76.5 ± 8.2 kg; experience 12.4 ± 3.0 years). [Methods] The specific muscle imbalance improvement training program was performed for 12 weeks and Pre-Post tests were to evaluate its effect on the experimental group. Measurements comprised anthropometry, test of balance, and movement analysis. [Results] After the training program, mediolateral sway of the nondominant lower limb and the balance scale showed statistically significant improvement. [Conclusion] The specific muscle imbalance improvement training program used in this research was proven to be effective for improving the muscle imbalance of elite fencers.

  15. Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences.

    Science.gov (United States)

    Duchêne, David; Duchêne, Sebastian; Ho, Simon Y W

    2015-07-01

    Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial samples of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular-clock analyses can be improved by increasing taxon sampling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance. © 2014 John Wiley & Sons Ltd.

  16. Social Management of Gender Imbalance in China: A Holistic Governance Framework.

    Science.gov (United States)

    Shuzhuo, Li; Zijuan, Shang; Feldman, Marcus W

    2013-08-31

    Since the 1980s, the sex ratio at birth (abbreviated as SRB) in China has been rising and has remained extremely high. With rapid social transition, gender imbalance has become one of the most significant issues of China's social management and has raised many problems and challenges. Innovation in the management principles and public policies of social management urgently needs a new perspective of holistic governance framework. Based on the latest trends in gender imbalance, using data from China's 2010 Population Census, this paper firstly reviews China's strategic policy responses and actions concerning the governance of the male-skewed SRB. With holistic governance theory, we focus on China's "Care for Girls" campaign to analyze the current public policy system. This paper then reveals fragmentation in the current management of China's gender imbalance. Finally we propose a social management framework for addressing China's gender imbalance. The public system needs to be strengthened, and the Chinese government should focus more on vulnerable groups such as forced bachelors in rural areas, and try to bring those groups into the policy framework for governance of gender imbalance. The proposed theoretical framework may help Chinese governments at various levels to design and implement improved social management of gender imbalance issues.

  17. Vibration-Induced Errors in MEMS Tuning Fork Gyroscopes with Imbalance.

    Science.gov (United States)

    Fang, Xiang; Dong, Linxi; Zhao, Wen-Sheng; Yan, Haixia; Teh, Kwok Siong; Wang, Gaofeng

    2018-05-29

    This paper discusses the vibration-induced error in non-ideal MEMS tuning fork gyroscopes (TFGs). Ideal TFGs which are thought to be immune to vibrations do not exist, and imbalance between two gyros of TFGs is an inevitable phenomenon. Three types of fabrication imperfections (i.e., stiffness imbalance, mass imbalance, and damping imbalance) are studied, considering different imbalance radios. We focus on the coupling types of two gyros of TFGs in both drive and sense directions, and the vibration sensitivities of four TFG designs with imbalance are simulated and compared. It is found that non-ideal TFGs with two gyros coupled both in drive and sense directions (type CC TFGs) are the most insensitive to vibrations with frequencies close to the TFG operating frequencies. However, sense-axis vibrations with in-phase resonant frequencies of a coupled gyros system result in severe error outputs to TFGs with two gyros coupled in the sense direction, which is mainly attributed to the sense capacitance nonlinearity. With increasing stiffness coupled ratio of the coupled gyros system, the sensitivity to vibrations with operating frequencies is cut down, yet sensitivity to vibrations with in-phase frequencies is amplified.

  18. Imbalance in multiple sclerosis and neuromyelitis optica: association with deep sensation disturbance.

    Science.gov (United States)

    Demura, Yutaka; Kinoshita, Masako; Fukuda, Osamu; Nose, Shouzou; Nakano, Hitoshi; Juzu, Akira; Murase, Nagako; Yamamoto, Kenji

    2016-12-01

    Abnormality in balance is one of the most important causes of gait disturbance which has a direct impact to disability and medical cost in multiple sclerosis (MS) and neuromyelitis optica (NMO). However, characteristics of imbalance in these two diseases have not been fully elucidated. The aim of this study was to evaluate the degree and features of imbalance using stabilography, the degree of deep sensation disturbance using tibial nerve somatosensory evoked potentials (SEP), and their association with clinical impairment, in patients with MS and NMO. Seven NMO patients and seven MS patients with balance disturbance were examined. The relationship among stabilography measurements representing the degree and features of imbalance, height-adjusted P38 peak latency of SEP, and neurological functional disability, were analyzed. Stabilography evaluation showed a significantly severer degree of imbalance in NMO than in MS. Romberg quotient of the patients with brainstem lesions was significantly larger than those without them. In all patients, length of excursion per second significantly correlated positively with anterio-posterior-axis power spectra at intermediate frequency band. In all patients and in NMO, P38 peak latency adjusted by height significantly correlated positively with anterio-posterior-axis power spectra at intermediate frequency band. These findings suggest that the degree of imbalance of MS and NMO possibly correlate with deep sensation disturbance, which could be evaluated by anterio-posterior-axis power spectra at intermediate frequency band by stabilography. Severer imbalance in NMO than MS may be associated with the severe longitudinally extensive spinal cord lesions.

  19. Allostatic Load and Effort-Reward Imbalance: Associations over the Working-Career

    Directory of Open Access Journals (Sweden)

    José Ignacio Cuitún Coronado

    2018-01-01

    Full Text Available Although associations between work stressors and stress-related biomarkers have been reported in cross-sectional studies, the use of single time measurements of work stressors could be one of the reasons for inconsistent associations. This study examines whether repeated reports of work stress towards the end of the working career predicts allostatic load, a measure of chronic stress related physiological processes. Data from waves 2 to 6 of the English Longitudinal Study of Ageing (ELSA were analysed, with a main analytical sample of 2663 older adults (aged 50+ who had at least one measurement of effort-reward imbalance between waves 2–6 and a measurement of allostatic load at wave 6. Cumulative work stress over waves 2–6 were measured by the effort-reward imbalance model. ELSA respondents who had reported two or more occasions of imbalance had a higher (0.3 estimate of the allostatic load index than those who did not report any imbalance, controlling for a range of health and socio-demographic factors, as well as allostatic load at baseline. More recent reports of imbalance were significantly associated with a higher allostatic load index, whereas reports of imbalance from earlier waves of ELSA were not. The accumulation of work related stressors could have adverse effects on chronic stress biological processes.

  20. Frequency of the GPR7 Tyr135Phe allelic variant in lean and obese subjects.

    Science.gov (United States)

    Pelosini, C; Maffei, M; Ceccarini, G; Marchi, M; Marsili, A; Galli, G; Scartabelli, G; Tamberi, A; Latrofa, F; Fierabracci, P; Vitti, P; Pinchera, A; Santini, F

    2013-10-01

    GPR7, the endogenous coupled receptor for neuropeptide B and neuropeptide W, is expressed in several regions of the central nervous system, which are involved in the regulation of feeding behavior. GPR7 affects the regulation of energy balance through a mechanism independent of leptin and melanocortin pathways. Aim of this study was to investigate whether GPR7 gene mutations can be detected in human subjects and, in that event, if they are differently distributed among lean and obese subjects. The coding region of GPR7 were sequenced in 150 obese patients and 100 normal-weight unrelated controls. Functional studies of the allelic variants were performed. One genetic GPR7 variant was found (Tyr135Phe - rs33977775) in obese subjects (13.3%) and lean control (25%). Functional studies did not reveal significant differences between the wild type and the Tyr135Phe allelic variants in their NPW-mediated capacity to inhibit forskolin-induced cAMP production. Screening of GPR7 gene mutations among lean and obese subjects revealed a Tyr135Phe allelic variant that was fairly common in the study population. As indicated by in vitro and in silico studies, this variant is unlikely to cause a functional derangement of the receptor.

  1. HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay

    Science.gov (United States)

    2009-01-01

    The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied. PMID:21637670

  2. Drop-out probabilities of IrisPlex SNP alleles

    DEFF Research Database (Denmark)

    Andersen, Jeppe Dyrberg; Tvedebrink, Torben; Mogensen, Helle Smidt

    2013-01-01

    In certain crime cases, information about a perpetrator's phenotype, including eye colour, may be a valuable tool if no DNA profile of any suspect or individual in the DNA database matches the DNA profile found at the crime scene. Often, the available DNA material is sparse and allelic drop-out...... of true alleles is possible. As part of the validation of the IrisPlex assay in our ISO17025 accredited, forensic genetic laboratory, we estimated the probability of drop-out of specific SNP alleles using 29 and 30 PCR cycles and 25, 50 and 100 Single Base Extension (SBE) cycles. We observed no drop-out...... when the amount of DNA was greater than 125 pg for 29 cycles of PCR and greater than 62 pg for 30 cycles of PCR. With the use of a logistic regression model, we estimated the allele specific probability of drop-out in heterozygote systems based on the signal strength of the observed allele...

  3. A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

    LENUS (Irish Health Repository)

    Prendergast, James G D

    2012-05-19

    AbstractBackgroundChromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. The aim of this study was to investigate the extent and characteristics of sites of ASHM in human embryonic stem cells (hESCs).ResultsUsing a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. We found that, although they were rare, sites of ASHM were substantially enriched at loci displaying ASE. Many were also found at known imprinted regions, hence sites of ASHM are likely to be better markers of imprinted regions than sites of ASM. We also found that sites of ASHM and ASE in hESCs colocalize at risk loci for developmental syndromes mediated by deletions, providing insights into the etiology of these disorders.ConclusionThese results demonstrate the potential importance of ASHM patterns in the interpretation of disease loci, and the protocol described provides a basis for similar studies of ASHM in other cell types to further our understanding of human disease susceptibility.

  4. Internal-external malalignment of the femoral component in kinematically aligned total knee arthroplasty increases tibial force imbalance but does not change laxities of the tibiofemoral joint.

    Science.gov (United States)

    Riley, Jeremy; Roth, Joshua D; Howell, Stephen M; Hull, Maury L

    2018-06-01

    the resection thickness of each posterior femoral condyle to within ± 0.5 mm of the thickness of the respective posterior region of the femoral component, the increase in imbalance can be effectively limited to 38 N. Generally laxities were unaffected within the ± 4º range tested indicating that instability is not a clinical concern and that manual testing of laxities is not useful to detect I-E malalignment.

  5. Implication of HLA-DMA Alleles in Corsican IDDM

    Directory of Open Access Journals (Sweden)

    P. Cucchi-Mouillot

    1998-01-01

    Full Text Available The HLA-DM molecule catalyses the CLIP/antigen peptide exchange in the classical class II peptide-binding groove. As such, DM is an antigen presentation regulator and may be linked to autoimmune diseases. Using PCR derived methods, a relationship was revealed between DM gene polymorphism and IDDM, in a Corsican population. The DMA*0101 allele was observed to confer a significant predisposition to this autoimmune disease while the DMA*0102 allele protected significantly. Experiments examining polymorphism of the HLA-DRB1 gene established that these relationships are not a consequence of linkage disequilibrium with HLA-DRB1 alleles implicated in this pathology. The study of the DMA gene could therefore be an additional tool for early IDDM diagnosis in the Corsican population.

  6. A common mutation associated with the Duarte galactosemia allele

    Energy Technology Data Exchange (ETDEWEB)

    Elsas, L.J.; Dembure, P.P.; Langley, S.; Paulk, E.M.; Hjelm, L.N.; Fridovich-Keil, J. (Emory Univ. School of Medicine, Atlanta, GA (United States))

    1994-06-01

    The human cDNA and gene for galactose-1-phosphate uridyl transferase (GALT) have been cloned and sequenced. A prevalant mutation (Q188R) is known to cause classic galactosemia (G/G). G/G galactosemia has an incidence of 1/38,886 in 1,396,766 Georgia live-born infants, but a more common variant of galactosemia, Duarte, has an unknown incidence. The proposed Duarte biochemical phenotypes of GALT are as follows: D/N, D/D, and D/G, which have [approximately]75%, 50%, and 25% of normal GALT activity, respectively. In addition, the D allele has isoforms of its enzyme that have more acidic pI than normal. Here the authors systematically determine (a) the prevalence of an A-to-G transition at base pair 2744 of exon 10 in the GALT gene, a transition that produces a codon change converting asparagine to aspartic acid at position 314 (N314D), and (b) the association of this mutation with the Duarte biochemical phenotype. The 2744G nucleotide change adds an AvaII (SinI) cut site, which was identified in PCR-amplified DNA. In 111 biochemically unphenotyped controls with no history of galactosemia, 13 N314D alleles were identified (prevalence 5.9%). In a prospective study, 40 D alleles were biochemically phenotyped, and 40 N314D alleles were found. By contrast, in 36 individuals known not to have the Duarte biochemical phenotype, no N314D alleles were found. The authors conclude that the N314D mutation is a common allele that probably causes the Duarte GALT biochemical phenotype and occurs in a predominantly Caucasian, nongalactosemic population, with a prevalence of 5.9%. 36 refs., 3 figs., 2 tabs.

  7. Evidence of heterozygosity and recombinant alleles in single cysts of Giardia duodenalis

    OpenAIRE

    Aguiar, Juliana Martins; Silva, Sheila Oliveira; Santos, Valdir Azevedo dos; Taniwaki, Sueli Akemi; Oliveira, Tricia Maria Ferreira de Sousa; Ferreira, Helena Lage; Keid, Lara Borges; Gregori, Fábio; Soares, Rodrigo Martins

    2016-01-01

    Abstract Giardia duodenalis is divided into eight assemblages (named A to H). Isolates of assemblage A are divided into four sub-assemblages (AI, AII, AIII and AIV). While isolates of sub-assemblage AII are almost exclusively detected in human hosts, isolates of assemblage B are encountered in a multitude of animal hosts and humans. Here, we isolated single cysts of G. duodenalis from a human stool sample and found that one of them had overlaps of assemblage AII and B alleles and an unexpecte...

  8. Applying cost-sensitive classification for financial fraud detection under high class-imbalance

    CSIR Research Space (South Africa)

    Moepya, SO

    2014-12-01

    Full Text Available , sensitivity, specificity, recall and precision using PCA and Factor Analysis. Weighted Support Vector Machines (SVM) were shown superior to the cost-sensitive Naive Bayes (NB) and K-Nearest Neighbors classifiers....

  9. The use of isotopes to detect moderate mineral imbalances in farm animals

    International Nuclear Information System (INIS)

    1982-09-01

    The publication comprises 12 articles of which 10 have been selected for inclusion in INIS. Their topic is the use of tracer techniques in studying the metabolism of trace amounts of mineral elements in domestic animals

  10. Large Clinically Consequential Imbalances Detected at the Breakpoints of Apparently Balanced and Inherited Chromosome Rearrangements

    OpenAIRE

    South, Sarah T.; Rector, Lyndsey; Aston, Emily; Rowe, Leslie; Yang, Samuel P.

    2010-01-01

    When a chromosome abnormality is identified in a child with a developmental delay and/or multiple congenital anomalies and the chromosome rearrangement appears balanced, follow-up studies often examine both parents for this rearrangement. If either clinically unaffected parent has a chromosome abnormality with a banding pattern identical to the affected child's study, then it is assumed that the chromosome rearrangement is balanced and directly inherited from the normal carrier parent. It is ...

  11. Reduced Height (Rht Alleles Affect Wheat Grain Quality.

    Directory of Open Access Journals (Sweden)

    Richard Casebow

    Full Text Available The effects of dwarfing alleles (reduced height, Rht in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c as well as those that retained GA-sensitivity (rht(tall, Rht8, Rht8 + Ppd-D1a, Rht12. Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0-450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05 reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there

  12. Reduced Height (Rht) Alleles Affect Wheat Grain Quality.

    Science.gov (United States)

    Casebow, Richard; Hadley, Caroline; Uppal, Rajneet; Addisu, Molla; Loddo, Stefano; Kowalski, Ania; Griffiths, Simon; Gooding, Mike

    2016-01-01

    The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0-450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (Pgrain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the strongest evidence for

  13. A common allele on chromosome 9 associated with coronary heartdisease

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R.; Hinds, David; Pennachio, Len; Tybjaerg-Hansen, Anne; Folsom, Aaron R.; Boerwinkle,Eric; Hobbs, Helen H.; Cohen, Jonathan C.

    2007-03-01

    Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.

  14. Effect of effort-reward imbalance and burnout on infection control among Ecuadorian nurses.

    Science.gov (United States)

    Colindres, C V; Bryce, E; Coral-Rosero, P; Ramos-Soto, R M; Bonilla, F; Yassi, A

    2018-06-01

    Nurses are frequently exposed to transmissible infections, yet adherence to infection control measures is suboptimal. There has been inadequate research into how the psychosocial work environment affects compliance with infection control measures, especially in low- and middle-income countries. To examine the association between effort-reward imbalance, burnout and adherence to infection control measures among nurses in Ecuador. A cross-sectional study linking psychosocial work environment indicators to infection control adherence. The study was conducted among 333 nurses in four Ecuadorian hospitals. Self-administered questionnaires assessed demographic variables, perceived infection risk, effort-reward imbalance, burnout and infection control adherence. Increased effort-reward imbalance was found to be a unique incremental predictor of exposure to burnout, and burnout was a negative unique incremental predictor of nurses' self-reported adherence with infection control measures. Results suggest an effort-reward imbalance-burnout continuum, which, at higher levels, contributes to reduce adherence to infection control. The Ecuadorean government has made large efforts to improve universal access to health care, yet this study suggests that workplace demands on nurses remain problematic. This study highlights the contribution of effort-reward-imbalance-burnout continuum to the chain of infection by decreased adherence to infection control of nurses. Health authorities should closely monitor the effect of new policies on psychosocial work environment, especially when expanding services and increasing public accessibility with limited resources. Additionally, organizational and psychosocial interventions targeting effort-reward imbalance and burnout in nurses should be considered part of a complete infection prevention and control strategy. Further study is warranted to identify interventions that best ameliorate effort-reward imbalance and burnout in low- and middle

  15. Robust energy storage scheduling for imbalance reduction of strategically formed energy balancing groups

    International Nuclear Information System (INIS)

    Chakraborty, Shantanu; Okabe, Toshiya

    2016-01-01

    Imbalance (on-line energy gap between contracted supply and actual demand, and associated cost) reduction is going to be a crucial service for a Power Producer and Supplier (PPS) in the deregulated energy market. PPS requires forward market interactions to procure energy as precisely as possible in order to reduce imbalance energy. This paper presents, 1) (off-line) an effective demand aggregation based strategy for creating a number of balancing groups that leads to higher predictability of group-wise aggregated demand, 2) (on-line) a robust energy storage scheduling that minimizes the imbalance energy and cost of a particular balancing group considering the demand prediction uncertainty. The group formation is performed by a Probabilistic Programming approach using Bayesian Markov Chain Monte Carlo (MCMC) method after applied on the historical demand statistics. Apart from the group formation, the aggregation strategy (with the help of Bayesian Inference) also clears out the upper-limit of the required storage capacity for a formed group, fraction of which is to be utilized in on-line operation. For on-line operation, a robust energy storage scheduling method is proposed that minimizes expected imbalance energy and cost (a non-linear function of imbalance energy) while incorporating the demand uncertainty of a particular group. The proposed methods are applied on the real apartment buildings' demand data in Tokyo, Japan. Simulation results are presented to verify the effectiveness of the proposed methods. - Highlights: • Strategic method for intelligent energy balancing group formation using Bayesian MCMC. • Stochastic programming based robust and online energy storage (battery) scheduling. • Imbalance cost (regulation) and energy reduction of a balancing group. • Imbalance cost reduction of 80% attainable by considerably lower battery capacity.

  16. Sagittal imbalance in patients with lumbar spinal stenosis and outcomes after simple decompression surgery.

    Science.gov (United States)

    Shin, E Kyung; Kim, Chi Heon; Chung, Chun Kee; Choi, Yunhee; Yim, Dahae; Jung, Whei; Park, Sung Bae; Moon, Jung Hyeon; Heo, Won; Kim, Sung-Mi

    2017-02-01

    Lumbar spinal stenosis (LSS) is the most common lumbar degenerative disease, and sagittal imbalance is uncommon. Forward-bending posture, which is primarily caused by buckling of the ligamentum flavum, may be improved via simple decompression surgery. The objectives of this study were to identify the risk factors for sagittal imbalance and to describe the outcomes of simple decompression surgery. This is a retrospective nested case-control study PATIENT SAMPLE: This was a retrospective study that included 83 consecutive patients (M:F=46:37; mean age, 68.5±7.7 years) who underwent decompression surgery and a minimum of 12 months of follow-up. The primary end point was normalization of sagittal imbalance after decompression surgery. Sagittal imbalance was defined as a C7 sagittal vertical axis (SVA) ≥40 mm on a 36-inch-long lateral whole spine radiograph. Logistic regression analysis was used to identify the risk factors for sagittal imbalance. Bilateral decompression was performed via a unilateral approach with a tubular retractor. The SVA was measured on serial radiographs performed 1, 3, 6, and 12 months postoperatively. The prognostic factors for sagittal balance recovery were determined based on various clinical and radiological parameters. Sagittal imbalance was observed in 54% (45/83) of patients, and its risk factors were old age and a large mismatch between pelvic incidence and lumbar lordosis. The 1-year normalization rate was 73% after decompression surgery, and the median time to normalization was 1 to 3 months. Patients who did not experience SVA normalization exhibited low thoracic kyphosis (hazard ratio [HR], 1.04; 95% confidence interval [CI], 1.02-1.10) (pimbalance was observed in more than 50% of LSS patients, but this imbalance was correctable via simple decompression surgery in 70% of patients. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Characterization of a New Pm2 Allele Conferring Powdery Mildew Resistance in the Wheat Germplasm Line FG-1

    Science.gov (United States)

    Ma, Pengtao; Xu, Hongxng; Li, Lihui; Zhang, Hongxia; Han, Guohao; Xu, Yunfeng; Fu, Xiaoyi; Zhang, Xiaotian; An, Diaoguo

    2016-01-01

    Powdery mildew has a negative impact on wheat production. Novel host resistance increases the diversity of resistance genes and helps to control the disease. In this study, wheat line FG-1 imported from France showed a high level of powdery mildew resistance at both the seedling and adult stages. An F2 population and F2:3 families from the cross FG-1 × Mingxian 169 both fit Mendelian ratios for a single dominant resistance gene when tested against multiple avirulent Blumeria tritici f. sp. tritici (Bgt) races. This gene was temporarily designated PmFG. PmFG was mapped on the multi-allelic Pm2 locus of chromosome 5DS using seven SSR, 10 single nucleotide polymorphism (SNP)-derived and two SCAR markers with the flanking markers Xbwm21/Xcfd81/Xscar112 (distal) and Xbwm25 (proximal) at 0.3 and 0.5 cM being the closest. Marker SCAR203 co-segregated with PmFG. Allelism tests between PmFG and documented Pm2 alleles confirmed that PmFG was allelic with Pm2. Line FG-1 produced a significantly different reaction pattern compared to other lines with genes at or near Pm2 when tested against 49 Bgt isolates. The PmFG-linked marker alleles detected by the SNP-derived markers revealed significant variation between FG-1 and other lines with genes at or near Pm2. It was concluded that PmFG is a new allele at the Pm2 locus. Data from seven closely linked markers tested on 31 wheat cultivars indicated opportunities for marker-assisted pyramiding of this gene with other genes for powdery mildew resistance and additional traits. PMID:27200022

  18. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

    Directory of Open Access Journals (Sweden)

    Roshan Mascarenhas

    Full Text Available mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs, and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs in lymphoblast cell lines (LCL and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T in ABCB1 (MDR1 on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

  19. Effort-reward imbalance and organisational injustice among aged nurses: a moderated mediation model.

    Science.gov (United States)

    Topa, Gabriela; Guglielmi, Dina; Depolo, Marco

    2016-09-01

    To test the effort-reward imbalance model among older nurses, expanding it to include the moderation of overcommitment and age in the stress-health complaints relationship, mediated by organisational injustice. The theoretical framework included the effort-reward imbalance, the uncertainty management and the socio-emotional selectivity models. Employing a two-wave design, the participants were 255 nurses aged 45 years and over, recruited from four large hospitals in Spain (Madrid and Basque Country). The direct effect of imbalance on health complaints was supported: it was significant when overcommitment was low but not when it was high. Organisational injustice mediated the influence of effort-reward imbalance on health complaints. The conditional effect of the mediation of organisational injustice was significant in three of the overcommitment/age conditions but it weakened, becoming non-significant, when the level of overcommitment was low and age was high. The study tested the model in nursing populations and expanded it to the settings of occupational health and safety at work. The results of this study highlight the importance of effort-reward imbalance and organisational justice for creating healthy work environments. © 2016 John Wiley & Sons Ltd.

  20. Carrier Frequency Offset Estimation and I/Q Imbalance Compensation for OFDM Systems

    Directory of Open Access Journals (Sweden)

    M. Omair Ahmad

    2007-01-01

    Full Text Available Two types of radio-frequency front-end imperfections, that is, carrier frequency offset and the inphase/quadrature (I/Q imbalance are considered for orthogonal frequency division multiplexing (OFDM communication systems. A preamble-assisted carrier frequency estimator is proposed along with an I/Q imbalance compensation scheme. The new frequency estimator reveals the relationship between the inphase and the quadrature components of the received preamble and extracts the frequency offset from the phase shift caused by the frequency offset and the cross-talk interference due to the I/Q imbalance. The proposed frequency estimation algorithm is fast, efficient, and robust to I/Q imbalance. An I/Q imbalance estimation/compensation algorithm is also presented by solving a least-square problem formulated using the same preamble as employed for the frequency offset estimation. The computational complexity of the I/Q estimation scheme is further reduced by using part of the short symbols with a little sacrifice in the estimation accuracy. Computer simulation and comparison with some of the existing algorithms are conducted, showing the effectiveness of the proposed method.

  1. Stress, autonomic imbalance, and the prediction of metabolic risk: A model and a proposal for research.

    Science.gov (United States)

    Wulsin, Lawson; Herman, James; Thayer, Julian F

    2018-03-01

    Devising novel prevention strategies for metabolic disorders will depend in part on the careful elucidation of the common pathways for developing metabolic risks. The neurovisceral integration model has proposed that autonomic imbalance plays an important role in the pathway from acute and chronic stress to cardiovascular disease. Though generally overlooked by clinicians, autonomic imbalance (sympathetic overactivity and/or parasympathetic underactivity) can be measured and modified by methods that are available in primary care. This review applies the neurovisceral integration concept to the clinical setting by proposing that autonomic imbalance plays a primary role in the development of metabolic risks. We present a testable model, a systematic review of the evidence in support of autonomic imbalance as a predictor for metabolic risks, and specific approaches to test this model as a guide to future research on the role of stress in metabolic disorders. We propose that autonomic imbalance deserves consideration by researchers, clinicians, and policymakers as a target for early interventions to prevent metabolic disorders. Published by Elsevier Ltd.

  2. Liquidity Effects on the Simultaneity of Trading Volume and Order Imbalance

    Directory of Open Access Journals (Sweden)

    Erman Denny Arfianto

    2016-10-01

    Full Text Available The purpose of this research is to analyze the simultaneity between trading volume and order imbalance, the influence of past performance, market risk, market capitalization, tick size to the trading volume and the influence of tick size, depth and bid-ask spread to the order imbalance of companies that were listed on LQ 45 index. The samples in this research were selected by using the purposive sampling method with some selected criteria. Fifty-five companies listed on 2014’s LQ 45 index were chosen as the sample. The results showed that the trading volume is simultaneously related to the order imbalance; past performance, market risk, and market capitalization have the positive and significant effect to the trading volume; tick size has the negative and significant effect to the trading volume; the order imbalance has the negative and insignificant effect to the trading volume; tick size, depth, bid-ask spread, and trading volume have no significant effect to the order imbalance.

  3. Type 2 Diabetes Risk Allele Loci in the Qatari Population.

    Directory of Open Access Journals (Sweden)

    Sarah L O'Beirne

    Full Text Available The prevalence of type 2 diabetes (T2D is increasing in the Middle East. However, the genetic risk factors for T2D in the Middle Eastern populations are not known, as the majority of studies of genetic risk for T2D are in Europeans and Asians.All subjects were ≥3 generation Qataris. Cases with T2D (n = 1,124 and controls (n = 590 were randomly recruited and assigned to the 3 known Qatari genetic subpopulations [Bedouin (Q1, Persian/South Asian (Q2 and African (Q3]. Subjects underwent genotyping for 37 single nucleotide polymorphisms (SNPs in 29 genes known to be associated with T2D in Europeans and/or Asian populations, and an additional 27 tag SNPs related to these susceptibility loci. Pre-study power analysis suggested that with the known incidence of T2D in adult Qataris (22%, the study population size would be sufficient to detect significant differences if the SNPs were risk factors among Qataris, assuming that the odds ratio (OR for T2D SNPs in Qatari's is greater than or equal to the SNP with highest known OR in other populations.Haplotype analysis demonstrated that Qatari haplotypes in the region of known T2D risk alleles in Q1 and Q2 genetic subpopulations were similar to European haplotypes. After Benjamini-Hochberg adjustment for multiple testing, only two SNPs (rs7903146 and rs4506565, both associated with transcription factor 7-like 2 (TCF7L2, achieved statistical significance in the whole study population. When T2D subjects and control subjects were assigned to the known 3 Qatari subpopulations, and analyzed individually and with the Q1 and Q2 genetic subpopulations combined, one of these SNPs (rs4506565 was also significant in the admixed group. No other SNPs associated with T2D in all Qataris or individual genetic subpopulations.With the caveats of the power analysis, the European/Asian T2D SNPs do not contribute significantly to the high prevalence of T2D in the Qatari population, suggesting that the genetic risks for T2D are

  4. Novel HLA Class I Alleles Associated with Indian Leprosy Patients

    Directory of Open Access Journals (Sweden)

    U. Shankarkumar

    2003-01-01

    A*0101, Cw*04011, and Cw*0602 leprosy patients was observed when compared to the controls. Further haplotype A*1102-B*4006-Cw*1502 was significantly increased among the lepromatous leprosy patients when compared to the controls. It seems that HLA class I alleles play vital roles in disease association/pathogenesis with leprosy among Indians.

  5. Molecular monitoring of resistant dhfr and dhps allelic haplotypes in ...

    African Journals Online (AJOL)

    Objective: The present study assesses the frequency of resistant dhfr and dhps alleles in Morogoro-Mvomero district in south eastern Tanzania and contrast their rate of change during 17 years of SP second line use against five years of SP first line use. Methodology: Cross sectional surveys of asymptomatic infections were ...

  6. Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis

    Science.gov (United States)

    Brock, M.K.; White, B.N.

    1991-01-01

    Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

  7. Allele frequency distribution for 21 autosomal STR loci in Bhutan.

    Science.gov (United States)

    Kraaijenbrink, Thirsa; van Driem, George L; Tshering of Gaselô, Karma; de Knijff, Peter

    2007-07-20

    We studied the allele frequency distribution of 21 autosomal STR loci contained in the AmpFlSTR Identifiler (Applied Biosystems), the Powerplex 16 (Promega) and the FFFL (Promega) multiplex PCR kits among 936 individuals from the Royal Kingdom of Bhutan. As such these are the first published autosomal DNA results from this country.

  8. Association of LEI0258 microsatellite alleles with antibody response ...

    African Journals Online (AJOL)

    SERVER

    2008-03-18

    Mar 18, 2008 ... (MHC) B region on chicken Micro-chromosome 16 has been demonstrated by many workers to be ... promising DNA markers in characterizing MHC B genes. Identifying marker alleles (bands) ..... SAS/STAT Users' Guide,. Release 6.12 Edition, SAS Institute Inc, Cary, North Carolina. USA. Taylor RL (2004).

  9. Distribution of HIV-1 resistance-conferring polymorphic alleles SDF ...

    Indian Academy of Sciences (India)

    Polymorphic allelic variants of chemokine receptors CCR2 and CCR5, as well as of stromal-derived factor-1 SDF-1, the ligand for the chemokine receptor CXCR4, are known to have protective effects against HIV-1 infection and to be involved with delay in disease progression. We have studied the DNA polymorphisms at ...

  10. HLA-A alleles differentially associate with severity to Plasmodium ...

    African Journals Online (AJOL)

    Human Leukocyte Antigen (HLA), particularly HLA-B and class II alleles have been differentially associated with disease outcomes in different populations following infection with the malaria Plasmodium falciparum. However, the effect of HLA-A on malaria infection and/or disease is not fully understood. Recently, HLA-A ...

  11. Clonal Ordering of 17p and 5q Allelic Losses in Barrett Dysplasia and Adenocarcinoma

    Science.gov (United States)

    Blount, Patricia L.; Meltzer, Stephen J.; Yin, Jing; Huang, Ying; Krasna, Mark J.; Reid, Brian J.

    1993-04-01

    Both 17p and 5q allelic losses appear to be involved in the pathogenesis or progression of many human solid tumors. In colon carcinogenesis, there is strong evidence that the targets of the 17p and 5q allelic losses are TP53, the gene encoding p53, and APC, respectively. It is widely accepted that 5q allelic losses precede 17p allelic losses in the progression to colonic carcinoma. The data, however, supporting this proposed order are largely based on the prevalence of 17p and 5q allelic losses in adenomas and unrelated adenocarcinomas from different patients. We investigated the order in which 17p and 5q allelic losses developed during neoplastic progression in Barrett esophagus by evaluating multiple aneuploid cell populations from the same patient. Using DNA content flow cytometric cell sorting and polymerase chain reaction, 38 aneuploid cell populations from 14 patients with Barrett esophagus who had high grade dysplasia, cancer or both were evaluated for 17p and 5q allelic losses. 17p allelic losses preceded 5q allelic losses in 7 patients, both 17p and 5q allelic losses were present in all aneuploid populations of 4 patients, and only 17p (without 5q) allelic losses were present in the aneuploid populations of 3 patients. In no patient did we find that a 5q allelic loss preceded a 17p allelic loss. Our data suggest that 17p allelic losses typically occur before 5q allelic losses during neoplastic progression in Barrett esophagus.

  12. Segregation of male-sterility alleles across a species boundary.

    Science.gov (United States)

    Weller, S G; Sakai, A K; Culley, T M; Duong, L; Danielson, R E

    2014-02-01

    Hybrid zones may serve as bridges permitting gene flow between species, including alleles influencing the evolution of breeding systems. Using greenhouse crosses, we assessed the likelihood that a hybrid zone could serve as a conduit for transfer of nuclear male-sterility alleles between a gynodioecious species and a hermaphroditic species with very rare females in some populations. Segregation patterns in progeny of crosses between rare females of hermaphroditic Schiedea menziesii and hermaphroditic plants of gynodioecious Schiedea salicaria heterozygous at the male-sterility locus, and between female S. salicaria and hermaphroditic plants from the hybrid zone, were used to determine whether male-sterility was controlled at the same locus in the parental species and the hybrid zone. Segregations of females and hermaphrodites in approximately equal ratios from many of the crosses indicate that the same nuclear male-sterility allele occurs in the parent species and the hybrid zone. These rare male-sterility alleles in S. menziesii may result from gene flow from S. salicaria through the hybrid zone, presumably facilitated by wind pollination in S. salicaria. Alternatively, rare male-sterility alleles might result from a reversal from gynodioecy to hermaphroditism in S. menziesii, or possibly de novo evolution of male sterility. Phylogenetic analysis indicates that some species of Schiedea have probably evolved separate sexes independently, but not in the lineage containing S. salicaria and S. menziesii. High levels of selfing and expression of strong inbreeding depression in S. menziesii, which together should favour females in populations, argue against a reversal from gynodioecy to hermaphroditism in S. menziesii. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  13. Somatic mutations, allele loss, and DNA methylation of the Cub and Sushi Multiple Domains 1 (CSMD1 gene reveals association with early age of diagnosis in colorectal cancer patients.

    Directory of Open Access Journals (Sweden)

    Austin Y Shull

    Full Text Available The Cub and Sushi Multiple Domains 1 (CSMD1 gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients.We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A.Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%. The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15:1, a ratio significantly higher than the expected 2:1 ratio (p = 0.014. This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%. Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years than those without somatic mutations (average age, 68 years. The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%, suggesting extensive cytosine methylation predisposing to somatic mutations.Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical

  14. Relationship between effort-reward imbalance and hair cortisol concentration in female kindergarten teachers.

    Science.gov (United States)

    Qi, Xingliang; Zhang, Jing; Liu, Yapeng; Ji, Shuang; Chen, Zheng; Sluiter, Judith K; Deng, Huihua

    2014-04-01

    The present study aims to investigate the relationship between effort-reward imbalance and hair cortisol concentration among teachers to examine whether hair cortisol can be a biomarker of chronic work stress. Hair samples were collected from 39 female teachers from three kindergartens. Cortisol was extracted from the hair samples with methanol, and cortisol concentrations were measured with high performance liquid chromatography-tandem mass spectrometry. Work stress was measured using the effort-reward imbalance scale. The ratio of effort to reward showed significantly positive association with hair cortisol concentration. The cortisol concentration in the system increases with the effort-reward imbalance. Measurement of hair cortisol can become a useful biomarker of chronic work stress. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Effort-Reward Imbalance, Work-Privacy Conflict, and Burnout Among Hospital Employees.

    Science.gov (United States)

    Häusler, Nadine; Bopp, Matthias; Hämmig, Oliver

    2018-04-01

    Studies investigating the relative importance of effort-reward imbalance and work-privacy conflict for burnout risk between professional groups in the health care sector are rare and analyses by educational attainment within professional groups are lacking. The study population consists of 1422 hospital employees in Switzerland. Multivariate linear regression analyses with standardized coefficients were performed for the overall study population and stratified for professional groups refined for educational attainment. Work-privacy conflict is a strong predictor for burnout and more strongly associated with burnout than effort-reward imbalance in the overall study population and across all professional groups. Effort-reward imbalance only had a minor effect on burnout in tertiary-educated medical professionals. Interventions aiming at increasing the compatibility of work and private life may substantially help to decrease burnout risk of professionals working in a health care setting.

  16. Cardiovascular dysfunctions and sympathovagal imbalance in hypertension and prehypertension: physiological perspectives.

    Science.gov (United States)

    Pal, Gopal Krushna; Pal, Pravati; Nanda, Nivedita; Amudharaj, Dharmalingam; Adithan, Chandrasekaran

    2013-01-01

    Hypertension (HTN) and prehypertension (pre-HTN) have been identified as independent risk factors for adverse cardiovascular events. Recently, increased psychosocial stress and work stress have contributed to the increased prevalence of HTN and pre-HTN, in addition to the contribution of obesity, diabetes, poor food habits and physical inactivity. Irrespective of the etiology, sympathetic overactivity has been recognized as the main pathophysiologic mechanism in the genesis of HTN and pre-HTN. Sympathovagal imbalance owing to sympathetic overactivity and vagal withdrawal is reported to be the basis of many clinical disorders. However, the role played by vagal withdrawal has been under-reported. In this review, we have analyzed the pathophysiologic involvement of sympathovagal imbalance in the development of HTN and pre-HTN, and the link of sympathovagal imbalance to cardiovascular dysfunctions. We have emphasized that adaptation to a healthier lifestyle will help improve sympathovagal homeostasis and prevent the occurrence of HTN and pre-HTN.

  17. Thermal imbalance force modelling for a GPS satellite using the finite element method

    Science.gov (United States)

    Vigue, Yvonne; Schutz, Bob E.

    1991-01-01

    Methods of analyzing the perturbation due to thermal radiation and determining its effects on the orbits of GPS satellites are presented, with emphasis on the FEM technique to calculate satellite solar panel temperatures which are used to determine the magnitude and direction of the thermal imbalance force. Although this force may not be responsible for all of the force mismodeling, conditions may work in combination with the thermal imbalance force to produce such accelerations on the order of 1.e-9 m/sq s. If submeter accurate orbits and centimeter-level accuracy for geophysical applications are desired, a time-dependent model of the thermal imbalance force should be used, especially when satellites are eclipsing, where the observed errors are larger than for satellites in noneclipsing orbits.

  18. Occupational imbalance and the role of perceived stress in predicting stress-related disorders.

    Science.gov (United States)

    Håkansson, Carita; Ahlborg, Gunnar

    2017-03-02

    Stress-related disorders are the main reason for sick leave in many European countries. The aim of the present study was to explore whether perceived occupational imbalance predicts stress-related disorders, potential gender differences, and to explore the mediating role of perceived stress. Longitudinal data on 2223 employees in a public organization in Sweden were collected by surveys, and analyzed by logistic regression. Occupational imbalance predicted stress-related disorders among both women and men. However, what aspects of occupational imbalance which predicted stress-related disorders differ by gender. Perceived stress was not a mediator in these associations. How women and men perceived their occupational balance affected the risk of stress-related disorders. The results may be used to develop effective strategies to decrease stress-related disorders.

  19. Asynchronous Cholinergic Drive Correlates with Excitation-Inhibition Imbalance via a Neuronal Ca2+ Sensor Protein

    Directory of Open Access Journals (Sweden)

    Keming Zhou

    2017-05-01

    Full Text Available Excitation-inhibition imbalance in neural networks is widely linked to neurological and neuropsychiatric disorders. However, how genetic factors alter neuronal activity, leading to excitation-inhibition imbalance, remains unclear. Here, using the C. elegans locomotor circuit, we examine how altering neuronal activity for varying time periods affects synaptic release pattern and animal behavior. We show that while short-duration activation of excitatory cholinergic neurons elicits a reversible enhancement of presynaptic strength, persistent activation results to asynchronous and reduced cholinergic drive, inducing imbalance between endogenous excitation and inhibition. We find that the neuronal calcium sensor protein NCS-2 is required for asynchronous cholinergic release in an activity-dependent manner and dampens excitability of inhibitory neurons non-cell autonomously. The function of NCS-2 requires its Ca2+ binding and membrane association domains. These results reveal a synaptic mechanism implicating asynchronous release in regulation of excitation-inhibition balance.

  20. New fuzzy support vector machine for the class imbalance problem in medical datasets classification.

    Science.gov (United States)

    Gu, Xiaoqing; Ni, Tongguang; Wang, Hongyuan

    2014-01-01

    In medical datasets classification, support vector machine (SVM) is considered to be one of the most successful methods. However, most of the real-world medical datasets usually contain some outliers/noise and data often have class imbalance problems. In this paper, a fuzzy support machine (FSVM) for the class imbalance problem (called FSVM-CIP) is presented, which can be seen as a modified class of FSVM by extending manifold regularization and assigning two misclassification costs for two classes. The proposed FSVM-CIP can be used to handle the class imbalance problem in the presence of outliers/noise, and enhance the locality maximum margin. Five real-world medical datasets, breast, heart, hepatitis, BUPA liver, and pima diabetes, from the UCI medical database are employed to illustrate the method presented in this paper. Experimental results on these datasets show the outperformed or comparable effectiveness of FSVM-CIP.

  1. New Fuzzy Support Vector Machine for the Class Imbalance Problem in Medical Datasets Classification

    Directory of Open Access Journals (Sweden)

    Xiaoqing Gu

    2014-01-01

    Full Text Available In medical datasets classification, support vector machine (SVM is considered to be one of the most successful methods. However, most of the real-world medical datasets usually contain some outliers/noise and data often have class imbalance problems. In this paper, a fuzzy support machine (FSVM for the class imbalance problem (called FSVM-CIP is presented, which can be seen as a modified class of FSVM by extending manifold regularization and assigning two misclassification costs for two classes. The proposed FSVM-CIP can be used to handle the class imbalance problem in the presence of outliers/noise, and enhance the locality maximum margin. Five real-world medical datasets, breast, heart, hepatitis, BUPA liver, and pima diabetes, from the UCI medical database are employed to illustrate the method presented in this paper. Experimental results on these datasets show the outperformed or comparable effectiveness of FSVM-CIP.

  2. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency

    NARCIS (Netherlands)

    Kiezun, Adam; Pulit, Sara L.; Francioli, Laurent C.; van Dijk, Freerk; Swertz, Morris; Boomsma, Dorret I.; van Duijn, Cornelia M.; Slagboom, P. Eline; van Ommen, G. J. B.; Wijmenga, Cisca; de Bakker, Paul I. W.; Sunyaev, Shamil R.

    Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral

  3. Multi-hop amplify-and-forward relaying cooperation in the presence of I/Q imbalance

    KAUST Repository

    Qi, Jian; Aï ssa, Sonia; Alouini, Mohamed-Slim

    2013-01-01

    In this paper, multi-hop cooperative networks implementing channel state information (CSI)-assisted amplify-and-forward (AF) relaying in the presence of in-phase and quadrature-phase (I/Q) imbalance are investigated. We propose a compensation algorithm for the I/Q imbalance. The performance of the multi-hop CSI-assisted AF cooperative networks with and without compensation for I/Q imbalance in Nakagami-m fading environment is evaluated in terms of average symbol error probability. Numerical results are provided and show that the proposed compensation method can effectively mitigate the impact of I/Q imbalance. © 2013 IEEE.

  4. Multi-hop amplify-and-forward relaying cooperation in the presence of I/Q imbalance

    KAUST Repository

    Qi, Jian

    2013-06-01

    In this paper, multi-hop cooperative networks implementing channel state information (CSI)-assisted amplify-and-forward (AF) relaying in the presence of in-phase and quadrature-phase (I/Q) imbalance are investigated. We propose a compensation algorithm for the I/Q imbalance. The performance of the multi-hop CSI-assisted AF cooperative networks with and without compensation for I/Q imbalance in Nakagami-m fading environment is evaluated in terms of average symbol error probability. Numerical results are provided and show that the proposed compensation method can effectively mitigate the impact of I/Q imbalance. © 2013 IEEE.

  5. The Relationship Between the Effort-Reward Imbalance and Psychosocial Health in Nurses

    Directory of Open Access Journals (Sweden)

    Fariborz Roshangar

    2017-09-01

    Full Text Available The health of nurses as providers of health affects the quality of care provided by health care organizations to patients. The effort-reward imbalance is accompanied by repressive responses that can lead to physical and psychological diseases as well as stressful experiences in nurses’ activity. Regarding the existence of some discrimination in the system of health, the present study was conducted to determine the relationship between the effort-reward imbalance and psychosocial health in nurses. In this descriptive cross-sectional study, 270 nurses working in five medical-educational centers in Tabriz participated through random-quota sampling. The research tool included a demographic questionnaire, Siegrist effort- reward imbalance questionnaire and Copenhagen Psychosocial questionnaire. Data were analyzed by SPSS V18 and descriptive and inferential statistics. In the present study, 54.8% of the patients were suffering from effort- reward imbalance model (occupational stress. The relatively high prevalence of this can be attributed to the conditions of the hospital's working environment. The results of this study showed a significant relationship between psychosocial health and balance of reward and effort in nurses and also the findings of the research showed a positive and significant relationship between mental and social health and the score of effort-reward imbalance model (0.95 = R, and P <0.05. There was a significant relationship between effort and work commitment and job burnout. Considering the stressful nature of the profession among many reasons, the mental health of nurses is at a higher risk than that of other groups in the society. Because some factors related to the imbalance in the effort and reward (stress is inevitable, it is necessary in the profession of nursing for managers to review their employees' position and characteristics to find out their staff’s attitudes and behaviors and direct them in the right path.

  6. Perceived work stress, imbalance between work and family/personal lives, and mental disorders.

    Science.gov (United States)

    Wang, Jian Li

    2006-07-01

    Occupational mental health research has been focusing on the relationship between work stress and depression. However, the impacts of work stress on anxiety disorders and of imbalance between work and family life on workers' mental health have not been well studied. This analysis investigated the association between levels of perceived work stress and of imbalance between work and family/personal lives and current mood/anxiety disorders. This was a cross-sectional study using data from the Canadian Community Health Survey-Mental Health and Well-being (CCHS-1.2) (n=36,984). Mood and anxiety disorders were measured using the World Mental Health-Composite International Diagnostic Interview. The 1-month prevalence of mood and anxiety disorders among those with a work stress score at the 75th percentile value and above was 3.6% and 4.0%. Among those who reported that their work and family/personal lives "never" balanced in the past month, the 1-month prevalence of mood and anxiety disorders was 21.2% and 17.9%. In multivariate analyses, work stress and imbalance between work and family/personal lives were independently associated with mood and anxiety disorders. There was no evidence that perceived work stress interacted with imbalance between work and family/personal lives to increase the likelihood of having mental disorders. Gender was associated with anxiety disorders, but not with major depressive disorder and mood disorders. Work stress and imbalance between work and family/personal lives may be part of the etiology of mood and anxiety disorders in the working population. Community based longitudinal studies are needed to delineate the causal relationships among work stress, imbalance between work and family/personal lives and mental disorders.

  7. Imbalances in the development of European currency integration: key issues and recent trends

    Directory of Open Access Journals (Sweden)

    Cornelia Sahling

    2017-12-01

    Full Text Available The recent financial and sovereign debt crises affected the Eurozone countries in different ways. The centre-periphery divide of the national economies exacerbated existing problems in the euro area. In this article an empirical analysis of the development of intra-European imbalances is provided. The analysis shows that the problem of internal imbalances remains unsolved. High unemployment and high public debt in Eurozone’s periphery reflects the internal imbalances. In some Northern countries the public debt ratios are becoming higher, too. Significant current account imbalances provide an important indicator of external imbalances. The co-existence of large current account surpluses in Germany and the Netherlands and deficits in Greece challenges the possibilities of deeper European integration. The provided analysis shows a reduction in external imbalances because of better performance of periphery current accounts. A real solution of European problems needs deeper macroeconomic policy cooperation between national authorities and European institutions. The article highlights the limits of European institutions in promoting common economic policy. It is necessary to boost competitiveness by coordinated structural reforms in the euro area; fiscal austerity policies are not enough to restore pre-crisis internal balance. For sustainable economic growth European investment projects should be implemented in the euro area. The recovery of national economies should be used to reduce the high public debt levels in both centre and periphery countries. In the absence of economic adjustment through the exchange rate in the euro area further improvement in European current accounts convergence is important for European economic integration.

  8. Determinants of Pre-Operative Shoulder Imbalance in Patients with Adolescent Idiopathic Scoliosis

    Directory of Open Access Journals (Sweden)

    Hassan Ghandhari

    2017-01-01

    Full Text Available Background Disfiguring complications of adolescent idiopathic scoliosis (AIS could significantly affect the patients’ satisfaction. In this regard, shoulder imbalance has recently received much attention in spite of its poorly understood challenge. Objectives While the majority of previous studies have attempted to explore preoperative determinants of postoperative shoulder imbalance, in this study we aimed to investigate the factors correlated with the preoperative shoulder imbalance. Methods A total of 72 AIS patients with no previous history of corrective surgery took part in this study. The study sample comprised 63 females and 9 males with the mean age of 15.72 ± 3.08 years, ranging from 11 to 26 years. Shoulder imbalance parameters including T1 tilt, first rib angle (FRA, and clavicle angle (CA were assessed and their correlation with radiographic characteristics of the curves and patients’ demographic data including age and sex was evaluated. Results T1 tilt was more severe in males (mean -8.2° than females (mean -2.8° (P = 0.04. Moreover, a significant correlation was found between age and FRA (P = 0.04. A significant correlation was also observed between main thoracic (MT curve size and all the three parameters of shoulder imbalance (P < 0.001. The reverse correlation of T5 - T12 kyphosis angle with FRA was also significant (P = 0.04. Conclusions According to our results, in AIS, pre-operative radiographic shoulder imbalance could be affected by some curve parameters including MT and kyphosis size and demographic characteristics of patients including age and gender.

  9. Estimating radiative feedbacks from stochastic fluctuations in surface temperature and energy imbalance

    Science.gov (United States)

    Proistosescu, C.; Donohoe, A.; Armour, K.; Roe, G.; Stuecker, M. F.; Bitz, C. M.

    2017-12-01

    Joint observations of global surface temperature and energy imbalance provide for a unique opportunity to empirically constrain radiative feedbacks. However, the satellite record of Earth's radiative imbalance is relatively short and dominated by stochastic fluctuations. Estimates of radiative feedbacks obtained by regressing energy imbalance against surface temperature depend strongly on sampling choices and on assumptions about whether the stochastic fluctuations are primarily forced by atmospheric or oceanic variability (e.g. Murphy and Forster 2010, Dessler 2011, Spencer and Braswell 2011, Forster 2016). We develop a framework around a stochastic energy balance model that allows us to parse the different contributions of atmospheric and oceanic forcing based on their differing impacts on the covariance structure - or lagged regression - of temperature and radiative imbalance. We validate the framework in a hierarchy of general circulation models: the impact of atmospheric forcing is examined in unforced control simulations of fixed sea-surface temperature and slab ocean model versions; the impact of oceanic forcing is examined in coupled simulations with prescribed ENSO variability. With the impact of atmospheric and oceanic forcing constrained, we are able to predict the relationship between temperature and radiative imbalance in a fully coupled control simulation, finding that both forcing sources are needed to explain the structure of the lagged-regression. We further model the dependence of feedback estimates on sampling interval by considering the effects of a finite equilibration time for the atmosphere, and issues of smoothing and aliasing. Finally, we develop a method to fit the stochastic model to the short timeseries of temperature and radiative imbalance by performing a Bayesian inference based on a modified version of the spectral Whittle likelihood. We are thus able to place realistic joint uncertainty estimates on both stochastic forcing and

  10. Distinct evolutionary mechanisms for genomic imbalances in high-risk and low-risk neuroblastomas

    Directory of Open Access Journals (Sweden)

    Gisselsson David

    2007-09-01

    Full Text Available Abstract Background Neuroblastoma (NB is the most common extracranial solid tumour of childhood. Several genomic imbalances correlate to prognosis in NB, with structural rearrangements, including gene amplification, in a near-diploid setting typically signifying high-risk tumours and numerical changes in a near-triploid setting signifying low-risk tumours. Little is known about the temporal sequence in which these imbalances occur during the carcinogenic process. Methods We have reconstructed the appearance of cytogenetic imbalances in 270 NBs by first grouping tumours and imbalances through principal component analysis and then using the number of imbalances in each tumour as an indicator of evolutionary progression. Results Tumours clustered in four sub-groups, dominated respectively by (1 gene amplification in double minute chromosomes and few other aberrations, (2 gene amplification and loss of 1p sequences, (3 loss of 1p and other structural aberrations including gain of 17q, and (4 whole-chromosome gains and losses. Temporal analysis showed that the structural changes in groups 1–3 were acquired in a step-wise fashion, with loss of 1p sequences and the emergence of double minute chromosomes as the earliest cytogenetic events. In contrast, the gains and losses of whole chromosomes in group 4 occurred through multiple simultaneous events leading to a near-triploid chromosome number. Conclusion The finding of different temporal patterns for the acquisition of genomic imbalances in high-risk and low-risk NBs lends strong support to the hypothesis that these tumours are biologically diverse entities, evolving through distinct genetic mechanisms.

  11. What is Driving Global Imbalances? The Global Savings Glut Hypothesis Reexamined

    Directory of Open Access Journals (Sweden)

    Jai-Won Ryou

    2009-12-01

    Full Text Available In the middle of the global financial crisis, global imbalances seem to have been resolved to some extent, but it remains to be seen whether these imbalances will emerge again along with economic recovery. In order to cope with this global issue, we need to clarify what caused global imbalances in the first place. This paper aims to evaluate the relative importance of the "global savings glut" to the U.S. external imbalances. Drawing on the portfolio balance model, we analyze how the process of interaction between the U.S. current account deficit, capital inflows, and the U.S. dollar exchange rate is linked to domestic and external factors. Our empirical analysis shows that the U.S. current account deficit maintained since the early 1990s is mainly driven by the domestic factors, such as a decrease in the U.S. national savings and an increase in money supply growth. The size of the negative effect of a "global savings glut" measured by an increase in the East Asian countries' national savings (i.e. China, Japan and Korea on the U.S. current account seems to be exaggerated. Meanwhile, current account does not appear to be sensitive to changes in the exchange rate. This finding implies that the rectification of global imbalances is hardly possible to achieve by means of depreciating the U.S. dollar alone while leaving the structural factors unchanged. In order to achieve global rebalancing, the U.S. should increase its savings rate, reduce fiscal deficit, and tighten its money supply. While an increase in the domestic demand in the surplus countries such as China and Japan may be helpful in rectifying global imbalances, it appears to be insufficient per se.

  12. Geographical gradient of the eIF4E alleles conferring resistance to potyviruses in pea (Pisum) germplasm.

    Science.gov (United States)

    Konečná, Eva; Šafářová, Dana; Navrátil, Milan; Hanáček, Pavel; Coyne, Clarice; Flavell, Andrew; Vishnyakova, Margarita; Ambrose, Mike; Redden, Robert; Smýkal, Petr

    2014-01-01

    The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the eIF4E gene to identify novel genetic diversity. Germplasm of 2803 pea accessions was screened for eIF4E intron 3 length polymorphism, resulting in the detection of four eIF4E(A-B-C-S) variants, whose distribution was geographically structured. The eIF4E(A) variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, eIF4E(B), was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The eIF4E(C) variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The eIF4E(S) variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (eIF4E(A-1-2-3-4-5-6-7), eIF4E(B-1), eIF4E(C-2)) conferred resistance to the P1 PSbMV pathotype. This work identified novel eIF4E alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible eIF4E(S1) allele. Despite high variation present in wild Pisum accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the

  13. Generation of charge imbalance in a superconductor by a temperature gradient

    International Nuclear Information System (INIS)

    Entin-Wohlman, O.; Orbach, R.

    1980-01-01

    The charge-imbalance voltage in a superconductor carrying a current in the presence of a temperature gradient is calculated from the Boltzmann equation in the clean limit. We demonstrate why the Green's-function approach in the dirty limit, first performed by Schmid and Schoem, generates the same Boltzmann-like equation for the distribution function. In addition, the charge-imbalance voltage in the absence of an impressed current is calculated. It is shown to depend on del 2 T+(delT) 2 /T, and not solely on (delT) 2 . The calculations are limited to the temperature regime near T/sub c/, such that Δ<< T

  14. The role of hormonal imbalance in the development of autoimmune dacryoadenitis in endocrine orbitopathy

    Directory of Open Access Journals (Sweden)

    V. G. Likhvantseva

    2014-07-01

    Full Text Available The authors analyzed the hormonal profile of patients with Graves’ disease and endocrine orbitopathy with or without autoimmune dacryoadenitis. Presented compelling evidence about the role of hormonal imbalance between thyreoglobulines and thyroidstimulating hormones in the development of autoimmune dacryoadenitis. The availability of this kind of imbalance increases the risk of involvement of lacrimal gland in the pathological process with 12.3 % up to 64.3 % in the population with Graves’ disease and endocrine orbitopathy.

  15. Widely Linear Equalization for IQ Imbalance and Skew Compensation in Optical Coherent Receivers

    DEFF Research Database (Denmark)

    Porto da Silva, Edson; Zibar, Darko

    2016-01-01

    In this paper, an alternative approach to design linear equalization algorithms for optical coherent receivers is introduced. Using widely linear complex analysis, a general analytical model it is shown, where In-phase/quadrature (IQ) imbalances and IQ skew at the coherent receiver front-end are ......In this paper, an alternative approach to design linear equalization algorithms for optical coherent receivers is introduced. Using widely linear complex analysis, a general analytical model it is shown, where In-phase/quadrature (IQ) imbalances and IQ skew at the coherent receiver front...

  16. Does correction of preoperative coronal imbalance make a difference in outcomes of adult patients with deformity?

    Science.gov (United States)

    Daubs, Michael D; Lenke, Lawrence G; Bridwell, Keith H; Kim, Yongjung J; Hung, Man; Cheh, Gene; Koester, Linda A

    2013-03-15

    Retrospective study with prospectively collected outcomes data. Determine the significance of coronal balance on spinal deformity surgery outcomes. Sagittal balance has been confirmed as an important radiographic parameter correlating with adult deformity treatment outcomes. The significance of coronal balance on functional outcomes is less clear. Eighty-five patients with more than 4 cm of coronal imbalance who underwent reconstructive spinal surgery were evaluated to determine the significance of coronal balance on functional outcomes as measured with the Oswestry Disability Index (ODI) and Scoliosis Research Society outcomes questionnaires. Sixty-two patients had combined coronal (>4 cm) and sagittal imbalance (>5 cm), while 23 patients had coronal imbalance alone. Postoperatively, 85% of patients demonstrated improved coronal balance. The mean improvement in the coronal C7 plumb line was 26 mm for a mean correction of 42%. The mean preoperative sagittal C7 plumb line in patients with combined coronal and sagittal imbalance was 118 mm (range, 50-310 mm) and improved to a mean 49 mm. The mean preoperative and postoperative ODI scores were 42 (range, 0-90) and 27 (range, 0-78), for a mean improvement of 15 (36%) (P = 0.00001; 95% CI, 12-20). The mean Scoliosis Research Society scores improved by 17 points (29%) (P = 0.00). Younger age (P = 0.008) and improvement in sagittal balance (P = 0.014) were positive predictors for improved ODI scores. Improvement in sagittal balance (P = 0.010) was a positive predictor for improved Scoliosis Research Society scores. In patients with combined coronal and sagittal imbalance, improvement in sagittal balance was the most significant predictor for improved ODI scores (P = 0.009). In patients with preoperative coronal imbalance alone, improvement in coronal balance trended toward, but was not a significant predictor for improved ODI (P = 0.092). Sagittal balance improvement is the strongest predictor of improved outcomes in

  17. Effort reward imbalance is associated with vagal withdrawal in Danish public sector employees

    DEFF Research Database (Denmark)

    Eller, Nanna Hurwitz; Blønd, Morten; Nielsen, Martin

    2011-01-01

    The current study analyzed the relationship between psychosocial work environment assessed by the Effort Reward Imbalance Model (ERI-model) and heart rate variability (HRV) measured at baseline and again, two years later, as this relationship is scarcely covered by the literature.......The current study analyzed the relationship between psychosocial work environment assessed by the Effort Reward Imbalance Model (ERI-model) and heart rate variability (HRV) measured at baseline and again, two years later, as this relationship is scarcely covered by the literature....

  18. Imbalance in resting state functional connectivity is associated with eating behaviors and adiposity in children

    Directory of Open Access Journals (Sweden)

    BettyAnn A. Chodkowski

    2016-01-01

    Conclusions: In the absence of any explicit eating-related stimuli, the developing brain is primed toward food approach and away from food avoidance behavior with increasing adiposity. Imbalance in resting state functional connectivity that is associated with non-homeostatic eating develops during childhood, as early as 8–13 years of age. Our results indicate the importance of identifying children at risk for obesity for earlier intervention. In addition to changing eating habits and physical activity, strategies that normalize neural functional connectivity imbalance are needed to maintain healthy weight. Mindfulness may be one such approach as it is associated with increased response inhibition and decreased impulsivity.

  19. Effects of PM2.5 exposure on the Notch signaling pathway and immune imbalance in chronic obstructive pulmonary disease

    International Nuclear Information System (INIS)

    Gu, Xing-yu; Chu, Xu; Zeng, Xiao-Li; Bao, Hai-Rong; Liu, Xiao-Ju

    2017-01-01

    Chronic Obstructive Pulmonary Disease (COPD) is associated with T lymphocytes subset (Th1/Th2, Th17/Treg) imbalance. Notch signaling pathway plays a key role in the development of the adaptive immunity. The immune disorder induced by fine particulate matter (PM2.5) is related to COPD. The aim of this study was to investigate the mechanism by which PM2.5 influences the Notch signaling pathway leading to worsening immune disorder and accelerating COPD development. A COPD mouse model was established by cigarette smoke exposure. PM2.5 exposure was performed by aerosol inhalation. γ-secretase inhibitor (GSI) was given using intraperitoneal injection. Splenic T lymphocytes were purified using a density gradient centrifugation method. CD4 + T lymphocyte subsets (Th1/Th2, Th17/Treg) were detected using flow cytometry. mRNA and proteins of Notch1/2/3/4, Hes1/5, and Hey1 were detected using RT-PCR and Western blot. Serum INF-γ, IL-4, IL-17 and IL-10 concentrations were measured using ELISA. The results showed that in COPD mice Th1% and Th17%, Th1/Th2 and Th17/Treg were increased, and the levels of mRNA and protein in Notch1/2/3/4, Hes1/5, and Hey1 and serum INF-γ and IL-17 concentrations were significantly increased, and Th2%, Treg%, and serum IL-4 and IL-10 concentrations were significantly decreased. COPD Mice have Th1- and Th17-mediated immune disorder, and the Notch signaling pathway is in an overactivated state. PM2.5 promotes the overactivation of the Notch signaling pathway and aggravates the immune disorder of COPD. GSI can partially inhibit the activation of the Notch signaling pathway and alleviate the immune disorder under basal state and the immune disorder of COPD caused by PM2.5. This result suggests that PM2.5 is involved in the immune disorder of mice with COPD by affecting the Notch signaling pathway and that PM2.5 aggravates COPD. - Highlights: • The COPD mice demonstrated Th1 and Th17 dominant immune imbalance. • PM2.5 aggravates the Th1/Th2 and Th

  20. Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR

    Directory of Open Access Journals (Sweden)

    Neng Chen

    2014-07-01

    Full Text Available Cystic fibrosis transmembrane conductance regulator (CFTR gene mutation analysis has been implemented for Cystic Fibrosis (CF carrier screening, and molecular diagnosis of CF and congenital bilateral absence of the vas deferens (CBAVD. Although poly-T allele analysis in intron 8 of CFTR is required when a patient is positive for R117H, it is not recommended for routine carrier screening. Therefore, commercial kits for CFTR mutation analysis were designed either to mask the poly-T allele results, unless a patient is R117H positive, or to have the poly-T analysis as a standalone reflex test using the same commercial platform. There are other standalone assays developed to detect poly-T alleles, such as heteroduplex analysis, High Resolution Melting (HRM curve analysis, allele-specific PCR (AS-PCR and Sanger sequencing. In this report, we developed a simple and easy-to-implement multiplex AS-PCR assay using unlabeled standard length primers, which can be used as a reflex or standalone test for CFTR poly-T track analysis. Out of 115 human gDNA samples tested, results from our new AS-PCR matched to the previous known poly-T results or results from Sanger sequencing.

  1. Hitchhiking and Selective Sweeps of Plasmodium falciparum Sulfadoxine and Pyrimethamine Resistance Alleles in a Population from Central Africa▿ †

    Science.gov (United States)

    McCollum, Andrea M.; Basco, Leonardo K.; Tahar, Rachida; Udhayakumar, Venkatachalam; Escalante, Ananias A.

    2008-01-01

    Sulfadoxine-pyrimethamine (SP) resistance in Plasmodium falciparum is encoded by a number of mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps) genes. Here, we have characterized point mutations in dhfr and dhps and microsatellite loci around dhfr on chromosome 4 and dhps on chromosome 8 as well as neutral markers on chromosomes 2 and 3 in 332 samples from Yaoundé, Cameroon. The triple mutant dhfr haplotype that originated in Southeast Asia is the most predominant in this sample set, but we also find additional independent haplotypes at low frequency and an incipient process of genetic differentiation among alleles of Southeast Asian origin. As reported for other African populations, we find evidence of a selective sweep for resistant dhfr mutants in this Cameroonian population due to drug selection. Although we find evidence for a selective sweep in dhps mutants associated with SP resistance, the dynamics of dhps mutants appear different than those observed for dhfr mutants. Overall, our results yield support for the use of microsatellite markers to track resistant parasites; however, the detection of resistant dhfr alleles in low frequency, the evidence of divergence among dhfr alleles that share a common evolutionary origin, and the distinct dynamics of resistant dhps alleles emphasize the importance of comprehensive, population-based investigations to evaluate the effects of drug selection on parasite populations. PMID:18765692

  2. A Simple, High-Throughput Assay for Fragile X Expanded Alleles Using Triple Repeat Primed PCR and Capillary Electrophoresis

    Science.gov (United States)

    Lyon, Elaine; Laver, Thomas; Yu, Ping; Jama, Mohamed; Young, Keith; Zoccoli, Michael; Marlowe, Natalia

    2010-01-01

    Population screening has been proposed for Fragile X syndrome to identify premutation carrier females and affected newborns. We developed a PCR-based assay capable of quickly detecting the presence or absence of an expanded FMR1 allele with high sensitivity and specificity. This assay combines a triplet repeat primed PCR with high-throughput automated capillary electrophoresis. We evaluated assay performance using archived samples sent for Fragile X diagnostic testing representing a range of Fragile X CGG-repeat expansions. Two hundred five previously genotyped samples were tested with the new assay. Data were analyzed for the presence of a trinucleotide “ladder” extending beyond 55 repeats, which was set as a cut-off to identify expanded FMR1 alleles. We identified expanded FMR1 alleles in 132 samples (59 premutation, 71 full mutation, 2 mosaics) and normal FMR1 alleles in 73 samples. We found 100% concordance with previous results from PCR and Southern blot analyses. In addition, we show feasibility of using this assay with DNA extracted from dried-blood spots. Using a single PCR combined with high-throughput fragment analysis on the automated capillary electrophoresis instrument, we developed a rapid and reproducible PCR-based laboratory assay that meets many of the requirements for a first-tier test for population screening. PMID:20431035

  3. Allelic Tests and Sequence Analysis of Three Genes for Resistance to Xanthomonas perforans Race T3 in Tomato

    Institute of Scientific and Technical Information of China (English)

    ZHAO Baimei; CAO Haipeng; DUAN Junjie; YANG Wencai

    2015-01-01

    Three crosses,Hawaii7981×PI128216,Hawaii7981×LA1589,and PI128216×LA1589,were made to develop F2 populations for testing allelism among three genes Xv3,Rx4,and RxLA1589 conferring resistance to bacterial spot caused by Xanthomonas perforans race T3 in tomato. Each population consisted of 535–1 655 individuals. An infiltration method was used to inoculate the leaves of the parental and F2 plants as well as the susceptible control OH88119 for detecting hypersensitive resistance(HR). The results showed that all the tomato plants except OH88119 had HR to race T3,indicating that Xv3,Rx4,and RxLA1589 were allelic genes. Genomic DNA fragments of the Rx4 alleles from Hawaii7981,PI128216,and LA1589 were amplified using gene-specific primers and sequenced. No sequence variation was observed in the coding region of Rx4 in the three resistant lines. Based on the published map positions of these loci as well as the allelic tests and sequence data obtained in this study,we speculated that Xv3,Rx4,and RxLA1589 were the same gene. The results will provide useful information for understanding the mechanism of resistance to race T3 and developing resistant tomato varieties.

  4. Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds.

    Science.gov (United States)

    Goldmann, W; Marier, E; Stewart, P; Konold, T; Street, S; Langeveld, J; Windl, O; Ortiz-Pelaez, A

    2016-02-13

    Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level. British Veterinary Association.

  5. [Acid-base imbalance in acute obstructive uropathies].

    Science.gov (United States)

    Belyĭ, L E

    2007-01-01

    The aim of this study was to evaluate impairment of acid-base balance (ABB) in acute obstructive uropathies. Evaluation of acid-base balance was performed by pH, partial carbon dioxide pressure, plasma bicarbonate concentration, buffer bases, basis excess, hydrogen ion concentration. An automatic gas analyzer was used, plasma anion gap was calculated. Characteristic ABB alterations in different acute obstructive uropathies were detected. Acidotic shifts in acute obstruction of the upper urinary tracts and its inflammatory complications were assessed pathophysiologically. A comparative study of pathological acid-base disorders in acute supra- and infravesical obstructive uropathies was performed.

  6. Reliability of a new method for measuring coronal trunk imbalance, the axis-line-angle technique.

    Science.gov (United States)

    Zhang, Rui-Fang; Liu, Kun; Wang, Xue; Liu, Qian; He, Jia-Wei; Wang, Xiang-Yang; Yan, Zhi-Han

    2015-12-01

    Accurate determination of the extent of trunk imbalance in the coronal plane plays a key role in an evaluation of patients with trunk imbalance, such as patients with adolescent idiopathic scoliosis. An established, widely used practice in evaluating trunk imbalance is to drop a plumb line from the C7 vertebra to a key reference axis, the central sacral vertical line (CSVL) in full-spine standing anterioposterior radiographs, and measuring the distance between them, the C7-CSVL. However, measuring the CSVL is subject to intraobserver differences, is error-prone, and is of poor reliability. Therefore, the development of a different way to measure trunk imbalance is needed. This study aimed to describe a new method to measure coronal trunk imbalance, the axis-line-angle technique (ALAT), which measures the angle at the intersection between the C7 plumb line and an axis line drawn from the vertebral centroid of the C7 to the middle of the superior border of the symphysis pubis, and to compare the reliability of the ALAT with that of the C7-CSVL. A prospective study at a university hospital was used. The patient sample consisted of sixty-nine consecutively enrolled men and women patients, aged 10-18 years, who had trunk imbalance defined as C7-CSVL longer than 20 mm on computed full-spine standing anterioposterior radiographs. Data were analyzed to determine the correlation between C7-CSVL and ALAT measurements and to determine intraobserver and interobserver reliabilities. Using a picture archiving and communication system, three radiologists independently evaluated trunk imbalance on the 69 computed radiographs by measuring the C7-CSVL and by measuring the angle determined by the ALAT. Data were analyzed to determine the correlations between the two measures of trunk imbalance, and to determine intraobserver and interobserver reliabilities of each of them. Overall results from the measurements by the C7-CSVL and the ALAT were significantly moderately correlated

  7. Using high-resolution human leukocyte antigen typing of 11,423 randomized unrelated individuals to determine allelic varieties, deduce probable human leukocyte antigen haplotypes, and observe linkage disequilibria between human leukocyte antigen-B and-C and human leukocyte antigen-DRB1 and-DQB1 alleles in the Taiwanese Chinese population

    Directory of Open Access Journals (Sweden)

    Kuo-Liang Yang

    2017-01-01

    Full Text Available Objective: We report here the human leukocyte antigen (HLA allelic variety and haplotype composition in a cohort of the Taiwanese Chinese population and their patterns of linkage disequilibria on HLA-B: HLA-C alleles and HLA-DRB1: HLA-DQB1 alleles at a high-resolution level. Materials and Methods: Peripheral whole blood from 11,423 Taiwanese Chinese unrelated individuals was collected in acid citrate dextrose. Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit. The DNA material was subjected to HLA genotyping for HLA-A,-B,-C,-DRB1, and-DQB1 loci using a commercial polymerase chain reaction-sequence-based typing (PCR-SBT kit, the SeCore® A/B/C/DRB1/DQB1 Locus Sequencing kit. High-resolution allelic sequencing was performed as previously described. Results: The number of individual HLA-B alleles detected was greater than the number of alleles recognized in the both the HLA-A and-DRB1 loci. Several novel alleles were discovered as a result of employing the SBT method and the high number of donors tested. In addition, we observed a genetic polymorphic feature of association between HLA-A and-B, HLA-B and-C, and HLA-DRB1 and-DQB1 alleles. Further, the homozygous haplotype frequencies of HLA-A and-B; HLA-A,-C, and-B; HLA-A,-C,-B, and-DRB1; and HLA-A,-C,-B,-DRB1, and-DQB1 in Taiwanese Chinese population are presented. Conclusion: As increasing number of HLA alleles are being discovered, periodic HLA profile investigation in a given population is essential to recognize the HLA complexity in that population. Population study can also provide an up-to-date strategic plan for future needs in terms of compatibility measurement for HLA matching between transplant donors and patients.

  8. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    Czech Academy of Sciences Publication Activity Database

    Baker, C.L.; Petkova, P.; Walker, M.; Flachs, Petr; Mihola, Ondřej; Trachtulec, Zdeněk; Petkov, P.M.; Paigen, K.

    2015-01-01

    Roč. 11, č. 9 (2015), e1005512-e1005512 ISSN 1553-7390 R&D Projects: GA ČR GAP305/10/1931; GA ČR(CZ) GA14-20728S; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:68378050 Keywords : recombination * PRDM9 * allelic competition Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.528, year: 2014

  9. [Phenotypic effects of puroindoline gene alleles of bread wheat].

    Science.gov (United States)

    Chebotar, S V; Kurakina, K O; Khokhlov, O M; Chebotar, H O; Syvolap, Iu M

    2012-01-01

    85 winter bread wheat varieties and lines that have been developed mostly in Ukraine were analyzed with NIR for parameters of hardness and protein content. The hardness data were compared with the data of puroindoline gene alleles analysis done earlier and the published data. Significant variation of parameters of hardness was revealed when there was low polymorphism of puroindoline genes indicating the presence of additional genes that influence the hardness parameters.

  10. TRPV6 alleles do not influence prostate cancer progression

    OpenAIRE

    Kessler, Thorsten; Wissenbach, Ulrich; Grobholz, Rainer; Flockerzi, Veit

    2009-01-01

    Abstract Background The transient receptor potential, subfamily V, member 6 (TRPV6) is a Ca2+ selective cation channel. Several studies have shown that TRPV6 transcripts are expressed in locally advanced prostatic adenocarcinoma, metastatic and androgen-insensitive prostatic lesions but are undetectable in healthy prostate tissue and benign prostatic hyperplasia. Two allelic variants of the human trpv6 gene have been identified which are transcribed into two independent mRNAs, TRPV6a and TRPV...

  11. Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L..

    Directory of Open Access Journals (Sweden)

    Jie Guo

    Full Text Available Common wheat is one of the most important crops in China, which is the largest producer in the world. A set of 230 cultivars was used to identify yield-related loci by association mapping. This set was tested for seven yield-related traits, viz. plant height (PH, spike length (SL, spikelet number per spike (SNPS, kernel number per spike (KNPS, thousand-kernel weight (TKW, kernel weight per spike (KWPS, and sterile spikelet number (SSN per plant in four environments. A total of 106 simple sequence repeat (SSR markers distributed on all 21 chromosomes were used to screen the set. Twenty-one and 19 of them were associated with KNPS and TKW, respectively. Association mapping detected 73 significant associations across 50 SSRs, and the phenotypic variation explained (R2 by the associations ranged from 1.54 to 23.93%. The associated loci were distributed on all chromosomes except 4A, 7A, and 7D. Significant and potentially new alleles were present on 8 chromosomes, namely 1A, 1D, 2A, 2D, 3D, 4B, 5B, and 6B. Further analysis showed that genetic effects of associated loci were greatly influenced by association panels, and the R2 of crucial loci were lower in modern cultivars than in the mini core collection, probably caused by strong selection in wheat breeding. In order to confirm the results of association analysis, yield-related favorable alleles Xgwm135-1A138, Xgwm337-1D186, Xgwm102-2D144, and Xgwm132-6B128 were evaluated in a double haploid (DH population derived from Hanxuan10 xLumai14.These favorable alleles that were validated in various populations might be valuable in breeding for high-yield.

  12. Mutant power: using mutant allele collections for yeast functional genomics.

    Science.gov (United States)

    Norman, Kaitlyn L; Kumar, Anuj

    2016-03-01

    The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  13. The protease inhibitor PI*S allele and COPD

    DEFF Research Database (Denmark)

    Hersh, C P; Ly, N P; Berkey, C S

    2005-01-01

    In many countries, the protease inhibitor (SERPINA1) PI*S allele is more common than PI*Z, the allele responsible for most cases of chronic obstructive pulmonary disease (COPD) due to severe alpha 1-antitrypsin deficiency. However, the risk of COPD due to the PI*S allele is not clear. The current...... authors located studies that addressed the risk of COPD or measured lung function in individuals with the PI SZ, PI MS and PI SS genotypes. A separate meta-analysis for each genotype was performed. Aggregating data from six studies, the odds ratio (OR) for COPD in PI SZ compound heterozygotes compared...... with PI MM (normal) individuals was significantly increased at 3.26 (95% confidence intervals (CI): 1.24-8.57). In 17 cross-sectional and case-control studies, the OR for COPD in PI MS heterozygotes was 1.19 (95%CI: 1.02-1.38). However, PI MS genotype was not associated with COPD risk after correcting...

  14. Higher FKBP5, COMT, CHRNA5, and CRHR1 allele burdens are associated with PTSD and interact with trauma exposure: implications for neuropsychiatric research and treatment

    Directory of Open Access Journals (Sweden)

    Boscarino JA

    2012-03-01

    Full Text Available Joseph A Boscarino1,2, Porat M Erlich1,3, Stuart N Hoffman4, Xiaopeng Zhang51Center for Health Research, Geisinger Clinic, Danville, PA, 2Department of Psychiatry, 3Department of Medicine, Temple University School of Medicine, Philadelphia, PA, 4Department of Neurology, 5Department of Anesthesiology, Geisinger Clinic, Danville, PA, USAObjective: The study aim was to assess the cumulative burden of polymorphisms located within four genetic loci previously associated with posttraumatic stress disorder (PTSD among outpatients at risk for PTSD.Methods: Diagnostic interviews were completed and DNA samples collected among 412 pain patients to determine if FKBP5 (rs9470080, COMT (rs4680, CHRNA5 (rs16969968, and CRHR1 (rs110402 single nucleotide polymorphisms were cumulatively associated with increased risk for PTSD.Results: In bivariate analyses, it was found that a count of specific PTSD risk alleles located within FKBP5, COMT, CHRNA5, and CRHR1 genetic loci (allele range = 0–6, mean count = 2.92, standard deviation = 1.36 was associated with lifetime (t [409] = 3.430, P = 0.001 and early onset PTSD (t [409] = 4.239, P = 0.000028. In logistic regression, controlling for demographic factors, personality traits, and trauma exposures, this risk allele count remained associated with both lifetime (odds ratio = 1.49, P = 0.00158 and early onset PTSD (odds ratio = 2.36, P = 0.000093. Interaction effects were also detected, whereby individuals with higher risk allele counts and higher trauma exposures had an increased risk of lifetime PTSD (allele count × high trauma, P = 0.026 and early onset PTSD (allele count × high trauma, P = 0.016 in these logistic regressions. Those with no or few risk alleles appeared resilient to PTSD, regardless of exposure history.Conclusion: A cumulative risk allele count involving four single nucleotide polymorphisms located within the FKBP5, COMT, CHRNA5, and CRHR1 genes are associated with PTSD. Level of trauma exposure

  15. Evaluation of electrolyte imbalance among tuberculosis patients receiving treatments in Southwestern Nigeria

    Directory of Open Access Journals (Sweden)

    Adebimpe Wasiu Olalekan

    2015-09-01

    Conclusion: Hyponatraemia, hyperkalaemia, and hypochloremia characterized some of the electrolyte imbalance among TB patients receiving treatments. The raised level of bicarbonate may be attributed to overcorrection of respiratory acidosis often found in patients with tuberculosis. Monitoring electrolytes is therefore an important component of TB management.

  16. SCOREBOARD AND THE POSSIBILITY OF EARLY STAGE IDENTIFICATION OF IMBALANCES IN THE EUROPEAN UNION

    Directory of Open Access Journals (Sweden)

    Marius, Gust

    2013-01-01

    Full Text Available In late 2011, the European Union (EU Council and European Parliament adopted a series of new rules on economic governance, perfecting the process begun in 2010 to strengthen the monitoring and prevention of macroeconomic imbalances, fiscal and competitiveness disparities among EU countries. In the same direction, of strengthening fiscal surveillance under the Stability and Growth Pact, also goes the Treaty on Stability, Coordination and Governance in the Economic and Monetary Union, through the fiscal Compact. Thus, the macroeconomic imbalances procedure provided in the new legislation requires as a first step the realization of a scoreboard consisting of 10 indicators, which, according to promoters, allow an early identification of imbalances, of both short-term, as well as structural, of longer-term. European Commission reports and statistics for EU Member States in 2010 and 2011, indicate that in the post-crisis period there has been a pronounced adjustment of external imbalances, but a number of countries continue to record higher values than indicative levels in the dashboard .

  17. Reverse knowledge and technology transfer: imbalances caused by cognitive barriers in asymmetric relationships

    NARCIS (Netherlands)

    Millar-Schijf, Carla C.J.M.; Choi, Chong-Ju

    2009-01-01

    An imbalance exists in almost any type of knowledge and technology transfer due to the information asymmetry of the relationship. However, this is especially the case for reverse technology and knowledge transfer which is epitomised for us by "transfers from an MNC's subsidiary to its headquarters".

  18. The validity and reliability of the Dutch Effort-Reward Imbalance Questionnaire

    NARCIS (Netherlands)

    Hanson, E. K.; Schaufeli, W.; Vrijkotte, T.; Plomp, N. H.; Godaert, G. L.

    2000-01-01

    The reliability and validity of the Effort-Reward Imbalance Questionnaire were tested in 775 blue- and white-collar workers in the Netherlands. Cronbach's alpha revealed sufficient internal consistency of all subscales except Need for Control. With exploratory probabilistic scaling (Mokken)

  19. Effort-Reward Imbalance for Learning Is Associated with Fatigue in School Children

    Science.gov (United States)

    Fukuda, Sanae; Yamano, Emi; Joudoi, Takako; Mizuno, Kei; Tanaka, Masaaki; Kawatani, Junko; Takano, Miyuki; Tomoda, Akemi; Imai-Matsumura, Kyoko; Miike, Teruhisa; Watanabe, Yasuyoshi

    2010-01-01

    We examined relationships among fatigue, sleep quality, and effort-reward imbalance for learning in school children. We developed an effort-reward for learning scale in school students and examined its reliability and validity. Self-administered surveys, including the effort reward for leaning scale and fatigue scale, were completed by 1,023…

  20. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Bonhenry, Daniel; Timr, Štěpán; Jungwirth, Pavel

    2016-01-01

    Roč. 12, č. 5 (2016), s. 2418-2425 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : membrane potential * molecular dynamics * ion imbalance Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.245, year: 2016

  1. Socio-Cultural Imbalances in AIED Research: Investigations, Implications and Opportunities

    Science.gov (United States)

    Blanchard, Emmanuel G.

    2015-01-01

    This paper investigates international representations in the Artificial Intelligence in Education (AIED) research field. Its methodological and theoretical groundings are inspired by Arnett (2008) and Henrich et al. (2010a) who addressed the same issue in psychology, and respectively a) discovered massive imbalances in representation in top-tier…

  2. Short-term strategies for Dutch wind power producers to reduce imbalance costs

    International Nuclear Information System (INIS)

    Chaves-Ávila, José Pablo; Hakvoort, Rudi A.; Ramos, Andrés

    2013-01-01

    The paper assesses bidding strategies for a wind power producer in the Netherlands. To this end, a three-stage stochastic optimization framework is used, maximizing wind power producer's profit using the day-ahead and cross-border intraday market, taking into account available interconnection capacity. Results show that the wind power producer can increase its profits by trading on the intraday market and – under certain imbalance prices – by intentionally creating imbalances. It has been considered uncertainties about prices, power forecast and interconnection capacity at the day-ahead and intraday timeframes. - Highlights: ► A cross-border bidding strategy model for wind power producers has been developed. ► The model was applied to a real case study of a Dutch offshore wind power producer. ► Under certain imbalance prices, it is not profitable to deliver all possible power. ► Intraday markets give the possibility to reduce imbalance costs. ► Integration of intraday markets will increase liquidity.

  3. A low-complexity feed-forward I/Q imbalance compensation algorithm

    NARCIS (Netherlands)

    Moseley, N.A.; Slump, Cornelis H.

    2006-01-01

    This paper presents a low-complexity adaptive feed- forward I/Q imbalance compensation algorithm. The feed-forward so- lution has guaranteed stability. Due to its blind nature the algorithm is easily incorporated into an existing receiver design. The algorithm uses three estimators to obtain the

  4. Coping, social support, job satisfaction, and work/life imbalance / Mianda Smith

    OpenAIRE

    Smith, Mianda

    2006-01-01

    This mini dissertation focuses on the effects of coping on job satisfaction when job insecurity is being experienced by a group of managers in a South African mining company. The second part of the dissertation deals with role conflict, goal clarity, and how social support affects work/life imbalance. Thesis (M.Com. (Industrial Psychology))--North-West University, Potchefstroom Campus, 2007.

  5. The impact of effort-reward imbalance on quality of life among Japanese working men.

    Science.gov (United States)

    Watanabe, Mayumi; Tanaka, Katsutoshi; Aratake, Yutaka; Kato, Noritada; Sakata, Yumi

    2008-07-01

    Health-related quality of life (HRQL) is an important measure of health outcome in working and healthy populations. Here, we investigated the impact of effort-reward imbalance (ERI), a representative work-stress model, on HRQL of Japanese working men. The study targeted 1,096 employees from a manufacturing plant in Japan. To assess HRQL and ERI, participants were surveyed using the Japanese version of the Short-Form 8 Health Survey (SF-8) and effort-reward imbalance model. Of the 1,096 employees, 1,057 provided valid responses to the questionnaire. For physical summary scores, the adjusted effort-reward imbalance odds ratios of middle vs. bottom and top vs. bottom tertiles were 0.24 (95% confidence interval, 0.08-0.70) and 0.09 (95% confidence interval, 0.03-0.28), respectively. For mental summary scores, ratios were 0.21 (95% confidence interval, 0.07-0.63) and 0.07 (95% confidence interval, 0.02-0.25), respectively. These findings demonstrate that effort-reward imbalance is independently associated with HRQL among Japanese employees.

  6. Effort-Reward Imbalance and Overcommitment in UK Academics: Implications for Mental Health, Satisfaction and Retention

    Science.gov (United States)

    Kinman, Gail

    2016-01-01

    This study utilises the effort-reward imbalance (ERI) model of job stress to predict several indices of well-being in academics in the UK: mental ill health, job satisfaction and leaving intentions. This model posits that (a) employees who believe that their efforts are not counterbalanced by sufficient rewards will experience impaired well-being…

  7. Quasiparticle Lifetime in Ultracold Fermionic Mixtures with Density and Mass Imbalance

    DEFF Research Database (Denmark)

    Lan, Zhihao; Bruun, Georg; Lobo, Carlos

    2013-01-01

    We show that atomic Fermi mixtures with density and mass imbalance exhibit a rich diversity of scaling laws for the quasiparticle decay rate beyond the quadratic energy and temperature dependence of conventional Fermi liquids. For certain densities and mass ratios, the decay rate is linear, whereas...

  8. Widely Linear Blind Adaptive Equalization for Transmitter IQ-Imbalance/Skew Compensation in Multicarrier Systems

    DEFF Research Database (Denmark)

    Porto da Silva, Edson; Zibar, Darko

    2016-01-01

    Simple analytical widely linear complex-valued models for IQ-imbalance and IQ-skew effects in multicarrier transmitters are presented. To compensate for such effects, a 4×4 MIMO widely linear adaptive equalizer is proposed and experimentally validated....

  9. Effects of novel tubing gait on neuromuscular imbalance in cerebral palsy.

    Science.gov (United States)

    Shin, Yoon Kyum; Lee, Dong Ryul; Kim, Do Hyun; Lee, Jae Jin; You, Sung Joshua Hyun; Yi, Chung Hwi; Jeon, Hye Seon

    2014-01-01

    Gait impairments from a neuromuscular imbalance are crucial issues in cerebral palsy. The purpose of our study was to compare the effects of the assistive tubing gait (ATG) and assistive-resistive tubing gait (ARTG) on improving the vasti and hamstring muscle imbalance during the initial contact to mid-stance phases in individuals with spastic diplegic cerebral palsy (CP). Fourteen age-matched individuals including seven normal individuals (11.7 years) and seven individuals with CP (12.9 years) were recruited. All participants underwent electromyography (EMG) measurement of the unilateral vasti and hamstring muscle activity during the three gait training conditions of no-tubing gait (NTG), ATG, and ARTG. A statistical one-way repeated-measure analysis of variance (ANOVA) was used to determine differences in the vasti and hamstring activity, the vasti/hamstring ratio, and the knee joint angle across the three gait training conditions for each group. The initial vasti and hamstring muscle imbalance in CP was significantly improved by applying the ARTG compared with the ATG. The vasti/hamstring ratio during the ARTG was compatible with the ratio value obtained from the NTG of normal individuals. The knee joint angle in CP was not improved in this short-term intervention. The ARTG proportionately increased the vasti activation and reciprocally inhibited the hamstring activity, subsequently improving the neuromuscular imbalance associated with the flexed-knee gait in individuals with spastic diplegic CP.

  10. The price path due to order imbalances: evidence from the Amsterdam agricultural futures exchange.

    NARCIS (Netherlands)

    Pennings, J.M.E.; Kuiper, W.E.; Hofstede, ter F.; Meulenberg, M.T.G.

    1998-01-01

    The lack of sufficient market depth particularly in many newly initiated futures markets results in relatively high hedging costs, and this inhibits the growth of futures contract volume. In this article the price path due to order imbalances is analyzed and a two-dimensional market depth measure is

  11. Frequency Shift of a Rotating Mass-Imbalance Immersed in an Acoustic Fluid

    International Nuclear Information System (INIS)

    Stephen R. Novascone; David M. Weinberg; Michael J. Anderson

    2005-01-01

    In this paper, we describe a physical mechanism that relates a measurable behavior of a vibrating device to the physical properties of a surrounding acoustic medium. The vibrating device under consideration is a rotating imbalance immersed in an unbounded acoustic fluid. It is assumed that the rotating imbalance is driven by an electromagnetic motor excited by a given DC voltage. If nonlinearities are ignored, the steady state operational frequency of such a device is determined by a balance between the applied electromagnetic and opposing frictional torque on the rotating imbalance. If nonlinearities are retained, it is shown that under certain circumstances, the surrounding acoustic medium exerts an additional time-averaged opposing torque on the rotating imbalance that reduces the operational frequency of the device. Consequently, the operational frequency of the device becomes linked to the physical properties of the surrounding medium. Analytical calculations showed that the radiative resistance of an acoustic fluid caused the opposing torque. The shift in frequency is proportional to the radiative resistance and the square of the rotating eccentricity, but inversely proportional the total transducer mass and the damping effect of the DC motor

  12. Mental health among Norwegian priests: associations with effort-reward imbalance and overcommitment.

    Science.gov (United States)

    Lau, Bjørn

    2018-01-01

    The aim of the study was to determine the prevalence of anxiety and depression symptoms among Norwegian priests and to examine their associations with effort-reward imbalance (ERI) and overcommitment. Eight hundred four priests in the Norwegian Church completed the Hospital Anxiety and Depression Scale (HADS), the Effort-Reward Imbalance Questionnaire (ERI-Q), and the Intrinsic Effort Scale, measuring overcommitment. A significant proportion of the priests (23.4%) had HADS scores indicating a possible anxiety problem. Somewhat fewer had depression problems (9.3%). Both anxiety and depression difficulties were associated with an imbalance between effort given and rewards received at work. Priests characterized by a combination of this imbalance and high scores on overcommitment had more anxiety and depression symptoms. There is a higher occurrence of mental health challenges among priests than among the regular population. This applies in particular to anxiety symptoms measured by the HADS. These findings also indicate that it may be fruitful to explore mental health conditions among priests who report different combinations of effort-reward and overcommitment.

  13. Analysis of the impact of imbalance settlement design on market behaviour in electricity balancing markets

    NARCIS (Netherlands)

    Van der Veen, R.A.C.; Abbasy, A.; Hakvoort, R.A.

    2010-01-01

    The imbalance settlement design is the part of an electricity balancing market design that stimulates so-called Balance Responsible Parties (BRPs) to balance their electricity production and consumption portfolio and to stick to their energy schedules by penalizing any deviations from these

  14. Studies of generalized elemental imbalances in neurological disease patients using INAA [instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Ehmann, W.D.; Vance, D.E.; Khare, S.S.; Kasarskis, E.J.; Markesbery, W.R.

    1988-01-01

    Evidence has been presented in the literature to implicate trace elements in the etiology of several age-related neurological diseases. Most of these studies are based on brain analyses. Using instrumental neutron activation analysis (INAA), we have observed trace element imbalances in brains of patients with Alzheimer's disease, amyotrophic lateral sclerosis (ALS), and Picks's disease. The most prevalent elemental imbalances found in the brain were for bromine, mercury, and the alkali metals. In this study the authors report INAA studies of trace elements in nonneural tissues from Alzheimer's disease and ALS patients. Samples from household relatives were collected for use as controls wherever possible. Hair samples were washed according to the International Atomic Energy Agency recommended procedure. Fingernail samples were scraped with a quartz knife prior to washing by the same procedure. For ALS patients, blood samples were also collected. These data indicate that elemental imbalances in Alzheimer's disease and ALS are not restricted to the brain. Many elements perturbed in the brain are also altered in the several nonneural tissues examined to date. The imbalances in different tissues, however, are not always in the same direction. The changes observed may represent causes, effects, or simply epiphenomena. Longitudinal studies of nonneural tissues and blood, as well as tissue microprobe analyses at the cellular and subcellular level, will be required in order to better assess the role of trace elements in the etiology of these diseases

  15. An Enhanced Islanding Microgrid Reactive Power, Imbalance Power, and Harmonic Power Sharing Scheme

    DEFF Research Database (Denmark)

    He, Jinwei; Lin, Yun Wei; Blaabjerg, Frede

    2015-01-01

    To address inaccurate power sharing problems in autonomous islanding microgrids, an enhanced droop control method through online virtual impedance adjustment is proposed. First, a term associated with DG reactive power, imbalance power, or harmonic power is added to the conventional real power...

  16. Ocean heat content and Earth's radiation imbalance. II. Relation to climate shifts

    International Nuclear Information System (INIS)

    Douglass, D.H.; Knox, R.S.

    2012-01-01

    In an earlier study of ocean heat content (OHC) we showed that Earth's empirically implied radiation imbalance has undergone abrupt changes. Other studies have identified additional such climate shifts since 1950. The shifts can be correlated with features in recently updated OHC data. The implied radiation imbalance may possibly alternate in sign at dates close to the climate shifts. The most recent shifts occurred during 2001–2002 and 2008–2009. The implied radiation imbalance between these dates, in the direction of ocean heat loss, was −0.03±0.06 W/m 2 , with a possible systematic error of [−0.00,+0.09] W/m 2 . -- Highlights: ► Ocean heat content (OHC) slope discontinuities match similar Earth climate features. ► OHC slopes between climate shifts give most of the implied radiation balance (IRI). ► IRI often alternates in sign at dates close to the climate shifts. ► IRI between climate shifts of 2001–2002 and 2008–2009 was −0.03±0.06 W/m 2 . ► Geothermal flux is relevant to analyses of radiation imbalance.

  17. Repetition and Power Imbalance in Bullying Victimization at School. Data Point. NCES 2018-093

    Science.gov (United States)

    Lessne, Deborah; Yanez, Christine

    2018-01-01

    For the 2014-2015 school year, 20.8 percent of students reported being bullied at school. This report examines these students' experiences of bullying by repetition and power imbalance, two components of the Center for Disease Control and Prevention's (CDC) uniform definition of bullying. The report reviews the association of these components with…

  18. Neurohormonal Imbalance: A Neglected Problem-And Potential Therapeutic Target-In Acute Heart Failure.

    Science.gov (United States)

    Goldsmith, Steven R; Bart, Bradley A; Pin A, Ileana L

    2017-12-16

    Decompensated or acute heart failure (AHF) is characterized by increased ventricular and atrial pressures which may lead to and be caused by circulatory congestion. Unless due to a primary decrease in cardiac function, congestion arises from volume expansion or vasoconstriction. In turn, volume expansion and vasoconstriction are due to neurohormonal imbalance since both result from activation of the sympathetic nervous system, the renin-angiotensin-aldosterone axis and excess secretion of arginine vasopressin. Outcomes in AHF remain dismal. Loop diuretics are the mainstay of therapy for AHF and may themselves aggravate neurohormonal imbalance. No adjunctive pharmacotherapy has yielded improvement in outcomes in AHF despite many attempts with various vasodilators and inotropes. We, therefore, propose that insufficient attention has been paid to neurohormonal imbalance in AHF. As in chronic HF, rectifying the effects of neurohormonal imbalance may lead to better outcomes. The use of alternative decongestive strategies or adjunctive pharmacotherapy directed at neurohormonal activation could yield benefit. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Effects of interaction imbalance in a strongly repulsive one-dimensional Bose gas

    DEFF Research Database (Denmark)

    Barfknecht, Rafael Emilio; Zinner, Nikolaj Thomas; Foerster, Angela

    2018-01-01

    We calculate the spatial distributions and the dynamics of a few-body two-component strongly interacting Bose gas confined to an effectively one-dimensional trapping potential. We describe the densities for each component in the trap for different interaction and population imbalances. We calculate...

  20. Charge imbalance waves and nonequilibrium dynamics near a superconducting phase-slip center

    International Nuclear Information System (INIS)

    Kadin, A.M.; Smith, L.N.; Skocpol, W.J.

    1980-01-01

    Using a generalized two-fluid picture to describe a quasi-one-dimensional superconductor near T/sub c/, we provide a heuristic derivation for a set of equations governing the temporal and spatial evolution of the charge imbalance (or branch imbalance) in the quasiparticles. We show that these equations are isomorphic to those that describe a simple electrical transmission line, so that charge imbalance waves may propagate in the superconductor in analogy with electrical signals that propagate down the transmission line. We propose as a model for a phase-slip center in a superconducting filament a localized Josephson oscillator coupled to the transmission line. Applying standard transmission-line theory to solve the problem, we show that the Josephson oscillations in the center generate charge imbalance waves that the propagate out to a frequency-dependent distance of the order of the quasiparticle diffusion length GAMMA/sub Q/*= (Dtau/sub Q/*)/sup 1/2/ before they damp out. The time-averaged behavior of the model reduces to the earlier model of Skocpol, Beasley, and Tinkham. A novel consequence of the model is a prediction of intrinsic hysteresis in the dc current--voltage relation. The model also provides a convenient framework for dealing with ac effects in phase-slip centers, including resonance and synchronization in systems of closely spaced phase-slip centers and microbridges

  1. Studies of trace element imbalances in Alzheimer's disease using sequential NAA

    International Nuclear Information System (INIS)

    Ehmann, W.D.; Markesbery, W.R.; Thompson, C.M.; Vance, D.E.; Mao, Y.

    1986-01-01

    Evidence has accumulated in the literature that trace elements may be implicated in the etiology of Alzheimer's disease (AD) and other age-related neurological diseases. Even if elemental imbalances do not prove to be causative factors, observed perturbations may be markers that could aid in diagnosis, or help elucidate pathological processes. In this paper the authors present new data for trace element levels in three areas of the human brain most severely affected by AD (hippocampus, amygdala, and nucleus basalis) and in AD hair and nail samples. In some cases the specific imbalances seen previously in the bulk brain analyses are amplified in these regions. Elevated bromine levels seen in AD brain are also observed in AD hair and nail. Significant alkali metal and mercury imbalances with respect to controls occur in AD nail samples. The role of these trace element alterations in the etiology of AD has still not been determined. However, some possible physiological effects include: membrane dysfunction (alkali metals), enzyme inhibition (mercury and bromine), and interference with neurotransmitter functions (mercury, bromine, and alkali metals). The simultaneous multielement capability of this sequential NAA procedure also permits interelement correlation studies. Elemental associations may help identify potential environmental factors that could contribute to the observed trace element imbalances

  2. Economic concepts to address future water supply-demand imbalances in Iran, Morocco and Saudi Arabia

    NARCIS (Netherlands)

    Hellegers, P.J.G.J.; Immerzeel, W.; Droogers, P.

    2013-01-01

    In Middle East and North Africa (MENA) countries, renewable groundwater and surface water supply are limited while demand for water is growing rapidly. Climate change is expected to increase water demand even further. The main aim of this paper is to evaluate the water supply–demand imbalances in

  3. A Novel DBC Layout for Current Imbalance Mitigation in SiC MOSFET Multichip Power Modules

    DEFF Research Database (Denmark)

    Li, Helong; Munk-Nielsen, Stig; Beczkowski, Szymon

    2016-01-01

    This letter proposes a novel direct bonded copper (DBC) layout for mitigating the current imbalance among the paralleled SiC MOSFET dies in multichip power modules. Compared to the traditional layout, the proposed DBC layout significantly reduces the circuit mismatch and current coupling effect...

  4. An accurate autonomous islanding microgrid reactive power, imbalance power and harmonic power sharing scheme

    DEFF Research Database (Denmark)

    He, Jinwei; Li, Yun Wei; Blaabjerg, Frede

    2013-01-01

    To address inaccurate power sharing problems in autonomous islanding microgrids, an enhanced droop control method through adaptive virtual impedance adjustment is proposed. First, a term associated with DG reactive power, imbalance power or harmonic power is added to the conventional real power...

  5. The impact of effort-reward imbalance and learning motivation on teachers' sickness absence.

    Science.gov (United States)

    Derycke, Hanne; Vlerick, Peter; Van de Ven, Bart; Rots, Isabel; Clays, Els

    2013-02-01

    The aim of this study was to analyse the impact of the effort-reward imbalance and learning motivation on sickness absence duration and sickness absence frequency among beginning teachers in Flanders (Belgium). A total of 603 teachers, who recently graduated, participated in this study. Effort-reward imbalance and learning motivation were assessed by means of self-administered questionnaires. Prospective data of registered sickness absence during 12 months follow-up were collected. Multivariate logistic regression analyses were performed. An imbalance between high efforts and low rewards (extrinsic hypothesis) was associated with longer sickness absence duration and more frequent absences. A low level of learning motivation (intrinsic hypothesis) was not associated with longer sickness absence duration but was significantly positively associated with sickness absence frequency. No significant results were obtained for the interaction hypothesis between imbalance and learning motivation. Further research is needed to deepen our understanding of the impact of psychosocial work conditions and personal resources on both sickness absence duration and frequency. Specifically, attention could be given to optimizing or reducing efforts spent at work, increasing rewards and stimulating learning motivation to influence sickness absence. Copyright © 2012 John Wiley & Sons, Ltd.

  6. Reviewing the effort-reward imbalance model: drawing up the balance of 45 empirical studies

    NARCIS (Netherlands)

    Vegchel, van N.; Jonge, de J.; Bosma, H.; Schaufeli, W.B.

    2005-01-01

    The present paper provides a review of 45 studies on the Effort–Reward Imbalance (ERI) Model published from 1986 to 2003 (inclusive). In 1986, the ERI Model was introduced by Siegrist et al. (Biological and Psychological Factors in Cardiovascular Disease, Springer, Berlin, 1986, pp. 104–126; Social

  7. Relationship between effort-reward imbalance and hair cortisol concentration in female kindergarten teachers

    NARCIS (Netherlands)

    Qi, Xingliang; Zhang, Jing; Liu, Yapeng; Ji, Shuang; Chen, Zheng; Sluiter, Judith K.; Deng, Huihua

    2014-01-01

    The present study aims to investigate the relationship between effort-reward imbalance and hair cortisol concentration among teachers to examine whether hair cortisol can be a biomarker of chronic work stress. Hair samples were collected from 39 female teachers from three kindergartens. Cortisol was

  8. Beyond excitation/inhibition imbalance in multidimensional models of neural circuit changes in brain disorders.

    Science.gov (United States)

    O'Donnell, Cian; Gonçalves, J Tiago; Portera-Cailliau, Carlos; Sejnowski, Terrence J

    2017-10-11

    A leading theory holds that neurodevelopmental brain disorders arise from imbalances in excitatory and inhibitory (E/I) brain circuitry. However, it is unclear whether this one-dimensional model is rich enough to capture the multiple neural circuit alterations underlying brain disorders. Here, we combined computational simulations with analysis of in vivo two-photon Ca 2+ imaging data from somatosensory cortex of Fmr1 knock-out (KO) mice, a model of Fragile-X Syndrome, to test the E/I imbalance theory. We found that: (1) The E/I imbalance model cannot account for joint alterations in the observed neural firing rates and correlations; (2) Neural circuit function is vastly more sensitive to changes in some cellular components over others; (3) The direction of circuit alterations in Fmr1 KO mice changes across development. These findings suggest that the basic E/I imbalance model should be updated to higher dimensional models that can better capture the multidimensional computational functions of neural circuits.

  9. Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

    Science.gov (United States)

    Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

    2014-01-01

    The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. HLA class II alleles and the presence of circulating Epstein-Barr virus DNA in greek patients with nasopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Karanikiotis, C.; Daniilidis, M.; Karyotis, N.; Nikolaou, A.; Bakogiannis, C.; Economopoulos, T.; Murray, S.; Papamichael, D.; Samantas, E.; Skoura, L.; Tselis, N.; Zamboglou, N.; Fountzilas, G.

    2008-01-01

    Background and purpose: nasopharyngeal carcinoma (NPC) represents a seldom malignancy in most developed countries. Nevertheless, NPC receives an endemic form in concrete racial entities. The aims of this study were to detect the presence of Epstein-Barr virus DNA (EBV-DNA) in peripheral blood of NPC patients, to molecularly define human leukocyte antigens (HLA) DRB1*, DQA1* and DQB1* allele frequencies, and, finally, to determine whether the genetic predisposition of an individual to NPC depends on the liability to EBV infection. Patients and methods: a total of 101 patients of Hellenic origin and nationality, with histologically proven NPC, participated in this study. EBV-DNA detection was also applied in 66 patients with EBV-related malignancies (Hodgkin's [HL] and non-Hodgkin's lymphoma [NHL]) and infectious mononucleosis (IM), as well as in 80 healthy EBV-seropositive controls. Results: 81% of the NPC patients, 77.8% with HL, 72.2% with NHL, and 66.7% with IM were EBV-DNA positive, whereas the EBV genome was detected only in 15% of the healthy controls. These differences were statistically significant in all cases. Analysis of HLA class II antigens showed decreased frequency of the DRB1*07 (p 0.003), DQA1*0103 (p = 0.002), and DQA1*0201 (p = 0.003) alleles among NPC patients. A significant association between the HLA-DR/DQ alleles and the presence of EBV-DNA in peripheral whole blood was not established. Conclusion: circulating EBV-DNA and specific HLA class II alleles may predispose to or protect from NPC. However, the results of this study suggest that the genetic predisposition of an individual to NPC is independent of the liability to EBV infection. (orig.)

  11. HLA class II alleles and the presence of circulating Epstein-Barr virus DNA in greek patients with nasopharyngeal carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Karanikiotis, C. [424 Army General Hospital, Thessaloniki (Greece); Daniilidis, M.; Karyotis, N.; Nikolaou, A. [AHEPA Hospital, Aristotle Univ. of Thessaloniki School of Medicine (Greece); Bakogiannis, C. [Hygeia Hospital, Athens (Greece); Economopoulos, T. [' Attikon' Univ. Hospital, Athens (Greece); Murray, S. [Metropolitan Hospital, Athens (Greece); Papamichael, D. [Bank of Cyprus Oncology Center, Nicosia, Cyprus (Greece); Samantas, E. [' Agii Anargiri' Cancer Hospital, Athens (Greece); Skoura, L. [' Hippokration' Hospital, Thessaloniki (Greece); Tselis, N.; Zamboglou, N. [Dept. of Radiotherapy, Offenbach Hospital (Germany); Fountzilas, G. [' Papageorgiou' Hospital, Aristotle Univ. of Thessaloniki School of Medicine (Greece)

    2008-06-15

    Background and purpose: nasopharyngeal carcinoma (NPC) represents a seldom malignancy in most developed countries. Nevertheless, NPC receives an endemic form in concrete racial entities. The aims of this study were to detect the presence of Epstein-Barr virus DNA (EBV-DNA) in peripheral blood of NPC patients, to molecularly define human leukocyte antigens (HLA) DRB1*, DQA1* and DQB1* allele frequencies, and, finally, to determine whether the genetic predisposition of an individual to NPC depends on the liability to EBV infection. Patients and methods: a total of 101 patients of Hellenic origin and nationality, with histologically proven NPC, participated in this study. EBV-DNA detection was also applied in 66 patients with EBV-related malignancies (Hodgkin's [HL] and non-Hodgkin's lymphoma [NHL]) and infectious mononucleosis (IM), as well as in 80 healthy EBV-seropositive controls. Results: 81% of the NPC patients, 77.8% with HL, 72.2% with NHL, and 66.7% with IM were EBV-DNA positive, whereas the EBV genome was detected only in 15% of the healthy controls. These differences were statistically significant in all cases. Analysis of HLA class II antigens showed decreased frequency of the DRB1*07 (p = 0.003), DQA1*0103 (p = 0.002), and DQA1*0201 (p = 0.003) alleles among NPC patients. A significant association between the HLA-DR/DQ alleles and the presence of EBV-DNA in peripheral whole blood was not established. Conclusion: circulating EBV-DNA and specific HLA class II alleles may predispose to or protect from NPC. However, the results of this study suggest that the genetic predisposition of an individual to NPC is independent of the liability to EBV infection. (orig.)

  12. The Study of Morphological Traits and Identification of Self-incompatibility Alleles in Almond Cultivars and Genotypes

    Directory of Open Access Journals (Sweden)

    Mousa Rasouli

    2017-12-01

    Full Text Available The evaluation of an almond collection using morphological variables and identification of self-incompatibility genotype  is useful for selecting pollinizers and for the design of crossing in almond breeding programs. In this study, important morphological traits and self-incompatibilities in 71 almond cultivars and genotypes were studied. Simple and multiplex specific PCR analyses were used in order to identify self-incompatibility alleles. Based on the results, cultivars and genotypes including ‘Dir Ras–e-Savojbolagh’, ‘D-124’, ‘D-99’, ‘Shahrood 12’, ‘Tuono’, ‘Nonpareil’, ‘Price’, ‘Mirpanj-e-Tehran’, ‘Pakotahe-e- Taleghan’, ‘V-13-34’, ‘V-16-8, ‘V-11-10’, ‘Zarghan 10’, ‘Uromiyeh 68’, ‘Barg dorosht-e-Hamedan’ and ‘Yazd 60’ were late flowering and had the highest quality of nut and kernel characters. The result of the PCR method using combined primers AS1II and AmyC5R showed amplification of ten self-incompatibility alleles (S1, S2, S3, S5, S6, S7, S8, S10, S12,and S unknown allele and three Sfalleles. Moreover, S1 had the highest frequencies in comparison with other known S-alleles. Also, unknown alleles with different sizes were detected and 58 new bands were found in some cultivars.

  13. Examining Longitudinal Relationship among Effort Reward Imbalance, Coping Strategies and Academic Burnout in Korean Middle School Students

    Science.gov (United States)

    Kim, Boyoung; Kim, Eunjoo; Lee, Sang Min

    2017-01-01

    The present study examined the longitudinal relationship between effort-reward imbalance as a stressor and academic burnout as a strain. The study also examined the moderation effect of coping strategies, a problem-focused coping and an emotion-focused coping, in the relationship between effort-reward imbalance as a stressor and middle school…

  14. Optimizing imbalance and loss in 2 x 2 3dB multimode interference couplers via access waveguide width

    NARCIS (Netherlands)

    Hill, M.T.; Leijtens, X.J.M.; Khoe, G.D.; Smit, M.K.

    2003-01-01

    The imbalance and excess loss in multimode interference couplers with fabrication errors are examined. Remarkably, there exists a number of optimum access waveguide widths which give a minimum imbalance. Furthermore, quite low excess loss can be simultaneously achieved by choosing one particular

  15. TRPV6 alleles do not influence prostate cancer progression

    International Nuclear Information System (INIS)

    Kessler, Thorsten; Wissenbach, Ulrich; Grobholz, Rainer; Flockerzi, Veit

    2009-01-01

    The transient receptor potential, subfamily V, member 6 (TRPV6) is a Ca 2+ selective cation channel. Several studies have shown that TRPV6 transcripts are expressed in locally advanced prostatic adenocarcinoma, metastatic and androgen-insensitive prostatic lesions but are undetectable in healthy prostate tissue and benign prostatic hyperplasia. Two allelic variants of the human trpv6 gene have been identified which are transcribed into two independent mRNAs, TRPV6a and TRPV6b. We now asked, whether the trpv6a allele is correlated with the onset of prostate cancer, with the Gleason score and the tumour stage. Genomic DNA of prostate cancer patients and control individuals was isolated from resections of prostatic adenocarcinomas and salivary fluid respectively. Genotyping of SNPs of the TRPV6 gene was performed by restriction length polymorphism or by sequencing analysis. RNA used for RT-PCR was isolated from prostate tissue. Data sets were analyzed by Chi-Square test. We first characterized in detail the five polymorphisms present in the protein coding exons of the trpv6 gene and show that these polymorphisms are coupled and are underlying the TRPV6a and the TRPV6b variants. Next we analysed the frequencies of the two TRPV6 alleles using genomic DNA from saliva samples of 169 healthy individuals. The homozygous TRPV6b genotype predominated with 86%, whereas no homozygous TRPV6a carriers could be identified. The International HapMap Project identified a similar frequency for an Utah based population whereas in an African population the a-genotype prevailed. The incidence of prostate cancer is several times higher in African populations than in non-African and we then investigated the TRPV6a/b frequencies in 141 samples of prostatic adenocarcinoma. The TRPV6b allele was found in 87% of the samples without correlation with Gleason score and tumour stage. Our results show that the frequencies of trpv6 alleles in healthy control individuals and prostate cancer patients

  16. TRPV6 alleles do not influence prostate cancer progression.

    Science.gov (United States)

    Kessler, Thorsten; Wissenbach, Ulrich; Grobholz, Rainer; Flockerzi, Veit

    2009-10-26

    The transient receptor potential, subfamily V, member 6 (TRPV6) is a Ca(2+) selective cation channel. Several studies have shown that TRPV6 transcripts are expressed in locally advanced prostatic adenocarcinoma, metastatic and androgen-insensitive prostatic lesions but are undetectable in healthy prostate tissue and benign prostatic hyperplasia. Two allelic variants of the human trpv6 gene have been identified which are transcribed into two independent mRNAs, TRPV6a and TRPV6b. We now asked, whether the trpv6a allele is correlated with the onset of prostate cancer, with the Gleason score and the tumour stage. Genomic DNA of prostate cancer patients and control individuals was isolated from resections of prostatic adenocarcinomas and salivary fluid respectively. Genotyping of SNPs of the TRPV6 gene was performed by restriction length polymorphism or by sequencing analysis. RNA used for RT-PCR was isolated from prostate tissue. Data sets were analyzed by Chi-Square test. We first characterized in detail the five polymorphisms present in the protein coding exons of the trpv6 gene and show that these polymorphisms are coupled and are underlying the TRPV6a and the TRPV6b variants. Next we analysed the frequencies of the two TRPV6 alleles using genomic DNA from saliva samples of 169 healthy individuals. The homozygous TRPV6b genotype predominated with 86%, whereas no homozygous TRPV6a carriers could be identified. The International HapMap Project identified a similar frequency for an Utah based population whereas in an African population the a-genotype prevailed. The incidence of prostate cancer is several times higher in African populations than in non-African and we then investigated the TRPV6a/b frequencies in 141 samples of prostatic adenocarcinoma. The TRPV6b allele was found in 87% of the samples without correlation with Gleason score and tumour stage. Our results show that the frequencies of trpv6 alleles in healthy control individuals and prostate cancer patients

  17. TRPV6 alleles do not influence prostate cancer progression

    Directory of Open Access Journals (Sweden)

    Flockerzi Veit

    2009-10-01

    Full Text Available Abstract Background The transient receptor potential, subfamily V, member 6 (TRPV6 is a Ca2+ selective cation channel. Several studies have shown that TRPV6 transcripts are expressed in locally advanced prostatic adenocarcinoma, metastatic and androgen-insensitive prostatic lesions but are undetectable in healthy prostate tissue and benign prostatic hyperplasia. Two allelic variants of the human trpv6 gene have been identified which are transcribed into two independent mRNAs, TRPV6a and TRPV6b. We now asked, whether the trpv6a allele is correlated with the onset of prostate cancer, with the Gleason score and the tumour stage. Methods Genomic DNA of prostate cancer patients and control individuals was isolated from resections of prostatic adenocarcinomas and salivary fluid respectively. Genotyping of SNPs of the TRPV6 gene was performed by restriction length polymorphism or by sequencing analysis. RNA used for RT-PCR was isolated from prostate tissue. Data sets were analyzed by Chi-Square test. Results We first characterized in detail the five polymorphisms present in the protein coding exons of the trpv6 gene and show that these polymorphisms are coupled and are underlying the TRPV6a and the TRPV6b variants. Next we analysed the frequencies of the two TRPV6 alleles using genomic DNA from saliva samples of 169 healthy individuals. The homozygous TRPV6b genotype predominated with 86%, whereas no homozygous TRPV6a carriers could be identified. The International HapMap Project identified a similar frequency for an Utah based population whereas in an African population the a-genotype prevailed. The incidence of prostate cancer is several times higher in African populations than in non-African and we then investigated the TRPV6a/b frequencies in 141 samples of prostatic adenocarcinoma. The TRPV6b allele was found in 87% of the samples without correlation with Gleason score and tumour stage. Conclusion Our results show that the frequencies of trpv6

  18. A new hybrid observer based rotor imbalance vibration control via passive autobalancer and active bearing actuation

    Science.gov (United States)

    Jung, DaeYi; DeSmidt, Hans

    2018-02-01

    Many researchers have explored the use of active bearings, such as non-contact Active Magnetic Bearings (AMB), to control imbalance vibration in rotor systems. Meanwhile, the advantages of a passive Auto-balancer device (ABD) eliminating the imbalance effect of rotor without using other active means have been recently studied. This paper develops a new hybrid imbalance vibration control approach for an ABD-rotor system supported by a normal passive bearing in augmented with an AMB to enhance the balancing and vibration isolation capabilities. Essentially, an ABD consists of several freely moving eccentric balancing masses mounted on the rotor, which, at supercritical operating speeds, act to cancel the rotor's imbalance at steady-state. However, due to the inherent nonlinearity of the ABD, the potential for other, non-synchronous limit-cycle behavior exists resulting in increased rotor vibration. To address this, the algorithm of proposed hybrid control is designed to guarantee globally asymptotic stability of the synchronous balanced condition. This algorithm also incorporates with a "Luenberger-like" observer that continuously estimates the states of a balancer ball circulating around within ABD. In particular, it is shown that the balanced equilibrium can be made globally attractive under the hybrid control strategy, and that the control power levels of AMB are significantly reduced via the addition of the ABD because the control is designed such that it is only switched on for the abnormal operation of ABD and will be disengaged otherwise. Moreover, unlike other imbalance vibration control applications based upon ABD such as rotor speed regulator [21,22], this approach enables the controller to achieve the desirable performance without altering rotor speed once the rotor initially reaches the target speed. These applications are relevant to limited power applications such as in satellite reaction wheels, flywheel energy storage batteries or CD-ROM application.

  19. Discrimination of acute ischemic stroke from nonischemic vertigo in patients presenting with only imbalance.

    Science.gov (United States)

    Honda, Shoji; Inatomi, Yuichiro; Yonehara, Toshiro; Hashimoto, Yoichiro; Hirano, Teruyuki; Ando, Yukio; Uchino, Makoto

    2014-01-01

    Some patients who present with an acute feeling of imbalance are experiencing an ischemic stroke that is not evident on computed tomography (CT) scans. The aim of this study was to compare ischemic stroke and nonischemic vertigo patient groups and to investigate independent factors associated with ischemic stroke. We examined 332 consecutive patients with an acute feeling of imbalance who showed no neurologic findings or responsible lesions on CT scan at the hyperacute phase. We examined their clinical backgrounds, physical findings, and laboratory examinations, with ischemic stroke diagnosed by later CT and/or magnetic resonance imaging (MRI). We identified 41 (12.3%) ischemic stroke patients. Atrial fibrillation (odds ratio 4.1; 95% confidence interval 1.4-11.5), white blood cell count (10(3)/μL, 1.4; 1.2-1.6), head and/or neck pain (4.6; 2.1-10.3), first attack of imbalance feeling (3.3; 1.1-12.2), and dizziness (3.7; 1.7-8.3) were significant and independent factors associated with ischemic stroke among patients with an acute feeling of imbalance. We used these factors to calculate an "imbalance score"; 1 point was given for the presence of each factor and a score of 3-5 points was independently associated with ischemic stroke. An awareness of these factors may indicate that further examinations including MRI are necessary to rule out ischemic stroke. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  20. Patterns of Energy Imbalance of the Meridians in Patients with Temporomandibular Dysfunction.

    Science.gov (United States)

    Rasera Zotelli, Vera L; Grillo, Cássia M; Bressiani Gil, Maria L; Wada, Ronaldo S; Sato, Jorge E; de Sousa, Maria da Luz R

    2018-02-01

    Temporomandibular dysfunction (TMD) is a set of changes that affects the muscles of mastication, temporomandibular joint, teeth, and associated periodontal and orofacial structures. According to Traditional Chinese Medicine, the imbalance of energy (Qi) circulating in the acupuncture meridians is always the primary etiologic cause of any physical manifestation. The aim of this study was to describe the patterns of Qi imbalance in patients with TMD by means of an objective measurement. The clinical study was conducted at the Piracicaba Dental School (FOP/Unicamp), in Piracicaba-SP, Brazil. We evaluated 40 adult volunteers with TMD. The Qi measurement was carried out by the researcher using the Ryodoraku method using 24 points representing the 12 acupuncture meridians: LU9 (Taiyuan), PC7 (Daling), HT7 (Shemen), SI5 (Yanggu), TE4 (Yangchi), LI5 (Yangxi), SP3 (Taibai), LR3 (Taichong), KI3 (Taixi), BL64 (Jinggu), GB40 (Qiuxu), and ST42 (Chongyang). The average total Qi of 40 volunteers (21.7 μA ± 1.5), was below the normal range (40-60 μA) and was classified as deficiency of Qi (empty). The coupled meridians that showed the highest Qi imbalance were the kidney (29.4 μA ± 2.8) and bladder (13.8 μA ± 1). The Qi planes with greatest imbalance were the Shao Yang and Shao Yin. In conclusion, volunteers with TMD presented a pattern of Qi deficiency, and the most prevalent imbalance patterns identified were in the kidney and bladder coupled meridians and in the energetic planes Shao Yin (heart/kidney) and Shao Yang (triple energizer/gall bladder). Copyright © 2017. Published by Elsevier B.V.