Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

PubMed Central

Rostoks, Nils; Ramsay, Luke; MacKenzie, Katrin; Cardle, Linda; Bhat, Prasanna R.; Roose, Mikeal L.; Svensson, Jan T.; Stein, Nils; Varshney, Rajeev K.; Marshall, David F.; Graner, Andreas; Close, Timothy J.; Waugh, Robbie

2006-01-01

Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs. PMID:17085595

Construction of a transfer vector for a clonal isolate of LdNPV

Treesearch

Shivanand T. Hiremath; Martha Fikes; Audrey Ichida

1991-01-01

Deoxyribonucleic acid from a clonal isolate of LdNPV (CI A2-1), obtained by in vivo cloning procedures, was used to construct genomic libraries in phage (lamda Gem 11) and cosmid (pHC79) vectors. Overlapping clones were selected to generate a restriction enzyme map. The restriction enzyme map, covering about 85% of the CI A2-1 genome, was determined...

Temporal analysis and spatial mapping of Lymantria dispar nuclear polyhedrosis virus transcripts and in-vitro translation products

Treesearch

James M. Slavicek; Nancy Hayes-Plazolles

1991-01-01

The Lymantria dispar nuclear polyhedrosis virus LdNPV) is being used as a biopesticide against the gypsy moth. We are attempting to enhance the potency of the LdNPV through recombinant DNA technology. As a prerequisite to genetic manipulation, we have characterized LdNPV gene expression in cell culture through the generation of transcription and...

Developing the Concept of Perimeter and Area in Students with Learning Disabilities (LD)

ERIC Educational Resources Information Center

Kozulin, Alex; Kazaz, Sigalit

2017-01-01

The present research is aimed at developing an educational program effective for the development of the concepts of perimeter and area in students with LD and testing this program. The study combined action research with quasi-experimental design involving experimental (LD) and comparison (non-LD) groups. The intervention program consisted of 12…

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

PubMed

Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

2008-12-01

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.

Comparison of the Performance of College Students Classified as ADHD, LD, and LD/ADHD in Foreign Language Courses

ERIC Educational Resources Information Center

Sparks, Richard L.; Javorsky, James; Philips, Lois

2005-01-01

In this study, college students classified as having attention deficit hyperactivity disorder (ADHD) who had fulfilled the foreign language (FL) requirement were compared with students classified as learning disabled (LD) or both LD and ADHD who had either substituted courses for the college FL requirement petition or had passed FL courses…

First-Year College Students with ADHD And/or LD: Differences in Engagement, Positive Core Self-Evaluation, School Preparation, and College Expectations

ERIC Educational Resources Information Center

DuPaul, George J.; Pinho, Trevor D.; Pollack, Brittany L.; Gormley, Matthew J.; Laracy, Seth D.

2017-01-01

Students with attention-deficit/hyperactivity disorder (ADHD) and/or learning disabilities (LD) experience significant challenges in making the transition from high school to college. This study examined the ways first-year college students with ADHD, LD, ADHD+LD, and comparison peers differ in engagement, core self-evaluation, high school…

Academic procrastination, emotional intelligence, academic self-efficacy, and GPA: a comparison between students with and without learning disabilities.

PubMed

Hen, Meirav; Goroshit, Marina

2014-01-01

Academic procrastination has been seen as an impediment to students' academic success. Research findings suggest that it is related to lower levels of self-regulated learning and academic self-efficacy and associated with higher levels of anxiety, stress, and illness. Emotional intelligence (EI) is the ability to assess, regulate, and utilize emotions and has been found to be associated with academic self-efficacy and a variety of better outcomes, including academic performance. Students with learning disabilities (LD) are well acquainted with academic difficulty and maladaptive academic behavior. In comparison to students without LD, they exhibit high levels of learned helplessness, including diminished persistence, lower academic expectations, and negative affect. This study examined the relationships among academic procrastination, EI, and academic performance as mediated by academic self-efficacy in 287 LD and non-LD students. Results indicated that the indirect effect of EI on academic procrastination and GPA was stronger in LD students than in non-LD students. In addition, results indicated that LD students scored lower than non-LD students on both EI and academic self-efficacy and higher on academic procrastination. No difference was found in GPA.

Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel.

PubMed

Sela, Hanan; Ezrati, Smadar; Ben-Yehuda, Pnina; Manisterski, Jacob; Akhunov, Eduard; Dvorak, Jan; Breiman, Adina; Korol, Abraham

2014-11-01

Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new stripe rust resistance genes were found. Genome-wide association mapping (GWAM) is becoming an important tool for the discovery and mapping of loci underlying trait variation in crops, but in the wild relatives of crops the use of GWAM has been limited. Critical factors for the use of GWAM are the levels of linkage disequilibrium (LD) and genetic diversity in mapped populations, particularly in those of self-pollinating species. Here, we report LD estimation in a population of 128 accessions of self-pollinating wild emmer, Triticum turgidum ssp. dicoccoides, the progenitor of cultivated wheat, collected in Israel. LD decayed fast along wild emmer chromosomes and reached the background level within 1 cM. We employed GWAM for the discovery and mapping of genes for resistance to three isolates of Puccinia striiformis, the causative agent of wheat stripe rust. The wild emmer population was genotyped with the wheat iSelect assay including 8643 gene-associated SNP markers (wheat 9K Infinium) of which 2,278 were polymorphic. The significance of association between stripe rust resistance and each of the polymorphic SNP was tested using mixed linear model implemented in EMMA software. The model produced satisfactory results and uncovered four significant associations on chromosome arms 1BS, 1BL and 3AL. The locus on 1BS was located in a region known to contain stripe rust resistance genes. These results show that GWAM is an effective strategy for gene discovery and mapping in wild emmer that will accelerate the utilization of this genetic resource in wheat breeding.

Biogeochemistry and Spatial Distribution of the Microbial-Mineral Interface Using I2LD-FTMS

NASA Astrophysics Data System (ADS)

Scott, J. R.; Kauffman, M. E.; Kauffman, M. E.; Tremblay, P. L.

2001-12-01

Previous studies indicate that biogeochemistry can vary within individual mineral specimens in contact with microorganisms. These same studies have shown that microcosms containing a mixture of minerals simulating a heterogeneous geologic matrix do not yield the same results as the naturally occurring rock. Therefore, it is of utmost importance to develop analytical tools that can provide spatially correlative biogeochemical data of the microbial-mineral interface within naturally occurring geologic matrices. Imaging internal laser desorption Fourier transform mass spectrometry (I2LD-FTMS) can provide elemental and molecular information of the microbial-mineral interface at a spatial resolution limited only by the optical diffraction limit of the final focusing lens (down to 2 μ m). Additionally, the I2LD-FTMS used in this study has exceptional reproducibility, which can provide successive mapping sequences for depth-profiling studies. Basalt core samples, taken from the Snake River Plain Aquifer in southeastern Idaho, were mapped prior to, and after, exposure to a bacterial culture. The bacteria-basalt interface spectra were collected using the I2LD-FTMS at the INEEL. Mass spectra were recorded over a mass-to-charge range of 30-2500 Da with an average peak resolution of 15,000 using 10 μ m spots. Two-dimensional maps were constructed depicting the spatial distribution of the minerals within the basalt as well as the spatial distribution of the bacteria on the basalt surface. This represents the first reported application of I2LD-FTMS in the field of biogeochemistry.

Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups.

PubMed

Chopra, Rupali; Ali, Shafat; Srivastava, Amit K; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K; Bhattacharya, Sambit N; Bamezai, Rameshwar N K

2013-01-01

Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations.

Mapping of PARK2 and PACRG Overlapping Regulatory Region Reveals LD Structure and Functional Variants in Association with Leprosy in Unrelated Indian Population Groups

PubMed Central

Chopra, Rupali; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K.; Bhattacharya, Sambit N.; Bamezai, Rameshwar N. K.

2013-01-01

Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations. PMID:23861666

A Comparison of Two Instructional Methods for Teaching Logo to Learning Disabled and Nonlearning Disabled Children.

ERIC Educational Resources Information Center

Mathinos, Debra A.; Leonard, Ann Scheier

The study examines the use of LOGO, a computer language, with 19 learning disabled (LD) and 19 non-LD students in grades 4-6. Ss were randomly assigned to one of two instructional groups: sequential or whole-task, each with 10 LD and 10 non-LD students. The sequential method features a carefully ordered plan for teaching LOGO commands; the…

A synthesis of mathematical and cognitive performances of students with mathematics learning disabilities.

PubMed

Shin, Mikyung; Bryant, Diane Pedrotty

2015-01-01

The purpose of this study was to synthesize the findings from 23 articles that compared the mathematical and cognitive performances of students with mathematics learning disabilities (LD) to (a) students with LD in mathematics and reading, (b) age- or grade-matched students with no LD, and (c) mathematical-ability-matched younger students with no LD. Overall results revealed that students with mathematics LD exhibited higher word problem-solving abilities and no significant group differences on working memory, long-term memory, and metacognition measures compared to students with LD in mathematics and reading. Findings also revealed students with mathematics LD demonstrated significantly lower performance compared to age- or grade-matched students with no LD on both mathematical and cognitive measures. Comparison between students with mathematics LD and younger students with no LD revealed mixed outcomes on mathematical measures and generally no significant group differences on cognitive measures. © Hammill Institute on Disabilities 2013.

Multilocus Association Mapping Using Variable-Length Markov Chains

PubMed Central

Browning, Sharon R.

2006-01-01

I propose a new method for association-based gene mapping that makes powerful use of multilocus data, is computationally efficient, and is straightforward to apply over large genomic regions. The approach is based on the fitting of variable-length Markov chain models, which automatically adapt to the degree of linkage disequilibrium (LD) between markers to create a parsimonious model for the LD structure. Edges of the fitted graph are tested for association with trait status. This approach can be thought of as haplotype testing with sophisticated windowing that accounts for extent of LD to reduce degrees of freedom and number of tests while maximizing information. I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests. PMID:16685642

Multilocus association mapping using variable-length Markov chains.

PubMed

Browning, Sharon R

2006-06-01

I propose a new method for association-based gene mapping that makes powerful use of multilocus data, is computationally efficient, and is straightforward to apply over large genomic regions. The approach is based on the fitting of variable-length Markov chain models, which automatically adapt to the degree of linkage disequilibrium (LD) between markers to create a parsimonious model for the LD structure. Edges of the fitted graph are tested for association with trait status. This approach can be thought of as haplotype testing with sophisticated windowing that accounts for extent of LD to reduce degrees of freedom and number of tests while maximizing information. I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests.

Genome-wide proteomics analysis on longissimus muscles in Qinchuan beef cattle.

PubMed

He, Hua; Chen, Si; Liang, Wei; Liu, Xiaolin

2017-04-01

To gain further insight into the molecular mechanism of bovine muscle development, we combined mass spectrometry characterization of proteins with Illumina deep sequencing of RNAs obtained from bovine longissimus muscle (LD) at prenatal and postnatal stages. For the proteomic study, each group of LD proteins was extracted and labeled using isobaric tags for relative and absolute quantitation (iTRAQ) method. Among the 1321 proteins identified from six samples, 390 proteins were differentially expressed in embryos at day 135 post-fertilization (Emb135d) vs. 30-month-old adult cattle (Emb135d vs. 30M) samples. Gene Ontology, Cluster of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes analyses were further conducted to better understand the different functions. Furthermore, we analyzed the relationship between transcript and protein regulation between samples by direct comparison of expression levels from transcriptomic and iTRAQ-based proteomics. Association results indicated that 1295 of 1321 proteins could be mapped to transcriptome sequencing data. This study provides the most comprehensive, targeted survey of bovine LD proteins to date and has shown the power of combining transcriptomic and proteomic approaches to provide molecular insights for understanding the developmental characteristics in bovine muscle, and even in other mammals. © 2016 Stichting International Foundation for Animal Genetics.

Leadership Development and Language Learning: A Foundational Framework

ERIC Educational Resources Information Center

Long, Sheri Spaine; Derby, LeAnn; Scharff, Lauren; LeLoup, Jean W.; Uribe, Daniel

2015-01-01

The ACTFL [American Council on the Teaching of Foreign Languages] 21st Century Skills Map (2011) proposes incorporating "leadership and responsibility" into language learning (LL). This study offers a foundational framework for combined LL and leadership development (LD) and contains a snapshot of the presence of LD in the language…

Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

PubMed Central

Abdallah, Jihad M; Goffinet, Bruno; Cierco-Ayrolles, Christine; Pérez-Enciso, Miguel

2003-01-01

Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance. PMID:12939203

Learning Disabilities and Anxiety: A Meta-Analysis

ERIC Educational Resources Information Center

Nelson, Jason M.; Harwood, Hannah

2011-01-01

This article presents the results of a meta-analysis of the empirical literature on anxious symptomatology among school-aged students with learning disabilities (LD) in comparison to their non-LD peers. Fifty-eight studies met inclusion criteria. Results indicate that students with LD had higher mean scores on measures of anxiety than did non-LD…

Syntactic and Reading Abilities in Normal and Learning Disabled Junior High School Students.

ERIC Educational Resources Information Center

Ferraro, Mary F.; Doyle, Beverly A.

The study involving 12 learning disabled (LD) junior high school students investigated whether LD students with reading comprehension difficulties were deficient in syntactic abilities as compared to normal students. Syntactic and reading tests were administered to each student. Comparison of the scores between the two groups showed that LD Ss…

Mechanical and wear characteristics of epoxy composites filled with industrial wastes: A comparative study

NASA Astrophysics Data System (ADS)

Purohit, A.; Satapathy, A.

2017-02-01

Use of industrial wastes, such as slag and sludge particles, as filler in polymers is not very common in the field of composite research. Therefore in this paper, a comparison of mechanical characteristics of epoxy based composites filled with LD sludge, BF slag and LD slag (wastes generated in iron and steel industries) were presented. A comparative study among these composites in regard to their dry sliding wear characteristics under similar test conditions was also included. Composites with different weight proportions (0, 5, 10, 15 and 20 wt.%) of LD sludge were fabricated by solution casting technique. Mechanical properties were evaluated as per ASTM test standards and sliding wear test was performed following a design of experiment approach based on Taguchi’s orthogonal array. The test results for epoxy-LD sludge composites were compared with those of epoxy-BF slag and epoxy-LD slag composites reported by previous investigators. The comparison reveals that epoxy filled with LD sludge exhibits superior mechanical and wear characteristics among the three types of composites considered in this study.

A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.

PubMed

De La Vega, Francisco M; Isaac, Hadar I; Scafe, Charles R

2006-01-01

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan SNP Genotyping Assays or the SNPlex Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.

The Social Acceptance of Secondary School Students with Learning Disabilities (LD)

ERIC Educational Resources Information Center

Lorger, Teja; Schmidt, Majda; Vukman, Karin Bakracevic

2015-01-01

This paper aims to shed light on the level of social acceptance among students with learning disabilities (LD) in various secondary school vocational programs in comparison with their peers without disabilities. Our findings are based on an empirical study that comprised 417 students, of whom 85 were students with LD. Based on sociometric analyses…

Cgl2 plays an essential role in cuticular wax biosynthesis in cabbage (Brassica oleracea L. var. capitata).

PubMed

Liu, Dongming; Tang, Jun; Liu, Zezhou; Dong, Xin; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao; Sun, Peitian; Liu, Yumei; Li, Zhansheng; Ye, Zhibiao; Fang, Zhiyuan; Yang, Limei

2017-11-28

The aerial parts of most land plants are covered with cuticular wax which is important for plants to avoid harmful factors. There is still no cloning study about wax synthesis gene of the alcohol-forming pathway in Brassica species. Scanning electron microscopy (SEM) showed that, compared with wild type (WT), wax crystal are severely reduced in both the adaxial and abaxial sides of cabbage (Brassica oleracea L. var. capitata L.) leaves from the LD10GL mutant. Genetic analysis results revealed that the glossy trait of LD10GL is controlled by a single recessive gene, and fine mapping results revealed that the target gene Cgl2 (Cabbage glossy 2) is located within a physical region of 170 kb on chromosome 1. Based on sequence analysis of the genes in the mapped region, the gene designated Bol013612 was speculated to be the candidate gene. Gene Bol013612 is homologous to Arabidopsis CER4, which encodes fatty acyl-coenzyme A reductase. Sequencing identified a single nucleotide substitution at an intron/exon boundary that results in an insertion of six nucleotides in the cDNA of Bol013612 in LD10GL. The phenotypic defect of LD10GL was confirmed by a functional complementation test with Arabidopsis mutant cer4. Our results indicated that wax crystals of cabbage mutant LD10GL are severely reduced and mutation of gene Bol013612 causes a glossy phenotype in the LD10GL mutant.

Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

PubMed Central

Farmer, Andrew D.; Huang, Wei; Ambachew, Daniel; Penmetsa, R. Varma; Carrasquilla-Garcia, Noelia; Assefa, Teshale; Cannon, Steven B.

2018-01-01

Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel. A whole genome genetic map was created that covered all eleven linkage groups (LG). The LGs were linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length in total was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as the use of gene-based markers. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters. LD levels were found to be stronger within the Mesoamerican genepool and decay more rapidly within the Andean genepool. The recombination rate across the genome was 2.13 cM / Mb but R was found to be highly repressed around centromeres and frequent outside peri-centromeric regions. These results have important implications for association and genetic mapping or crop improvement in common bean. PMID:29522524

Uneven recombination and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD) and recombination (R) analyses are the basis for plant breeding. LD and R vary by breeding system, by generation of inbreeding or outcrossing and by region of the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome and n=...

Supervised versus unsupervised technology-based levodopa monitoring in Parkinson's disease: an intrasubject comparison.

PubMed

Lopane, Giovanna; Mellone, Sabato; Corzani, Mattia; Chiari, Lorenzo; Cortelli, Pietro; Calandra-Buonaura, Giovanna; Contin, Manuela

2018-06-01

We aimed to assess the intrasubject reproducibility of a technology-based levodopa (LD) therapeutic monitoring protocol administered in supervised versus unsupervised conditions in patients with Parkinson's disease (PD). The study design was pilot, intrasubject, single center, open and prospective. Twenty patients were recruited. Patients performed a standardized monitoring protocol instrumented by an ad hoc embedded platform after their usual first morning LD dose in two different randomized ambulatory sessions: one under a physician's supervision, the other self-administered. The protocol is made up of serial motor and non-motor tests, including alternate finger tapping, Timed Up and Go test, and measurement of blood pressure. Primary motor outcomes included comparisons of intrasubject LD subacute motor response patterns over the 3-h test in the two experimental conditions. Secondary outcomes were the number of intrasession serial test repetitions due to technical or handling errors and patients' satisfaction with the unsupervised LD monitoring protocol. Intrasubject LD motor response patterns were concordant between the two study sessions in all patients but one. Platform handling problems averaged 4% of total planned serial tests for both sessions. Ninety-five percent of patients were satisfied with the self-administered LD monitoring protocol. To our knowledge, this study is the first to explore the potential of unsupervised technology-based objective motor and non-motor tasks to monitor subacute LD dosing effects in PD patients. The results are promising for future telemedicine applications.

A study of viscous interaction effects on hypersonic waveriders. Ph.D. Thesis, Dec. 1991

NASA Technical Reports Server (NTRS)

Chang, Jinhwa

1992-01-01

The effects of viscous interaction in the analysis and design of improved classes of viscous optimized hypersonic waveriders is examined. The Corda computer program is used to generate viscous optimized hypersonic waveriders from conical flow fields without viscous interaction. Each waverider is optimized for maximum L/D, and comparison studies are made between cases with and without viscous interaction. The results show that aerodynamic performance of the viscous interaction waveriders are reduced due mainly to a large increase in skin-friction drag associated with the viscous interaction phenomena that grows with increasing Mach number and altitude, but some of this performance loss can be recouped by including viscous interactions within the optimization procedure. When the waverider is optimized for viscous interaction, the shape can change dramatically. A significant result of the present work delineates on a velocity-altitude map the region where viscous interaction effects are significant for modern hypersonic waveriders by performing parametric runs to produce L/D, C sub L, and C sub D contour plots for Mach numbers from 6 to 30 at altitudes from 30 to 80 km.

The impact of shock wave therapy at varied energy and dose levels on functional and structural changes in erectile tissue.

PubMed

Müller, Alexander; Akin-Olugbade, Yemi; Deveci, Serkan; Donohue, John F; Tal, Raanan; Kobylarz, Keith A; Palese, Michael; Mulhall, John P

2008-03-01

Only minimal literature exists on consequences of shock wave therapy (SWT) on erectile function in treatment of Peyronie's disease (PD). This study was undertaken to define SWT impact at varied energy/dose levels at different time points on functional and structural changes in erectile tissue. In 45 rats 2000 shock waves (sw) at 2 BAR were applied to the penis weekly sorted by one, two, and three sessions (high-dose/energy level, HD-1, HD-2, HD-3). Each group was followed for 1, 7, or 28 d before measuring intracavernosal pressure (ICP) and mean arterial pressure (MAP). Fifteen control animals (C1, C7, C28) underwent anesthesia alone. Another 15 animals were exposed to three SWT sessions applying 1000 sw at 1 BAR and analyzed identically (low-dose/energy level, LD-3-1, -7, -28). Terminal deoxynucleotidyl transferase biotin-dUTP nick-end labeling assay was used to define the apoptotic index (AI) and Masson's trichrome (MT) staining was prepared to evaluate smooth muscle-to-collagen ratios. ICP/MAP ratios for all C groups displayed a mean of 64%. All SWT groups demonstrated significantly reduced ICP/MAP ratios compared to their corresponding C groups (p<0.05). The LD-3 groups showed a trend toward improved ICP/MAP ratios. LD-3-28 demonstrated significant recovery compared to HD-3-28 (55+/-8% vs. 41+/-10%, p=0.004), but remained reduced compared to C28 (63+/-5%, p=0.03). No statistical differences were seen for MT staining in SWT groups compared to C (p>0.05). AIs for the LD-3 groups were significantly lower compared to the HD-3 groups (p<0.001), but all AIs were significantly increased compared to C groups (p<0.01). Overall, at both energy/dose levels, SWT resulted in a time- and treatment-dependent reduction of ICP/MAP ratios, which might be mediated partly through apoptosis and collagenization of corporal smooth muscle.

Can social stories enhance the interpersonal conflict resolution skills of children with LD?

PubMed

Kalyva, Efrosini; Agaliotis, Ioannis

2009-01-01

Since many children with learning disabilities (LD) face interpersonal conflict resolution problems, this study examines the efficacy of social stories in helping them choose more appropriate interpersonal conflict resolution strategies. A social story was recorded and played to the 31 children with LD in the experimental group twice a week for a period of 1 month, while the 32 children with LD in the control group did not receive any intervention. The effects of the intervention were systematically examined by means of an interview with the participants, while teachers completed the T-MESSY (Matson, J. L. (1990). Matson Evaluation of Social Skills With Youngsters: Manual. Worthington, OR: International Diagnostic Systems). All children chose mainly avoidance and hostile strategies before the intervention, but children in the experimental group chose predominantly positive strategies both after the intervention and at follow-up in comparison to control children. Furthermore, children with LD who received the intervention were rated by their teachers as engaging in significantly less inappropriate social behaviors after the intervention and at follow-up in comparison to control children. The recorded changes in the choice of interpersonal conflict resolution strategies and the more positive teacher ratings for the experimental group indicate that social stories constitute a powerful intervention for the enhancement of the social competence of children with LD.

Prevalence of LD From Parental and Professional Perspectives: A Comparison of the Data From the National Survey of Children's Health and the Office of Special Education Programs' Reports to Congress.

PubMed

Pullen, Paige C

Since the emergence of the field of learning disabilities (LD) in the late 1960s and early 1970s, controversy has surrounded issues regarding methods used for identification. The prevalence of students identified as LD increased steadily from the 1970s until the beginning of the 21st century, at which time it has decreased until at least 2011 (the most current data available from the U.S. Office of Education). In this article, I compare the prevalence rates of children aged 6 to 17 years being served in schools according to the Office of Special Education Programs with the prevalence rates as reported by parents on the National Survey of Children's Health. To date, no such comparison has been made that takes into account parents' knowledge of their children's disabilities. Results of the analyses reveal that parents report that their children have LD at a significantly higher rate than what is reported by schools of students receiving LD services. Most important, the longitudinal trend from 2001 to 2011 indicates that parents are reporting a slight increase whereas the Office of Special Education Programs is reporting a dramatic decrease in LD.

HapMap tagSNP transferability in multiple populations: general guidelines

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Watkins, W. Scott; Zhang, Yuhua; Tolpinrud, Whitney; Jorde, Lynn B.

2008-01-01

This PDF receipt will only be used as the basis for generating PubMed Central (PMC) documents. PMC documents will be made available for review after conversion (approx. 2–3 weeks time). Any corrections that need to be made will be done at that time. No materials will be released to PMC without the approval of an author. Only the PMC documents will appear on PubMed Central -- this PDF Receipt will not appear on PubMed Central. Linkage disequilibrium (LD) has received much recent attention because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations. PMID:18482828

Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel.

PubMed

Khatkar, Mehar S; Nicholas, Frank W; Collins, Andrew R; Zenger, Kyall R; Cavanagh, Julie A L; Barris, Wes; Schnabel, Robert D; Taylor, Jeremy F; Raadsma, Herman W

2008-04-24

The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are based on microsatellite markers or small numbers of single nucleotide polymorphisms (SNPs) covering one or only a few chromosomes. This is the first comprehensive study on the extent of LD in cattle by analyzing data on 1,546 Holstein-Friesian bulls genotyped for 15,036 SNP markers covering all regions of all autosomes. Furthermore, most studies in cattle have used relatively small sample sizes and, consequently, may have had biased estimates of measures commonly used to describe LD. We examine minimum sample sizes required to estimate LD without bias and loss in accuracy. Finally, relatively little information is available on comparative LD structures including other mammalian species such as human and mouse, and we compare LD structure in cattle with public-domain data from both human and mouse. We computed three LD estimates, D', Dvol and r2, for 1,566,890 syntenic SNP pairs and a sample of 365,400 non-syntenic pairs. Mean D' is 0.189 among syntenic SNPs, and 0.105 among non-syntenic SNPs; mean r2 is 0.024 among syntenic SNPs and 0.0032 among non-syntenic SNPs. All three measures of LD for syntenic pairs decline with distance; the decline is much steeper for r2 than for D' and Dvol. The value of D' and Dvol are quite similar. Significant LD in cattle extends to 40 kb (when estimated as r2) and 8.2 Mb (when estimated as D'). The mean values for LD at large physical distances are close to those for non-syntenic SNPs. Minor allelic frequency threshold affects the distribution and extent of LD. For unbiased and accurate estimates of LD across marker intervals spanning < 1 kb to > 50 Mb, minimum sample sizes of 400 (for D') and 75 (for r2) are required. The bias due to small samples sizes increases with inter-marker interval. LD in cattle is much less extensive than in a mouse population created from crossing inbred lines, and more extensive than in humans. For association mapping in Holstein-Friesian cattle, for a given design, at least one SNP is required for each 40 kb, giving a total requirement of at least 75,000 SNPs for a low power whole-genome scan (median r2 > 0.19) and up to 300,000 markers at 10 kb intervals for a high power genome scan (median r2 > 0.62). For estimation of LD by D' and Dvol with sufficient precision, a sample size of at least 400 is required, whereas for r2 a minimum sample of 75 is adequate.

A new method for large-scale assessment of change in ecosystem functioning in relation to land degradation

NASA Astrophysics Data System (ADS)

Horion, Stephanie; Ivits, Eva; Verzandvoort, Simone; Fensholt, Rasmus

2017-04-01

Ongoing pressures on European land are manifold with extreme climate events and non-sustainable use of land resources being amongst the most important drivers altering the functioning of the ecosystems. The protection and conservation of European natural capital is one of the key objectives of the 7th Environmental Action Plan (EAP). The EAP stipulates that European land must be managed in a sustainable way by 2020 and the UN Sustainable development goals define a Land Degradation Neutral world as one of the targets. This implies that land degradation (LD) assessment of European ecosystems must be performed repeatedly allowing for the assessment of the current state of LD as well as changes compared to a baseline adopted by the UNCCD for the objective of land degradation neutrality. However, scientifically robust methods are still lacking for large-scale assessment of LD and repeated consistent mapping of the state of terrestrial ecosystems. Historical land degradation assessments based on various methods exist, but methods are generally non-replicable or difficult to apply at continental scale (Allan et al. 2007). The current lack of research methods applicable at large spatial scales is notably caused by the non-robust definition of LD, the scarcity of field data on LD, as well as the complex inter-play of the processes driving LD (Vogt et al., 2011). Moreover, the link between LD and changes in land use (how land use changes relates to change in vegetation productivity and ecosystem functioning) is not straightforward. In this study we used the segmented trend method developed by Horion et al. (2016) for large-scale systematic assessment of hotspots of change in ecosystem functioning in relation to LD. This method alleviates shortcomings of widely used linear trend model that does not account for abrupt change, nor adequately captures the actual changes in ecosystem functioning (de Jong et al. 2013; Horion et al. 2016). Here we present a new methodology for assessing gradual and abrupt changes in ecosystem functioning in Europe. Based on segmented trend analysis of water-use efficiency (WUE) time series, an Ecosystem Change Type (ECT) map was produced over Europe at 1km resolution for the period 1999 to 2013. An analysis of auxiliary data on land use/cover change, drought trends, and soil threats was performed over hotspot areas to better understand the observed changes in ecosystem functioning and their driving mechanisms. The ECT map was validated using the case study sites from the EU-funded RECARE project. Overall, the ECT map accurately highlighted areas characterized by a major change in pathways of ecosystem functioning as well as indicated the type and timing of changes. Allan, R. et al. (2007). Climate and land degradation. Verlag Berlin Heidelberg: Springer. de Jong, R et al. (2013). Remote Sensing, 5, 1117-1133 Horion, S. et al. (2016). Global Change Biology, 22, 2801-2817 Vogt, J. V et al. (2011). Land Degradation & Development, 22: 150-165.

Mucuna pruriens in Parkinson Disease: A Kinetic-Dynamic Comparison With Levodopa Standard Formulations.

PubMed

Contin, Manuela; Lopane, Giovanna; Passini, Andrea; Poli, Ferruccio; Iannello, Carmelina; Guarino, Maria

2015-01-01

We compared levodopa (LD) kinetic-dynamic profile of a dose of LD/aromatic amino acid decarboxylase peripheral inhibitors versus a nominally equivalent dose of a commercial Mucuna pruriens (Mucuna) seeds extract in 2 patients with Parkinson disease chronically taking LD standard combined with self-prescribed Mucuna. Patients were challenged with a fasting morning dose of 100 mg LD/25 mg carbidopa (patient 1) or benserazide (patient 2) versus 100 mg LD from Mucuna capsules in 2 different sessions, after a 12-hour standard LD formulations' washout. They underwent kinetic-dynamic LD monitoring based on LD dose intake and simultaneous serial assessments of plasma drug concentrations and motor test performances. Quantitative analysis of LD in Mucuna capsules was also performed. Levodopa bioavailability was markedly lower after Mucuna administration compared with LD standard formulations: in patient 1, peak plasma LD concentration (Cmax) decreased from 2.0 to 1.0 mg/L and the area under the plasma concentration time curve from 137 to 33.6 mg/L per minute; in patient 2, Cmax was 0.7 mg/L after LD/benserazide and nearly undetectable after Mucuna. In patient 1, impaired LD bioavailability from Mucuna resulted in reduced duration and overall extent of drug response compared with LD/carbidopa. In patient 2, no significant subacute LD motor response was observed in either condition. Quantitative analysis of Mucuna formulation confirmed the 100 mg LD content for the utilized capsules. Our results show an impaired LD bioavailability from Mucuna preparation, as expected by the lacking aromatic amino acid decarboxylase inhibitors coadministration, which might explain the suggested lower dyskinetic potential of Mucuna compared with standard LD formulations.

The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

PubMed

Huang, J; Jiang, Y

2001-01-01

We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy

PubMed Central

Xu, Shuhua; Huang, Wei; Qian, Ji; Jin, Li

2008-01-01

The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 < r2 < 0.8 when ancestry-informative markers (AIMs) were used. The size of chromosomal segments that were derived from East Asian and European ancestries averaged 2.4 cM and 4.1 cM, respectively. Both the magnitude of LD and fragmentary ancestral chromosome segments indicated a long history of Uyghur. Under the assumption of a hybrid isolation (HI) model, we estimated that the admixture event of UIG occurred about 126 [107∼146] generations ago, or 2520 [2140∼2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but ∼10-fold AIMs are necessary for a whole-genome scan. PMID:18355773

Comparison of synchronization of primate circadian rhythms by light and food

NASA Technical Reports Server (NTRS)

Sulzman, F. M.; Fuller, C. A.; Moore-Ede, M. C.

1978-01-01

It is a well-documented fact that cycles of light and dark (LD) are the major entraining agent or 'zeitgeber' for circadian rhythms and that cycles of eating and fasting (EF) are capable of synchronizing a few circadian rhythms in the squirrel monkey. In this paper, by contrasting how these rhythms are timed by LD and EF cycles, the differential coupling to the oscillating system within adult male squirrel monkeys is examined. The variables measured are the rhythms of drinking, colonic temperature, and urinary potassium and water excretion. Attention is given to a comparison of the reproducibility of the averaged waveforms of the rhythms, the stability of the timing of a phase reference point, and the rate of resynchronization of these rhythms following an abrupt 8-hr phase delay in the zeitgeber. It is shown that the colonic temperature rhythm is more tightly controlled by LD than EF cycles, and that the drinking and urinary rhythms are more tightly coupled to EF than LD cycles.

Volumetric-modulated Arc Therapy Lung Stereotactic Body Radiation Therapy Dosimetric Quality Assurance: A Comparison between Radiochromic Film and Chamber Array.

PubMed

Colodro, Juan Fernando Mata; Berná, Alfredo Serna; Puchades, Vicente Puchades; Amores, David Ramos; Baños, Miguel Alcaraz

2017-01-01

The aim of this work is to verify the use of radiochromic film in the quality assurance (QA) of volumetric-modulated arc therapy (VMAT) lung stereotactic body radiation therapy (SBRT) plans and compare the results with those obtained using an ion chamber array. QA was performed for 14 plans using a two-dimensional-array seven29 and EBT3 film. Dose values per session ranged between 7.5 Gy and 18 Gy. The multichannel method was used to obtain a dose map for film. The results obtained were compared with treatment planning system calculated profiles through gamma analysis. Passing criteria were 3%/3 mm, 2%/2 mm and 3%/1.5 mm with maximum and local dose (LD) normalization. Mean gamma passing rate (GPR) (percentage of points presenting a gamma function value of <1) was obtained and compared. Calibration curves were obtained for each color channel within the dose range 0-16 Gy. Mean GPR values for film were >98.9% for all criteria when normalizing per maximum dose. When using LD, normalization was >92.7%. GPR values for the array were lower for all criteria; this difference being statistically significant when normalizing at LD, reaching 12% for the 3%/1.5 mm criterion. Both detectors provide satisfactory results for the QA of plans for VMAT lung SBRT. The film provided greater mean GPR values, afforded greater spatial resolution and was more efficient overall.

Volumetric-modulated Arc Therapy Lung Stereotactic Body Radiation Therapy Dosimetric Quality Assurance: A Comparison between Radiochromic Film and Chamber Array

PubMed Central

Colodro, Juan Fernando Mata; Berná, Alfredo Serna; Puchades, Vicente Puchades; Amores, David Ramos; Baños, Miguel Alcaraz

2017-01-01

Introduction: The aim of this work is to verify the use of radiochromic film in the quality assurance (QA) of volumetric-modulated arc therapy (VMAT) lung stereotactic body radiation therapy (SBRT) plans and compare the results with those obtained using an ion chamber array. Materials and Methods: QA was performed for 14 plans using a two-dimensional-array seven29 and EBT3 film. Dose values per session ranged between 7.5 Gy and 18 Gy. The multichannel method was used to obtain a dose map for film. Results: The results obtained were compared with treatment planning system calculated profiles through gamma analysis. Passing criteria were 3%/3 mm, 2%/2 mm and 3%/1.5 mm with maximum and local dose (LD) normalization. Mean gamma passing rate (GPR) (percentage of points presenting a gamma function value of <1) was obtained and compared. Calibration curves were obtained for each color channel within the dose range 0–16 Gy. Mean GPR values for film were >98.9% for all criteria when normalizing per maximum dose. When using LD, normalization was >92.7%. GPR values for the array were lower for all criteria; this difference being statistically significant when normalizing at LD, reaching 12% for the 3%/1.5 mm criterion. Conclusion: Both detectors provide satisfactory results for the QA of plans for VMAT lung SBRT. The film provided greater mean GPR values, afforded greater spatial resolution and was more efficient overall. PMID:28974858

The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets

PubMed Central

McCaskie, Pamela A; Carter, Kim W; McCaskie, Simon R; Palmer, Lyle J

2005-01-01

We used our newly developed linkage disequilibrium (LD) plotting software, JLIN, to plot linkage disequilibrium between pairs of single-nucleotide polymorphisms (SNPs) for three chromosomes of the Genetic Analysis Workshop 14 Aipotu simulated population to assess the effect of missing data on LD calculations. Our haplotype analysis program, SIMHAP, was used to assess the effect of missing data on haplotype-phenotype association. Genotype data was removed at random, at levels of 1%, 5%, and 10%, and the LD calculations and haplotype association results for these levels of missingness were compared to those for the complete dataset. It was concluded that ignoring individuals with missing data substantially affects the number of regions of LD detected which, in turn, could affect tagging SNPs chosen to generate haplotypes. PMID:16451612

Significant evidence for linkage disequilibrium over a 5-cM region among Afrikaners.

PubMed

Gordon, D; Simonic, I; Ott, J

2000-05-15

We explore the extent of deviations from Hardy-Weinberg equilibrium (HWE) at a marker locus and linkage disequilibrium (LD) between pairs of marker loci in the Afrikaner population of South Africa. DNA samples were used for genotyping of 23 loci on six chromosomes. The samples were collected from 91 healthy unrelated Afrikaner adults. Exact tests were used to determine evidence for deviations from HWE at a single marker locus or LD between pairs of marker loci. At the 0.05 level of significance, evidence was found for deviation from HWE at only one of the 23 loci. At the same level of significance, LD was found among 8 of the 34 intrachromosomal pairs of loci. On chromosome 21, there was evidence for LD (P = 0.02) between a pair of loci with a genetic distance of 5.51 cM. On chromosome 2, there was evidence for LD between a pair of loci with a genetic distance of 5.28 cM (P = 0.002) and a pair of loci with a genetic distance of 3.68 cM (P = 0.0004). Detailed analysis of LD for one locus pair indicated that only a few of all alleles participated in the LD and that strong LD was most often positive. Our findings indicate that Afrikaans-speaking Afrikaners represent one of those special populations deemed particularly suitable for disequilibrium mapping. Copyright 2000 Academic Press.

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

PubMed Central

Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca e; Mundim, Gabriel Borges

2016-01-01

Abstract The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

PubMed

Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca E; Mundim, Gabriel Borges

2016-03-01

The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

A Study of the School to Work Transition for Learning Disabled Students and the Learning Disabled Adult in Society in the Netherlands and Denmark. Final Report, April 14, 1984 to May 26, 1984.

ERIC Educational Resources Information Center

Gerber, Paul Jay

The report summarizes findings of 6 weeks spent in the Netherlands and Denmark to study services provided to learning disabled (LD) young adults and adults. The school to work transition for LD students is examined along with the LD adult in society, and comparisons are made between Dutch and Danish approaches. The Dutch system, highly structured…

Prevalence of LD from Parental and Professional Perspectives: A Comparison of the Data from the National Survey of Children's Health and the Office of Special Education Programs' Reports to Congress

ERIC Educational Resources Information Center

Pullen, Paige C.

2017-01-01

Since the emergence of the field of learning disabilities (LD) in the late 1960s and early 1970s, controversy has surrounded issues regarding methods used for identification. The prevalence of students identified as LD increased steadily from the 1970s until the beginning of the 21st century, at which time it has decreased until at least 2011 (the…

Perception of Nonverbal Social Cues by Regular Education, ADHD, and ADHD/LD Students.

ERIC Educational Resources Information Center

Hall, Cathy W.; Peterson, Andrea D.; Webster, Raymond E.; Bolen, Larry M.; Brown, Michael B.

1999-01-01

Study examined ability of attention deficit hyperactive disorder (ADHD) children with and without learning disability to perceive nonverbal social cues. ADHD/LD children demonstrated significant difficulty in comparison to their peers in effectively perceiving paralanguage cues. This group also showed significant improvement on the Postures and…

Divergence between human populations estimated from linkage disequilibrium.

PubMed

Sved, John A; McRae, Allan F; Visscher, Peter M

2008-12-01

Observed linkage disequilibrium (LD) between genetic markers in different populations descended independently from a common ancestral population can be used to estimate their absolute time of divergence, because the correlation of LD between populations will be reduced each generation by an amount that, approximately, depends only on the recombination rate between markers. Although drift leads to divergence in allele frequencies, it has less effect on divergence in LD values. We derived the relationship between LD and time of divergence and verified it with coalescent simulations. We then used HapMap Phase II data to estimate time of divergence between human populations. Summed over large numbers of pairs of loci, we find a positive correlation of LD between African and non-African populations at levels of up to approximately 0.3 cM. We estimate that the observed correlation of LD is consistent with an effective separation time of approximately 1,000 generations or approximately 25,000 years before present. The most likely explanation for such relatively low separation times is the existence of substantial levels of migration between populations after the initial separation. Theory and results from coalescent simulations confirm that low levels of migration can lead to a downward bias in the estimate of separation time.

A linked GeoData map for enabling information access

USGS Publications Warehouse

Powell, Logan J.; Varanka, Dalia E.

2018-01-10

OverviewThe Geospatial Semantic Web (GSW) is an emerging technology that uses the Internet for more effective knowledge engineering and information extraction. Among the aims of the GSW are to structure the semantic specifications of data to reduce ambiguity and to link those data more efficiently. The data are stored as triples, the basic data unit in graph databases, which are similar to the vector data model of geographic information systems (GIS); that is, a node-edge-node model that forms a graph of semantically related information. The GSW is supported by emerging technologies such as linked geospatial data, described below, that enable it to store and manage geographical data that require new cartographic methods for visualization. This report describes a map that can interact with linked geospatial data using a simulation of a data query approach called the browsable graph to find information that is semantically related to a subject of interest, visualized using the Data Driven Documents (D3) library. Such a semantically enabled map functions as a map knowledge base (MKB) (Varanka and Usery, 2017).A MKB differs from a database in an important way. The central element of a triple, alternatively called the edge or property, is composed of a logic formalization that structures the relation between the first and third parts, the nodes or objects. Node-edge-node represents the graphic form of the triple, and the subject-property-object terms represent the data structure. Object classes connect to build a federated graph, similar to a network in visual form. Because the triple property is a logical statement (a predicate), the data graph represents logical propositions or assertions accepted to be true about the subject matter. These logical formalizations can be manipulated to calculate new triples, representing inferred logical assertions, from the existing data.To demonstrate a MKB system, a technical proof-of-concept is developed that uses geographically attributed Resource Description Framework (RDF) serializations of linked data for mapping. The proof-of-concept focuses on accessing triple data from visual elements of a geographic map as the interface to the MKB. The map interface is embedded with other essential functions such as SPARQL Protocol and RDF Query Language (SPARQL) data query endpoint services and reasoning capabilities of Apache Marmotta (Apache Software Foundation, 2017). An RDF database of the Geographic Names Information System (GNIS), which contains official names of domestic feature in the United States, was linked to a county data layer from The National Map of the U.S. Geological Survey. The county data are part of a broader Government Units theme offered to the public as Esri shapefiles. The shapefile used to draw the map itself was converted to a geographic-oriented JavaScript Object Notation (JSON) (GeoJSON) format and linked through various properties with a linked geodata version of the GNIS database called “GNIS–LD” (Butler and others, 2016; B. Regalia and others, University of California-Santa Barbara, written commun., 2017). The GNIS–LD files originated in Terse RDF Triple Language (Turtle) format but were converted to a JSON format specialized in linked data, “JSON–LD” (Beckett and Berners-Lee, 2011; Sorny and others, 2014). The GNIS–LD database is composed of roughly three predominant triple data graphs: Features, Names, and History. The graphs include a set of namespace prefixes used by each of the attributes. Predefining the prefixes made the conversion to the JSON–LD format simple to complete because Turtle and JSON–LD are variant specifications of the basic RDF concept.To convert a shapefile into GeoJSON format to capture the geospatial coordinate geometry objects, an online converter, Mapshaper, was used (Bloch, 2013). To convert the Turtle files, a custom converter written in Java reconstructs the files by parsing each grouping of attributes belonging to one subject and pasting the data into a new file that follows the syntax of JSON–LD. Additionally, the Features file contained its own set of geometries, which was exported into a separate JSON–LD file along with its elevation value to form a fourth file, named “features-geo.json.” Extracted data from external files can be represented in HyperText Markup Language (HTML) path objects. The goal was to import multiple JSON–LD files using this approach.

Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

USDA-ARS?s Scientific Manuscript database

The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and po...

Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium.

PubMed

Pasaniuc, Bogdan; Zaitlen, Noah; Lettre, Guillaume; Chen, Gary K; Tandon, Arti; Kao, W H Linda; Ruczinski, Ingo; Fornage, Myriam; Siscovick, David S; Zhu, Xiaofeng; Larkin, Emma; Lange, Leslie A; Cupples, L Adrienne; Yang, Qiong; Akylbekova, Ermeg L; Musani, Solomon K; Divers, Jasmin; Mychaleckyj, Joe; Li, Mingyao; Papanicolaou, George J; Millikan, Robert C; Ambrosone, Christine B; John, Esther M; Bernstein, Leslie; Zheng, Wei; Hu, Jennifer J; Ziegler, Regina G; Nyante, Sarah J; Bandera, Elisa V; Ingles, Sue A; Press, Michael F; Chanock, Stephen J; Deming, Sandra L; Rodriguez-Gil, Jorge L; Palmer, Cameron D; Buxbaum, Sarah; Ekunwe, Lynette; Hirschhorn, Joel N; Henderson, Brian E; Myers, Simon; Haiman, Christopher A; Reich, David; Patterson, Nick; Wilson, James G; Price, Alkes L

2011-04-01

While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations.

Endurance exercise modulates levodopa induced growth hormone release in patients with Parkinson's disease.

PubMed

Müller, Thomas; Welnic, Jacub; Woitalla, Dirk; Muhlack, Siegfried

2007-07-11

Acute levodopa (LD) application and exercise release human growth hormone (GH). An earlier trial showed, that combined stimulus of exercise and LD administration is the best provocative test for GH response in healthy participants. Objective was to show this combined effect of LD application and exercise on GH response and to investigate the impact on LD metabolism in 20 previously treated patients with Parkinson's disease (PD). We measured GH- and LD plasma concentrations following soluble 200 mg LD/50 mg benserazide administration during endurance exercise and rest on two separate consecutive days. GH concentrations significantly increased on both days, but GH release was significantly delayed during rest. LD metabolism was not altered due to exercise in a clinical relevant manner. Exercise induced a significant faster LD stimulated GH release in comparison with the rest condition. We did not find the supposed increase of LD induced GH release by endurance exercise. We assume, that only a limited amount of GH is available for GH release in the anterior pituitary following an acute 200 mg LD administration. GH disposal also depends on growth hormone releasing hormone (GHRH), which is secreted into hypothalamic portal capillaries. During the exercise condition, the resulting higher blood pressure supports blood flow and thus GHRH transport towards the GH producing cells in the pituitary. This might additionally have caused the significant faster GH release during exercise.

Patterns of Cognitive Strengths and Weaknesses: Identification Rates, Agreement, and Validity for Learning Disabilities Identification

PubMed Central

Miciak, Jeremy; Fletcher, Jack M.; Stuebing, Karla; Vaughn, Sharon; Tolar, Tammy D.

2014-01-01

Purpose Few empirical investigations have evaluated LD identification methods based on a pattern of cognitive strengths and weaknesses (PSW). This study investigated the reliability and validity of two proposed PSW methods: the concordance/discordance method (C/DM) and cross battery assessment (XBA) method. Methods Cognitive assessment data for 139 adolescents demonstrating inadequate response to intervention was utilized to empirically classify participants as meeting or not meeting PSW LD identification criteria using the two approaches, permitting an analysis of: (1) LD identification rates; (2) agreement between methods; and (3) external validity. Results LD identification rates varied between the two methods depending upon the cut point for low achievement, with low agreement for LD identification decisions. Comparisons of groups that met and did not meet LD identification criteria on external academic variables were largely null, raising questions of external validity. Conclusions This study found low agreement and little evidence of validity for LD identification decisions based on PSW methods. An alternative may be to use multiple measures of academic achievement to guide intervention. PMID:24274155

Rab5 Isoforms Specifically Regulate Different Modes of Endocytosis in Leishmania.

PubMed

Rastogi, Ruchir; Verma, Jitender Kumar; Kapoor, Anjali; Langsley, Gordon; Mukhopadhyay, Amitabha

2016-07-08

Differential functions of Rab5 isoforms in endocytosis are not well characterized. Here, we cloned, expressed, and characterized Rab5a and Rab5b from Leishmania and found that both of them are localized in the early endosome. To understand the role of LdRab5 isoforms in different modes of endocytosis in Leishmania, we generated transgenic parasites overexpressing LdRab5a, LdRab5b, or their dominant-positive (LdRab5a:Q93L and LdRab5b:Q80L) or dominant-negative mutants (LdRab5a:N146I and LdRab5b:N133I). Using LdRab5a or its mutants overexpressing parasites, we found that LdRab5a specifically regulates the fluid-phase endocytosis of horseradish peroxidase and also specifically induced the transport of dextran-Texas Red to the lysosomes. In contrast, cells overexpressing LdRab5b or its mutants showed that LdRab5b explicitly controls receptor-mediated endocytosis of hemoglobin, and overexpression of LdRab5b:WT enhanced the transport of internalized Hb to the lysosomes in comparison with control cells. To unequivocally demonstrate the role of Rab5 isoforms in endocytosis in Leishmania, we tried to generate null-mutants of LdRab5a and LdRab5b parasites, but both were lethal indicating their essential functions in parasites. Therefore, we used heterozygous LdRab5a(+/-) and LdRab5b(+/-) cells. LdRab5a(+/-) Leishmania showed 50% inhibition of HRP uptake, but hemoglobin endocytosis was uninterrupted. In contrast, about 50% inhibition of Hb endocytosis was observed in LdRab5b(+/-) cells without any significant effect on HRP uptake. Finally, we tried to identify putative LdRab5a and LdRab5b effectors. We found that LdRab5b interacts with clathrin heavy chain and hemoglobin receptor. However, LdRab5a failed to interact with the clathrin heavy chain, and interaction with hemoglobin receptor was significantly less. Thus, our results showed that LdRab5a and LdRab5b differentially regulate fluid phase and receptor-mediated endocytosis in Leishmania. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.

PubMed

Machiela, Mitchell J; Chanock, Stephen J

2015-11-01

Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. mitchell.machiela@nih.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Linkage Disequilibrium Mapping in Domestic Dog Breeds Narrows the Progressive Rod-Cone Degeneration (prcd) Interval and Identifies Ancestral Disease Transmitting Chromosome

PubMed Central

Goldstein, Orly; Zangerl, Barbara; Pearce-Kelling, Sue; Sidjanin, Duska J.; Kijas, James W.; Felix, Jeanette; Acland, Gregory M; Aguirre, Gustavo D.

2014-01-01

Canine progressive rod-cone degeneration (prcd) is a retinal disease previously mapped to a broad, gene-rich centromeric region of canine chromosome 9. As allelic disorders are present in multiple breeds, we used linkage disequilibrium (LD) to narrow the ∼6.4 Mb interval candidate region. Multiple dog breeds, each representing genetically isolated populations, were typed for SNPs and other polymorphisms identified from BACs. The candidate region was initially localized to a 1.5 Mb zero recombination interval between growth factor receptor-bound protein 2 (GRB2) and SEC14-like 1 (SEC14L). A fine-scale haplotype of the region was developed which reduced the LD interval to 106 Kb, and identified a conserved haplotype of 98 polymorphisms present in all prcd-affected chromosomes from 14 different dog breeds. The findings strongly suggest that a common ancestor transmitted the prcd disease allele to many of the modern dog breeds, and demonstrate the power of LD approach in the canine model. PMID:16859891

Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts.

PubMed

Barros-Álvarez, Ximena; Kerchner, Keshia M; Koh, Cho Yeow; Turley, Stewart; Pardon, Els; Steyaert, Jan; Ranade, Ranae M; Gillespie, J Robert; Zhang, Zhongsheng; Verlinde, Christophe L M J; Fan, Erkang; Buckner, Frederick S; Hol, Wim G J

2017-07-01

The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 Å resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains. Comparing the two independent chains in the asymmetric unit reveals that the two pseudo-monomers of LdTyrRS can bend with respect to each other essentially as rigid bodies. This flexibility might be useful in the positioning of tRNA for catalysis since both pseudo-monomers in the LdTyrRS chain are needed for charging tRNA Tyr . An "extra pocket" (EP) appears to be present near the adenine binding region of LdTyrRS. Since this pocket is absent in the two human homologous enzymes, the EP provides interesting opportunities for obtaining selective drugs for treating infections caused by L. donovani, a unicellular parasite causing visceral leishmaniasis, or kala azar, which claims 20,000 to 30,000 deaths per year. Sequence and structural comparisons indicate that the EP is a characteristic which also occurs in the active site of several other important pathogenic protozoa. Therefore, the structure of LdTyrRS could inspire the design of compounds useful for treating several different parasitic diseases. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Maternal Stress in Nonverbal Learning Disorder: A Comparison with Reading Disorder

ERIC Educational Resources Information Center

Antshel, Kevin M.; Joseph, Guy-Ronald

2006-01-01

Maternal stress was assessed in mothers of children ages 8 to 11 years with learning disorders (LD). Age-, gender-, and IQ-matched children with reading disorders (RD; n = 31), children with nonverbal learning disorders (NVLD; n = 21), and typically developing control participants (n = 23) participated. Mothers of children with LD reported higher…

Learned Helplessness: Perceived Effects of Ability and Effort on Academic Performance Among EH and LD/EH Children.

ERIC Educational Resources Information Center

Luchow, Jed P.; And Others

The Intellectual Achievement Responsibility Questionnaire, which measures perceived locus of control of academic outcomes, was administered to 28 emotionally handicapped (EH) and 25 learning disabled (LD)/EH children. Between group comparison revealed that EH children took significantly more personal responsibility for academic failure than did…

Anxiety, Depression, and Coping Skills Among Mexican School Children: A Comparison of Students With and Without Learning Disabilities

PubMed Central

Gallegos, Julia; Langley, Audra; Villegas, Diana

2012-01-01

The purpose of this study was to compare severity and risk status for anxiety and depression with coping skills among 130 Mexican school children with learning disabilities (LD) and 130 school children without LD. This research is the first to explore the emotional difficulties of Mexican children with LD. Children completed the Spanish version of the Spence Children’s Anxiety Scale and Children’s Depression Inventory, and the Cuestionario de Afrontamiento (Coping Skills Questionnaire). Results indicated that a higher percentage of children with LD were at risk for anxiety (22.3% vs. 11.5%) and depression (32% vs. 18%). No statistically significant differences were found for coping skills. Results support the idea that there is an increased awareness of comorbid depression and anxiety among students with LD and a need to promote early identification and intervention in schools. Efforts should focus on better understanding the relationship between social-emotional difficulties and academic achievement and on developing effective interventions to support children with LD. PMID:24223470

Private speech of learning disabled and normally achieving children in classroom academic and laboratory contexts.

PubMed

Berk, L E; Landau, S

1993-04-01

Learning disabled (LD) children are often targets for cognitive-behavioral interventions designed to train them in effective use of a self-directed speech. The purpose of this study was to determine if, indeed, these children display immature private speech in the naturalistic classroom setting. Comparisons were made of the private speech, motor accompaniment to task, and attention of LD and normally achieving classmates during academic seatwork. Setting effects were examined by comparing classroom data with observations during academic seatwork and puzzle solving in the laboratory. Finally, a subgroup of LD children symptomatic of attention-deficit hyperactivity disorder (ADHD) was compared with pure LD and normally achieving controls to determine if the presumed immature private speech is a function of a learning disability or externalizing behavior problems. Results indicated that LD children used more task-relevant private speech than controls, an effect that was especially pronounced for the LD/ADHD subgroup. Use of private speech was setting- and task-specific. Implications for intervention and future research methodology are discussed.

The Leishmania donovani histidine acid ecto-phosphatase LdMAcP: insight into its structure and function.

PubMed

Papadaki, Amalia; Politou, Anastasia S; Smirlis, Despina; Kotini, Maria P; Kourou, Konstadina; Papamarcaki, Thomais; Boleti, Haralabia

2015-05-01

Acid ecto-phosphatase activity has been implicated in Leishmania donovani promastigote virulence. In the present study, we report data contributing to the molecular/structural and functional characterization of the L. donovani LdMAcP (L. donovani membrane acid phosphatase), member of the histidine acid phosphatase (HAcP) family. LdMAcP is membrane-anchored and shares high sequence identity with the major secreted L. donovani acid phosphatases (LdSAcPs). Sequence comparison of the LdMAcP orthologues in Leishmania sp. revealed strain polymorphism and species specificity for the L. donovani complex, responsible for visceral leishmaniasis (Khala azar), proposing thus a potential value of LdMAcP as an epidemiological or diagnostic tool. The extracellular orientation of the LdMAcP catalytic domain was confirmed in L. donovani promastigotes, wild-type (wt) and transgenic overexpressing a recombinant LdMAcP-mRFP1 (monomeric RFP1) chimera, as well as in transiently transfected mammalian cells expressing rLdMAcP-His. For the first time it is demonstrated in the present study that LdMAcP confers tartrate resistant acid ecto-phosphatase activity in live L. donovani promastigotes. The latter confirmed the long sought molecular identity of at least one enzyme contributing to this activity. Interestingly, the L. donovani rLdMAcP-mRFP1 promastigotes generated in this study, showed significantly higher infectivity and virulence indexes than control parasites in the infection of J774 mouse macrophages highlighting thereby a role for LdMAcP in the parasite's virulence.

Functional Characterization of Monomeric GTPase Rab1 in the Secretory Pathway of Leishmania*

PubMed Central

Bahl, Surbhi; Parashar, Smriti; Malhotra, Himanshu; Raje, Manoj; Mukhopadhyay, Amitabha

2015-01-01

Leishmania secretes a large number of its effectors to the extracellular milieu. However, regulation of the secretory pathway in Leishmania is not well characterized. Here, we report the cloning, expression, and characterization of the Rab1 homologue from Leishmania. We have found that LdRab1 localizes in Golgi in Leishmania. To understand the role of LdRab1 in the secretory pathway of Leishmania, we have generated transgenic parasites overexpressing GFP-LdRab1:WT, GFP-LdRab1:Q67L (a GTPase-deficient dominant positive mutant of Rab1), and GFP-LdRab1:S22N (a GDP-locked dominant negative mutant of Rab1). Surprisingly, our results have shown that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N does not disrupt the trafficking and localization of hemoglobin receptor in Leishmania. To determine whether the Rab1-dependent secretory pathway is conserved in parasites, we have analyzed the role of LdRab1 in the secretion of secretory acid phosphatase and Ldgp63 in Leishmania. Our results have shown that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N significantly inhibits the secretion of secretory acid phosphatase by Leishmania. We have also found that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N retains RFP-Ldgp63 in Golgi and blocks the secretion of Ldgp63, whereas the trafficking of RFP-Ldgp63 in GFP-LdRab1:WT-expressing cells is unaltered in comparison with control cells. Taken together, our results have shown that the Rab1-regulated secretory pathway is well conserved, and hemoglobin receptor trafficking follows an Rab1-independent secretory pathway in Leishmania. PMID:26499792

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

PubMed Central

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

2013-01-01

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers.

PubMed

Pardo, Luba M; Piras, Giovanna; Asproni, Rosanna; van der Gaag, Kristiaan J; Gabbas, Attilio; Ruiz-Linares, Andres; de Knijff, Peter; Monne, Maria; Rizzu, Patrizia; Heutink, Peter

2012-09-01

Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of genome-wide association studies (GWAS). We revisited this issue by examining the genetic make-up of a sample from North-East Sardinia using a dense set of autosomal, Y chromosome and mitochondrial markers to assess the potential of the sample for GWAS and fine mapping studies. We genotyped individuals for 500K single-nucleotide polymorphisms, Y chromosome markers and sequenced the mitochondrial hypervariable (HVI-HVII) regions. We identified major haplogroups and compared these with other populations. We estimated linkage disequilibrium (LD) and haplotype diversity across autosomal markers, and compared these with other populations. Our results show that within Sardinia there is no major population substructure and thus it can be considered a genetically homogenous population. We did not find substantial differences in the extent of LD in Sardinians compared with other populations. However, we showed that at least 9% of genomic regions in Sardinians differed in LD structure, which is helpful for identifying functional variants using fine mapping. We concluded that Sardinia is a powerful setting for genetic studies including GWAS and other mapping approaches.

Mapping of yellow mosaic virus (YMV) resistance in soybean (Glycine max L. Merr.) through association mapping approach.

PubMed

Kumar, Bhupender; Talukdar, Akshay; Verma, Khushbu; Bala, Indu; Harish, G D; Gowda, Sarmrat; Lal, S K; Sapra, R L; Singh, K P

2015-02-01

Yellow Mosaic Virus (YMV) is a serious disease of soybean. Resistance to YMV was mapped in 180 soybean genotypes through association mapping approach using 121 simple sequence repeats (SSR) and four resistance gene analogue (RGA)-based markers. The association mapping population (AMP) (96 genotypes) and confirmation population (CP) (84 genotypes) was tested for resistance to YMV at hot-spot consecutively for 3 years (2007-2009). The genotypes exhibited significant variability for YMV resistance (P < 0.01). Molecular genotyping and population structure analysis with 'admixture' co-ancestry model detected seven optimal sub-populations in the AMP. Linkage disequilibrium (LD) between the markers extended up to 35 and 10 cM with r2 > 0.15, and >0.25, respectively. The 4 RGA-based markers showed no association with YMV resistance. Two SSR markers, Satt301 and GMHSP179 on chromosome 17 were found to be in significant LD with YMV resistance. Contingency Chi-square test confirmed the association (P < 0.01) and the utility of the markers was validated in the CP. It would pave the way for marker assisted selection for YMV resistance in soybean. This is the first report of its kind in soybean.

Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

PubMed

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T H; Tan, Adrian K S; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S; Ku, Chee-Seng; Lee, Edmund J D; Seielstad, Mark; Chia, Kee-Seng

2009-11-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.

Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations

PubMed Central

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T.H.; Tan, Adrian K.S.; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S.; Ku, Chee-Seng; Lee, Edmund J.D.; Seielstad, Mark; Chia, Kee-Seng

2009-01-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser. PMID:19700652

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

PubMed Central

Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement. PMID:25942004

Implications of climate change on the distribution of the tick vector Ixodes scapularis and risk for Lyme disease in the Texas-Mexico transboundary region.

PubMed

Feria-Arroyo, Teresa P; Castro-Arellano, Ivan; Gordillo-Perez, Guadalupe; Cavazos, Ana L; Vargas-Sandoval, Margarita; Grover, Abha; Torres, Javier; Medina, Raul F; de León, Adalberto A Pérez; Esteve-Gassent, Maria D

2014-04-25

Disease risk maps are important tools that help ascertain the likelihood of exposure to specific infectious agents. Understanding how climate change may affect the suitability of habitats for ticks will improve the accuracy of risk maps of tick-borne pathogen transmission in humans and domestic animal populations. Lyme disease (LD) is the most prevalent arthropod borne disease in the US and Europe. The bacterium Borrelia burgdorferi causes LD and it is transmitted to humans and other mammalian hosts through the bite of infected Ixodes ticks. LD risk maps in the transboundary region between the U.S. and Mexico are lacking. Moreover, none of the published studies that evaluated the effect of climate change in the spatial and temporal distribution of I. scapularis have focused on this region. The area of study included Texas and a portion of northeast Mexico. This area is referred herein as the Texas-Mexico transboundary region. Tick samples were obtained from various vertebrate hosts in the region under study. Ticks identified as I. scapularis were processed to obtain DNA and to determine if they were infected with B. burgdorferi using PCR. A maximum entropy approach (MAXENT) was used to forecast the present and future (2050) distribution of B. burgdorferi-infected I. scapularis in the Texas-Mexico transboundary region by correlating geographic data with climatic variables. Of the 1235 tick samples collected, 109 were identified as I. scapularis. Infection with B. burgdorferi was detected in 45% of the I. scapularis ticks collected. The model presented here indicates a wide distribution for I. scapularis, with higher probability of occurrence along the Gulf of Mexico coast. Results of the modeling approach applied predict that habitat suitable for the distribution of I. scapularis in the Texas-Mexico transboundary region will remain relatively stable until 2050. The Texas-Mexico transboundary region appears to be part of a continuum in the pathogenic landscape of LD. Forecasting based on climate trends provides a tool to adapt strategies in the near future to mitigate the impact of LD related to its distribution and risk for transmission to human populations in the Mexico-US transboundary region.

A Comparison of How Gifted/LD and Average/LD Boys Cope with School Frustration.

ERIC Educational Resources Information Center

Coleman, Mary Ruth

1992-01-01

Gifted learning-disabled and average learning-disabled middle school boys (n=42) in grades 6-9 were compared on ways they cope with difficult school situations. Although no group differences were found on the Coping Resources Inventory, significant differences were found in the actual strategies the groups reported using, with gifted students…

A Longitudinal Comparison of Systems Used to Identify Subgroups of Learning Disabled Children.

ERIC Educational Resources Information Center

Goldstein, David; Dundon, William D.

This paper addresses the problem of heterogeneity of samples of learning disabled (LD) children by comparing five different systems for identifying homogeneous subgroups in terms of their ability to predict longitudinal reading and mathematics scores. One hundred and sixty LD children served as subjects. Three of the five subgrouping systems were…

A Cross-National Comparison of Attributional Patterns toward Students with and without Learning Disabilities

ERIC Educational Resources Information Center

Woodcock, Stuart; Jiang, Han

2018-01-01

Claims of the importance of having positive perceptions and expectations of students with learning disabilities (LD) have been repeatedly made over recent years. This article aims to raise awareness of the importance of attributional beliefs in relation to the educational outcomes of students with LD in Australia and China. Australian and Chinese…

Graphic organizers and their effects on the reading comprehension of students with LD: a synthesis of research.

PubMed

Kim, Ae-Hwa; Vaughn, Sharon; Wanzek, Jeanne; Wei, Shangjin

2004-01-01

Previous research studies examining the effects of graphic organizers on reading comprehension for students with learning disabilities (LD) are reviewed. An extensive search of the professional literature between 1963 and June 2001 yielded a total of 21 group design intervention studies that met the criteria for inclusion in the synthesis. Using graphic organizers (i.e., semantic organizers, framed outlines, cognitive maps with and without a mnemonic) was associated with improved reading comprehension overall for students with LD. Compared to standardized reading measures, researcher-developed comprehension measures were associated with higher effect sizes. Initial gains demonstrated when using graphic organizers were not revealed during later comprehension tasks or on new comprehension tasks.

Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

PubMed Central

Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

2002-01-01

Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

Acute oral toxicity: variability, reliability, relevance and interspecies comparison of rodent LD50 data from literature surveyed for the ACuteTox project.

PubMed

Hoffmann, Sebastian; Kinsner-Ovaskainen, Agnieszka; Prieto, Pilar; Mangelsdorf, Inge; Bieler, Christian; Cole, Thomas

2010-12-01

The ACuteTox project has aimed to optimise and prevalidate an in vitro testing strategy for predicting human acute toxicity. Ninety-seven reference substances were selected and an in vivo acute toxicity database was compiled. Comprehensive statistical analyses of the in vivo LD50 data to evaluate variability and reliability, interspecies correlation, predictive capacities with regard to EU and GHS toxicity categories, and deduction of performance criteria for in vitro methods is presented. For the majority of substances variability among rodent data followed a log normal distribution where good reproducibility was found. Rat and mouse interspecies comparison of LD50 studies by ordinary regression showed high correlation, with coefficients of determination, ranging between 0.8 and 0.9. Substance specific differences were only significant for warfarin and cycloheximide. No correlation of compound LD50 range with presumed study quality rank (by assigning Klimisch reliability scores) was found. Modelling based on LD50 variability showed that with at least 90% probability ∼54% of the substances would fall into only one GHS category and ∼44% would fall within two adjacent categories. These results could form the basis for deriving a predictive capacity that should be expected from alternative approaches to the conventional in vivo acute oral toxicity test. Copyright © 2010 Elsevier Inc. All rights reserved.

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

PubMed Central

Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

2015-01-01

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

Fine-scale mapping of a locus for severe bipolar mood disorder on chromosome 18p11.3 in the Costa Rican population

PubMed Central

McInnes, L. Alison; Service, Susan K.; Reus, Victor I.; Barnes, Glenn; Charlat, Olga; Jawahar, Satya; Lewitzky, Steve; Yang, Qing; Duong, Quyen; Spesny, Mitzi; Araya, Carmen; Araya, Xinia; Gallegos, Alvaro; Meza, Luis; Molina, Julio; Ramirez, Rolando; Mendez, Roxana; Silva, Sandra; Fournier, Eduardo; Batki, Steven L.; Mathews, Carol A.; Neylan, Thomas; Glatt, Charles E.; Escamilla, Michael A.; Luo, David; Gajiwala, Paresh; Song, Terry; Crook, Stephen; Nguyen, Jasmine B.; Roche, Erin; Meyer, Joanne M.; Leon, Pedro; Sandkuijl, Lodewijk A.; Freimer, Nelson B.; Chen, Hong

2001-01-01

We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3. We further investigated this region by creating a physical map and developing 4 new microsatellite and 26 single-nucleotide polymorphism markers for typing in the pedigree and population samples. We report the results of fine-scale association analyses in the population sample, as well as evaluation of haplotypes in pedigree CR001. Our results suggest a candidate region containing six genes but also highlight the complexities of LD mapping of common disorders. PMID:11572994

Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types

PubMed Central

2013-01-01

Background Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Results Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Conclusions Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits. PMID:23647851

Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types.

PubMed

Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie

2013-05-06

Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.

Technetium-99m Pyrophosphate: Comparison of ED50 for Tetany and Acidosis with Acute LD500

DTIC Science & Technology

electrocardiogram and chemical analysis revealed that the hypocalcemic effect occurs at a much lower dosage than for the LD50. Polyphosphate was found to be more...toxic by the LD50 analysis than pyrophosphate. It is emphasized that the hypocalcemic toxic effects should be the determining factor in deciding what...to 1 with regard to the first signs of hypocalcemia by electrocardiographic measurements (i.e., 2 mg/kg). On this basis an injection of no more than 1 mg/kg is recommended to maintain a safety factor of around 10 to 1.

Orion Entry Performance-Based Center-of-Gravity Box

NASA Technical Reports Server (NTRS)

Rea, Jeremy R.

2010-01-01

The Orion capsule is designed both for Low Earth Orbit missions to the ISS and for missions to the moon. For ISS class missions, the capsule will use an Apollo-style direct entry. For lunar return missions, depending on the timing of the mission, the capsule could perform a direct entry or a skip entry of up to 4800 n.mi. in order to land in the coastal waters of California. The physics of atmospheric re-entry determine the capability of the Orion vehicle. For a given vehicle mass and shape, physics tells us that the driving parameters for an entry vehicle are the hypersonic lift-to-drag ratio (L/D) and the flight path angle at entry interface (gamma(sub EI)). The design of the Orion atmospheric re-entry must meet constraints during both nominal and dispersed flight conditions on landing accuracy, heating rate, total heat load, sensed acceleration, and proper disposal of the Service Module. These constraints define an entry corridor in the space of L/D-gamma(sub EI); if the vehicle falls within this corridor, then all constraints are met. The gamma(sub EI) dimension of the corridor can be further constrained by the gloads experienced during emergency entries. Thus, the entry performance for the Orion vehicle can be described completely by the L/D. Bounds on the hypersonic L/D necessary to achieve all the mission requirements can be defined for the given entry corridor. Landing accuracy performance drives the lower limit on L/D. In order to achieve the desired landing accuracy, a minimum L/D must be ensured. The design of the Thermal Protection System (TPS) drives the upper limit on L/D. A higher L/D can drive mass into the design of the TPS. Conversely, once the TPS is designed, the L/D must be ensured to stay below a certain limit in order for the TPS to stay within its design envelop. The L/D must stay within its upper and lower bounds during dispersed flight conditions. L/D is a function of both the aerodynamics and the center-of-gravity (CG) of the vehicle. The aerodynamics of the vehicle are determined by Computational Fluid Mechanics (CFD) and wind tunnel tests. However, the aerodynamics are not known precisely. Instead, an aerodynamic database has been developed where the aerodynamic coefficients are known to fall within a probabilistic band defined by upper and lower bounds. It is expected that the probabilistic band will shrink after the first missions are flown and real-world data is collected. Until that time, the Orion must be designed to the current aerodynamic database. Thus, for a given aerodynamic database with given uncertainties, the allowable range in L/D can be mapped to an allowable box for the CG location. The CG box is used to set requirements on the dispersions allowed for vehicle packaging and cargo storage. As the aerodynamic uncertainties decrease, the size of the CG box can increase. This paper discusses the technique used to map the minimum and maximum L/D bounds set by the entry performance requirements to the allowable dispersions in CG while accounting for aerodynamic uncertainties. The L/D is defined as the ratio of the lift force to the drag force. It is equivalent to the ratio of lift coefficient (C(sub L)) over drag coefficient (C(sub D)). C(sub L) and C(sub D) are functions of Mach number (M) and angle of attack (alpha). A Mach number of 25 is used as a measuring point of the hypersonic L/D. Variations in C(sub L), C(sub D) and alpha cause variations in L/D. Equation (1) shows the three contributions to the variation in L/D.

Quality of Life of Children with Learning Disabilities: A Comparison of Self-Reports and Proxy Reports

ERIC Educational Resources Information Center

Sakiz, Halis; Sart, Zeynep Hande; Börkan, Bengü; Korkmaz, Baris; Babür, Nalan

2015-01-01

This study aimed to explore how children with learning disabilities (LD) perceive their quality of life (QoL) and to compare self-reports and proxy reports regarding their QoL. Children with LD, their typically developing peers, their parents and teachers responded to the child, parent, and teacher forms of KINDL® Questionnaire for Measuring…

Children with and without Learning Disabilities: A Comparison of Processes and Outcomes Following Group Counseling

ERIC Educational Resources Information Center

Leichtentritt, Judith; Shechtman, Zipora

2010-01-01

This study compared outcomes and processes in counseling groups of an expressive-supportive modality for children with learning disabilities (LD) and without them (NLD). Participants were 266 students (ages 10-18), all referred for emotional, social, and behavioral difficulties; of these, 123 were identified with LD and 143 were not. There were 40…

Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

PubMed

Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J; Xiao, Yingjie; Liu, Kede

2016-01-01

High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.

Story Mapping and Its Effects on the Writing Fluency and Word Diversity of Students with Learning Disabilities

ERIC Educational Resources Information Center

Li, Daqi

2007-01-01

Students with learning disabilities (LD) often experience difficulties in writing fluently and using a diversity of words. To help these students, specific and effective writing strategies must be incorporated into instruction and demonstrated to them through modeling. This study examined the effectiveness of using a story map and story map…

Temporal analysis and spatial mapping of Lymantria dispar nuclear polyhedrosis virus transcripts and in vitro translation polypeptides

Treesearch

James M. Slavicek

1991-01-01

Genomic expression of the Lymantriu dispar multinucleocapsid nuclear polyhedrosis virus (LdMNPV) was studied. Viral specific transcripts expressed in cell culture at various times from 2 through 72 h postinfection were identified and their genomic origins mapped through Northern analysis. Sixty-five distinct transcripts were identified in this...

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-gro...

Fine-Mapping Angiotensin-Converting Enzyme Gene: Separate QTLs Identified for Hypertension and for ACE Activity

PubMed Central

Chung, Chia-Min; Wang, Ruey-Yun; Fann, Cathy S. J.; Chen, Jaw-Wen; Jong, Yuh-Shiun; Jou, Yuh-Shan; Yang, Hsin-Chou; Kang, Chih-Sen; Chen, Chien-Chung; Chang, Huan-Cheng; Pan, Wen-Harn

2013-01-01

Angiotensin-converting enzyme (ACE) has been implicated in multiple biological system, particularly cardiovascular diseases. However, findings associating ACE insertion/deletion polymorphism with hypertension or other related traits are inconsistent. Therefore, in a two-stage approach, we aimed to fine-map ACE in order to narrow-down the function-specific locations. We genotyped 31 single nucleotide polymorphisms (SNPs) of ACE from 1168 individuals from 305 young-onset (age ≤40) hypertension pedigrees, and found four linkage disequilibrium (LD) blocks. A tag-SNP, rs1800764 on LD block 2, upstream of and near the ACE promoter, was significantly associated with young-onset hypertension (p = 0.04). Tag-SNPs on all LD blocks were significantly associated with ACE activity (p-value: 10–16 to <10–33). The two regions most associated with ACE activity were found between exon13 and intron18 and between intron 20 and 3′UTR, as revealed by measured haplotype analysis. These two major QTLs of ACE activity and the moderate effect variant upstream of ACE promoter for young-onset hypertension were replicated by another independent association study with 842 subjects. PMID:23469169

Extent of Linkage Disequilibrium in the Domestic Cat, Felis silvestris catus, and Its Breeds

PubMed Central

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A.

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r 2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits. PMID:23308248

Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

PubMed

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A; Gandolfi, Barbara; Mullikin, James C; Cole, Shelley A; Gruffydd-Jones, Timothy J; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

Do Processing Patterns of Strengths and Weaknesses Predict Differential Treatment Response?

PubMed

Miciak, Jeremy; Williams, Jacob L; Taylor, W Pat; Cirino, Paul T; Fletcher, Jack M; Vaughn, Sharon

2016-08-01

No previous empirical study has investigated whether the LD identification decisions of proposed methods to operationalize processing strengths and weaknesses (PSW) approaches for LD identification are associated with differential treatment response. We investigated whether the identification decisions of the concordance/discordance model (C/DM; Hale & Fiorello, 2004) and Cross Battery Assessment approach (XBA method; Flanagan, Ortiz, & Alfonso, 2007) were consistent and whether they predicted intervention response beyond that accounted for by pretest performance on measures of reading. Psychoeducational assessments were administered at pretest to 203 4 th graders with low reading comprehension and individual results were utilized to identify students who met LD criteria according to the C/DM and XBA methods and students who did not. Resulting group status permitted an investigation of agreement for identification methods and whether group status at pretest (LD or not LD) was associated with differential treatment response to an intensive reading intervention. The LD identification decisions of the XBA and C/DM demonstrated poor agreement with one another (κ = -.10). Comparisons of posttest performance for students who met LD criteria and those who did not meet were largely null, with small effect sizes across all measures. LD status, as identified through the C/DM and XBA approaches, was not associated with differential treatment response and did not contribute educationally meaningful information about how students would respond to intensive reading intervention. These results do not support the value of cognitive assessment utilized in this way as part of the LD identification process.

Athletic performance outcomes following lumbar discectomy in professional basketball players.

PubMed

Anakwenze, Okechukwu A; Namdari, Surena; Auerbach, Joshua D; Baldwin, Keith; Weidner, Zachary D; Lonner, Baron S; Huffman, G R; Sennett, Brian J

2010-04-01

Retrospective case-control study. To quantify the athletic performance profiles after lumbar discectomy (LD) in a cohort of National Basketball Association (NBA) players in comparison with a control group of matched NBA players who did not undergo LD during the same study period. LD provides symptomatic relief and improved functional outcomes in the majority of patients as assessed by validated measures such as Oswestry Disability Index, Visual Analog Scale, and Short Form-36 (SF-36). Among professional athletes, however, the goal of lumbar HNP treated by discectomy is not only to improve functional status but also, ultimately, to return the player to preinjury athletic performance levels. No study to date has compared the athletic performance profiles before and after discectomy in professional athletes. An analysis of NBA games summaries, weekly injury reports, player profiles, and press releases was performed to identify 24 NBA players who underwent LD for symptomatic lumbar HNP between 1991 and 2007. A 1:2 case: control study was performed using players without history of lumbar HNP who were matched for age, position, experience, and body mass index as control subjects (n = 48). Paired t tests were conducted on the following parameters: games played, minutes per game, points per 40 minutes, rebounds per 40 minutes, assists per 40 minutes, steals per 40 minutes, blocks per 40 minutes, and shooting percentage. For each athletic performance outcome, between-group comparisons evaluating preindex to postindex season performance were done (index season = season of surgery). In the LD group, 18 of 24 players (75%) returned to play again in the NBA, compared with 42 of 48 players (88%, P = 0.31) in the control group. One year after surgery, between-group comparisons revealed statistically significant increase in blocked shots per 40 minutes in the LD (0.18) versus control group (-0.33; P = 0.008) and a smaller decrease in rebounds per 40 minutes in the LD (-0.25) versus control group (-1.42; P = 0.049). No other performance variable was found to be significantly different between the study and control group. Compared with a closely matched control cohort, we found that 75% of surgical patients returned to play again in the NBA, compared with 88% in control subjects who did not undergo surgery. For those players who returned, overall athletic performance was slightly improved or no worse than control subjects.

Functional Characterization of Monomeric GTPase Rab1 in the Secretory Pathway of Leishmania.

PubMed

Bahl, Surbhi; Parashar, Smriti; Malhotra, Himanshu; Raje, Manoj; Mukhopadhyay, Amitabha

2015-12-11

Leishmania secretes a large number of its effectors to the extracellular milieu. However, regulation of the secretory pathway in Leishmania is not well characterized. Here, we report the cloning, expression, and characterization of the Rab1 homologue from Leishmania. We have found that LdRab1 localizes in Golgi in Leishmania. To understand the role of LdRab1 in the secretory pathway of Leishmania, we have generated transgenic parasites overexpressing GFP-LdRab1:WT, GFP-LdRab1:Q67L (a GTPase-deficient dominant positive mutant of Rab1), and GFP-LdRab1:S22N (a GDP-locked dominant negative mutant of Rab1). Surprisingly, our results have shown that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N does not disrupt the trafficking and localization of hemoglobin receptor in Leishmania. To determine whether the Rab1-dependent secretory pathway is conserved in parasites, we have analyzed the role of LdRab1 in the secretion of secretory acid phosphatase and Ldgp63 in Leishmania. Our results have shown that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N significantly inhibits the secretion of secretory acid phosphatase by Leishmania. We have also found that overexpression of GFP-LdRab1:Q67L or GFP-LdRab1:S22N retains RFP-Ldgp63 in Golgi and blocks the secretion of Ldgp63, whereas the trafficking of RFP-Ldgp63 in GFP-LdRab1:WT-expressing cells is unaltered in comparison with control cells. Taken together, our results have shown that the Rab1-regulated secretory pathway is well conserved, and hemoglobin receptor trafficking follows an Rab1-independent secretory pathway in Leishmania. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Linkage disequilibrium compared between five populations of domestic sheep.

PubMed

Meadows, Jennifer R S; Chan, Eva K F; Kijas, James W

2008-09-30

The success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation. High density SNP arrays are currently in development for the sheep genome, however little is known about the behaviour of LD in this livestock species. This study examined the behaviour of LD within five sheep populations using two LD metrics, D' and x2'. Four economically important Australian sheep flocks, three pure breeds (White Faced Suffolk, Poll Dorset, Merino) and a crossbred population (Merino x Border Leicester), along with an inbred Australian Merino museum flock were analysed. Short range LD (0 - 5 cM) was observed in all five populations, however the persistence with increasing distance and magnitude of LD varied considerably between populations. Average LD (x2') for markers spaced up to 20 cM exceeded the non-syntenic average within the White Faced Suffolk, Poll Dorset and Macarthur Merino. LD decayed faster within the Merino and Merino x Border Leicester, with LD below or consistent with observed background levels. Using marker-marker LD as a guide to the behaviour of marker-QTL LD, estimates of minimum marker spacing were made. For a 95% probability of detecting QTL, a microsatellite marker would be required every 0.1 - 2.5 centimorgans, depending on the population used. Sheep populations were selected which were inbred (Macarthur Merino), highly heterogeneous (Merino) or intermediate between these two extremes. This facilitated analysis and comparison of LD (x2') between populations. The strength and magnitude of LD was found to differ markedly between breeds and aligned closely with both observed levels of genetic diversity and expectations based on breed history. This confirmed that breed specific information is likely to be important for genome wide selection and during the design of successful genome scans where tens of thousands of markers will be required.

Extended Linkage Disequilibrium Surrounding the Hemoglobin E Variant Due to Malarial Selection

PubMed Central

Ohashi, Jun ; Naka, Izumi ; Patarapotikul, Jintana ; Hananantachai, Hathairad ; Brittenham, Gary ; Looareesuwan, Sornchai ; Clark, Andrew G. ; Tokunaga, Katsushi 

2004-01-01

The hemoglobin E variant (HbE; β26Glu→Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240–4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection. PMID:15114532

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.

PubMed

Ohashi, Jun; Naka, Izumi; Patarapotikul, Jintana; Hananantachai, Hathairad; Brittenham, Gary; Looareesuwan, Sornchai; Clark, Andrew G; Tokunaga, Katsushi

2004-06-01

The hemoglobin E variant (HbE; ( beta )26Glu-->Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240-4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection.

Effect of exogenous melatonin and different photoperiods on oxidative status and antioxidant enzyme activity in Chhotanagpuri ewe.

PubMed

Choudhary, Pankaj Kumar; Ishwar, Ajay Kumar; Kumar, Rajesh; Niyogi, Debasish; Kumar, Mukesh

2018-02-01

The present study was conducted to evaluate the effect of exogenous melatonin under different photoperiods on oxidative status in Chhotanagpuri ewe. A total of 42 non-pregnant, non-lactating Chhotanagpuri ewe, having body weight ranging between 14.11±0.09 and 15.38±0.06 kg, were selected and were isolated from rams 2 months before melatonin administration. The selected animals were allocated randomly into seven groups, namely, Group I (normal control), Group II (long day [LD] control), Group III (LD+melatonin administration orally, 3 mg/day), Group IV (LD+melatonin administration subcutaneously, 1 mg/day), Group V (short day [SD] control), Group VI (SD+melatonin administration orally, 3 mg/day), and Group VII (SD+melatonin administration subcutaneously, 1 mg/day) comprising six animals in each group. Rams were then introduced into each group after completion of exogenous administration of melatonin. Blood samples with anticoagulant in vials were collected from each animal day before the start of the experiment and thereafter every month up to 5 th month. Hemolysate was prepared for estimation of oxidative stress parameters such as malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT). It was observed that the level of MDA was significantly (p<0.05) higher in LD groups (Group II, III and IV) in comparison to control and SD groups (VI and VII) at 1 st month. MDA concentration after exogenous administration of melatonin was significantly (p<0.05) decreased in Group IV and VI in comparison to 1 st month. SOD was significantly (p<0.05) higher in SD groups (V, VI, and VII) at the 1 st month in comparison to 0 day. After exogenous administration of melatonin, SOD concentration was significantly (p<0.05) higher in Groups III and IV in comparison to 1 st month. CAT was significantly (p<0.05) higher in SD groups (V, VI, and VII) in comparison to control and LD groups. After exogenous administration of melatonin, CAT concentration was significantly (p<0.05) higher in Groups III, IV, VI, and VIII in comparison to Groups I, II, and V. At the 3 rd month, CAT concentration significantly (p<0.05) decreased in Groups III, IV, VI, and VII in comparison to 2 nd month of experiment. However, a decreasing trend of CAT was observed in all the groups from 3 rd to 5 th month. The present experiment revealed that exogenous melatonin was able to reduce significantly the level of MDA and increased the activity of SOD and CAT in Chhotanagpuri ewe.

Mapping asthma-associated variants in admixed populations

PubMed Central

Mersha, Tesfaye B.

2015-01-01

Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease–associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders. PMID:26483834

[Neurological and neuropsychological comparison between subjects with learning disorder and those suffering from learning difficulties when eeg abnormalities are detected at pediatric age].

PubMed

Borsetti, L; Viberti, B; Ariano, C; Isocrono, A

2015-12-01

The objective of the study is to compare data and investigate the points of overlap between the two clinical conditions. The hypothesis is to observe a similar cognitive and neuropsychological profile in LD children and subjects with electroencephalogram (EEG) abnormalities. The present study consists of a descriptive analysis of 35 children who have been tested for suspected learning disorder (LD). The diagnostic protocol includes a detailed cognitive and neuropsychological evaluation, as well as logopedic and neuropsychomotor assessment. Children carried neurological visit, EEG in waking and encephalic nuclear magnetic resonance (NMR). In this study, anamnestic data and the results of some of the neuropsychological tests were administrated to children and subsequently were analyzed. Depending on EEG report (positive or negative), subjects were split in two subsample: subjects with "pure" LD and subjects who showed significant paroxysmal abnormalities at the EEG. This comparison shows that the profile of the two subsamples matches for many aspects. The only statistically significant differences are the increased impairment of meta-phonological skills and reading speed in children with EEG abnormalities. On the other hand, children with "pure" LD are inclined to manifest more frequently difficulties in highly-modularized processes, such as counting. In conclusion, the substantial overlap of the two profiles causes a reflection about the difficulty in making differential diagnosis in children who show a suspected LD, in absence of an accurate neurophysiological and neuroradiological investigation. The study did not find out useful markers to select subjects who should carry EEG and encephalic NMR. Our team established to keep EEG in waking in the diagnostic protocol, for all children with LD diagnosis. Only in case of abnormalities at the track, we prescribed EEG in sleeping and encephalic NMR.

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

PubMed Central

Ma, Yue; Tuskan, Gerald A.

2018-01-01

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln(L) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level. PMID:29686995

Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

PubMed

Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto

2016-06-21

QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

PubMed Central

Nice, Liana M.; Steffenson, Brian J.; Brown-Guedira, Gina L.; Akhunov, Eduard D.; Liu, Chaochih; Kono, Thomas J. Y.; Morrell, Peter L.; Blake, Thomas K.; Horsley, Richard D.; Smith, Kevin P.; Muehlbauer, Gary J.

2016-01-01

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm. PMID:27182953

The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

PubMed

Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

2012-01-01

The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

Magma-tectonic Interaction at Laguna del Maule, Chile

NASA Astrophysics Data System (ADS)

Keranen, K. M.; Peterson, D. E.; Miller, C. A.; Garibaldi, N.; Tikoff, B.; Williams-Jones, G.

2016-12-01

The Laguna del Maule Volcanic Field (LdM), Chile, the largest concentration of rhyolite <20 kyr globally, exhibits crustal deformation at rates higher than any non-erupting volcano. The interaction of large magmatic systems with faulting is poorly understood, however, the Chaitén rhyolitic system demonstrated that faults can serve as magma pathways during an eruption. We present a complex fault system at LdM in close proximity to the magma reservoir. In March 2016, 18 CHIRP seismic reflection lines were acquired at LdM to identify faults and analyze potential spatial and temporal impacts of the fault system on volcanic activity. We mapped three key horizons on each line, bounding sediment packages between Holocene onset, 870 ybp, and the present date. Faults were mapped on each line and offset was calculated across key horizons. Our results indicate a system of normal-component faults in the northern lake sector, striking subparallel to the mapped Troncoso Fault SW of the lake. These faults correlate to prominent magnetic lineations mapped by boat magnetic data acquired February 2016 which are interpreted as dykes intruding along faults. We also imaged a vertical fault, interpreted as a strike-slip fault, and a series of normal faults in the SW lake sector near the center of magmatic inflation. Isochron and fault offset maps illuminate areas of growth strata and indicate migration and increase of fault activity from south to north through time. We identify a domal structure in the SW lake sector, coincident with an area of low magnetization, in the region of maximum deformation from InSAR results. The dome experienced 10 ms TWT ( 10 meters) of uplift throughout the past 16 kybp, which we interpret as magmatic inflation in a shallow magma reservoir. This inflation is isolated to a 1.5 km diameter region in the hanging wall of the primary normal fault system, indicating possible fault-facilitated inflation.

Absence of individual chromosomes and radiation sensitivity of bread wheat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jagathesan, D.; Swaminathan, M. S.

Seeds of twenty different monosomics of bread wheat of the variety Chinese Spring were treated with different doses of x rays to determine LD-50. Dormant seeds with an embryo moisture content of 4 to 5% were irradiated with doses from 5000 to 50000 r. The seeds were sown immediately after irradiation. Germination and survival counts were made 15 days after sowing. The LD-50 rates found are tabulated and show that the monosomics are more radiosensitive than the disonics. Monosomtics for D genome chromosomes have generally a higher LD-50 dosage in comparison with A and B genomes. (J.S.R.)

1059 and 1328nm LD pumped Nd:S-FAP solid state laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun Lianke; Zhang Shaojun; Zhao Shengzhi

In this paper the authors introduce a new laser crystal--Nd{sup 3+}:Sr{sub 5}(PO{sub 4}){sub 3}F, Nd:S-FAP, and present its optical and physical characteristics. Based on the experiment lasing performance of CW LD pumped Nd:S-FAP crystal is reported here: the threshold and slope efficiency of 1059 nm Nd:S-FAP laser pumped by CW LD at 805nm are 7mW and 41%, and that of 1328nm Nd:S-FAP laser are 19mW and 35%. The comparison between experimental result and theoretical calculation is also discussed in this paper.

Cognitive control in children with learning disabilities: neuromarker for deficient executive functions.

PubMed

Alahmadi, Nsreen A

2017-08-02

The neural underpinnings of learning disabilities (LD) are still not known. Recent discussions focus over whether domain-specific and/or domain-unspecific reasons might be responsible for LD either alone or in combination with each other. This study applied standard nonverbal Go-NoGo tasks (visual continuous performance test) to LD and healthy control children to examine whether they show deficient executive functions. During this Go-NoGo task, electroencephalogram was measured in addition to reaction times, hits, omissions, and commissions to the Go and NoGo stimuli. It was shown that children with LD reacted slower with variable responses to Go stimuli and made more omission errors in comparison with the healthy control children. The analysis of the event-related potential indicated that the deficient behavior in this task is associated with smaller - and in part nonexistent - P3d amplitudes. This neural activation indicates a different neural activation pattern during action inhibition in LD children. The neural networks involved in controlling action inhibition are mostly located in frontal brain areas, for which it has been shown that children with LD show neural activation deficiencies. This is possibly a consequence of a maturational delay of the frontal cortex.

Implications of climate change on the distribution of the tick vector Ixodes scapularis and risk for Lyme disease in the Texas-Mexico transboundary region

PubMed Central

2014-01-01

Background Disease risk maps are important tools that help ascertain the likelihood of exposure to specific infectious agents. Understanding how climate change may affect the suitability of habitats for ticks will improve the accuracy of risk maps of tick-borne pathogen transmission in humans and domestic animal populations. Lyme disease (LD) is the most prevalent arthropod borne disease in the US and Europe. The bacterium Borrelia burgdorferi causes LD and it is transmitted to humans and other mammalian hosts through the bite of infected Ixodes ticks. LD risk maps in the transboundary region between the U.S. and Mexico are lacking. Moreover, none of the published studies that evaluated the effect of climate change in the spatial and temporal distribution of I. scapularis have focused on this region. Methods The area of study included Texas and a portion of northeast Mexico. This area is referred herein as the Texas-Mexico transboundary region. Tick samples were obtained from various vertebrate hosts in the region under study. Ticks identified as I. scapularis were processed to obtain DNA and to determine if they were infected with B. burgdorferi using PCR. A maximum entropy approach (MAXENT) was used to forecast the present and future (2050) distribution of B. burgdorferi-infected I. scapularis in the Texas-Mexico transboundary region by correlating geographic data with climatic variables. Results Of the 1235 tick samples collected, 109 were identified as I. scapularis. Infection with B. burgdorferi was detected in 45% of the I. scapularis ticks collected. The model presented here indicates a wide distribution for I. scapularis, with higher probability of occurrence along the Gulf of Mexico coast. Results of the modeling approach applied predict that habitat suitable for the distribution of I. scapularis in the Texas-Mexico transboundary region will remain relatively stable until 2050. Conclusions The Texas-Mexico transboundary region appears to be part of a continuum in the pathogenic landscape of LD. Forecasting based on climate trends provides a tool to adapt strategies in the near future to mitigate the impact of LD related to its distribution and risk for transmission to human populations in the Mexico-US transboundary region. PMID:24766735

Predictive value of hippocampal MR imaging-based high-dimensional mapping in mesial temporal epilepsy: preliminary findings.

PubMed

Hogan, R E; Wang, L; Bertrand, M E; Willmore, L J; Bucholz, R D; Nassif, A S; Csernansky, J G

2006-01-01

We objectively assessed surface structural changes of the hippocampus in mesial temporal sclerosis (MTS) and assessed the ability of large-deformation high-dimensional mapping (HDM-LD) to demonstrate hippocampal surface symmetry and predict group classification of MTS in right and left MTS groups compared with control subjects. Using eigenvector field analysis of HDM-LD segmentations of the hippocampus, we compared the symmetry of changes in the right and left MTS groups with a group of 15 matched controls. To assess the ability of HDM-LD to predict group classification, eigenvectors were selected by a logistic regression procedure when comparing the MTS group with control subjects. Multivariate analysis of variance on the coefficients from the first 9 eigenvectors accounted for 75% of the total variance between groups. The first 3 eigenvectors showed the largest differences between the control group and each of the MTS groups, but with eigenvector 2 showing the greatest difference in the MTS groups. Reconstruction of the hippocampal deformation vector fields due solely to eigenvector 2 shows symmetrical patterns in the right and left MTS groups. A "leave-one-out" (jackknife) procedure correctly predicted group classification in 14 of 15 (93.3%) left MTS subjects and all 15 right MTS subjects. Analysis of principal dimensions of hippocampal shape change suggests that MTS, after accounting for normal right-left asymmetries, affects the right and left hippocampal surface structure very symmetrically. Preliminary analysis using HDM-LD shows it can predict group classification of MTS and control hippocampi in this well-defined population of patients with MTS and mesial temporal lobe epilepsy (MTLE).

7 CFR 1753.47 - Plans and specifications (P&S).

Code of Federal Regulations, 2014 CFR

2014-01-01

... the Loan Design (LD) shall be revised to reflect any needed changes (See § 1753.3). (ii) Deviations... units and guide drawings, if any. (4) Key, detail, and cable layout maps. (5) RUS Contract Form 787...

7 CFR 1753.47 - Plans and specifications (P&S).

Code of Federal Regulations, 2011 CFR

2011-01-01

... the Loan Design (LD) shall be revised to reflect any needed changes (See § 1753.3). (ii) Deviations... units and guide drawings, if any. (4) Key, detail, and cable layout maps. (5) RUS Contract Form 787...

7 CFR 1753.47 - Plans and specifications (P&S).

Code of Federal Regulations, 2012 CFR

2012-01-01

... the Loan Design (LD) shall be revised to reflect any needed changes (See § 1753.3). (ii) Deviations... units and guide drawings, if any. (4) Key, detail, and cable layout maps. (5) RUS Contract Form 787...

7 CFR 1753.47 - Plans and specifications (P&S).

Code of Federal Regulations, 2013 CFR

2013-01-01

... the Loan Design (LD) shall be revised to reflect any needed changes (See § 1753.3). (ii) Deviations... units and guide drawings, if any. (4) Key, detail, and cable layout maps. (5) RUS Contract Form 787...

7 CFR 1753.47 - Plans and specifications (P&S).

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Loan Design (LD) shall be revised to reflect any needed changes (See § 1753.3). (ii) Deviations... units and guide drawings, if any. (4) Key, detail, and cable layout maps. (5) RUS Contract Form 787...

The Effects of a Story-Mapping Procedure to Improve the Comprehension Skills of Expository Text Passages for Elementary Students with Learning Disabilities

ERIC Educational Resources Information Center

Stagliano, Christina; Boon, Richard T.

2009-01-01

The purpose of this study was to examine the effects of using a story-mapping procedure to improve and enhance the reading comprehension skills using expository text passages for 3 fourth-grade students with learning disabilities (LD). The study was conducted in the resource classroom in which the participants regularly received reading…

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

PubMed Central

Song, Bao-Hua; Windsor, Aaron J.; Schmid, Karl J.; Ramos-Onsins, Sebastian; Schranz, M. Eric; Heidel, Andrew J.; Mitchell-Olds, Thomas

2009-01-01

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ∼45% higher recombination per kilobase than outcrossing A. lyrata. PMID:19104077

Validation of the SCIAN LD-735 wrist blood pressure monitor for home blood pressure monitoring according to the European Society of Hypertension International Protocol revision 2010.

PubMed

Kang, Yuan-Yuan; Chen, Qi; Li, Yan; Wang, Ji-Guang

2016-08-01

This study aimed to evaluate the accuracy of the automated oscillometric wrist blood pressure monitor SCIAN LD-735 for home blood pressure monitoring according to the International Protocol of the European Society of Hypertension revision 2010. Systolic and diastolic blood pressures were measured sequentially in 33 adult Chinese participants (10 women, mean age 44.8 years) using a mercury sphygmomanometer (two observers) and the SCIAN LD-735 device (one supervisor). A total of 99 pairs of comparisons were obtained from 33 participants for judgments in two parts with three grading phases. The SCIAN LD-735 device achieved the targets in part 1 of the validation study. The number of absolute differences between device and observers within 5, 10, and 15 mmHg was 86/99, 97/99, and 98/99, respectively, for systolic blood pressure and 85/99, 98/99, and 99/99, respectively, for diastolic blood pressure. The device also fulfilled the criteria in part 2 of the validation study. In total, 30 and 33 participants for systolic and diastolic blood pressure, respectively, had at least two of the three device-observer differences within 5 mmHg (required ≥24). No participant had all of the three device-observer comparisons greater than 5 mmHg for systolic or diastolic blood pressure. The SCIAN wrist blood pressure monitor LD-735 has passed the requirements of the International Protocol revision 2010, and hence can be recommended for home use in adults.

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

PubMed

Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

2017-07-05

The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

Pharmacogenetics.

PubMed

Roses, A D

2001-10-01

Pharmacogenetics is the variability of drug response due to inherited characteristics in individuals. Drug metabolizing enzymes have been studied for decades, first as chemical reactions and, more recently, as specific polymorphisms of known molecules. With the availability of whole-genome single-nucleotide polymorphism (SNP) maps, it will soon be possible to create an SNP profile for patients who experience adverse events (AEs) or who respond clinically to the medicine (efficacy). Proof-of-principle experiments have demonstrated that high density SNP maps in chromosomal regions of genetic linkage facilitate the identification of susceptibility disease genes. Whole-genome SNP mapping analyses aimed at determining linkage disequilibrium (LD) profiles along an ordered human genome backbone are in progress. SNP 'fingerprints' or SNP PRINTs(sm) will be used to identify patients at greater risk of an AE, or those patients with a greater chance of responding to a medicine. As LD maps for various ethnic populations are constructed, the number of SNPs necessary to measure for an individual will decrease. Standardized pharmacogenetic maps for drug registration and post-marketing surveillance will result in safer, more effective and more cost-efficient medicines. The timing of these pharmacogenetic applications will occur over the next 5 years. In contrast, the benefits of pharmacogenomic applications such as the identification of new tractable targets will not be visible as new medicines for 7-12 years, due to the lengthy drug development and registration processes.

Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina

PubMed Central

Zhu, Yuan; Valter, Krisztina; Bisti, Silvia; Eells, Janis; Stone, Jonathan

2010-01-01

Purpose To identify the genes and noncoding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary antioxidant (saffron) and of photobiomodulation (PBM). Methods We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12 h 5 lux, 12 h darkness) were challenged by 24 h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1 mg/kg/day for 21 days) or PBM (9 J/cm2 at the eye, daily for 5 days). RNA from one eye of four animals in each of the six experimental groups (control, light damage [LD], saffron, PBM, saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate the microarray results. Results LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (p<0.05 in comparison with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes. By contrast, ncRNAs were prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62%, respectively). Conclusions Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given before retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for the more focused study of their mechanisms. PMID:20844572

Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

PubMed

Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

2015-09-01

Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Quality of life in newly diagnosed children with specific learning disabilities (SpLD) and differences from typically developing children: a study of child and parent reports.

PubMed

Ginieri-Coccossis, M; Rotsika, V; Skevington, S; Papaevangelou, S; Malliori, M; Tomaras, V; Kokkevi, A

2013-07-01

Research on quality of life (QoL) of school children with specific learning disabilities (SpLD) and their parents is scarce. The present study explores QoL deficits in newly diagnosed children with SpLD and their parents, in comparison to a similar age group of typically developing children. Possible associations between parental and child QoL were statistically explored in both groups of children. 70 newly diagnosed children with SpLD [International Classification of Diseases-10 (ICD-10) criteria] (38 boys, 32 girls, mean age 10.1 years) and a control group of 69 typically developing children of the same age (40 boys, 29 girls, mean age 10.6 years) were recruited. Children were of normal intelligence quotient, attending mainstream schools. Their parents were also recruited so a child's scores could be associated with corresponding parental scores (mother or father). Children's QoL was assessed by the German questionnaire for measuring quality of life in children and adolescents (KINDL(R) ) questionnaire and parental QoL by World Health Organization Quality of Life brief questionnaire (WHOQOL-BREF) of the World Health Organization. Children with SpLD in comparison to typically developing children reported according to the KINDL(R) measurement poorer emotional well-being, lower self-esteem and satisfaction in their relationships with family and friends. Surprisingly, school functioning was not reported by these children as an area of concern. Parents of children with SpLD indicated experiencing lower satisfaction in the WHOQOL-BREF domains of social relationships and environment. Correlational and regression analysis with parental-child QoL scores provided evidence that in the SpLD group, parental scores on WHOQOL-BREF social relationships and psychological health domains could be predictors of the child's emotional well-being, satisfaction with family, friends and school functioning. Stepwise regression analysis verified the effect of parents' WHOQOL-BREF social relationships domain on several dimensions of children's KINDL(R) QoL.   The results may suggest certain significant effects of the SpLD condition on newly diagnosed children's QoL. Emotional and social deficits seem to be experienced by this cohort of children and their parents. Investigation into the possible interrelationships between parental and child QoL seems to indicate that parental social wellbeing may to a certain extend influence some dimensions of the child's QoL. The findings are useful for policy making and specialized interventions for children with SpLD and their families. © 2012 John Wiley & Sons Ltd.

Why are they late? Timing abilities and executive control among students with learning disabilities.

PubMed

Grinblat, Nufar; Rosenblum, Sara

2016-12-01

While a deficient ability to perform daily tasks on time has been reported among students with learning disabilities (LD), the underlying mechanism behind their 'being late' is still unclear. This study aimed to evaluate the organization in time, time estimation abilities, actual performance time pertaining to specific daily activities, as well as the executive functions of students with LD in comparison to those of controls, and to assess the relationships between these domains among each group. The participants were 27 students with LD, aged 20-30, and 32 gender and age-matched controls who completed the Time Organization and Participation Scale (TOPS) and the Behavioral Rating Inventory of Executive Function-Adult version (BRIEF-A). In addition, their ability to estimate the time needed to complete the task of preparing a cup of coffee as well as their actual performance time were evaluated. The results indicated that in comparison to controls, students with LD showed significantly inferior organization in time (TOPS) and executive function abilities (BRIEF-A). Furthermore, their time estimation abilities were significantly inferior and they required significantly more time to prepare a cup of coffee. Regression analysis identified the variables that predicted organization in time and task performance time among each group. The significance of the results for both theoretical and clinical implications are discussed. What this paper adds? This study examines the underlying mechanism of the phenomena of being late among students with LD. Following a recent call for using ecologically valid assessments, the functional daily ability of students with LD to prepare a cup of coffee and to organize time were investigated. Furthermore, their time estimation and executive control abilities were examined as a possible underlying mechanism for their lateness. Although previous studies have indicated executive control deficits among students with LD, to our knowledge, this is the first analysis of the relationships between their executive control and time estimation deficits and their influence upon their daily function and organization in time abilities. Our findings demonstrate that students with LD need more time in order to execute simple daily activities, such as preparing a cup of coffee. Deficient working memory, retrospective time estimation ability and inhibition predicted their performance time and organization in time abilities. Therefore, this paper sheds light on the mechanism behind daily performance in time among students with LD and emphasizes the need for future development of focused intervention programs to meet their unique needs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mapping the Rust Resistant Loci MXC3 and MER in P. trichocarpa and Assessing the Intermarker Linkage Disequilibrium in MXC3 Region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Tongming; Difazio, Stephen P.; Gunter, Lee E

In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa, we have mapped two resistance loci, MXC3 and MER, and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations. We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3. The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16more » kb, respectively. The MXC3 region also contained six disease-resistance candidate genes. The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker-aided selection.« less

Erosion wear response of epoxy composites filled with steel industry slag and sludge particles: A comparative study

NASA Astrophysics Data System (ADS)

Purohit, Abhilash; Satapathy, Alok

2018-03-01

In the field of composite research, use of industrial wastes such as slag and sludge particles as filler in wear resistant polymer composites has not been very common. Owing to the very high cost of conventional filler materials in polymer composites, exploring the possibility of using low cost minerals and industrial wastes for this purpose has become the need of the hour. In this context this work explores the possibility of such polymer composites filled with low cost industrial wastes and presents a comparison of mechanical characteristics among three types of epoxy based composites filled with Linz - Donawitz sludge (LD sludge), blast furnace slag (BF slag) and Linz - Donawitz slag (LD slag) respectively. A comparative study in regard to their solid particle erosion wear characteristics under similar test conditions is also included. Composites with different weight proportions (0, 5, 10, 15 and 20 wt. %) of LD sludge are fabricated by solution casting technique. Mechanical properties such as micro- hardness, tensile strength and flexural strength of three types of composites have been evaluated as per ASTM test standards and solid particle erosion wear test is performed following a design of experiment approach based on Taguchi’s orthogonal array. Five control factors (impact velocity, erodent size, filler content, impingement angle and erodent temperature) each at five levels are considered to conduct erosion wear tests. The test results for epoxy-LD sludge composites are compared with those of epoxy-BF slag and epoxy-LD slag composites reported by previous investigators. The comparison reveals that epoxy filled with LD sludge exhibits superior mechanical and erosion wear characteristics among the three types of composites considered in this study. This work also opens up a new avenue for value added utilization of an abundant industrial waste in the making of epoxy based functional composites.

Mapping microscopic order in plant and mammalian cells and tissues: novel differential polarization attachment for new generation confocal microscopes (DP-LSM)

NASA Astrophysics Data System (ADS)

Steinbach, G.; Pawlak, K.; Pomozi, I.; Tóth, E. A.; Molnár, A.; Matkó, J.; Garab, G.

2014-03-01

Elucidation of the molecular architecture of complex, highly organized molecular macro-assemblies is an important, basic task for biology. Differential polarization (DP) measurements, such as linear (LD) and circular dichroism (CD) or the anisotropy of the fluorescence emission (r), which can be carried out in a dichrograph or spectrofluorimeter, respectively, carry unique, spatially averaged information about the molecular organization of the sample. For inhomogeneous samples—e.g. cells and tissues—measurements on macroscopic scale are not satisfactory, and in some cases not feasible, thus microscopic techniques must be applied. The microscopic DP-imaging technique, when based on confocal laser scanning microscope (LSM), allows the pixel by pixel mapping of anisotropy of a sample in 2D and 3D. The first DP-LSM configuration, which, in fluorescence mode, allowed confocal imaging of different DP quantities in real-time, without interfering with the ‘conventional’ imaging, was built on a Zeiss LSM410. It was demonstrated to be capable of determining non-confocally the linear birefringence (LB) or LD of a sample and, confocally, its FDLD (fluorescence detected LD), the degree of polarization (P) and the anisotropy of the fluorescence emission (r), following polarized and non-polarized excitation, respectively (Steinbach et al 2009 Acta Histochem.111 316-25). This DP-LSM configuration, however, cannot simply be adopted to new generation microscopes with considerably more compact structures. As shown here, for an Olympus FV500, we designed an easy-to-install DP attachment to determine LB, LD, FDLD and r, in new-generation confocal microscopes, which, in principle, can be complemented with a P-imaging unit, but specifically to the brand and type of LSM.

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

DOE PAGES

Guo, Hao-Bo; Ma, Yue; Tuskan, Gerald A.; ...

2018-01-01

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here)more » from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.« less

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Hao-Bo; Ma, Yue; Tuskan, Gerald A.

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here)more » from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.« less

Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays

PubMed Central

2011-01-01

Background The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. Results The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Conclusions Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses. PMID:21798003

Leishmania donovani Argininosuccinate Synthase Is an Active Enzyme Associated with Parasite Pathogenesis

PubMed Central

Lakhal-Naouar, Ines; Jardim, Armando; Strasser, Rona; Luo, Shen; Kozakai, Yukiko; Nakhasi, Hira L.; Duncan, Robert C.

2012-01-01

Background Gene expression analysis in Leishmania donovani (Ld) identified an orthologue of the urea cycle enzyme, argininosuccinate synthase (LdASS), that was more abundantly expressed in amastigotes than in promastigotes. In order to characterize in detail this newly identified protein in Leishmania, we determined its enzymatic activity, subcellular localization in the parasite and affect on virulence in vivo. Methodology/Principal Findings Two parasite cell lines either over expressing wild type LdASS or a mutant form (G128S) associated with severe cases of citrullinemia in humans were developed. In addition we also produced bacterially expressed recombinant forms of the same proteins. Our results demonstrated that LdASS has argininosuccinate synthase enzymatic activity that is abolished using an ASS specific inhibitor (MDLA: methyl-D-L-Aspartic acid). However, the mutant form of the protein is inactive. We demonstrate that though LdASS has a glycosomal targeting signal that binds the targeting apparatus in vitro, only a small proportion of the total cellular ASS is localized in a vesicle, as indicated by protection from protease digestion of the crude organelle fraction. The majority of LdASS was found to be in the cytosolic fraction that may include large cytosolic complexes as indicated by the punctate distribution in IFA. Surprisingly, comparison to known glycosomal proteins by IFA revealed that LdASS was located in a structure different from the known glycosomal vesicles. Significantly, parasites expressing a mutant form of LdASS associated with a loss of in vitro activity had reduced virulence in vivo in BALB/c mice as demonstrated by a significant reduction in the parasite load in spleen and liver. Conclusion/Significance Our study suggests that LdASS is an active enzyme, with unique localization and essential for parasite survival and growth in the mammalian host. Based on these observations LdASS could be further explored as a potential drug target. PMID:23094117

Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.

PubMed Central

Rossi, Monica; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Rau, Domenico; Attene, Giovanna; Papa, Roberto

2009-01-01

Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes. PMID:25567895

Towards a Remote Sensing Based Assessment of Land Susceptibility to Degradation: Examining Seasonal Variation in Land Use-Land Cover for Modelling Land Degradation in a Semi-Arid Context

NASA Astrophysics Data System (ADS)

Mashame, Gofamodimo; Akinyemi, Felicia

2016-06-01

Land degradation (LD) is among the major environmental and anthropogenic problems driven by land use-land cover (LULC) and climate change worldwide. For example, poor LULC practises such as deforestation, livestock overstocking, overgrazing and arable land use intensification on steep slopes disturbs the soil structure leaving the land susceptible to water erosion, a type of physical land degradation. Land degradation related problems exist in Sub-Saharan African countries such as Botswana which is semi-arid in nature. LULC and LD linkage information is still missing in many semi-arid regions worldwide.Mapping seasonal LULC is therefore very important in understanding LULC and LD linkages. This study assesses the impact of seasonal LULC variation on LD utilizing Remote Sensing (RS) techniques for Palapye region in Central District, Botswana. LULC classes for the dry and rainy seasons were classified using LANDSAT 8 images at Level I according to the Food and Agriculture Organization (FAO) International Organization of Standardization (ISO) code 19144. Level I consists of 10 LULC classes. The seasonal variations in LULC are further related to LD susceptibility in the semi-arid context. The results suggest that about 985 km² (22%) of the study area is susceptible to LD by water, major LULC types affected include: cropland, paved/rocky material, bare land, built-up area, mining area, and water body. Land degradation by water susceptibility due to seasonal land use-land cover variations is highest in the east of the study area where there is high cropland to bare land conversion.

Assessing browse trend at the landscape level Part 2: Monitoring

USGS Publications Warehouse

Keigley, R.B.; Frisina, M.R.; Fager, C.W.

2002-01-01

In Part 1, we assessed browse trend across a wide geographic area of Mt. Haggin Wildlife Management Area by conducting surveys of browsing-related architectures. Those data were qualitative. Below we describe the periodic collection of quantitative data from permanently marked locations; we refer to this phase of the trend assessment program as "monitoring." Trend was monitored by three methods: 1 Repeat photography. 2 Comparison of the height of live stems with the height of stems killed by browsing (LD Index). 3 Net annual stem growth rate (NAGRL3). The photography provides an assessment of trend from the comparison of photographs taken at intervals of a few years. The LD Index and NAGRL3 measurements provide an immediate assessment of trend.

Haplotype diversity in 11 candidate genes across four populations.

PubMed

Beaty, T H; Fallin, M D; Hetmanski, J B; McIntosh, I; Chong, S S; Ingersoll, R; Sheng, X; Chakraborty, R; Scott, A F

2005-09-01

Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.

Mucuna pruriens in Parkinson disease: A double-blind, randomized, controlled, crossover study.

PubMed

Cilia, Roberto; Laguna, Janeth; Cassani, Erica; Cereda, Emanuele; Pozzi, Nicolò G; Isaias, Ioannis U; Contin, Manuela; Barichella, Michela; Pezzoli, Gianni

2017-08-01

To investigate whether Mucuna pruriens (MP), a levodopa-containing leguminous plant growing in all tropical areas worldwide, may be used as alternative source of levodopa for indigent individuals with Parkinson disease (PD) who cannot afford long-term therapy with marketed levodopa preparations. We investigated efficacy and safety of single-dose intake of MP powder from roasted seeds obtained without any pharmacologic processing. Eighteen patients with advanced PD received the following treatments, whose sequence was randomized: (1) dispersible levodopa at 3.5 mg/kg combined with the dopa-decarboxylase inhibitor benserazide (LD+DDCI; the reference treatment); (2) high-dose MP (MP-Hd; 17.5 mg/kg); (3) low-dose MP (MP-Ld; 12.5 mg/kg); (4) pharmaceutical preparation of LD without DDCI (LD-DDCI; 17.5 mg/kg); (5) MP plus benserazide (MP+DDCI; 3.5 mg/kg); (6) placebo. Efficacy outcomes were the change in motor response at 90 and 180 minutes and the duration of on state. Safety measures included any adverse event (AE), changes in blood pressure and heart rate, and the severity of dyskinesias. When compared to LD+DDCI, MP-Ld showed similar motor response with fewer dyskinesias and AEs, while MP-Hd induced greater motor improvement at 90 and 180 minutes, longer ON duration, and fewer dyskinesias. MP-Hd induced less AEs than LD+DDCI and LD-DDCI. No differences in cardiovascular response were recorded. Single-dose MP intake met all noninferiority efficacy and safety outcome measures in comparison to dispersible levodopa/benserazide. Clinical effects of high-dose MP were similar to levodopa alone at the same dose, with a more favorable tolerability profile. NCT02680977. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Skin blood flow: a comparison of transcutaneous oximetry and laser Doppler flowmetry.

PubMed

Allen, P I; Goldman, M

1987-10-01

In normal limbs skin blood flow (SBF) falls on standing, but in ischaemic limbs there is a characteristic blush on dependancy. We studied the effect of changing posture in a range of ischaemic limbs, using two non-invasive techniques--laser Doppler (LD) and transcutaneous oximetry (TcPO2). Warmed TcPO2 and LD probes were placed over the first metatarsal cleft and SBF recorded with the limb horizontal, dependant and elevated. Ankle to brachial pressure ratios (A:B) were also measured. Twelve patients with lower limb ischaemia, mean A:B ratio 0.5 +/- 0.21 (+/- S.D.) were compared with 21 asymptomatic controls, mean A:B ratio 1.2 +/- 0.15. In the controls, neither TcPO2 nor LD values changed significantly with limb position. Both flux and oxygen tension were significantly lower in ischaemic limbs in all positions; on lowering the ischaemic limb, flux unexpectedly rose to 23.5 +/- 17.7 V from a mean of 14 + 9.0 V (horizontal). Both TcPO2 and LD correlated well with A:B ratio in two positions: horizontal r (TcPO2) = 0.73, r(LD) = 0.57; elevated r(TcPO2) = 0.78, r(LD) = 0.68. Overall there was a highly significant correlation between LD and TcPO2 (r = 0.6, P less than 0.001, Student's test), but this was strongest in the elevated position (r = 0.87, P less than 0.001). LD and TcPO2 relate to A:B ratio and to each other, particularly in the stressed limb; in the well perfused limb, the poorer correlation suggests skin perfusion is not linearly related to tissue oxygen tension.

[Memory characteristic in boys with attention deficit/hyperactivity disorder comorbid learning disability].

PubMed

Wu, Zhaomin; Wang, Na; Qian, Qiujin; Yang, Li; Qian, Ying; Liu, Lu; Liu, Yuxin; Cheng, Jia; Sun, Li; Cao, Qingjiu; Wang, Yufeng

2014-06-10

To explore the memory characteristic in boys with attention-deficit/hyperactivity disorder (ADHD) plus learning disability (LD). A total of 97 ADHD boys with comorbid LD (ADHD+LD), 97 ADHD boys without comorbid LD (ADHD-LD) and 97 healthy controls (based on the criteria of DSM-IV) were recruited from the outpatient clinic of Peking University Sixth Hospital from December 2003 to September 2012. Individuals across three groups were matched by ages, intelligence quotient (IQ) and ADHD subtypes. The Wechsler Memory Scale (WMS) was used to access the characteristics of several memory domains. ADHD +LD group performed the worst and control group the best in memory quotient (MQ) (90 ± 15 vs 98 ± 14 & 104 ± 14) and long-term memory domain ((36.0 ± 10.2) vs (42.1 ± 7.8) & (45.6 ± 6.7) score, all P < 0.05) . ADHD+LD group scored significantly lower than the control group in short-term memory ( (53.0 ± 9.2) vs (58.0 ± 9.7) score, P < 0.05) and immediate memory domains ((10.0 ± 3.3) vs (11.3 ± 3.5) score, P < 0.05). However, ADHD+LD group scored slightly but not significantly lower than the ADHD-LD group ((54.9 ± 10.7),(10.8 ± 3.2) score, P > 0.05). In most subscales of WMS, ADHD+LD group scored significantly lower than both ADHD-LD and control group in current information and orientation, mental control (1→100) , mental control (100→1) and associate learning subscales ( (8.8 ± 3.1) vs (10.0 ± 3.0) & (9.9 ± 2.3) score, (8.7 ± 4.1) vs (10.0 ± 3.9) & (11.1 ± 3.6) score, (10.7 ± 3.9) vs (12.9 ± 2.8) & (13.7 ± 2.2) score, (9.8 ± 3.1) vs (10.8 ± 2.6) & (11.1 ± 2.1) score, all P < 0.05) . In mental control (accumulation) subscale, all pairwise comparisons were statistically significant (all P < 0.05) . In subscales of figure memory, visual reproduction and digit span, ADHD+LD scored significantly lower than the control group (all P < 0.05), but not the ADHD-LD group (all P > 0.05). Boys with ADHD comorbid LD show deficits in overall memory function and long-term memory while short-term memory is partially damaged. Impairment in immediate memory is not detected.

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances.

PubMed

Li, X; Yang, S; Dong, K; Tang, Z; Li, K; Fan, B; Wang, Z; Liu, B

2017-10-01

Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.

Adolescent athletes with learning disability display atypical maturational trajectories on concussion baseline testing: Implications based on a Finnish sample.

PubMed

Peltonen, Kati; Vartiainen, Matti; Laitala-Leinonen, Tiina; Koskinen, Sanna; Luoto, Teemu; Pertab, Jon; Hokkanen, Laura

2018-05-21

Previous research has reported lower cognitive test scores on baseline testing in athletes reporting multiple previous concussions or a history of learning disability (LD). Age also has an important influence on cognitive performance. While these factors have been considered individually in previous studies, the present study is the first to explore the interaction of age, self-reported LD, and history of concussion on baseline Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT®) in a nationwide study of adolescent athletes. ImPACT® was administered to 1823 Finnish male ice hockey players (aged 12-21 years old) prior to the 2015-2016 or 2016-2017 playing seasons. Linear regressions and simple slopes analyses were used for clarifying the impact of LD and previous concussion history on maturational trajectories. In comparison to typically developing athletes, athletes with LD had lower neurocognitive scores in all composites and differing maturational trajectory in verbal memory and visual motor speed. The number of previous concussions did not impair neurocognitive performance at baseline assessment. Application of standard age-based norms to adolescent athletes with a history of LD has the potential to negatively skew clinical decision-making. Separate reference values for LD athletes are warranted due to their unique developmental cognitive trajectories. The reference values for the Finnish participants in this study are presented.

Historical Relevance: NCLB in Relation to Exclusion of Prince George's County ADHD and LD Students

ERIC Educational Resources Information Center

Watt, Lawrence

2013-01-01

The implications of No Child Left Behind made comparisons of all students in the American education system with students in other countries. NCLB also made historical comparisons with students from previous generations. The purpose of this study was to point out the impropriety of making these comparisons. Students who attended school prior to the…

The effects of repeated low-dose sarin exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shih, T.-M.; Hulet, S.W.; McDonough, J.H.

2006-09-01

This project assessed the effects of repeated low-dose exposure of guinea pigs to the organophosphorus nerve agent sarin. Animals were injected once a day, 5 days per week (Monday-Friday), for 2 weeks with fractions (0.3x, 0.4x, 0.5x, or 0.6x) of the established LD{sub 5} dose of sarin (42 {mu}g/kg, s.c.). The animals were assessed for changes in body weight, red blood cell (RBC) acetylcholinesterase (AChE) levels, neurobehavioral reactions to a functional observational battery (FOB), cortical electroencephalographic (EEG) power spectrum, and intrinsic acetylcholine (ACh) neurotransmitter (NT) regulation over the 2 weeks of sarin exposure and for up to 12 days postinjection.more » No guinea pig receiving 0.3, 0.4 or 0.5 x LD{sub 5} of sarin showed signs of cortical EEG seizures despite decreases in RBC AChE levels to as low as 10% of baseline, while seizures were evident in animals receiving 0.6 x LD{sub 5} of sarin as early as the second day; subsequent injections led to incapacitation and death. Animals receiving 0.5 x LD{sub 5} sarin showed obvious signs of cholinergic toxicity; overall, 2 of 13 animals receiving 0.5 x LD{sub 5} sarin died before all 10 injections were given, and there was a significant increase in the angle of gait in the animals that lived. By the 10th day of injection, the animals receiving saline were significantly easier to remove from their cages and handle and significantly less responsive to an approaching pencil and touch on the rump in comparison with the first day of testing. In contrast, the animals receiving 0.4 x LD{sub 5} sarin failed to show any significant reductions in their responses to an approaching pencil and a touch on the rump as compared with the first day. The 0.5 x LD{sub 5} sarin animals also failed to show any significant changes to the approach and touch responses and did not adjust to handling or removal from the cage from the first day of injections to the last day of handling. Thus, the guinea pigs receiving the 0.4 and 0.5 x LD{sub 5} doses of sarin failed to habituate to some aspects of neurobehavioral testing. Spectral analysis of EEG data suggested that repeated sarin exposure may disrupt normal sleeping patterns (i.e., lower frequency bandwidths). While these EEG changes returned to relative normalcy 6 days after the last injection in animals receiving 0.4 x LD{sub 5} sarin, these changes were still observed in the animals that received 0.5 x LD{sub 5} sarin. Ten to twelve days after the last sarin injection (in 0.4 x LD{sub 5} group only), neurochemical data showed that striatal choline levels were reduced in comparison to the saline group. At this time, atropine sulfate (5 mg/kg, i.p.) challenge resulted in a transient elevation in striatal ACh levels in animals exposed to repeated 0.4 x LD{sub 5} sarin as well as in control animals. No evidence of brain or heart pathology was found in any guinea pig that survived all 10 sarin injections.« less

Minority carrier diffusion length extraction in Cu2ZnSn(Se,S)4 solar cells

NASA Astrophysics Data System (ADS)

Gokmen, Tayfun; Gunawan, Oki; Mitzi, David B.

2013-09-01

We report measurement of minority carrier diffusion length (Ld) for high performance Cu2ZnSn(S,Se)4 (CZTSSe) solar cells in comparison with analogous Cu(In,Ga)(S,Se)2 (CIGSSe) devices. Our Ld extraction method involves performing systematic measurements of the internal quantum efficiency combined with separate capacitance-voltage measurement. This method also enables the measurement of the absorption coefficient of the absorber material as a function of wavelength in a finished device. The extracted values of Ld for CZTSSe samples are at least factor of 2 smaller than those for CIGSSe samples. Combined with minority carrier lifetime (τ) data measured by time-resolved photoluminescence, we deduce the minority carrier mobility (μe), which is also relatively low for the CZTSSe samples.

Semiconductor laser using multimode interference principle

NASA Astrophysics Data System (ADS)

Gong, Zisu; Yin, Rui; Ji, Wei; Wu, Chonghao

2018-01-01

Multimode interference (MMI) structure is introduced in semiconductor laser used in optical communication system to realize higher power and better temperature tolerance. Using beam propagation method (BPM), Multimode interference laser diode (MMI-LD) is designed and fabricated in InGaAsP/InP based material. As a comparison, conventional semiconductor laser using straight single-mode waveguide is also fabricated in the same wafer. With a low injection current (about 230 mA), the output power of the implemented MMI-LD is up to 2.296 mW which is about four times higher than the output power of the conventional semiconductor laser. The implemented MMI-LD exhibits stable output operating at the wavelength of 1.52 μm and better temperature tolerance when the temperature varies from 283.15 K to 293.15 K.

Identifying disease polymorphisms from case-control genetic association data.

PubMed

Park, L

2010-12-01

In case-control association studies, it is typical to observe several associated polymorphisms in a gene region. Often the most significantly associated polymorphism is considered to be the disease polymorphism; however, it is not clear whether it is the disease polymorphism or there is more than one disease polymorphism in the gene region. Currently, there is no method that can handle these problems based on the linkage disequilibrium (LD) relationship between polymorphisms. To distinguish real disease polymorphisms from markers in LD, a method that can detect disease polymorphisms in a gene region has been developed. Relying on the LD between polymorphisms in controls, the proposed method utilizes model-based likelihood ratio tests to find disease polymorphisms. This method shows reliable Type I and Type II error rates when sample sizes are large enough, and works better with re-sequenced data. Applying this method to fine mapping using re-sequencing or dense genotyping data would provide important information regarding the genetic architecture of complex traits.

Effect of facial material softness and applied force on face mask dead volume, face mask seal, and inhaled corticosteroid delivery through an idealized infant replica.

PubMed

Carrigy, Nicholas B; O'Reilly, Connor; Schmitt, James; Noga, Michelle; Finlay, Warren H

2014-08-01

During the aerosol delivery device design and optimization process, in vitro lung dose (LD) measurements are often performed using soft face models, which may provide a more clinically relevant representation of face mask dead volume (MDV) and face mask seal (FMS) than hard face models. However, a comparison of MDV, FMS, and LD for hard and soft face models is lacking. Metal, silicone, and polyurethane represented hard, soft, and very soft facial materials, respectively. MDV was measured using a water displacement technique. FMS was measured using a valved holding chamber (VHC) flow rate technique. The LD of beclomethasone dipropionate (BDP) delivered via a 100-μg Qvar® pressurized metered dose inhaler with AeroChamber Plus® Flow-Vu® VHC and Small Mask, defined as that which passes through the nasal airways of the idealized infant geometry, was measured using a bias tidal flow system with a filter. MDV, FMS, and LD were measured at 1.5 lb and 3.5 lb of applied force. A mathematical model was used to predict LD based on experimental measurements of MDV and FMS. Experimental BDP LD measurements for ABS, silicone, and polyurethane at 1.5 lb were 0.9 (0.6) μg, 2.4 (1.9) μg, and 19.3 (0.9) μg, respectively. At 3.5 lb, the respective LD was 10.0 (1.5) μg, 13.8 (1.4) μg, and 14.2 (0.9) μg. Parametric analysis with the mathematical model showed that differences in FMS between face models had a greater impact on LD than differences in MDV. The use of soft face models resulted in higher LD than hard face models, with a greater difference at 1.5 lb than at 3.5 lb. A lack of a FMS led to decreased dose consistency; therefore, a sealant should be used when measuring LD with a hard ABS or soft silicone face model at 1.5 lb of applied force or less.

Comparison of tolerance to sunlight between spatially distant and genetically different strains of Lymantria dispar nucleopolyhedrovirus.

PubMed

Akhanaev, Yuriy B; Belousova, Irina A; Ershov, Nikita I; Nakai, Madoka; Martemyanov, Vyacheslav V; Glupov, Viktor V

2017-01-01

Baculoviruses are a family of insect-specific pathogenic viruses can persist outside for long periods through the formation of occlusion bodies. In spite of this ability, the UV of sunlight is an essential factor that limits the survival of baculoviruses outside the host. In the current study, we compared the UV tolerance of two strains of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV), which were isolated in spatially different regions (LdMNPV-27/0 in Western Siberia (Russia) and LdMNPV-45/0 in North America (USA)) and dramatically differ in their potency. We exposed the studied strains to sunlight in an open area for 0.25, 0.5, 1, and 2 hours and later perorally inoculated host larvae with the same doses of virus (5x105) and with doses leading to same effect (LD90). We observed that strain LdMNPV-45/0, which previously showed high virulence against L. dispar larvae, was more sensitive to UV irradiation (estimated as the relative rate of inactivation (r, h -1) and as the half-life of the virus (τ1/2, h)) compared to LdMNPV-27/0. Exposure to sunlight induced a significant delay of LdMNPV-45/0-induced pathogenesis already after 0.25 h of sunlight exposure, while for LdMNPV-27/0 this delay was occurred only after 2 h exposure in spite of used concentrations. We also compared the sequences of the main structural proteins of the studied strains as UV light contributes not only to genome damage in viruses but also to structural protein damage. The most prominent genetic difference between the structural proteins of the strains was related to the loss of the virus enhancin factor-1 (vef-1) gene in the LdMNPV-27/0 strain. Thus initially highly potent viral strain (such as LdMNPV-45/0) is not recommend to use in the regions (or forest stand density) with high UV load. The role of virus enhancin factor-1 in baculovirus tolerance to UV needs for following studies.

Differential effect of predictors of bone mineral density and hip geometry in postmenopausal women: a cross-sectional study.

PubMed

Singh, Rekha; Gupta, Sushil; Awasthi, Ashish

2015-01-01

Osteoporosis is an important health problem in postmenopausal women. Lactation duration (LD), parity, menopause duration (MD), and body mass index (BMI) are important predictors of bone mineral density (BMD) and osteoporotic fractures in them. In addition, they have site-specific effects on BMD. Osteoporosis is especially prevalent in postmenopausal women. The aim of the study was to determine the effects of age, parity, LD, MD, and BMI on BMD at different sites and hip geometry in postmenopausal women. In this cross-sectional study, 87 women (45 years and above and at least 5 years postmenopausal) were enrolled. Subjects were divided into three parity groups (group 1: ≤ 2 children, group: 3-4 children, and group 3: > 4 children) and three LD groups (group 1: < 4 years, group 2: 4-8 years, and group 3: > 8 years). BMD was measured at neck of femur (BMD-NF), trochanter (BMD-TR), inter-trochanter (BMD-IT), spine (BMD-LS), and forearm (BMD-FA). Hip geometry was analyzed based on dual energy X-ray absorptiometry. One way ANOVA was used for comparisons of groups, and Bonferroni correction was used as post-hoc test. p value < 0.05 was considered significant. A significant difference in mean BMD was found between parity groups 1 and 3 at BMD-NF, BMD-TR, and BMD-LS, and between LD groups 1 and 3 at BMD-NF, BMD-TR, BMD-IT, and BMD-LS. Mean buckling ratio (BR) at IT was significantly different between parity groups 1 and 3, and LD groups 1 and 3. In multivariate regression analysis, BMI, age, and parity were significant predictors for BMD-NF; parity, BMI, and MD for BMD-TR; BMI, MD, and LD for BMD-IT; BMI and LD for BMD-LS; and age, LD, and BMI for BMD-FA. BMI and LD were significant predictors of IT-BR, while MD and BMI of narrow neck BR. MD, LD, parity, BMI, and age are important factors influencing BMD at hip and spine in postmenopausal women, and have site-specific effects on BMD.

Accounting for linkage disequilibrium in association analysis of diverse populations.

PubMed

Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

2014-04-01

The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases. © 2014 WILEY PERIODICALS, INC.

All-cause and incremental per patient per year cost associated with chronic hepatitis C virus and associated liver complications in the United States: a managed care perspective.

PubMed

McAdam-Marx, Carrie; McGarry, Lisa J; Hane, Christopher A; Biskupiak, Joseph; Deniz, Baris; Brixner, Diana I

2011-09-01

Approximately 3.2-3.9 million U.S. residents are infected with the hepatitis C virus (HCV). Total annual costs (direct and indirect) in the United States for HCV were estimated to be $5.46 billion in 1997, and direct medical costs have been predicted to increase to $10.7 billion for the 10-year period from 2010 through 2019, due in part to the increasing number of HCV patients developing advanced liver disease (AdvLD). To quantify in a sample of commercially insured enrollees (a) total per patient per year (PPPY) all-cause costs to the payer, overall and by the stage of liver disease, for patients diagnosed with HCV; and (b) incremental all-cause costs for patients diagnosed with HCV relative to a matched non-HCV cohort. This retrospective, matched cohort study included patients aged at least 18 years and with at least 6 months of continuous enrollment in a large managed care organization (MCO) claims database from July 1, 2001, through March 31, 2010. Patients with a diagnosis of HCV (ICD-9-CM codes 070.54, 070.70) were identified and stratified into those with and without AdvLD, defined as decompensated cirrhosis (ICD-9-CM codes 070.44, 070.71, 348.3x, 456.0, 456.1, 456.2x, 572.2, 572.3, 572.4, 782.4, 789.59); hepatocellular carcinoma (HCC, ICD-9-CM code 155); or liver transplant (ICD-9-CM codes V42.7, 50.5 or CPT codes 47135, 47136). For patients without AdvLD, the index date was the first HCV diagnosis date observed at least 6 months after the first enrollment date, and at least 6 months of continuous enrollment after the index date were required. HCV patients without AdvLD were stratified into those with and without compensated cirrhosis (ICD-9-CM codes 571.2, 571.5, 571.6). For patients with AdvLD, the index date was the date of the first AdvLD diagnosis observed at least 6 months after the first enrollment date, and at least 1 day of enrollment after the index date was required. Cases were matched in an approximate 1:10 ratio to comparison patients without an HCV diagnosis or AdvLD diagnosis who met all other inclusion criteria based on gender, age, hospital referral region state, pre-index health care costs, alcoholism, human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS), and a modified Charlson Comorbidity Index. For the HCV and comparison patient cohorts, PPPY all-cause costs to the payer were calculated as total allowed charges summed across all patients divided by total patient-days of follow-up for the cohort, multiplied by 365, inflation-normalized to 2009 dollars. Because the calculation of PPPY cost generated a single value for each cohort, bootstrapping was used to generate descriptive statistics. Incremental PPPY costs for HCV patients relative to non-HCV patients were calculated as between-group differences in PPPY costs. T-tests for independent samples were used to compare costs between case and comparison cohorts. A total of 34,597 patients diagnosed with HCV, 78.0% with HCV without AdvLD, 4.4% with compensated cirrhosis, 12.3% with decompensated cirrhosis, 2.8% with HCC, and 2.6% with liver transplant, were matched to 330,435 comparison patients. Mean (SD) age of all HCV cases was 49.9 (8.5) years; 61.7% were male. Incremental mean (SD) PPPY costs in 2009 dollars for all HCV patients relative to comparison patients were $ 9,681 ($176) PPPY. Incremental PPPY costs were $5,870 ($157) and $5,330 ($491) for HCV patients without liver disease and with compensated cirrhosis, respectively. Incremental PPPY costs for patients with AdvLD were $27,845 ($ 965) for decompensated cirrhosis, $43,671 ($2,588) for HCC, and $ 93,609 ($4,482) for transplant. Incremental prescription drug costs, including the cost of antiviral drugs, were $2,739 ($37) for HCV patients overall, $2,659 ($41) for HCV without liver involvement, and $3,102 ($157) for HCV with compensated cirrhosis. These between-group differences were statistically significant at P<0.001. Based on a retrospective analysis of data from a large, MCO claims database, patients diagnosed with HCV had annual all-cause medical costs that were almost twice as high as those of enrollees without a diagnosis of HCV. Health care costs increased dramatically with AdvLD. Data from this study may help MCOs project future HCV costs and facilitate planning for HCV patient management efforts.

Detecting drought and human-induced land degradation using time series trend analysis in Northeastern Brazil drylands

NASA Astrophysics Data System (ADS)

Mariano, D. A.; Costa dos Santos, C. A.; Wardlow, B.

2017-12-01

Land degradation (LD) is one of the most catastrophic outcomes of long-lasting drought events and anthropogenic activities. Assessing climate and human-induced impacts on land can provide information for decision makers to mitigate the effects associated to thereof. The Northeastern region of Brazil (NEB) is the most populous dryland on the planet, making it a highly vulnerable ecosystem especially when considering the lingering drought that started in 2012. The present work consisted on detecting trends in biomass [gross primary productivity (GPP)] and albedo anomalies as indicators of land degradation in NEB. Both GPP and albedo data were derived from MODIS/Terra sensor at 8-day temporal and 500m spatial resolutions. For precipitation z-scores, we relied on CHIRPS-v2 10-day temporal and 5km spatial resolution data. For detecting trends, we applied linear regressions on time series of MODIS GPP and albedo images. Trend analysis was performed for the periods ranging from 2002-2012 (no severe droughts) and 2002-2016 (includes the last drought). The first analysis highlights the human-induced LD whereas the last detected drought induced LD. About 4.5% of the area undergone human-induced degradation whereas drought was responsible for 13%, although, not mutually exclusive. As reported in the literature and official data, grazing intensification was the main driver for human-induced LD. GPP trends were more pronounced and had a stronger signal than albedo, thus, is considered more efficient on mapping LD. Finally, the effects of LD on evapotranspiration anomalies [evaporative stress index (ESI)] were assessed as a way to link it to the hydrological cycle. GPP and ET relations are very site-specific; thus, we found that these variables are highly correlated in regions where LD was intense. We conclude that, in fact, drought led to severe LD in NEB and, the degradation cycle has a positive feedback derived from ET reduction resulting in an increased net moisture deficit. The study warns of the desertification risk that NEB is facing and the need for the authorities to take action to stop these trends.

Circadian and extracircadian exploration during daytime hours of circulating corticosterone and other endocrine chronomes.

PubMed

Jozsa, R; Olah, A; Cornélissen, G; Csernus, V; Otsuka, K; Zeman, M; Nagy, G; Kaszaki, J; Stebelova, K; Csokas, N; Pan, W; Herold, M; Bakken, E E; Halberg, F

2005-10-01

During 7 consecutive days, blood and several tissues were collected during daytime working hours only, three times per day at 4-h intervals from inbred Wistar rats, which had been previously standardized for 1 month in two rooms on a regimen of 12 h of light (L) alternating with 12 h of darkness (LD12:12). In one room, lights were on from 09:00 to 21:00 and in the other room, lights were on from 21:00 to 09:00 (DL12:12; reversed lighting regimen). This setup provides a convenient design to study circadian and extracircadian variations over long (e.g., 7-day) spans. Prior checking of certain circadian rhythms in animals reared in the room on reversed lighting (DL) as compared with animals in the usual (LD) regimen provided evidence that the 180 degrees phase-shift had occurred. These measurements were limited to the circadian (and not extended to infradian) variation. As marker rhythm, the core temperature of a subsample of rats was measured every 4 h around the clock (by night as well as by day) before the start of the 7-day sampling. An antiphase of the circadian rhythm in core temperature was thus demonstrated between rats in the LD vs. DL rooms. A sex difference in core temperature was also found in each room. A reversed rhythm in animals kept in DL and an antiphase between rats kept in DL vs. LD was again shown for the circulating corticosterone rhythm documented in subsamples of 8 animals of each sex sampled around the clock during the first approximately 1.5 day of the 7-day sampling. The findings were in keeping with the proposition that sampling rats at three timepoints 4 h apart during daytime from two rooms on opposite lighting regimens allows the assessment of circadian changes, the daytime samples from animals kept on the reversed lighting regimen accounting for the samples that would have to be obtained by night from animals kept in the room with the usual lighting regimen. During the 7-day-long follow-up, circadian and extracircadian spectral components were mapped for serum corticosterone, taking into account the large day-to-day variability. A third check on the synchronization of the animals to their respective lighting regimen was a comparison (and a good agreement) between studies carried out earlier on the same variables and the circadian results obtained on core temperature and serum corticosterone in this study as a whole. The present study happened to start on the day of the second extremum of a moderate double magnetic storm. The study of any associations of corticosterone with the storm is beyond our scope herein, as are the results on circulating prolactin, characterized by a greater variability and a larger sex difference than corticosterone. Sex differences and extracircadian aspects of prolactin and endothelin determined in the same samples are reported elsewhere, as are results on melatonin. Prior studies on melatonin were confirmed insofar as a circadian profile is concerned by sampling on two antiphasic lighting regimens, as also reported elsewhere. Accordingly, a circadian map for the rat will eventually be extended by the result of this study and aligned with other maps with the qualification of the unassessed contribution in this study of a magnetic storm.

Cognitive Science Program. Hierarchical Distributed Networks in the Neuropsychology of Selective Attention.

DTIC Science & Technology

1985-05-15

The -. . . . . . . . . . ..- L 12 example, Hughes & Zimba (1985) have argued that attention acts simply by inhibiting the hemifield to which one is...and control of attention. Brain 104, 1981, 861-872. Hughes, H.C. & Zimba , L.D. Spatial maps of directed attention. Paper presented to the Psychonmics

Convergent and divergent functional connectivity patterns in patients with long-term left-sided and right-sided deafness.

PubMed

Zhang, Yanyang; Mao, Zhiqi; Feng, Shiyu; Wang, Wenxin; Zhang, Jun; Yu, Xinguang

2018-02-05

Cortical reorganization may be induced in long-term single-sided deafness (SD); however, the influence of the deafness side on the functional changes remains poorly understood. Here, we investigated whole-brain functional connectivity patterns in long-term SD patients. The normalized voxel-based functional connectivity strength (FCS) was determined using resting-state fMRI (rs-fMRI) in 17 left-sided deafness (LD) patients, 21 right-sided deafness (RD) patients and 21 healthy controls (HCs). Relative to the HCs, both the LD and RD patients exhibited a reduction in the FCS in the ipsilateral visual cortex. However, compared to that in the HCs, a significantly higher FCS was observed in some regions in the salience and default-mode networks in the RD patients, but this FCS alternation pattern was not observed in the LD patients. A direct comparison of the two patient groups revealed a significantly increased FCS in the supplemental motor area in the LD group. Altogether, the long-term SD groups with LD and RD exhibited convergent and divergent functional connectivity patterns in whole-brain networks, providing promising evidence that the functional changes in long-term SD are highly deafness-side-dependent. Copyright © 2017 Elsevier B.V. All rights reserved.

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

PubMed Central

Money, Daniel; Gardner, Kyle; Migicovsky, Zoë; Schwaninger, Heidi; Zhong, Gan-Yuan; Myles, Sean

2015-01-01

Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates. PMID:26377960

Direct Reconstruction of CT-Based Attenuation Correction Images for PET With Cluster-Based Penalties

NASA Astrophysics Data System (ADS)

Kim, Soo Mee; Alessio, Adam M.; De Man, Bruno; Kinahan, Paul E.

2017-03-01

Extremely low-dose (LD) CT acquisitions used for PET attenuation correction have high levels of noise and potential bias artifacts due to photon starvation. This paper explores the use of a priori knowledge for iterative image reconstruction of the CT-based attenuation map. We investigate a maximum a posteriori framework with cluster-based multinomial penalty for direct iterative coordinate decent (dICD) reconstruction of the PET attenuation map. The objective function for direct iterative attenuation map reconstruction used a Poisson log-likelihood data fit term and evaluated two image penalty terms of spatial and mixture distributions. The spatial regularization is based on a quadratic penalty. For the mixture penalty, we assumed that the attenuation map may consist of four material clusters: air + background, lung, soft tissue, and bone. Using simulated noisy sinogram data, dICD reconstruction was performed with different strengths of the spatial and mixture penalties. The combined spatial and mixture penalties reduced the root mean squared error (RMSE) by roughly two times compared with a weighted least square and filtered backprojection reconstruction of CT images. The combined spatial and mixture penalties resulted in only slightly lower RMSE compared with a spatial quadratic penalty alone. For direct PET attenuation map reconstruction from ultra-LD CT acquisitions, the combination of spatial and mixture penalties offers regularization of both variance and bias and is a potential method to reconstruct attenuation maps with negligible patient dose. The presented results, using a best-case histogram suggest that the mixture penalty does not offer a substantive benefit over conventional quadratic regularization and diminishes enthusiasm for exploring future application of the mixture penalty.

Influences of twilight on diurnal variation of core temperature, its nadir, and urinary 6-hydroxymelatonin sulfate during nocturnal sleep and morning drowsiness.

PubMed

Kondo, Masayuki; Tokura, Hiromi; Wakamura, Tomoko; Hyun, Ki-Ja; Tamotsu, Satoshi; Morita, Takeshi; Oishi, Tadashi

2009-03-01

This study aimed at elucidating the physiological significance of dusk and dawn in the circadian rhythm of core temperature (T(core)) and urinary 6-hydroxymelatonin sulfate in humans during sleep and the waking sensation just after rising. Seven female and four male students served as participants. Participants retired at 2300 h and rose at 0700 h. They were requested to sit on a chair and spend time as quietly as possible during wakefulness, reading a book or listening to recorded light music. Two lighting conditions were provided for each participant: 1) Light-Dark (LD)-rectangular light change with abrupt decrease from 3,000 lx to 100 lx at 1800 h, abrupt increase from 0 lx to 3,000 lx at 0700 h. 2) LD-twilight light change with gradual decrease from 3,000 lx to 100 lx starting at 1700 h (twilight period about 2 h), with gradual increase from 0 lx to 3,000 lx starting at 0500 h (twilight period about 2 h). The periods of 0 lx at night were from 2300 h to 0700 h on the first day and from 2300 to 0500 h on the second day. Nadir time advanced significantly under the influence of the LD-twilight condition. The amount of 6-hydroxymelatonin sulfate in urine collected at 0200 h was significantly higher under LD-twilight in comparison with LD-rectangular light. Morning drowsiness tended to be lower under LD-twilight. Our results suggest that in architectural design of indoor illumination it is important to provide LD-twilight in the evening and early morning for sleep promotion in healthy normal people and/or light treatment in elderly patients with advanced dementia.

The relevance of detection and attribution for loss and damage policy

NASA Astrophysics Data System (ADS)

Stone, D. A.; Huggel, C.; Auffhammer, M.; Cramer, W.; Eicken, H.; Hansen, G.; Wallimann, I.

2015-12-01

The concept of loss and damage (L&D), the residual adverse impacts of climate change beyond what can be addressed by adaptation, has featured as a central component of recent discussions on international climate policy, most notably in negotiations under the United Nations Framework Convention on Climate Change. However, it remains unclear what sort of scientific evidence will be required to inform L&D activities, including with respect to issues of responsibility, liability, compensation, and financing. Possible types of scientific evidence include simple observation of the occurrence of weather-related disaster, understanding of causation and the role of anthropogenic emissions, and the comparison of understanding of causation versus observations of long-term trends through detection and attribution (D&A) analysis.In this presentation we will discuss these questions in detail and consider the implications. If L&D policy leans towards a compensation rationale, then it will likely require the most comprehensive form of evidence of the role of anthropogenic emissions in observed L&D, in other words D&A analysis. However, this has restrictive requirements, for instance in the retrospective availability of long-term monitoring, that may be prohibitive in many situations. Unfortunately, conditions that lead to a dearth of sustained long-term monitoring often also lead to greater vulnerability and exposure, and are thus exactly the conditions that L&D activities are intended to address. On the other hand, if L&D activities are motivated as a mechanism for supporting adaptation they may not necessarily require D&A evidence, but can nevertheless benefit from the confirmation and calibration that D&A provides. Thus, even if L&D policy is not focused on compensation, building resources and capacity in long-term monitoring and its analysis remains a priority.

Effects of soybean ingestion on pharmacokinetics of levodopa and motor symptoms of Parkinson's disease--In relation to the effects of Mucuna pruriens.

PubMed

Nagashima, Yasuhiro; Kondo, Tomoyoshi; Sakata, Mayumi; Koh, Jinsoo; Ito, Hidefumi

2016-02-15

Mucuna pruriens is a levodopa-containing legume and its favorable effects on motor complications in Parkinson disease patients have been reported. The aim of this study was to investigate the effects of another legume, soybeans, on the pharmacokinetics and metabolism of levodopa. Seven parkinsonian patients with the wearing-off phenomenon and dyskinesia and five healthy volunteers participated in this study. We conducted a crossover study of the clinical effects on the participants before and after taking either levodopa (100mg)/carbidopa (10mg) only (LD/CD) or levodopa/carbidopa with 11 g of ground soybeans (LD/CD/soy). Parkinsonism and dyskinesia before and after ingestion of these substances were evaluated using UPDRS part III, the modified Abnormal Involuntary Movement Scale (mAIMS) and a self-rating scale. The concentrations of plasma levodopa and its major metabolites were measured by high-performance liquid chromatography. Clinical assessment and blood sampling were conducted before and three hours after the ingestion of ground soybeans. When the patients took LD/CD/soy, they had a significantly longer on-period (p=0.028) and a lower mAIMS score (p<0.001). From the comparison of the results of pharmacokinetic study before and after taking LD/CD or LD/CD/soy, the estimated marginal mean (EMM) of HVA after LD/CD/soy increased in the PD group. EMMs of 3-OMD after LD/CD/soy significantly decreased both in PD patients and healthy controls. These results indicate that soy partly increased the bioavailability of levodopa and suppressed levodopa degradation through COMT. Soybeans may have favorable effects on the motor complications occurring under current levodopa therapy. Further investigation to clarify the mechanism underlying such effects is required. Copyright © 2015 Elsevier B.V. All rights reserved.

Clinical Pharmacokinetics of IPX066: Evaluation of Dose Proportionality and Effect of Food in Healthy Volunteers

PubMed Central

Yao, Hsuan-Ming; Hsu, Ann; Gupta, Suneel; Modi, Nishit B.

2016-01-01

Objectives IPX066 is an oral, extended-release capsule formulation of carbidopa-levodopa (CD-LD) available in 4 strengths. The goals of this investigation were to assess the dose proportionality of IPX066 and to study the effects of a high-fat, high-calorie meal and of sprinkling the capsule contents on applesauce on the pharmacokinetics of IPX066 in healthy volunteers. Methods Three open-label studies were conducted. In the first study, subjects received 1 capsule of each IPX066 strength (23.75–95, 36.25–145, 48.75–195, and 61.25–245 mg of CD-LD). In the second study, subjects received 1 and 2 capsules of IPX066 245-mg LD under fasting conditions. In the third study, subjects received 2 capsules of IPX066 245-mg LD under 3 conditions: fasting; following a high-fat, high-calorie breakfast; and with the capsule contents sprinkled on applesauce under fasting conditions. Results Peak plasma concentrations (Cmax) and systemic exposure (AUCt, AUCinf) for LD and CD increased dose-proportionally over the range of the IPX066 capsule strengths. Comparison of 1 and 2 IPX066 245-mg LD capsules showed dose-proportional pharmacokinetics for Cmax and AUCt. Sprinkling the capsule contents on applesauce did not affect the pharmacokinetics. A high-fat, high-calorie meal delayed the initial increase in LD concentration by approximately 1 to 2 hours, reduced Cmax by 21%, and increased AUCinf by 13% compared with the fasted state. Conclusions IPX066 shows dose-proportional pharmacokinetics. Sprinkling the capsule contents on applesauce does not affect the pharmacokinetics; a high-fat, high-calorie meal delayed absorption by 1 to 2 hours, slightly reduced Cmax, and slightly increased extent of absorption. PMID:26626430

Experimental assessment of film cooling performance of short cylindrical holes on a flat surface

NASA Astrophysics Data System (ADS)

Singh, Kuldeep; Premachandran, B.; Ravi, M. R.

2016-12-01

The present study is an experimental investigation of film-cooling over a flat surface from the short cylindrical holes. The film cooling holes used in the combustion chamber and the afterburner liner of an aero engine has length-to-diameter (L/D) typically in the range 1-2, while the cooling holes used in turbine blades has L/D > 3. Based on the classification given in the literature, cooling holes with L/D ≤ 3 are named as short holes and cooling holes with L/D > 3 are named as long holes. Short film cooling holes cause jetting of the secondary fluid whereas the secondary fluid emerging from long holes has characteristics similar to fully developed turbulent flow in pipe. In order to understand the difference in the film cooling performance of long and short cooling holes, experimental study is carried out for five values of L/D in the range 1-5, five injection angles, α = 15°-90° and five mainstream Reynolds number 1.25 × 105-6.25 × 105 and two blowing ratios, M = 0.5-1.0. The surface temperature of the test plate is monitored using infrared thermography. The results obtained from the present study showed that the film-cooling effectiveness is higher for the longest holes (L/D = 5) investigated in the present work in comparison to that for the shorter holes. Short holes are found to give better effectiveness at the lowest investigated injection angle i.e. α = 15° in the near cooling hole region, whereas film cooling effectiveness obtained at injection angle, α = 45° is found to be better than other injection angles for longest investigated holes, i.e. L/D = 5.

Clinical Pharmacokinetics of IPX066: Evaluation of Dose Proportionality and Effect of Food in Healthy Volunteers.

PubMed

Yao, Hsuan-Ming; Hsu, Ann; Gupta, Suneel; Modi, Nishit B

2016-01-01

IPX066 is an oral, extended-release capsule formulation of carbidopa-levodopa (CD-LD) available in 4 strengths. The goals of this investigation were to assess the dose proportionality of IPX066 and to study the effects of a high-fat, high-calorie meal and of sprinkling the capsule contents on applesauce on the pharmacokinetics of IPX066 in healthy volunteers. Three open-label studies were conducted. In the first study, subjects received 1 capsule of each IPX066 strength (23.75-95, 36.25-145, 48.75-195, and 61.25-245 mg of CD-LD). In the second study, subjects received 1 and 2 capsules of IPX066 245-mg LD under fasting conditions. In the third study, subjects received 2 capsules of IPX066 245-mg LD under 3 conditions: fasting; following a high-fat, high-calorie breakfast; and with the capsule contents sprinkled on applesauce under fasting conditions. Peak plasma concentrations (Cmax) and systemic exposure (AUCt, AUCinf) for LD and CD increased dose-proportionally over the range of the IPX066 capsule strengths. Comparison of 1 and 2 IPX066 245-mg LD capsules showed dose-proportional pharmacokinetics for Cmax and AUCt. Sprinkling the capsule contents on applesauce did not affect the pharmacokinetics. A high-fat, high-calorie meal delayed the initial increase in LD concentration by approximately 1 to 2 hours, reduced Cmax by 21%, and increased AUCinf by 13% compared with the fasted state. IPX066 shows dose-proportional pharmacokinetics. Sprinkling the capsule contents on applesauce does not affect the pharmacokinetics; a high-fat, high-calorie meal delayed absorption by 1 to 2 hours, slightly reduced Cmax, and slightly increased extent of absorption.

A Synthesis of Reading and Spelling Interventions and Their Effects on Spelling Outcomes for Students With Learning Disabilities

PubMed Central

Williams, Kelly J.; Walker, Melodee A.; Vaughn, Sharon; Wanzek, Jeanne

2016-01-01

Spelling is one of the most challenging areas for students with learning disabilities (LD), and improving spelling outcomes for these students is of high importance. In this synthesis, we examined the effects of spelling and reading interventions on spelling outcomes for students with LD in Grades K through 12. A systematic search of peer-reviewed literature published between 2004 and 2014 was conducted using electronic databases and hand searches of relevant journals. To be eligible for inclusion, studies had to meet the following criteria: (a) Participants were identified with LD and were in Grades K through 12, (b) designs were either treatment/comparison or single case, (c) a reading or spelling intervention was implemented, (d) at least one spelling outcome was measured, and (e) instruction was in English. Ten studies met criteria for inclusion in the synthesis, and effectiveness ranged from ineffective to highly effective. Findings demonstrated that spelling outcomes for taught words were improved for students with LD with the use of explicit instruction or self-correction strategies. PMID:26733209

A Synthesis of Reading and Spelling Interventions and Their Effects on Spelling Outcomes for Students With Learning Disabilities.

PubMed

Williams, Kelly J; Walker, Melodee A; Vaughn, Sharon; Wanzek, Jeanne

Spelling is one of the most challenging areas for students with learning disabilities (LD), and improving spelling outcomes for these students is of high importance. In this synthesis, we examined the effects of spelling and reading interventions on spelling outcomes for students with LD in Grades K through 12. A systematic search of peer-reviewed literature published between 2004 and 2014 was conducted using electronic databases and hand searches of relevant journals. To be eligible for inclusion, studies had to meet the following criteria: (a) Participants were identified with LD and were in Grades K through 12, (b) designs were either treatment/comparison or single case, (c) a reading or spelling intervention was implemented, (d) at least one spelling outcome was measured, and (e) instruction was in English. Ten studies met criteria for inclusion in the synthesis, and effectiveness ranged from ineffective to highly effective. Findings demonstrated that spelling outcomes for taught words were improved for students with LD with the use of explicit instruction or self-correction strategies.

Psychosis and the Control of Lucid Dreaming.

PubMed

Mota, Natália B; Resende, Adara; Mota-Rolim, Sérgio A; Copelli, Mauro; Ribeiro, Sidarta

2016-01-01

Dreaming and psychosis share important features, such as intrinsic sense perceptions independent of external stimulation, and a general lack of criticism that is associated with reduced frontal cerebral activity. Awareness of dreaming while a dream is happening defines lucid dreaming (LD), a state in which the prefrontal cortex is more active than during regular dreaming. For this reason, LD has been proposed to be potentially therapeutic for psychotic patients. According to this view, psychotic patients would be expected to report LD less frequently, and with lower control ability, than healthy subjects. Furthermore, psychotic patients able to experience LD should present milder psychiatric symptoms, in comparison with psychotic patients unable to experience LD. To test these hypotheses, we investigated LD features (occurrence, control abilities, frequency, and affective valence) and psychiatric symptoms (measure by PANSS, BPRS, and automated speech analysis) in 45 subjects with psychotic symptoms [25 with Schizophrenia (S) and 20 with Bipolar Disorder (B) diagnosis] versus 28 non-psychotic control (C) subjects. Psychotic lucid dreamers reported control of their dreams more frequently (67% of S and 73% of B) than non-psychotic lucid dreamers (only 23% of C; S > C with p = 0.0283, B > C with p = 0.0150). Importantly, there was no clinical advantage for lucid dreamers among psychotic patients, even for the diagnostic question specifically related to lack of judgment and insight. Despite some limitations (e.g., transversal design, large variation of medications), these preliminary results support the notion that LD is associated with psychosis, but falsify the hypotheses that we set out to test. A possible explanation is that psychosis enhances the experience of internal reality in detriment of external reality, and therefore lucid dreamers with psychotic symptoms would be more able to control their internal reality than non-psychotic lucid dreamers. Training dream lucidity is likely to produce safe psychological strengthening in a non-psychotic population, but in a psychotic population LD practice may further empower deliria and hallucinations, giving internal reality the appearance of external reality.

Psychosis and the Control of Lucid Dreaming

PubMed Central

Mota, Natália B.; Resende, Adara; Mota-Rolim, Sérgio A.; Copelli, Mauro; Ribeiro, Sidarta

2016-01-01

Dreaming and psychosis share important features, such as intrinsic sense perceptions independent of external stimulation, and a general lack of criticism that is associated with reduced frontal cerebral activity. Awareness of dreaming while a dream is happening defines lucid dreaming (LD), a state in which the prefrontal cortex is more active than during regular dreaming. For this reason, LD has been proposed to be potentially therapeutic for psychotic patients. According to this view, psychotic patients would be expected to report LD less frequently, and with lower control ability, than healthy subjects. Furthermore, psychotic patients able to experience LD should present milder psychiatric symptoms, in comparison with psychotic patients unable to experience LD. To test these hypotheses, we investigated LD features (occurrence, control abilities, frequency, and affective valence) and psychiatric symptoms (measure by PANSS, BPRS, and automated speech analysis) in 45 subjects with psychotic symptoms [25 with Schizophrenia (S) and 20 with Bipolar Disorder (B) diagnosis] versus 28 non-psychotic control (C) subjects. Psychotic lucid dreamers reported control of their dreams more frequently (67% of S and 73% of B) than non-psychotic lucid dreamers (only 23% of C; S > C with p = 0.0283, B > C with p = 0.0150). Importantly, there was no clinical advantage for lucid dreamers among psychotic patients, even for the diagnostic question specifically related to lack of judgment and insight. Despite some limitations (e.g., transversal design, large variation of medications), these preliminary results support the notion that LD is associated with psychosis, but falsify the hypotheses that we set out to test. A possible explanation is that psychosis enhances the experience of internal reality in detriment of external reality, and therefore lucid dreamers with psychotic symptoms would be more able to control their internal reality than non-psychotic lucid dreamers. Training dream lucidity is likely to produce safe psychological strengthening in a non-psychotic population, but in a psychotic population LD practice may further empower deliria and hallucinations, giving internal reality the appearance of external reality. PMID:27014118

Lean diabetes in middle-aged adults: A joint analysis of the German DIVE and DPV registries.

PubMed

Hartmann, Bettina; Lanzinger, Stefanie; Bramlage, Peter; Groß, Felix; Danne, Thomas; Wagner, Siegfried; Krakow, Dietmar; Zimmermann, Artur; Malcharzik, Christian; Holl, Reinhard W

2017-01-01

To assess differences in demographics, treatment and outcome of lean (LD) compared to overweight and obese people with diabetes clinically classified as type 2 diabetes mellitus (T2DM). We combined data from the German DIVE (Diabetes Versorgungs-Evaluation) and DPV (Diabetes-Patienten-Verlaufsdokumentation) databases to produce a large cohort of people with T2DM. The characteristics of people with Body Mass Index (BMI) <25 kg/m2, ≥25-30 kg/m2 and ≥30 kg/m2 aged 30 to 50 years were compared, including demographics, cardiovascular (CV) risk factors, comorbidities and outcomes. A total of 37,870 people were included in the analysis, 3,191 of these (8.4%) had a BMI < 25 kg/m2. LD reported more nicotine (41.6% of 2,070 vs. 38.1% of 6,070 and 33.4% of 16,823; P<0.001)and alcohol consumption (12.0% of 1,282, 10.3% of 3,594 and 6.6% of 9,418; P<0.001)compared to overweight and obese people. More LD were treated with insulin in comparison to the other subgroups (short acting insulin 33.1% of 3,191 vs. 28.4% of 9,234 and 28.0% of 25,445; P <0.001; long acting insulin 31.3% of 3,191 vs. 28.9% of 9,234 and 29.3% of 25,445; P = 0.043). Regression models adjusted for age, gender and diabetes duration showed a 2.50 times higher odds ratio (OR) for hypoglycemia and a 2.52 higher OR for mortality in LD compared to the BMI subgroup ≥30 kg/m2. LD is associated with an increased risk of hypoglycaemia and death. Patients are characterized by male gender, lifestyle habits as smoking and alcohol consumption while cardiovascular comorbidities are less important. In comparison to patients of the other weight groups they are treated with insulin more often and considerably less with metformin.

[Light pollution increases morbidity and mortality rate from different causes in male rats].

PubMed

Bukalev, A V; Vinogradova, I A; Zabezhinskiĭ, M A; Semenchenko, A V; Anisimov, V N

2012-01-01

The influence of different light regimes (constant light--LL; constant darkness--DD; standard light regime--LD, 12 hours light 12 hours darkness; natural lightening of the North-West of Russia--NL) on the dynamics of life's morbidity rate, spontaneous tumorigenesis and frequency of some kinds of non-tumor pathology revealed at the post-mortem examination of male rats was studied. It was found out that the maintenance of animals at LL and NL conditions led to the increase of the number of infectious diseases, substantially faster development of spontaneous tumors and the increase of non-tumor diseases in comparison with the animals kept at LD (standard light) regime. Light deprivation (DD) led to substantial reduction of development of new growth, of non-tumor and infectious diseases in comparison with the similar parameters in standard light regime.

Comparisons of Self-Determination among Students with Autism, Intellectual Disability, and Learning Disabilities: A Multivariate Analysis

ERIC Educational Resources Information Center

Chou, Yu-Chi; Wehmeyer, Michael L.; Palmer, Susan B.; Lee, Jaehoon

2017-01-01

This study examined differences in self-determination among students with autism spectrum disorders (ASD), students with intellectual disability (ID), and students with learning disabilities (LD). A total of 222 participants with an equal size group for each of the three disability categories were selected to participate in the comparison of total…

Recombinant NAD-dependent SIR-2 protein of Leishmania donovani: immunobiochemical characterization as a potential vaccine against visceral leishmaniasis.

PubMed

Baharia, Rajendra K; Tandon, Rati; Sharma, Tanuj; Suthar, Manish K; Das, Sanchita; Siddiqi, Mohammad Imran; Saxena, Jitendra Kumar; Sundar, Shaym; Sunder, Shyam; Dube, Anuradha

2015-03-01

The development of a vaccine conferring long-lasting immunity remains a challenge against visceral leishmaniasis (VL). Immunoproteomic characterization of Leishmania donovani proteins led to the identification of a novel protein NAD+-dependent Silent Information regulatory-2 (SIR2 family or sirtuin) protein (LdSir2RP) as one of the potent immunostimulatory proteins. Proteins of the SIR2 family are characterized by a conserved catalytic domain that exerts unique NAD-dependent deacetylase activity. In the present study, an immunobiochemical characterization of LdSir2RP and further evaluation of its immunogenicity and prophylactic potential was done to assess for its possible involvement as a vaccine candidate against leishmaniasis. LdSir2RP was successfully cloned, expressed and purified. The gene was present as a monomeric protein of ~45 kDa and further established by the crosslinking experiment. rLdSir2RP shown cytosolic localization in L. donovani and demonstrating NAD+-dependent deacetylase activity. Bioinformatic analysis also confirmed that LdSir2RP protein has NAD binding domain. The rLdSir2RP was further assessed for its cellular response by lymphoproliferative assay and cytokine ELISA in cured Leishmania patients and hamsters (Mesocricetus auratus) in comparison to soluble Leishmania antigen and it was observed to stimulate the production of IFN-γ, IL-12 and TNF-α significantly but not the IL-4 and IL-10. The naïve hamsters when vaccinated with rLdSir2RP alongwith BCG resisted the L. donovani challenge to the tune of ~75% and generated strong IL-12 and IFN-γ mediated Th1 type immune response thereof. The efficacy was further supported by remarkable increase in IgG2 antibody level which is indicative of Th1 type of protective response. Further, with a possible implication in vaccine design against VL, identification of potential T-cell epitopes of rLdSir2RP was done using computational approach. The immunobiochemical characterization strongly suggest the potential of rLdSir2RP as vaccine candidate against VL and supports the concept of its being effective T-cell stimulatory antigen.

Dopa decarboxylase (Ddc) affects variation in Drosophila longevity.

PubMed

De Luca, Maria; Roshina, Nataliya V; Geiger-Thornsberry, Gretchen L; Lyman, Richard F; Pasyukova, Elena G; Mackay, Trudy F C

2003-08-01

Mutational analyses in model organisms have shown that genes affecting metabolism and stress resistance regulate life span, but the genes responsible for variation in longevity in natural populations are largely unidentified. Previously, we mapped quantitative trait loci (QTLs) affecting variation in longevity between two Drosophila melanogaster strains. Here, we show that the longevity QTL in the 36E;38B cytogenetic interval on chromosome 2 contains multiple closely linked QTLs, including the Dopa decarboxylase (Ddc) locus. Complementation tests to mutations show that Ddc is a positional candidate gene for life span in these strains. Linkage disequilibrium (LD) mapping in a sample of 173 alleles from a single population shows that three common molecular polymorphisms in Ddc account for 15.5% of the genetic contribution to variance in life span from chromosome 2. The polymorphisms are in strong LD, and the effects of the haplotypes on longevity suggest that the polymorphisms are maintained by balancing selection. DDC catalyzes the final step in the synthesis of the neurotransmitters, dopamine and serotonin. Thus, these data implicate variation in the synthesis of bioamines as a factor contributing to natural variation in individual life span.

Association Analysis in Rice: From Application to Utilization

PubMed Central

Zhang, Peng; Zhong, Kaizhen; Shahid, Muhammad Qasim; Tong, Hanhua

2016-01-01

Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding. PMID:27582745

Non-contrast CT at comparable dose to an abdominal radiograph in patients with acute renal colic; impact of iterative reconstruction on image quality and diagnostic performance.

PubMed

McLaughlin, P D; Murphy, K P; Hayes, S A; Carey, K; Sammon, J; Crush, L; O'Neill, F; Normoyle, B; McGarrigle, A M; Barry, J E; Maher, M M

2014-04-01

The aim was to assess the performance of low-dose non-contrast CT of the urinary tract (LD-CT) acquired at radiation exposures close to that of abdominal radiography using adaptive statistical iterative reconstruction (ASiR). Thirty-three patients with clinically suspected renal colic were prospectively included. Conventional dose (CD-CT) and LD-CT data sets were contemporaneously acquired. LD-CT images were reconstructed with 40 %, 70 % and 90 % ASiR. Image quality was subjectively and objectively measured. Images were also clinically interpreted. Mean ED was 0.48 ± 0.07 mSv for LD-CT compared with 4.43 ± 3.14 mSv for CD-CT. Increasing the percentage ASiR resulted in a step-wise reduction in mean objective noise (p < 0.001 for all comparisons). Seventy % ASiR LD-CT images had higher diagnostic acceptability and spatial resolution than 90 % ASiR LD-CT images (p < 0.001). Twenty-seven calculi (diameter = 5.5 ± 1.7 mm), including all ureteric stones, were correctly identified using 70 % ASiR LD-CT with two false positives and 16 false negatives (diameter = 2.3 ± 0.7 mm) equating to a sensitivity and specificity of 72 % and 94 %. Seventy % ASiR LD-CT had a sensitivity and specificity of 87 % and 100 % for detection of calculi >3 mm. Reconstruction of LD-CT images with 70 % ASiR resulted in superior image quality than FBP, 40 % ASIR and 90 % ASIR. LD-CT with ASIR demonstrates high sensitivity and specificity for detection of calculi >3 mm. • Low-dose CT studies for urinary calculus detection were performed with a mean dose of 0.48 ± 0.07 mSv • Low-dose CT with 70 % ASiR detected calculi >3 mm with a sensitivity and specificity of 87 % and 100 % • Reconstruction with 70 % ASiR was superior to filtered back projection, 40 % ASiR and 90 % ASiR images.

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

PubMed Central

2014-01-01

Background Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. Methods By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. Results For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. Conclusions The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. PMID:24592996

Model-based iterative reconstruction in low-dose CT colonography-feasibility study in 65 patients for symptomatic investigation.

PubMed

Vardhanabhuti, Varut; James, Julia; Nensey, Rehaan; Hyde, Christopher; Roobottom, Carl

2015-05-01

To compare image quality on computed tomographic colonography (CTC) acquired at standard dose (STD) and low dose (LD) using filtered-back projection, adaptive statistical iterative reconstruction, and model-based iterative reconstruction (MBIR) techniques. A total of 65 symptomatic patients were prospectively enrolled for the study and underwent STD and LD CTC with filtered-back projection, adaptive statistical iterative reconstruction, and MBIR to allow direct per-patient comparison. Objective image noise, subjective image analyses, and polyp detection were assessed. Objective image noise analysis demonstrates significant noise reduction using MBIR technique (P < .05) despite being acquired at lower doses. Subjective image analyses were superior for LD MBIR in all parameters except visibility of extracolonic lesions (two-dimensional) and visibility of colonic wall (three-dimensional) where there were no significant differences. There was no significant difference in polyp detection rates (P > .05). Doses: LD (dose-length product, 257.7), STD (dose-length product, 483.6). LD MBIR CTC objectively shows improved image noise using parameters in our study. Subjectively, image quality is maintained. Polyp detection shows no significant difference but because of small numbers needs further validation. Average dose reduction of 47% can be achieved. This study confirms feasibility of using MBIR in this context of CTC in symptomatic population. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Close packing of rods on spherical surfaces

NASA Astrophysics Data System (ADS)

Smallenburg, Frank; Löwen, Hartmut

2016-04-01

We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in the geometry of the closest-packed configuration as a function of the aspect ratio L/D, where L is the cylinder length and D the diameter of the rods. We find a rich variety of cluster structures. For larger clusters, we find that the best-packed configurations up to around 100 particles are highly dependent on the exact number of particles and aspect ratio. For even larger clusters, we find largely disordered clusters for very short rods (L/D = 0.25), while slightly longer rods (L/D = 0.5 or 1) prefer a global baseball-like geometry of smectic-like domains, similar to the behavior of large-scale nematic shells. Intriguingly, we observe that when compared to their optimal flat-plane packing, short rods adapt to the spherical geometry more efficiently than both spheres and longer rods. Our results provide predictions for experimentally realizable systems of colloidal rods trapped at the interface of emulsion droplets.

Fluctuating observation time ensembles in the thermodynamics of trajectories

NASA Astrophysics Data System (ADS)

Budini, Adrián A.; Turner, Robert M.; Garrahan, Juan P.

2014-03-01

The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This ‘thermodynamics of trajectories’ approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there are a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show how the LD functions that describe an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates can be mapped to those of the fixed-time ensemble. We discuss how the correspondence between generalized ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

PubMed

Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

2012-08-01

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Clinical manifestations of reported Lyme disease cases in Ontario, Canada: 2005–2014

PubMed Central

Nelder, Mark P.; Russell, Curtis; Li, Ye; Badiani, Tina; Sander, Beate; Sider, Douglas; Patel, Samir N.

2018-01-01

Lyme disease (LD) is the most common vector-borne disease in Ontario, Canada. We describe the epidemiology and clinical manifestations of LD in Ontario and examine trends in the incidence of non-disseminated and disseminated LD. LD surveillance data from the integrated Public Health Information System (iPHIS) from 2005–2014 were mapped to symptoms according to syndrome groups (erythema migrans (EM), flu-like, cardiac, neurologic or arthritic) and disease stages (early localized, early disseminated or late disseminated). During the study period, 1,230 cases due to Borrelia burgdoferi were reported in Ontario with annual incidence rates ranging from 0.32 (2006) to 2.16 (2013) cases per 100,000 population. Seventy percent of cases had EM and the proportion of cases with EM increased over time. Other clinical manifestations included flu-like (75%), arthritic (42%), neurologic (41%) and cardiac (6%) symptoms. Early localized disease (n = 415) manifested with EM (87%) and flu-like (57%) symptoms; early disseminated disease (n = 216) manifested with neurologic (94%), cardiac (10%) and EM (63%) symptoms; and late disseminated disease (n = 475) manifested with EM (62%), neurologic (55%), cardiac (9%), and arthritic symptoms (i.e., arthralgia (93%) and arthritis (7%)). Early localized and early disseminated cases (88% each) occurred primarily from May through September, compared to late disseminated cases (81%). The proportion of cases reported to public health within 30 days of illness onset increased during the study period, while the proportion of cases reported within 1–3 months and >3 months decreased. Geographical variations characterized by higher incidence of early localized disease and earlier public health notification (within 30 days of illness onset) occurred in regions with established or recently established LD risk areas, while later public health notification (>3 months after illness onset) was reported more frequently in regions with recently established or no identified risk areas. This is the first study to describe the clinical manifestations of LD in Ontario, Canada. The observed geographical variations in the epidemiology of LD in Ontario reinforce the need for regionally focused public health strategies aimed at increasing awareness, promoting earlier recognition and reporting, and encouraging greater uptake of preventive measures. PMID:29856831

The Role of Local Ancestry Adjustment in Association Studies Using Admixed Populations

PubMed Central

Zhang, Jianqi; Stram, Daniel O.

2016-01-01

Association analysis using admixed populations imposes challenges and opportunities for disease mapping. By developing some explicit results for the variance of an allele of interest conditional on either local or global ancestry and by simulation of recently admixed genomes we evaluate power and false-positive rates under a variety of scenarios concerning linkage disequilibrium (LD) and the presence of unmeasured variants. Pairwise LD patterns were compared between admixed and nonadmixed populations using the HapMap phase 3 data. Based on the above, we showed that as follows: For causal variants with similar effect size in all populations, power is generally higher in a study using admixed population than using nonadmixed population, especially for highly differentiated SNPs. This gain of power is achieved with adjustment of global ancestry, which completely removes any cross-chromosome inflation of type I error rates, and addresses much of the intrachromosome inflation.If reliably estimated, adjusting for local ancestry precisely recovers the localization that could have been achieved in a stratified analysis of source populations. Improved localization is most evident for highly differentiated SNPs; however, the advantage of higher power is lost on exactly the same differentiated SNPs.In the real admixed populations such as African Americans and Latinos, the expansion of LD is not as dramatic as in our simulation.While adjustment for global ancestry is required prior to announcing a novel association seen in an admixed population, local ancestry adjustment may best be regarded as a localization tool not strictly required for discovery purposes. PMID:25043967

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.

PubMed

Money, Daniel; Gardner, Kyle; Migicovsky, Zoë; Schwaninger, Heidi; Zhong, Gan-Yuan; Myles, Sean

2015-09-15

Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates. Copyright © 2015 Money et al.

Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching.

PubMed

Nambeesan, Savithri U; Mandel, Jennifer R; Bowers, John E; Marek, Laura F; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H; Knapp, Steven J; Burke, John M

2015-03-11

Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.

ReVeaLD: a user-driven domain-specific interactive search platform for biomedical research.

PubMed

Kamdar, Maulik R; Zeginis, Dimitris; Hasnain, Ali; Decker, Stefan; Deus, Helena F

2014-02-01

Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biomedical discovery. Despite the popularity of semantic web technologies in tackling the integrative bioinformatics challenge, there are many obstacles towards its usage by non-technical research audiences. In particular, the ability to fully exploit integrated information needs using improved interactive methods intuitive to the biomedical experts. In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed sources. ReVeaLD facilitates query formulation using a domain-specific language (DSL) identified by biomedical experts and mapped to a self-updated catalogue of elements from external sources. ReVeaLD was implemented in a cancer research setting; queries included retrieving data from in silico experiments, protein modeling and gene expression. ReVeaLD was developed using Scalable Vector Graphics and JavaScript and a demo with explanatory video is available at http://www.srvgal78.deri.ie:8080/explorer. A set of user-defined graphic rules controls the display of information through media-rich user interfaces. Evaluation of ReVeaLD was carried out as a game: biomedical researchers were asked to assemble a set of 5 challenge questions and time and interactions with the platform were recorded. Preliminary results indicate that complex queries could be formulated under less than two minutes by unskilled researchers. The results also indicate that supporting the identification of the elements of a DSL significantly increased intuitiveness of the platform and usability of semantic web technologies by domain users. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Anovulatory hamster: a comparison of the effects of short photoperiod and daily melatonin injections on the induction and termination of ovarian acyclicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stetson, M.H.; Hamilton, B.

1981-02-01

Cyclic female hamsters were rendered anovulatory by daily subcutaneous melatonin injections (25 microgram/0.1 ml oil) in 29 days or by transfer to a short light cycle, LD 6:18 (lights 1000-1600 hrs) in 33 days. Estrous cyclicity was reinitiated in these animals in 44 or 45 days following cessation of melatonin injections or transfer to long light cycles (LD 14:10, lights 0600-2000 hrs), respectively. Exposure of both groups to LD 6:18 after reinitiation of estrous cyclicity caused a second cessation of ovulation in 75 (melatonin group) or 61 (short light cycle group) days. Thus, although both treatments disrupted estrous cyclicity formore » nearly 6 weeks, this was not sufficient to induce photorefractoriness (failure to respond to short light cycles with continued estrous cyclicity). Rather, every animal responded to LD 6:18 and ceased ovulating. Melatonin-induced anovulatory hamsters showed daily gonadotropin release patterns identical to those reported in hamsters in other anovulatory states (lactating, prepubertal, and photoinduced anovulatory hamsters); that is, peak LH and FSH release at 1700 hrs daily.« less

Designing a Moodle Course with the CADMOS Learning Design Tool

ERIC Educational Resources Information Center

Katsamani, Maria; Retalis, Symeon; Boloudakis, Michail

2012-01-01

CADMOS is a graphical learning design (LD) authoring tool that helps a teacher design a unit of learning in two layers: (i) the conceptual layer, which seems like a concept map and contains the learning activities with their associated learning resources and (ii) the flow layer, which contains the orchestration of these activities. One of CADMOS'…

Learning Strategies: Secondary LD Students in the Mainstream.

ERIC Educational Resources Information Center

D'Antoni, Alice; And Others

The paper presents four learning strategy techniques--the SQ3R method of study, the Multipass Strategy, the Advanced Study Guide Technique, and Cognitive Mapping--for use with secondary level learning disabled students. The SQ3R method involves the five steps of survey, question, read, recite, and review. An adaption of the SQ3R method, the…

Fidelity of life and death molluscan assemblages from carbonate tidal flats in the Persian (Arabian) Gulf

NASA Astrophysics Data System (ADS)

García-Ramos, Diego A.; Albano, Paolo G.; Harzhauser, Mathias; Piller, Werner E.; Zuschin, Martin

2016-04-01

Live-dead (LD) studies aim to help understand how faithfully fossil assemblages can be used to quantitatively infer the structure of the original living communities that generated them. To this purpose, LD comparisons have been conducted in different terrestrial and aquatic environments to assess how environment-specific differences in quality and intensity of taphonomic factors affect LD fidelity. In sub-tropical and tropical settings, most LD studies have focused on hard substrates or seagrass bottoms. Here we present results on molluscan assemblages from soft carbonate sediments in tidal flats of the Persian (Arabian) Gulf (Indo-West Pacific biogeographic province). We analyzed a total of 7193 mollusks collected from six sites comprising time-averaged death assemblages (DAs) and snapshot living assemblages (LAs). All analyses were performed at site and at habitat scales after correcting for sample-size differences. We found a good match in proportional abundance and a notable mismatch in species composition. In fact, species richness in DAs is 6 times larger than in LAs at site scale, and 4 times at habitat scale. Additionally, we found a good fidelity of evenness, and rank abundance of feeding guilds. Other studies have shown that molluscan DAs from subtidal carbonate environments can display lower time-averaging than those from siliciclastic environments due to high rates of shell loss to bioerosion and dissolution. For our case study of tidal flat carbonate settings, we interpret that despite temporal autocorrelation (good fidelity of proportional abundance), substantial differences in species richness and composition can be explained by early cementation, lateral mixing, intense bioturbation and moderate sedimentation rates. Our results suggest that tidal flat carbonate environments can potentially lead to a wider window of time-averaging in comparison with subtidal carbonate settings.

Downregulated Translation Initiation Signaling Predisposes Low-Birth-Weight Neonatal Pigs to Slower Rates of Muscle Protein Synthesis

PubMed Central

Chen, Ying; McCauley, Sydney R.; Johnson, Sally E.; Rhoads, Robert P.; El-Kadi, Samer W.

2017-01-01

Low-birth-weight (LBWT) neonates experience restricted muscle growth in their perinatal life. Our aim was to investigate the mechanisms that contribute to slower skeletal muscle growth of LBWT neonatal pigs. Twenty-four 1-day old male LBWT (816 ± 55 g) and normal-birth-weight (NBWT; 1,642 ± 55 g) littermates (n = 12) were euthanized to collect blood and longissimus dorsi (LD) muscle subsamples. Plasma glucose, insulin, and insulin-like growth factor-I (IGF-I) were lower in LBWT compared with NBWT pigs. Muscle IGF-I mRNA expression were lower in LBWT than NBWT pigs. However, IGF-I receptor mRNA and protein abundance was greater in LD of LBWT pigs. Abundance of myostatin and its receptors, and abundance and phosphorylation of smad3 were lower in LBWT LD by comparison with NBWT LD. Abundance of eukaryotic initiation factor (eIF) 4E binding protein 1 and mitogen-activated protein kinase-interacting kinases was lower in muscle of LBWT pigs compared with NBWT siblings, while eIF4E abundance and phosphorylation did not differ between the two groups. Furthermore, phosphorylation of ribosomal protein S6 kinase 1 (S6K1) was less in LBWT muscle, possibly due to lower eIF3e abundance. In addition, abundance and phosphorylation of eIF4G was reduced in LBWT pigs by comparison with NBWT littermates, suggesting translation initiation complex formation is compromised in muscle of LBWT pigs. In conclusion, diminished S6K1 activation and translation initiation signaling are likely the major contributors to impaired muscle growth in LBWT neonatal pigs. The upregulated IGF-I R expression and downregulated myostatin signaling seem to be compensatory responses for the reduction in protein synthesis signaling. PMID:28744224

Use of butterflies as nontarget insect test species and the acute toxicity and hazard of mosquito control insecticides.

PubMed

Hoang, Tham C; Pryor, Rachel L; Rand, Gary M; Frakes, Robert A

2011-04-01

Honeybees are the standard insect test species used for toxicity testing of pesticides on nontarget insects for the U.S. Environmental Protection Agency (U.S. EPA) under the Federal Insecticide Fungicide and Rodenticide Act (FIFRA). Butterflies are another important insect order and a valued ecological resource in pollination. The current study conducted acute toxicity tests with naled, permethrin, and dichlorvos on fifth larval instar (caterpillars) and adults of different native Florida, USA, butterfly species to determine median lethal doses (24-h LD50), because limited acute toxicity data are available with this major insect group. Thorax- and wing-only applications of each insecticide were conducted. Based on LD50s, thorax and wing application exposures were acutely toxic to both caterpillars and adults. Permethrin was the most acutely toxic insecticide after thorax exposure to fifth instars and adult butterflies. However, no generalization on acute toxicity (sensitivity) of the insecticides could be concluded based on exposures to fifth instars versus adult butterflies or on thorax versus wing exposures of adult butterflies. A comparison of LD50s of the butterflies from this study (caterpillars and adults) with honeybee LD50s for the adult mosquito insecticides on a µg/organism or µg/g basis indicates that several butterfly species are more sensitive to these insecticides than are honeybees. A comparison of species sensitivity distributions for all three insecticides shows that permethrin had the lowest 10th percentile. Using a hazard quotient approach indicates that both permethrin and naled applications in the field may present potential acute hazards to butterflies, whereas no acute hazard of dichlorvos is apparent in butterflies. Butterflies should be considered as potential test organisms when nontarget insect testing of pesticides is suggested under FIFRA. Copyright © 2011 SETAC.

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

PubMed Central

Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

Circadian and estrous cycle-dependent variations in blood pressure and heart rate in female rats.

PubMed

Takezawa, H; Hayashi, H; Sano, H; Saito, H; Ebihara, S

1994-11-01

To determine whether cardiovascular functions are controlled by the endogenous circadian system and whether they change with the estrous cycle in female rats, we measured mean arterial pressure (MAP), heart rate (HR), and spontaneous activity (ACT) of female rats using an implantable radiotelemetry device and a computerized data-collecting system. Under a 12:12-h light-dark (LD) cycle, these parameters exhibited daily rhythms that were entrained to the photic cycle. The patterns of the daily rhythms varied with estrous cycles, and variations were particularly marked in the proestrous stage. During the dark period of this stage, ACT levels were significantly higher, but HR was significantly lower than in other stages. Although the peak MAP occurred within 2 h after the onset of the dark phase in three of the estrous stages, it occurred around midnight in the proestrous stage. Such estrous cycle-dependent variations were eliminated by ovariectomy. The implantation of 17 beta-estradiol produced a gradual increase in MAP and an abrupt decrease in HR. During constant darkness, all three parameters were free running, maintaining the same internal phase relationships with each other as during LD cycles. These results indicate that daily variations in these parameters were controlled by the endogenous circadian oscillating system, that they vary with the estrous cycle in female rats, and that estrogen may be responsible for these estrous cycle-dependent variations.

Phenotypic characterization and genealogical tracing in an Afrikaner schizophrenia database.

PubMed

Karayiorgou, Maria; Torrington, Marie; Abecasis, Gonçalo R; Pretorius, Herman; Robertson, Brian; Kaliski, Sean; Lay, Stephen; Sobin, Christina; Möller, Natalie; Lundy, S Laura; Blundell, Maude L; Gogos, Joseph A; Roos, J Louw

2004-01-01

Founder populations hold tremendous promise for mapping genes for complex traits, as they offer less genetic and environmental heterogeneity and greater potential for genealogical research. Not all founder populations are equally valuable, however. The Afrikaner population meets several criteria that make it an ideal population for mapping complex traits, including founding by a small number of initial founders that likely allowed for a relatively restricted set of mutations and a large current population size that allows identification of a sufficient number of cases. Here, we examine the potential to conduct genealogical research in this population and present initial results indicating that accurate genealogical tracing for up to 17 generations is feasible. We also examine the clinical similarities of schizophrenia cases diagnosed in South Africa and those diagnosed in other, heterogeneous populations, specifically the US. We find that, with regard to basic sample descriptors and cardinal symptoms of disease, the two populations are equivalent. It is, therefore, likely that results from our genetic study of schizophrenia will be applicable to other populations. Based on the results presented here, the history and current size of the population, as well as our previous analysis addressing the extent of background linkage disequilibrium (LD) in the Afrikaners, we conclude that the Afrikaner population is likely an appropriate founder population to map genes for schizophrenia using both linkage and LD approaches. Copyright 2003 Wiley-Liss, Inc.

X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations

PubMed Central

Laan, Maris; Wiebe, Victor; Khusnutdinova, Elza; Remm, Maido; Pääbo, Svante

2005-01-01

Linkage disequilibrium structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225-DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25-40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasise the importance of understanding the history, structure and variation of a study population. PMID:15657606

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

PubMed

Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

2009-02-01

The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.

Reducing dosing frequency of carbidopa/levodopa: double-blind crossover study comparing twice-daily bilayer formulation of carbidopa/levodopa (IPX054) versus 4 daily doses of standard carbidopa/levodopa in stable Parkinson disease patients.

PubMed

Hinson, Vanessa K; Goetz, Christopher G; Leurgans, Sue; Fan, Wenqing; Nguyen, Tiffany; Hsu, Ann

2009-01-01

We compared IPX054, a bilayer tablet of immediate- and extended-release carbidopa/levodopa (CD/LD) given twice daily to standard CD/LD given 4 times daily in patients with stable Parkinson disease (PD). Twelve PD patients with no or mild fluctuations on CD/LD 25/100 mg 4 times daily were randomized to a double-blind crossover comparison with IPX054 (50/200 mg) twice daily. At the end of each 2-week treatment, patients were video recorded while performing a modified Unified Parkinson's Disease Rating Scale motor examination and Rush Dyskinesia Rating Scale at 30-minute intervals over 8.5 hours. The primary outcome measure was the number of videotape epochs rated as "ON" without troublesome dyskinesia by a blinded observer (Wilcoxon signed rank tests). The 9 men and 3 women had a mean age of 69 years and mean PD duration of 6 years. IPX054 and CD/LD showed no significant differences in the primary outcome measure (mean number of video epochs rated as ON without troublesome dyskinesia; P = 0.14). The mean time to ON was improved with IPX054 (P = 0.014), and the mean modified Unified Parkinson's Disease Rating Scale scores slightly favored IPX054 (14.4 vs 16.9; P = 0.052). Mean Rush Dyskinesia Rating Scale scores were not significantly different between IPX054 and CD/LD (0.45 vs 0.69; P = 0.25). No patient developed troublesome dyskinesias. In stable PD patients, no difference was detected between twice-daily treatment with IPX054 and CD/LD given 4 times daily. In this group, substitution with IPX054 reduced dosing frequency while maintaining CD/LD efficacy. In clinical practice, this ease of administration may offer improved treatment compliance.

Association mapping of seed and disease resistance traits in Theobroma cacao L.

PubMed

Motilal, Lambert A; Zhang, Dapeng; Mischke, Sue; Meinhardt, Lyndel W; Boccara, Michel; Fouet, Olivier; Lanaud, Claire; Umaharan, Pathmanathan

2016-12-01

Microsatellite and single nucleotide polymorphism markers that could be used in marker assisted breeding of cacao were identified for number of filled seeds, black pod resistance and witches' broom disease resistance. An association mapping approach was employed to identify markers for seed number and resistance to black pod and witches' broom disease (WBD) in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms (SNPs) were assessed on 483 unique trees in the International Cocoa Genebank Trinidad (ICGT). Linkage disequilibrium (LD) and association mapping studies were conducted to identify markers to tag the phenotypic traits. Decay of LD occurred over an average 9.3 cM for chromosomes 1-9 and 2.5 cM for chromosome 10. Marker/trait associations were generally identified based on general linear models (GLMs) that incorporated principal components from molecular information on relatedness factor. Seven markers (mTcCIR 8, 66, 126, 212; TcSNP368, 697, 1370) on chromosomes 1 and 9 were identified for number of filled seeds (NSEED). A single marker was found for black pod resistance (mTcCIR280) on chromosome 3, whereas six markers on chromosomes 4, 5, 6, 8, and 10 were detected for WBD (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374). It is expected that this association mapping study in cacao would contribute to the knowledge of the genetic determinism of cocoa traits and that the markers identified herein would prove useful in marker assisted breeding of cacao.

Mucuna pruriens in Parkinson disease

PubMed Central

Laguna, Janeth; Cassani, Erica; Cereda, Emanuele; Pozzi, Nicolò G.; Isaias, Ioannis U.; Contin, Manuela; Barichella, Michela; Pezzoli, Gianni

2017-01-01

Objective: To investigate whether Mucuna pruriens (MP), a levodopa-containing leguminous plant growing in all tropical areas worldwide, may be used as alternative source of levodopa for indigent individuals with Parkinson disease (PD) who cannot afford long-term therapy with marketed levodopa preparations. Methods: We investigated efficacy and safety of single-dose intake of MP powder from roasted seeds obtained without any pharmacologic processing. Eighteen patients with advanced PD received the following treatments, whose sequence was randomized: (1) dispersible levodopa at 3.5 mg/kg combined with the dopa-decarboxylase inhibitor benserazide (LD+DDCI; the reference treatment); (2) high-dose MP (MP-Hd; 17.5 mg/kg); (3) low-dose MP (MP-Ld; 12.5 mg/kg); (4) pharmaceutical preparation of LD without DDCI (LD−DDCI; 17.5 mg/kg); (5) MP plus benserazide (MP+DDCI; 3.5 mg/kg); (6) placebo. Efficacy outcomes were the change in motor response at 90 and 180 minutes and the duration of on state. Safety measures included any adverse event (AE), changes in blood pressure and heart rate, and the severity of dyskinesias. Results: When compared to LD+DDCI, MP-Ld showed similar motor response with fewer dyskinesias and AEs, while MP-Hd induced greater motor improvement at 90 and 180 minutes, longer ON duration, and fewer dyskinesias. MP-Hd induced less AEs than LD+DDCI and LD−DDCI. No differences in cardiovascular response were recorded. Conclusion: Single-dose MP intake met all noninferiority efficacy and safety outcome measures in comparison to dispersible levodopa/benserazide. Clinical effects of high-dose MP were similar to levodopa alone at the same dose, with a more favorable tolerability profile. ClinicalTrials.gov identifier: NCT02680977. PMID:28679598

Structural and functional insights into the interaction between the Cas family scaffolding protein p130Cas and the focal adhesion-associated protein paxillin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chi; Miller, Darcie J.; Guibao, Cristina D.

The Cas family scaffolding protein p130Cas is a Src substrate localized in focal adhesions (FAs) and functions in integrin signaling to promote cell motility, invasion, proliferation, and survival. p130Cas targeting to FAs is essential for its tyrosine phosphorylation and downstream signaling. Although the N-terminal SH3 domain is important for p130Cas localization, it has also been reported that the C-terminal region is involved in p130Cas FA targeting. The C-terminal region of p130Cas or Cas family homology domain (CCHD) has been reported to adopt a structure similar to that of the focal adhesion kinase C-terminal focal adhesion-targeting domain. The mechanism by whichmore » the CCHD promotes FA targeting of p130Cas, however, remains unclear. In this study, using a calorimetry approach, we identified the first LD motif (LD1) of the FA-associated protein paxillin as the binding partner of the p130Cas CCHD (in a 1:1 stoichiometry with a Kd ~4.2 μM) and elucidated the structure of the p130Cas CCHD in complex with the paxillin LD1 motif by X-ray crystallography. Of note, a comparison of the CCHD/LD1 complex with a previously solved structure of CCHD in complex with the SH2-containing protein NSP3 revealed that LD1 had almost identical positioning of key hydrophobic and acidic residues relative to NSP3. Because paxillin is one of the key scaffold molecules in FAs, we propose that the interaction between the p130Cas CCHD and the LD1 motif of paxillin plays an important role in p130Cas FA targeting.« less

Effects of Temperature and Humidity on Laser Diffraction Measurements to Jet Nebulizer and Comparison with NGI.

PubMed

Song, Xinghan; Hu, Junhua; Zhan, Shuyao; Zhang, Rui; Tan, Wen

2016-04-01

Laser diffraction (LD) and next generation impactor (NGI) are commonly used for the evaluation of inhaled drug formulations. In this study, the effect of temperature and humidity on the assessment of the nebulizer particle size distribution (PSD) by LD was investigated, and the consistency between NGI and LD measurements was evaluated. There was an increase in particle size with higher temperature or lower humidity. The particle population with a diameter less than 1 μm was significant at a temperature of 5°C or at relative humidity >90%; however, the same particle population became undetectable when temperature increased to 39°C or at relative humidity of 30-45%. The results of the NGI and LD measurements of aerosol generated from three types of jet nebulizers were compared. A poor correlation between the NGI and LD measurements was observed for PARI LC (2.2 μm) (R (2) = 0.893) and PARI LC (2.9 μm) (R (2) = 0.878), while a relatively good correlation (R (2) = 0.977) was observed for the largest particle size nebulizer (PARI TIA (8.6 μm)). We conclude that the ambient environment and the nebulizer have significant impacts on the performance and consistency between these instruments. These factors should be controlled in the evaluation of inhaled aerosol drug formulations when these instruments are used individually or in combination.

Comparison of fluid types for resuscitation after acute blood loss in mallard ducks (Anas platyrhynchos).

PubMed

Lichtenberger, Marla; Orcutt, Connie; Cray, Carolyn; Thamm, Douglas H; DeBehnke, Daniel; Page, Cheryl; Mull, Lori; Kirby, Rebecca

2009-10-01

The purpose of this study was to determine the LD(50) for acute blood loss in mallard ducks (Anas platyrhynchos), compare the mortality rate among 3 fluid resuscitation groups, and determine the time required for a regenerative RBC response. Prospective study. Medical College of Wisconsin Research facility. Eighteen mallard ducks were included for the LD(50) study and 28 for the fluid resuscitation study. Phlebotomy was performed during both the LD(50) and fluid resuscitation studies. Ducks in the fluid resuscitation study received a 5 mL/kg intravenous bolus of crystalloids, hetastarch (HES), or a hemoglobin-based oxygen-carrying solution (HBOCS). The LD(50) for acute blood loss was 60% of total blood volume. This blood volume was removed in the fluid resuscitation study to create a model of acute blood loss. Following fluid administration, 6 birds in the crystalloid group (66%), 4 birds in the HES group (40%), and 2 birds in the HBOCS group (20%) died. No statistical difference in mortality rate was seen among the 3 fluid resuscitation groups. Relative polychromasia evaluated post-phlebotomy demonstrated regeneration starting at 24 hours and continuing through 48 hours. The LD(50) for acute blood loss in mallard ducks was 60% of their total blood volume. Although no statistical difference in mortality rate was appreciated among the 3 fluid resuscitation groups, a trend of decreased mortality rate was observed in the HBOCS group. An early regenerative response was apparent following acute blood loss.

Oral acute toxic class method: a successful alternative to the oral LD50 test.

PubMed

Schlede, Eva; Genschow, Elke; Spielmann, Horst; Stropp, Gisela; Kayser, Detlev

2005-06-01

The oral acute toxic class method (ATC method) was developed as an alternative to replace the oral LD50 test. The ATC method is a sequential testing procedure using only three animals of one sex per step at any of the defined dose levels. Depending on the mortality rate three but never more than six animals are used per dose level. This approach results in the reduction of numbers of animals used in comparison to the LD50 test by 40-70%. The principle of the oral ATC method is based on the Probit model and it was first evaluated on a biometric basis before a national and subsequently an international ring study were conducted. The results demonstrated an excellent agreement between the toxicity and the animal numbers predicted biometrically and observed in the validation studies. The oral ATC method was adopted as an official test guideline by OECD in 1996 and was slightly amended in 2001. The ATC method has been successfully used in Germany and in 2003 >85% of all tests on acute oral toxicity testing was conducted as oral ATC tests. In member states of the European Union the ATC method is used in the range of 50% of all tests conducted. Meanwhile the oral LD50 test has been deleted by OECD, by the European Union and by the USA, making the use of alternatives to the oral LD50 test mandatory.

Wear Characteristics and Volume Loss of CAD/CAM Ceramic Materials.

PubMed

Zurek, Alec D; Alfaro, Maria F; Wee, Alvin G; Yuan, Judy Chia-Chun; Barao, Valentim A; Mathew, Mathew T; Sukotjo, Cortino

2018-03-06

In the field of prosthodontics, patients often require complex and extensive restorative care. This can involve the use of dental restorations to restore teeth on both the maxillary and mandibular arch. Current literature has evaluated the wear properties of different dental ceramics against enamel, but studies regarding dental ceramics opposing one another are limited. The purpose of this study was to assess the wear potential and wear behavior of CAD/CAM zirconia (ZR) and lithium disilicate (LD) materials against a similar ceramic material, and how the surface finish of these dental ceramics might affect patterns of wear. Using a sphere-on-plate tribometer system, different surface finishes (glazed-G and glazed then polished-GP) of ZR and LD were evaluated following wear simulation. Artificial saliva of physiologic pH was used as a lubricant during wear simulation at 37°C. The coefficient of friction (COF) was calculated during the wear simulation. After wear simulation was complete, volume loss, surface roughness, and surface characterization of the specimens were analyzed using white-light interferometry and scanning electron microscopy (SEM). Statistical significance between materials and surface finish was established with two-way ANOVA and Bonferroni post hoc test (α = 0.05). Based on the 2-way ANOVA, material (p = 0.002) significantly affected the COF. LD showed a higher COF (p = 0.002) than ZR. Material (p < 0.001) and surface finish (p = 0.004) significantly affected the surface roughness inside the scar. ZR had significantly lower surface roughness compared to LD (p < 0.001). For outside scar, surface finish (p < 0.001) significantly affected the surface roughness. Polished specimens showed significantly higher roughness compared to glazed specimens for both inside (p = 0.004) and outside scar (p < 0.001). For volume loss, material (p < 0.001) and the interaction between material and surface finish (p < 0.001) were statistically significant. LD had higher volume loss than ZR (p < 0.001). For both glazed and polished finished, LD-G and LD-GP had significantly higher volume loss than ZR-G (p = 0.028), and ZR-GP (p < 0.001), respectively. SEM analysis indicated particle build-up and a grooving mechanism of wear for the LD-GP specimens. This suggested a three-body wear phenomenon occurring for LD-GP specimens, which was not visible in SEM imaging for other specimen types. This study demonstrated the resistance to wear and low abrasiveness of ZR when compared to LD in a simulated masticatory environment. This can be best explained by the increased strength of ZR, and the introduction of three-body wear to LD specimens from the accumulation of embedded wear debris onto its surface. Wear data and comparison of SEM images following wear simulation confirmed this interpretation. © 2018 by the American College of Prosthodontists.

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

Treesearch

S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

2004-01-01

Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

Genome-wide differentiation of various melon horticultural groups for use in genome wide association study for fruit firmness and construction of a high resolution genetic map

USDA-ARS?s Scientific Manuscript database

We generated 13,789 single nucleotide plymorphism (SNP) markers from 97 melon accessions using genotyping by sequencing and anchored them to chromosomes to understand genome-wide fixation index between various melon morphotypes and linkage disequilibrium (LD) decay for inodorus and cantalupensis, th...

STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.

PubMed

Shen, Judong; Song, Kijoung; Slater, Andrew J; Ferrero, Enrico; Nelson, Matthew R

2017-09-01

We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes. This database can be used for a multitude of investigations into the genes and genetic mechanisms underlying inter-individual variation in human traits, as well as supporting drug discovery applications. Shell, R, Perl and Python scripts and STOPGAP R data files (version 2.5.1 at publication) are available at https://github.com/StatGenPRD/STOPGAP . Some of the most useful STOPGAP fields can be queried through an R Shiny web application at http://stopgapwebapp.com . matthew.r.nelson@gsk.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Simulations of Bluff Body Flow Interaction for Noise Source Modeling

NASA Technical Reports Server (NTRS)

Khorrami, Medi R.; Lockard David P.; Choudhari, Meelan M.; Jenkins, Luther N.; Neuhart, Dan H.; McGinley, Catherine B.

2006-01-01

The current study is a continuation of our effort to characterize the details of flow interaction between two cylinders in a tandem configuration. This configuration is viewed to possess many of the pertinent flow features of the highly interactive unsteady flow field associated with the main landing gear of large civil transports. The present effort extends our previous two-dimensional, unsteady, Reynolds Averaged Navier-Stokes computations to three dimensions using a quasilaminar, zonal approach, in conjunction with a two-equation turbulence model. Two distinct separation length-to-diameter ratios of L/D = 3.7 and 1.435, representing intermediate and short separation distances between the two cylinders, are simulated. The Mach 0.166 simulations are performed at a Reynolds number of Re = 1.66 105 to match the companion experiments at NASA Langley Research Center. Extensive comparisons with the measured steady and unsteady surface pressure and off-surface particle image velocimetry data show encouraging agreement. Both prominent and some of the more subtle trends in the mean and fluctuating flow fields are correctly predicted. Both computations and the measured data reveal a more robust and energetic shedding process at L/D = 3.7 in comparison with the weaker shedding in the shorter separation case of L/D = 1.435. The vortex shedding frequency based on the computed surface pressure spectra is in reasonable agreement with the measured Strouhal frequency.

Oral toxicity of p-aminopropiophenone to brushtail possums (Trichosurus vulpecula), dama wallabies (Macropus eugenii), and mallards (Anas platyrhynchos).

PubMed

Fisher, P; O'Connor, C E; Morriss, G

2008-07-01

Development of p-aminopropiophenone (PAPP) as a toxicant for pest predator management in New Zealand and Australia prompted investigation of its toxicity to potential nontarget species. Acute oral toxicity of PAPP in brushtail possums (Trichosurus vulpecula), dama wallabies (Macropus eugenii), and Mallards (Anas platyrhynchos) was estimated in pen trials, carried out between February 2000 and September 2001. The susceptibility of possums (LD50>or=500 mg kg(-1)) and wallabies (LD50 89 mg kg(-1)) to PAPP was low in comparison to noncarnivorous placental mammal species, but ducks (LD50 38 mg kg(-1)) were more susceptible than other bird species. These results suggest that the nontarget hazard to possums and wallabies from PAPP bait applied for pest predator control would be low. However, future development of PAPP as a vertebrate pest control agent should include rigorous assessments of the hazard posed by bait formulations to bird species and provision for delivery techniques that could mitigate exposure of nontarget birds.

A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics.

PubMed

Pare, Guillaume; Mao, Shihong; Deng, Wei Q

2016-06-08

Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD). We now propose a novel method, LD Adjusted Regional Genetic Variance (LARGV), to estimate phenotypic variance explained by regional associations using summary statistics while accounting for LD. Our method is asymptotically equivalent to a multiple linear regression model when no interaction or haplotype effects are present. It has several applications, such as ranking of genetic regions according to variance explained or comparison of variance explained by two or more regions. Using height and BMI data from the Health Retirement Study (N = 7,776), we show that most genetic variance lies in a small proportion of the genome and that previously identified linkage peaks have higher than expected regional variance.

A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics

PubMed Central

Pare, Guillaume; Mao, Shihong; Deng, Wei Q.

2016-01-01

Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD). We now propose a novel method, LD Adjusted Regional Genetic Variance (LARGV), to estimate phenotypic variance explained by regional associations using summary statistics while accounting for LD. Our method is asymptotically equivalent to a multiple linear regression model when no interaction or haplotype effects are present. It has several applications, such as ranking of genetic regions according to variance explained or comparison of variance explained by two or more regions. Using height and BMI data from the Health Retirement Study (N = 7,776), we show that most genetic variance lies in a small proportion of the genome and that previously identified linkage peaks have higher than expected regional variance. PMID:27273519

Measuring the potency labelling of onabotulinumtoxinA (Botox(®)) and incobotulinumtoxinA (Xeomin (®)) in an LD50 assay.

PubMed

Dressler, Dirk; Mander, Gerd; Fink, Klaus

2012-01-01

The biological potency of botulinum toxin (BT) drugs is determined by a standardised LD50 assay. However, the potency labelling varies vary amongst different BT drugs. One reason for this may be differences in the LD50 assays applied. When five unexpired batches of onabotulinumtoxinA (Botox(®)) and incobotulinumtoxinA (Xeomin(®)) are compared in the Xeomin(®) batch release assay, the potency variability of both BT drugs fell within the range allowed by the European Pharmacopoiea. Statistical analyses failed to detect differences in the potency labelling of both products. Although the existence of a conversion ratio has been questioned recently, our experimental data are in line with previous clinical experience showing that Botox(®) and Xeomin(®) can be compared using a 1:1 conversion ratio. Identical potency labelling allows easy exchange of both BT drugs in a therapeutic setting, and direct comparison of efficacy, adverse effects and costs.

Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa.

PubMed

Wang, Longxin; Wang, Bowen; Du, Qingzhang; Chen, Jinhui; Tian, Jiaxing; Yang, Xiaohui; Zhang, Deqiang

2017-02-01

Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development. Analysis of nucleotide diversity and LD revealed that PtoPsbW has low single-nucleotide polymorphism (SNP) diversity (π tot  = 0.0048 and θ w  = 0.0050) and relatively low average value of LD (0.1500), indicating that PtoPsbW is conserved due to its indispensable function. Using single-SNP associations in an association population of 435 individuals, we identified five significant associations at the threshold of P ≤ 0.05, explaining 3.28-15.98 % of the phenotypic variation. Haplotype-based association analyses indicated that 13 haplotypes (P ≤ 0.05) from six blocks were associated with photosynthesis, growth, and wood properties. Our work shows that identifying allelic variation and LD can help to decipher the genetic basis of photosynthesis and could potentially be applied for molecular marker-assisted selection in Populus.

Do the symptoms of language disorder align with treatment goals? An exploratory study of primary-grade students' IEPs.

PubMed

Schmitt, Mary Beth; Justice, Laura M; Logan, Jessica A R; Schatschneider, Christopher; Bartlett, Christopher W

2014-01-01

Individual Education Plans (IEPs) are legal documents that guide the treatment of students with language disorder (LD). This exploratory study investigated the extent to which students' symptoms of LD align with goals on their IEPs. A total of 99 kindergarten and first-grade students receiving treatment for LD in the public schools participated. IEPs were collected and coded for each student and norm-referenced measures were used to assess students' grammar, vocabulary, listening comprehension, and literacy skills in the fall of the academic year. Results showed there to be alignment between students' symptoms and IEP goals only in the area of vocabulary, such that students who had an IEP goal for vocabulary had lower scores on a vocabulary assessment than those without a goal. In general, there is limited alignment between observed symptoms of LD and treated symptoms as identified on students' IEPs. The limited alignment found in this study suggests more investigation is needed to understand the extent to which IEP goals, as potential indicators of treatment foci, should map on to students' symptoms. Readers will be able to: (1) explain the theoretical and practical relevance of treatment goals aligning to symptoms for children with language impairment; (2) identify three analytic methods used to investigate alignment between treatment goals and symptoms; and (3) describe the extent to which IEP goals align to children's symptoms in a sample of children receiving services in the public schools. Copyright © 2014 Elsevier Inc. All rights reserved.

Transethnic differences in GWAS signals: A simulation study.

PubMed

Zanetti, Daniela; Weale, Michael E

2018-05-07

Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. Previous studies have reported differences in the strength and even the direction of GWAS signals across different populations. These differences could be due to a combination of (1) lack of power, (2) allele frequency differences, (3) linkage disequilibrium (LD) differences, and (4) true differences in causal variant effect sizes. To determine whether properties (1)-(3) on their own might be sufficient to explain the patterns previously noted in strong GWAS signals, we simulated case-control data of European, Asian and African ancestry, applying realistic allele frequencies and LD from 1000 Genomes data but enforcing equal causal effect sizes across populations. Much of the observed differences in strong GWAS signals could indeed be accounted for by allele frequency and LD differences, enhanced by the Euro-centric SNP bias and lower SNP coverage found in older GWAS panels. While we cannot rule out a role for true transethnic effect size differences, our results suggest that strong causal effects may be largely shared among human populations, motivating the use of transethnic data for fine-mapping. © 2018 John Wiley & Sons Ltd/University College London.

Comparison of Data on Mutation Frequencies of Mice Caused by Radiation with Low Dose Model

NASA Astrophysics Data System (ADS)

Manabe, Yuichiro; Bando, Masako

2013-09-01

We propose low dose (LD) model, the extension of LDM model which was proposed in the previous paper [Y. Manabe et al.: J. Phys. Soc. Jpn. 81 (2012) 104004] to estimate biological damage caused by irradiation. LD model takes account of cell death effect in addition to the proliferation, apoptosis, repair which were included in LDM model. As a typical example of estimation, we apply LD model to the experiment of mutation frequency on the responses induced by the exposure to low levels of ionizing radiation. The most famous and extensive experiments are those summarized by Russell and Kelly [Proc. Natl. Acad. Sci. U.S.A. 79 (1982) 539], which are known as ``mega-mouse project''. This provides us with important information of the frequencies of transmitted specific-locus mutations induced in mouse spermatogonia stem-cells. It is found that the numerical results of the mutation frequency of mice are in reasonable agreement with the experimental data: the LD model reproduces the total dose and dose rate dependence of data reasonably. In order to see such dose-rate dependence more explicitly, we introduce the dose-rate effectiveness factor (DREF). This represents a sort of dose rate dependent effect, which are to be competitive with proliferation effect of broken cells induced by irradiation.

Tityus serrulatus Scorpion Venom: In Vitro Tests and Their Correlation with In Vivo Lethal Dose Assay

PubMed Central

Cajado-Carvalho, Daniela; Galvão, Juliana; Kuniyoshi, Alexandre K.; Carneiro, Patrícia dos Santos; Paes Leme, Adriana Franco; Pauletti, Bianca Alves; Marengo, Eliana Blini; Portaro, Fernanda V.

2017-01-01

Scorpion stings are the main cause of human envenomation in Brazil and, for the treatment of victims, the World Health Organization (WHO) recommends the use of antivenoms. The first step to achieve effective antivenom is to use a good quality venom pool and to evaluate it, with LD50 determination as the most accepted procedure. It is, however, time-consuming and requires advanced technical training. Further, there are significant ethical concerns regarding the number of animals required for testing. Hence, we investigated the correspondence between LD50 results, in vitro assays, and a strong correlation with proteolytic activity levels was observed, showing, remarkably, that proteases are potential toxicity markers for Tityus serrulatus venom. The comparison of reversed-phase chromatographic profiles also has a potential application in venoms’ quality control, as there were fewer neurotoxins detected in the venom with high LD50 value. These results were confirmed by mass spectrometry analysis. Therefore, these methods could precede the LD50 assay to evaluate the venom excellence by discriminating—and discarding—poor-quality batches, and, consequently, with a positive impact on the number of animals used. Notably, proposed assays are fast and inexpensive, being technically and economically feasible in Tityus serrulatus venom quality control to produce effective antivenoms. PMID:29168766

A Comprehensive Linkage Map of the Dog Genome

PubMed Central

Wong, Aaron K.; Ruhe, Alison L.; Dumont, Beth L.; Robertson, Kathryn R.; Guerrero, Giovanna; Shull, Sheila M.; Ziegle, Janet S.; Millon, Lee V.; Broman, Karl W.; Payseur, Bret A.; Neff, Mark W.

2010-01-01

We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with ∼3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with ∼1500 loci. An additional ∼1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from ∼22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map. PMID:19966068

Fine-Scale Map of Encyclopedia of DNA Elements Regions in the Korean Population

PubMed Central

Yoo, Yeon-Kyeong; Ke, Xiayi; Hong, Sungwoo; Jang, Hye-Yoon; Park, Kyunghee; Kim, Sook; Ahn, TaeJin; Lee, Yeun-Du; Song, Okryeol; Rho, Na-Young; Lee, Moon Sue; Lee, Yeon-Su; Kim, Jaeheup; Kim, Young J.; Yang, Jun-Mo; Song, Kyuyoung; Kimm, Kyuchan; Weir, Bruce; Cardon, Lon R.; Lee, Jong-Eun; Hwang, Jung-Joo

2006-01-01

The International HapMap Project aims to generate detailed human genome variation maps by densely genotyping single-nucleotide polymorphisms (SNPs) in CEPH, Chinese, Japanese, and Yoruba samples. This will undoubtedly become an important facility for genetic studies of diseases and complex traits in the four populations. To address how the genetic information contained in such variation maps is transferable to other populations, the Korean government, industries, and academics have launched the Korean HapMap project to genotype high-density Encyclopedia of DNA Elements (ENCODE) regions in 90 Korean individuals. Here we show that the LD pattern, block structure, haplotype diversity, and recombination rate are highly concordant between Korean and the two HapMap Asian samples, particularly Japanese. The availability of information from both Chinese and Japanese samples helps to predict more accurately the possible performance of HapMap markers in Korean disease-gene studies. Tagging SNPs selected from the two HapMap Asian maps, especially the Japanese map, were shown to be very effective for Korean samples. These results demonstrate that the HapMap variation maps are robust in related populations and will serve as an important resource for the studies of the Korean population in particular. PMID:16702437

Mapping of a disease susceptibility locus in chromosome 6p in Japanese patients with ulcerative colitis.

PubMed

Nomura, E; Kinouchi, Y; Negoro, K; Kojima, Y; Oomori, S; Sugimura, M; Hiroki, M; Takagi, S; Aihara, H; Takahashi, S; Hiwatashi, N; Shimosegawa, T

2004-09-01

Ulcerative colitis (UC) is a multifactorial disorder with both genetic and environmental factors. HLA-B*52 and DRB1*1502 are reported to be strongly associated with UC in Japan. However, the actual susceptible gene has not been identified yet. In this study, to map precisely the susceptible locus for UC, we performed association mapping in the chromosome 6p using 24 microsatellite markers distributed over 16 Mb. A total of 183 patients with UC and 186 healthy controls (HC) were included in this study. In all, 15 markers around the human leukocyte antigen (HLA) region showed statistical significance in the genotypic differentiation test concerned with the allelic distribution between the UC and HC. Especially, the markers between the centromeric region of HLA class I and the telomeric region of class III showed remarkably low P-values and the allele239 of C2-4-4 in class I marker showed the strongest association (Pc=2.9 x 10(-9): OR=3.74, 95% CI=2.50-5.60). Furthermore, we found strong linkage disequilibrium (LD) between the allele239 of C2-4-4 and HLA-B*52 in haplotype analysis. These results provide evidence that, in Japanese, important determinants of disease susceptibility to UC may exist in HLA, especially between the centromeric region of class I and the telomeric region of class III, under the strong LD with HLA-B*52.

Evidence for large inversion polymorphisms in the human genome from HapMap data

PubMed Central

Bansal, Vikas; Bashir, Ali; Bafna, Vineet

2007-01-01

Knowledge about structural variation in the human genome has grown tremendously in the past few years. However, inversions represent a class of structural variation that remains difficult to detect. We present a statistical method to identify large inversion polymorphisms using unusual Linkage Disequilibrium (LD) patterns from high-density SNP data. The method is designed to detect chromosomal segments that are inverted (in a majority of the chromosomes) in a population with respect to the reference human genome sequence. We demonstrate the power of this method to detect such inversion polymorphisms through simulations done using the HapMap data. Application of this method to the data from the first phase of the International HapMap project resulted in 176 candidate inversions ranging from 200 kb to several megabases in length. Our predicted inversions include an 800-kb polymorphic inversion at 7p22, a 1.1-Mb inversion at 16p12, and a novel 1.2-Mb inversion on chromosome 10 that is supported by the presence of two discordant fosmids. Analysis of the genomic sequence around inversion breakpoints showed that 11 predicted inversions are flanked by pairs of highly homologous repeats in the inverted orientation. In addition, for three candidate inversions, the inverted orientation is represented in the Celera genome assembly. Although the power of our method to detect inversions is restricted because of inherently noisy LD patterns in population data, inversions predicted by our method represent strong candidates for experimental validation and analysis. PMID:17185644

Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections.

PubMed

Qin, Hongde; Chen, Min; Yi, Xianda; Bie, Shu; Zhang, Cheng; Zhang, Youchang; Lan, Jiayang; Meng, Yanyan; Yuan, Youlu; Jiao, Chunhai

2015-01-01

Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1-2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.

Map showing bottom topography of the Pacific Continental Margin, Cape Mendocino to Point Conception

USGS Publications Warehouse

Chase, T.E.; Wilde, Pat; Normark, W.R.; Evenden, G.I.; Miller, C.P.; Seekins, B.A.; Young, J. D.; Grim, M.S.; Lief, C.J.

1992-01-01

Wilde, Pat, Chase, T.E., Holmes, M.L., Normark, W.R., Thomas, J.A., McCulloch, D.S., and Kulm, L.D., 1978, Oceanographic data off northern California-southern Oregon 40° to 43° North including the Gorda Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 251, scale 1:815,482 at 42° latitude.

HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics.

PubMed

Zheng, Jie; Rodriguez, Santiago; Laurin, Charles; Baird, Denis; Trela-Larsen, Lea; Erzurumluoglu, Mesut A; Zheng, Yi; White, Jon; Giambartolomei, Claudia; Zabaneh, Delilah; Morris, Richard; Kumari, Meena; Casas, Juan P; Hingorani, Aroon D; Evans, David M; Gaunt, Tom R; Day, Ian N M

2017-01-01

Fine mapping is a widely used approach for identifying the causal variant(s) at disease-associated loci. Standard methods (e.g. multiple regression) require individual level genotypes. Recent fine mapping methods using summary-level data require the pairwise correlation coefficients ([Formula: see text]) of the variants. However, haplotypes rather than pairwise [Formula: see text], are the true biological representation of linkage disequilibrium (LD) among multiple loci. In this article, we present an empirical iterative method, HAPlotype Regional Association analysis Program (HAPRAP), that enables fine mapping using summary statistics and haplotype information from an individual-level reference panel. Simulations with individual-level genotypes show that the results of HAPRAP and multiple regression are highly consistent. In simulation with summary-level data, we demonstrate that HAPRAP is less sensitive to poor LD estimates. In a parametric simulation using Genetic Investigation of ANthropometric Traits height data, HAPRAP performs well with a small training sample size (N < 2000) while other methods become suboptimal. Moreover, HAPRAP's performance is not affected substantially by single nucleotide polymorphisms (SNPs) with low minor allele frequencies. We applied the method to existing quantitative trait and binary outcome meta-analyses (human height, QTc interval and gallbladder disease); all previous reported association signals were replicated and two additional variants were independently associated with human height. Due to the growing availability of summary level data, the value of HAPRAP is likely to increase markedly for future analyses (e.g. functional prediction and identification of instruments for Mendelian randomization). The HAPRAP package and documentation are available at http://apps.biocompute.org.uk/haprap/ CONTACT: : jie.zheng@bristol.ac.uk or tom.gaunt@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Validation of the HONSUN LD-578 blood pressure monitor for home blood pressure monitoring according to the European Society of Hypertension International Protocol.

PubMed

Zhang, Yi; Wang, Jie; Huang, Qi-Fang; Sheng, Chang-Sheng; Li, Yan; Wang, Ji-Guang

2009-06-01

This study aimed to evaluate the accuracy of the automated oscillometric upper arm blood pressure monitor LD-578 (HONSUN Group, Shanghai, China) for home blood pressure monitoring according to the International Protocol. Systolic and diastolic blood pressures were sequentially measured in 33 adult Chinese using a mercury sphygmomanometer (two observers) and the LD-578 device (one supervisor). Ninety-nine pairs of comparisons were obtained from 15 participants in phase 1 and a further 18 participants in phase 2 of the validation study. Data analysis was performed using the ESHIP Analyzer. The LD-578 device successfully passed phase 1 of the validation study with a number of absolute differences between device and observers within 5, 10, and 15 mmHg for at least 32 of 45, 41 of 45, and 45 of 45 measurements (required 25, 35, and 40), respectively. The device also achieved the targets for phase 2.1, with 67 of 99, 90 of 99, and 98 of 99 differences within 5, 10, and 15 mmHg, respectively, for systolic blood pressure, and with 69 of 99, 95 of 99, and 98 of 99 within 5, 10, and 15 mmHg, respectively, for diastolic blood pressure. In phase 2.2, 24 participants had at least two of the three device-observers differences within 5 mmHg (required >or=22) for systolic and diastolic blood pressure. The HONSUN upper arm blood pressure monitor LD-578 can be recommended for home use in adults.

A 16-channel combined loop-dipole transceiver array for 7 Tesla body MRI.

PubMed

Ertürk, M Arcan; Raaijmakers, Alexander J E; Adriany, Gregor; Uğurbil, Kâmil; Metzger, Gregory J

2017-02-01

To develop a 16-channel transceive body imaging array at 7.0 T with improved transmit, receive, and specific absorption rate (SAR) performance by combining both loop and dipole elements and using their respective and complementary near and far field characteristics. A 16-channel radiofrequency (RF) coil array consisting of eight loop-dipole blocks (16LD) was designed and constructed. Transmit and receive performance was quantitatively investigated in phantom and human model simulations, and experiments on five healthy volunteers inside the prostate. Comparisons were made with 16-channel microstrip line (16ML) and 10-channel fractionated dipole antenna (10DA) arrays. The 16LD was used to acquire anatomic and functional images of the prostate, kidneys, and heart. The 16LD provided > 14% improvements in the signal-to-noise ratio (SNR), peak B1+, B1+ transmit, and SAR efficiencies over the 16ML and 10DA in simulations inside the prostate. Experimentally, the 16LD had > 20% higher SNR and B1+ transmit efficiency compared with other arrays, and achieved up to 51.8% higher peak B1+ compared with 10DA. Combining loop and dipole elements provided a body imaging array with high channel count and density while limiting inter-element coupling. The 16LD improved both near and far-field performance compared with existing 7.0T body arrays and provided high-quality MRI of the prostate kidneys and heart. Magn Reson Med 77:884-894, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

SU-F-18C-06: Prospective Patient Evaluation of Iterative Reconstruction in Radiation Oncology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, R; Vance, S; Cattaneo, R

2014-06-15

Purpose: This work incorporates iterative reconstruction (IR) into a dose reduction study to characterize image quality metrics, delineation, and dosimetric assessment, with the goal of reducing imaging dose in Radiation Oncology. Methods: Three-dimensional noise power spectrum (NPS) analysis characterized noise magnitude/texture (120 kVp, 50–200 mAs, IR levels 1–6 yielding noise reduction of 0.89–0.55 compared to filtered backprojection (FBP)). Task-specific Modulation Transfer Functions (MTFtask) were characterized across varied subject contrasts. A prospective dose reduction study (500 to 150 mAs) was conducted for 12 patients (43 inter-fraction CTs) for high-dose rate brachytherapy. Three physicians performed qualitative image assessment between full-dose FBP (FD-FBP,more » 500 mAs), low-dose FBP (LD-FBP, 150–250 mAs), and low-dose IRL5-6 (LD-IR) scans for image noise, cuff/bladder interface detectability, spatial resolution, texture, and segmentation confidence. Comparisons between LD-FBP and LD-IR were conducted for the following metrics: delineation (bladder and rectum evaluated via overlap indices (OI) and Dice similarity coefficients (DSC)), noise, boundary changes, dose calculation, and digitally reconstructed radiographs (DRRs). Results: NPS showed ∼50% reduction in noise magnitude and ∼0.1 1/mm spatial frequency shift with IRL6. The largest MTFtask decrease between FBP and IR was 0.08 A.U. Qualitative patient image evaluation revealed LD-IR was equivalent or slightly worse than FD-FBP, and superior to LD-FBP for all metrics except low contrast interface and texture. The largest CT number discrepancy from FBP occurred at a bone/tissue interface using IRL6 (−1.2 ± 4.9 HU (range: −17.6 – 12.5 HU)). No significant contour differences (OIs and DSCs = 0.85 – 0.95) and dose calculation discrepancy (<0.02%) were observed. DRRs preserved anatomical detail and demonstrated <2% difference in intensity between LD-FBP and LD-IRL6. Conclusion: While phantom analysis showed slight noise texture differences with IR, patient results revealed that image quality, contouring ability, and dosimetric parameters were not adversely affected, thus support integrating IR into treatment planning. Research supported in part by a grant from Philips HealthCare.« less

Comparing the effects of Yasmin® and LD™ (low-dose estrogen) as contraceptive methods on menstrual cycle changes in women referred to the health care centers of Isfahan

PubMed Central

Fathizadeh, Nahid; Bafghi, Raziye Karimain; Boroumandfar, Khadijeh; Savabi, Mitra

2010-01-01

BACKGROUND: One of the biggest problem today that most developing countries are faced with is the uncontrolled population growth; a serious threat to the international community. One of the most accessible contraceptive methods is the hormonal methods in which low-dose estrogen (LD) combined pills are considered as the most common among them. The most important reason for discontinuation of the combination pills is the side effects and following the discontinuation, it can lead to unwanted pregnancy. Promotion of more new methods and providing better methods with lesser side effects can be an important step towards solving some of the problems and increasing the usage percentages of contraceptive methods. This study therefore aimed to compare the effects of Yasmin and LD on menstrual cycle changes. METHODS: In this clinical trial study, 60 women referred to the Family Planning Health Center of Isfahan in 2008 were studied that finally after the sample loss, 27 and 24 samples were placed in Yasmin and LD groups, respectively. A questionnaire was used in order to collect the data. Content validity test and re-test also were used to confirm the validity and reliability of the questionnaire. To analyze the data, SPSS software and descriptive and inferential statistical methods were used. RESULTS: The results of this study indicated that the bleeding rate in the Yasmin group within the next six month compared to taking them before was significantly lower than that in LD group (p = 0.02); but there was no significant difference in terms of menstrual bleeding duration and the two menstruation interval between the two groups (p = 0.2). There was no significant difference between the Yasmin and LD groups in terms of delay in menstruation and dysmenorrheal. Spotting rate significantly was higher in Yasmin group than that in LD group (p = 0.02). There was a significant reduction in terms of bleeding rate changes and menstrual bleeding duration in both Yasmin and LD group at the following next six months in comparison with before the consumption (p < 0.05). CONCLUSIONS: According to the results obtained, the oral combination of Yasmin pills has fewer side effects than LD pills. Therefore, it is recommended to start using Yasmin pill in the family planning units in Iran. PMID:22049290

TCA High Lift Preliminary Assessment

NASA Technical Reports Server (NTRS)

Wyatt, G. H.; Polito, R. C.; Yeh, D. T.; Elzey, M. E.; Tran, J. T.; Meredith, Paul T.

1999-01-01

This paper presents a TCA (Technology Concept Airplane) High lift Preliminary Assessment. The topics discussed are: 1) Model Description; 2) Data Repeatability; 3) Effect of Inboard L.E. (Leading Edge) Flap Span; 4) Comparison of 14'x22' TCA-1 With NTF (National Transonic Facility) Modified Ref. H; 5) Comparison of 14'x22' and NTF Ref. H Results; 6) Effect of Outboard Sealed Slat on TCA; 7) TCA Full Scale Build-ups; 8) Full Scale L/D Comparisons; 9) TCA Full Scale; and 10) Touchdown Lift Curves. This paper is in viewgraph form.

Mapping quantitative trait loci for fear-like behaviors in mice.

PubMed

Gershenfeld, H K; Paul, S M

1997-11-15

Two mouse models developed for screening anxiolytic drugs were selected for genetic analysis, namely "wall-seeking" tendency in an open field ("thigmotaxis") and the light-to-dark transition (LD) paradigm, a conflict test. These tests measure differences in naturalistic tendencies of mice to explore a novel environment and to avoid a bright light or the center of an open field. In an F2 intercross of two strains of mice (A/J and C57BL/6J) that differ markedly in these behaviors, we estimated a broad sense heritability ranging from 0.3 to 0.59. With this intercross (n = 518), we have mapped several quantitative trait loci (QTL) for these behaviors by performing a genome-wide search. A significant QTL on chromosome 10 (near D10Mit237; LOD of 9.3) that affects LD behavior was identified, and suggestive QTL (LOD > 2.8) were mapped to chromosomes 6, 15, 19, and X. For center time behaviors, QTL were identified on chromosome 1 (LOD of 7.7 and 4.0 for the initial 5-min epoch and the first trial average of the next two 5-min epochs, respectively), and suggestive QTL (LOD > 2.8) were mapped to chromosomes 6 and 14. These QTL individually explain from 2.3 to 8.4% of the phenotypic variance. Collectively, the multiple independent QTL explain from 3.5 to 26.5% of the F2 population's phenotypic variance, depending on the trait. The complexity and heterogeneity of the genetic factors underlying these fear-like behaviors are illustrated by the lack of shared QTL between paradigms and by mapping different QTL for repeated trials of behavior. The identification of QTL affecting individual differences in fear-like behavior may lead to the identification of new gene products and pathways that modulate behavior, providing targets for rational drug design.

Effect of Crystallization Firing on Marginal Gap of CAD/CAM Fabricated Lithium Disilicate Crowns.

PubMed

Gold, Steven A; Ferracane, Jack L; da Costa, Juliana

2018-01-01

To evaluate the marginal gaps of CAD/CAM (CEREC 3) produced crowns made from leucite-reinforced glass-ceramic (IPS Empress CAD) blocks (LG), and lithium-disilicate (IPS e.max CAD) blocks before (LD-B), and after (LD-A) crystallization firing. A human molar tooth (#19) was mounted with adjacent teeth on a typodont and prepared for a full-coverage ceramic crown. The typodont was assembled in the mannequin head to simulate clinical conditions. After tooth preparation 15 individual optical impressions were taken by the same operator using titanium dioxide powder and a CEREC 3 camera per manufacturer's instructions. One operator designed and machined the crowns in leucite-reinforced glass-ceramic blocks (n = 5) and lithium-disilicate blocks (n = 10) using the CEREC 3 system. The crowns were rigidly seated on the prepared tooth, and marginal gaps (μm) were measured with an optical microscope (500×) at 12 points, 3 on each of the M, B, D, and L surfaces of the leucite-reinforced glass-ceramic crowns and the lithium-disilicate crowns before and after crystallization firing. Results were analyzed by two-way ANOVA followed by a Tukey's post hoc multiple comparison test (α = 0.05). The overall mean marginal gaps (μm) for the crowns evaluated were: LG = 49.2 ± 5.5, LD-B = 42.9 ± 12.2, and LD-A = 57.2 ± 16.0. The marginal gaps for LG and LD-B were not significantly different, but both were significantly less than for LD-A. The type of ceramic material did not affect the marginal gap of CAD/CAM crowns. The crystallization firing process required for lithium-disilicate crowns resulted in a significant increase in marginal gap size, likely due to shrinkage of the ceramic during the crystallization process. The marginal gap of CAD/CAM-fabricated lithium disilicate crowns increases following crystallization firing. The marginal gap still remains within clinically acceptable parameters. © 2017 by the American College of Prosthodontists.

Anabolic androgenic steroid use is associated with ventricular dysfunction on cardiac MRI in strength trained athletes.

PubMed

Luijkx, Tim; Velthuis, Birgitta K; Backx, Frank J G; Buckens, Constantinus F M; Prakken, Niek H J; Rienks, Rienk; Mali, Willem P Th M; Cramer, Maarten J

2013-08-10

Uncertainty remains about possible cardiac adaptation to resistance training. Androgenic anabolic steroids (AAS) use plays a potential role and may have adverse cardiovascular effects. To elucidate the effect of resistance training and of AAS-use on cardiac dimensions and function. Cardiac magnetic resonance (CMR) were performed in 156 male subjects aged 18-40 years: 52 non-athletes (maximum of 3 exercise hours/week), 52 strength-endurance (high dynamic-high static, HD-HS) athletes and 52 strength (low dynamic-high static, LD-HS) trained athletes (athletes ≥ 6 exercise hours/week). 28 LD-HS athletes denied and 24 admitted to AAS use for an average duration of 5 years (range 3 months-20 years). No significant differences were found between non-athletes and non-AAS-using LD-HS athletes. AAS-using LD-HS athletes had significantly larger LV and RV volumes and LV wall mass than non-AAS-using LD-HS athletes, but lower than HD-HS athletes. In comparison to all other groups AAS-using LD-HS athletes showed lower ejection fractions of both ventricles (LV/RV EF 51/48% versus 55-57/51-52%) and lower E/A ratios (LV/RV 1.5/1.2 versus 1.9-2.0/1.4-1.5) as an indirect measure of diastolic function. Linear regression models demonstrated a significant effect of AAS-use on LV EDV, LV EDM, systolic function and mitral valve E/A ratio (all ANOVA-tests p<0.05). Strength athletes who use AAS show significantly different cardiac dimensions and biventricular systolic dysfunction and impaired ventricular inflow as compared to non-athletes and non-AAS-using strength athletes. Increased ventricular volume and mass did not exceed that of strength-endurance athletes. These findings may help raise awareness of the consequences of AAS use. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Pharmacodynamic Comparison of Prasugrel Versus Ticagrelor in Patients With Type 2 Diabetes Mellitus and Coronary Artery Disease: The OPTIMUS (Optimizing Antiplatelet Therapy in Diabetes Mellitus)-4 Study.

PubMed

Franchi, Francesco; Rollini, Fabiana; Aggarwal, Niti; Hu, Jenny; Kureti, Megha; Durairaj, Ashwin; Duarte, Valeria E; Cho, Jung Rae; Been, Latonya; Zenni, Martin M; Bass, Theodore A; Angiolillo, Dominick J

2016-09-13

Patients with diabetes mellitus (DM) are at increased risk of atherothrombotic events, underscoring the importance of effective platelet inhibiting therapies. Prasugrel and ticagrelor reduce thrombotic complications to a greater extent than clopidogrel. Subgroup analyses of pivotal clinical trials testing prasugrel and ticagrelor versus clopidogrel showed DM patients to have benefits that were consistent with the overall trial populations, although the magnitude of the ischemic risk reduction appeared to be enhanced with prasugrel. Whether these findings may be attributed to differences in the pharmacodynamic profiles of these drugs in DM patients remains poorly explored and represented the aim of this study. In this prospective, randomized, double-blind, double-dummy, crossover pharmacodynamic study, aspirin-treated DM patients (n=50) with coronary artery disease were randomly assigned to receive prasugrel (60 mg loading dose [LD]/10 mg maintenance dose once daily) or ticagrelor (180 mg LD/90 mg maintenance dose twice daily) for 1 week. Pharmacodynamic assessments were conducted using 4 different assays, including VerifyNow P2Y12, vasodilator-stimulated phosphoprotein, light transmittance aggregometry, and Multiplate, which allowed us to explore ADP- and non-ADP-induced (arachidonic acid-, collagen-, thrombin receptor-activating, peptide-induced) platelet signaling pathways. The acute (baseline, 30 minutes, and 2 hours post-LD) and maintenance (1 week) effects of therapy were assessed. The primary end point of the study was the comparison of P2Y12 reaction units determined by VerifyNow P2Y12 at 1 week between prasugrel and ticagrelor. ADP- and non-ADP-induced measures of platelet reactivity reduced significantly with both prasugrel and ticagrelor LD and maintenance dose. P2Y12 reaction units defined by VerifyNow were similar between prasugrel and ticagrelor at 30 minutes and 2 hours post-LD. At 1 week, P2Y12 reaction units were significantly lower with ticagrelor than with prasugrel (52 [32-72] versus 83 [63-103]; least-square means difference: -31; 95% confidence interval, -57 to -4; P=0.022; primary end point). Pharmacodynamic assessments measured by vasodilator-stimulated phosphoprotein, light transmittance aggregometry, and Multiplate were similar between prasugrel and ticagrelor at each time point, including at 1 week. Rates of high on-treatment platelet reactivity were similar between groups with all assays at all time points. In DM patients with coronary artery disease, ticagrelor exerts similar or greater inhibition of ADP-induced platelet reactivity in comparison with prasugrel in the acute and chronic phases of treatment, whereas the inhibition of measures of non-ADP-induced platelet reactivity was not significantly different between the 2 agents. URL: http://www.clinicaltrials.gov. Unique identifier: NCT01852214. © 2016 American Heart Association, Inc.

Identification of a novel Lymantria dispar nucleopolyhedrovirus mutant that exhibits abnormal polyhedron formation and virion occlusion.

PubMed

Slavicek, J M; Mercer, M J; Pohlman, D; Kelly, M E; Bischoff, D S

1998-07-01

In previous studies on the formation of Lymantria dispar nuclear polyhedrosis virus (LdMNPV) few polyhedra (FP) mutants, several polyhedron formation mutants (PFM) were identified that appeared to be unique. These viral mutants are being characterized to investigate the processes of polyhedron formation and virion occlusion. LdMNPV isolate PFM-1 is one of these mutants, and is described in this report. Genetic techniques were used to determine if isolate PFM-1 contained a mutation in the polyhedrin or 25K FP gene. Wild-type viruses were recovered after coinfection of Ld652Y cells with isolate PFM-1 and a FP mutant, and with isolates PFM-1 and PFM-C (isolate PFM-C contains a mutation in the polyhedrin gene). These viruses were analyzed by genomic restriction endonuclease digestion and found to be chimeras of the original PFMs used in the coinfections. Marker rescue studies mapped the mutation in isolate PFM-1 to a genomic region that does not include the polyhedrin or 25K FP genes. Isolate PFM-1 produced approximately 14-fold fewer polyhedra than LdMNPV isolate A21-MPV, an isolate that produces wild-type levels of polyhedra, and approximately 2-fold more polyhedra compared to the FP isolate 122-2. Polyhedra generated by isolate PFM-1 were normal in size and shape but contained very few viral nucleocapsids. The same amount of budded virus (BV) was released from cells infected with isolates PFM-1 and A21-MPV. In contrast, isolate 122-2 yielded significantly more BV than isolates PFM-1 and A21-MPV.

Collaborative Strategic Reading for Students with Learning Disabilities in Upper Elementary Classrooms

ERIC Educational Resources Information Center

Boardman, Alison G.; Vaughn, Sharon; Buckley, Pamela; Reutebuch, Colleen; Roberts, Greg; Klingner, Janette

2016-01-01

Sixty fourth- and fifth-grade general education teachers were randomly assigned to teach Collaborative Strategic Reading (CSR; Klingner, Vaughn, Boardman, & Swanson, 2012), a set of reading comprehension strategies, or to a business-as-usual comparison group. Results demonstrate that students with learning disabilities (LD) who received CSR…

Relationships between Learning Disability, Executive Function, and Psychopathology in Children with ADHD

ERIC Educational Resources Information Center

Mattison, Richard E.; Mayes, Susan Dickerson

2012-01-01

Objective: Learning disabilities (LD), executive function (EF), and psychopathology were investigated to clarify their relationships in 595 children with ADHD. Method: Standard instruments for IQ, achievement, EF, and parent and teacher ratings of psychopathology were obtained at the time of outpatient evaluation. Results: Comparisons between the…

A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR.

PubMed

Sgourakis, Nikolaos G; May, Nathan A; Boyd, Lisa F; Ying, Jinfa; Bax, Ad; Margulies, David H

2015-11-27

As part of its strategy to evade detection by the host immune system, murine cytomegalovirus (MCMV) encodes three proteins that modulate cell surface expression of major histocompatibility complex class I (MHC-I) molecules: the MHC-I homolog m152/gp40 as well as the m02-m16 family members m04/gp34 and m06/gp48. Previous studies of the m04 protein revealed a divergent Ig-like fold that is unique to immunoevasins of the m02-m16 family. Here, we engineer and characterize recombinant m06 and investigate its interactions with full-length and truncated forms of the MHC-I molecule H2-L(d) by several techniques. Furthermore, we employ solution NMR to map the interaction footprint of the m06 protein on MHC-I, taking advantage of a truncated H2-L(d), "mini-H2-L(d)," consisting of only the α1α2 platform domain. Mini-H2-L(d) refolded in vitro with a high affinity peptide yields a molecule that shows outstanding NMR spectral features, permitting complete backbone assignments. These NMR-based studies reveal that m06 binds tightly to a discrete site located under the peptide-binding platform that partially overlaps with the β2-microglobulin interface on the MHC-I heavy chain, consistent with in vitro binding experiments showing significantly reduced complex formation between m06 and β2-microglobulin-associated MHC-I. Moreover, we carry out NMR relaxation experiments to characterize the picosecond-nanosecond dynamics of the free mini-H2-L(d) MHC-I molecule, revealing that the site of interaction is highly ordered. This study provides insight into the mechanism of the interaction of m06 with MHC-I, suggesting a structural manipulation of the target MHC-I molecule at an early stage of the peptide-loading pathway. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Map showing bottom topography of the Pacific Continental Margin, Strait of Juan de Fuca to Cape Mendocino

USGS Publications Warehouse

Grim, M.S.; Chase, T.E.; Evenden, G.I.; Holmes, M.L.; Normark, W.R.; Wilde, Pat; Fox, C.J.; Lief, C.J.; Seekins, B.A.

1992-01-01

Wilde, Pat, Chase, T.E., Holmes, M.L., Normark, W.R., Thomas, J.A., McCulloch, D.S., and Kulm, L.D., 1978, Oceanographic data off northern California-southern Oregon 40° to 43° North including the Gorda Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 251, scale 1:815,482 at 42° latitude.

Plausible Reasoning in Tactical Planning.

DTIC Science & Technology

1987-04-01

different contexts and tasks that give rise to mappings, and the set of issues and different resolutions to these issues that have been proposed in the...humans use in reasoning about the wo~ ld ( Polya , 1958; Collins, 1978a). Our work attempts to formalize the plausible inferences that frequently occur in...are interconnected by traces. Each hierarchy represents knowledge about a class of concepts arranged in a tree structure according to some viewpoint

A High-Level Symbolic Representation for Intelligent Agents Across Multiple Architectures

DTIC Science & Technology

2004-07-01

components of Soar that map to these concepts (instantiation support, selected operator). Fik Ed" Vie Go Boolbmo .’ lookb Wind , Help 1B w ,’ F:ld 1.ý fie...AnswerSpeedRequest ((msg> isa RequestSpeedChange consider (sel’>. pmsg (msg> end 0 St=ndadd irttezf•cc fo1.1 goals . ~interface lGoal s l’n sa,,invq this goail Ys "rt

Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels.

PubMed

Zhang, Ruijie; Lv, Wenhua; Luan, Meiwei; Zheng, Jiajia; Shi, Miao; Zhu, Hongjie; Li, Jin; Lv, Hongchao; Zhang, Mingming; Shang, Zhenwei; Duan, Lian; Jiang, Yongshuai

2015-11-24

Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had lower SNP densities, and higher degrees of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.

Comparison of intestine and bone marrow radiosensitivity of the BALB/c and the C57BL/6 mouse strains and their B6CF1 offspring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, W.R.; Fry, R.J.; Sallese, A.R.

1987-06-01

The radiosensitivity as measured by LD50/6 or LD50/30 of the F1 hybrid B6CF1 (C57BL/6 X BALB/c) is similar to that of C57BL/6 mice but markedly different from BALB/c. The LD50/6 for BALB/c mice was about 8.8 Gy compared to 16.4 Gy for the B6CF1. The difference in LD50/6 between the parent strains or between BALB/c and the F1 hybrid could not be explained by any differences in crypt cell number, cell cycle time, or transit time. Likewise, the observed differences in the LD50/6 do not appear to result from marked differences in the radiosensitivity of marrow stem cells (CFU-S) sincemore » the D0's for the three genotypes of mice were similar. Also, there were no apparent differences in the red blood cell contents of several enzymes associated with antioxidant defenses. The microcolony assay was used to determine the D0 for the crypt clonogenic cells and the D0 values for 60Co gamma rays were about 0.8 Gy for BALB/c mice and 1.4 Gy for B6CF1 mice. However, the D0 values for JANUS fission neutrons were similar; 0.6 Gy for the BALB/c mice and 0.5 for the B6CF1 mice. A comparison of clonogenic cell kinetics, using prolonged colcemid block to distinguish between slowly and rapidly cycling cells suggest that, normally, the stem cells are slowly cycling in both the BALB/c and the B6CF1 hybrid. However, the stem cells of the B6CF1 appear to go into rapid cell cycle more rapidly than those of the BALB/c following irradiation or prolonged colcemid treatment. The more rapid recovery in intestinal epihelial cell production in the B6CF1 hybrid after irradiation may provide an increased mucosal barrier and may, in part, explain the difference in the response to radiation compared to that in the BALB/c.« less

Outcomes for kidney transplants at the National University Health System: comparison with overseas transplants.

PubMed

Vathsala, Anantharaman

2010-01-01

The 5-year and 10-year graft survivals for 186 deceased donor (DD) transplants performed at National University Health System (NUHS) were 79.9% and 58.4% respectively. 5-year and 10-year patient survivals for DD transplants performed at NUHS were 94.2% and 83.4%. The 5-year and 10-year graft survivals for 128 living donor (LD) transplants performed at NUHS were 90.2% and 72% respectively. 5-year and 10-year patient survivals for DD transplants performed at NUHS were 98.6% and 95.1%. The projected graft half lives were 14.6 and 20.6 years for DD and LD transplants respectively. These results compare favorably with the 10-year survival rates of 40% and 58% for DD and LD grafts reported by the United States Renal Data System (USRDS) in 2010. The younger age and the lower prevalence of diabetes and HLAmismatch in the DD and LD transplant study populations, in comparison to the USRDS population and perhaps better access and compliance to maintenance immunosuppression, could have contributed to these excellent outcomes. The 5-year and 10-year graft survivals for 162 transplants receiving what were likely deceased donor kidneys from China were 89.2% and 69.2% respectively. Although these survivals were apparently better than that for DD performed at NUHS, the advantage for China Tx disappeared when DD with primary non function or vascular thrombosis were excluded from analysis. The 5-year and 10-year patient survivals for 30 transplants receiving live non-related transplants from India were 82.3% and 60.1%. Both groups were considered to have received commercial transplants based on various aspects of history from the patients. Among those receiving China_Tx or India Tx, there were a disproportionate number of males and Chinese; and a significant proportion underwent pre-emptive transplant or transplant after only a short period of dialysis. Prevalence of post-transplant hepatitis B was significantly higher among China_Tx than their DD counterparts (7.7% vs. 1.2%, P = 0.005); likewise, post transplant hepatitis C was significantly higher for India_Tx than their LD counterparts (23.1% vs. 3.4%, P = 0.003). These results suggest that commercialization in transplant, results in inequities to access to transplantation and is associated with compromise in screening for infections among potential donors or in observing safety precautions during dialysis.

Comparison of the sensitivity of the Legionella urinary antigen EIA kits from Binax and Biotest with urine from patients with infections caused by less common serogroups and subgroups of Legionella.

PubMed

Olsen, C W; Elverdal, P; Jørgensen, C S; Uldum, S A

2009-07-01

The detection of urinary antigen is the most widely used method to diagnose Legionnaires' disease (LD), so it is important that these assays have a high sensitivity for the disease. In this study, we compare two kits for their ability to detect urinary antigen in urine samples from patients infected with Legionella species and L. pneumophila sero- and subgroups not considered as the most common causes of LD. Urine samples (n = 33) from 30 culture-proven cases of L. pneumophila serogroup (sg) 1, subgroup non-Pontiac infection, and urine samples (n = 35) from 32 cases of non-L. pneumophila species or non-sg 1 infection were examined using the Binax EIA and Biotest EIA kits. For both groups, the overall diagnostic sensitivity of the Binax kit was significantly better than the sensitivity of the Biotest kits (P < 0.0001). For the non-Pontiac group, the sensitivity was 81.8 and 42.4%, respectively, and for the non-sg1 group, it was 51.4 and 28.6%, respectively. It was concluded that the Binax kit was more suitable for the general diagnosis of LD than the Biotest kit, but we still need urinary antigen detection methods with higher sensitivity for non-sg1 LD.

Quantitative determination of biological activity of botulinum toxins utilizing compound muscle action potentials (CMAP), and comparison of neuromuscular transmission blockage and muscle flaccidity among toxins.

PubMed

Torii, Yasushi; Goto, Yoshitaka; Takahashi, Motohide; Ishida, Setsuji; Harakawa, Tetsuhiro; Sakamoto, Takashi; Kaji, Ryuji; Kozaki, Shunji; Ginnaga, Akihiro

2010-01-01

The biological activity of various types of botulinum toxin has been evaluated using the mouse intraperitoneal LD(50) test (ip LD(50)). This method requires a large number of mice to precisely determine toxin activity, and so has posed a problem with regard to animal welfare. We have used a direct measure of neuromuscular transmission, the compound muscle action potential (CMAP), to evaluate the effect of different types of botulinum neurotoxin (NTX), and we compared the effects of these toxins to evaluate muscle relaxation by employing the digit abduction scoring (DAS) assay. This method can be used to measure a broad range of toxin activities the day after administration. Types A, C, C/D, and E NTX reduced the CMAP amplitude one day after administration at below 1 ip LD(50), an effect that cannot be detected using the mouse ip LD(50) assay. The method is useful not only for measuring toxin activity, but also for evaluating the characteristics of different types of NTX. The rat CMAP test is straightforward, highly reproducible, and can directly determine the efficacy of toxin preparations through their inhibition of neuromuscular transmission. Thus, this method may be suitable for pharmacology studies and the quality control of toxin preparations. Copyright 2009 Elsevier Ltd. All rights reserved.

Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C.

PubMed

Wang, Feng; Wan, Hua; Hu, Jian-Ping; Chang, Shan

2015-01-01

Botulinum neurotoxins (BoNTs) are known as the most poisonous biological substances, and they are also used to treat a wide range of medical conditions as well as in the cosmetic applications. Recently, the complex structures of the BoNT/A receptor-binding domain (BoNT/A-RBD) and the synaptic vesicle protein 2C luminal domain (SV2C-LD) were determined by X-ray crystallography. In this article, the wild type (WT) and four mutants of the new structure are studied by molecular dynamics (MD) simulations. The differently decreased structural stabilities of the mutants relative to WT are shown to be consistent with the experimental data of binding affinities. The conformational changes of the five systems are explored by using principal component analysis (PCA) and free energy landscape (FEL) methods. Based on the calculation of interactions at the binding interface, we divide the interface between BoNT/A-RBD and SV2C-LD into two crucial binding regions. Through the comparison of WT and four mutants, we further propose the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions. This study would provide some new insights into the understanding of the dynamics and the interaction mechanism of BoNT/A-RBD:SV2C-LD.

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)

NASA Astrophysics Data System (ADS)

Snyder, David A.; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase.

Void fraction development in gas-liquid flow after a U-bend in a vertically upwards serpentine-configuration large-diameter pipe

NASA Astrophysics Data System (ADS)

Almabrok, Almabrok A.; Aliyu, Aliyu M.; Baba, Yahaya D.; Lao, Liyun; Yeung, Hoi

2018-01-01

We investigate the effect of a return U-bend on flow behaviour in the vertical upward section of a large-diameter pipe. A wire mesh sensor was employed to study the void fraction distributions at axial distances of 5, 28 and 47 pipe diameters after the upstream bottom bend. The study found that, the bottom bend has considerable impacts on up-flow behaviour. In all conditions, centrifugal action causes appreciable misdistribution in the adjacent straight section. Plots from WMS measurements show that flow asymmetry significantly reduces along the axis at L/D = 47. Regime maps generated from three axial locations showed that, in addition to bubbly, intermittent and annular flows, oscillatory flow occurred particularly when gas and liquid flow rates were relatively low. At this position, mean void fractions were in agreement with those from other large-pipe studies, and comparisons were made with existing void fraction correlations. Among the correlations surveyed, drift flux-type correlations were found to give the best predictive results.

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

PubMed Central

Nimmakayala, Padma; Abburi, Venkata L.; Saminathan, Thangasamy; Alaparthi, Suresh B.; Almeida, Aldo; Davenport, Brittany; Nadimi, Marjan; Davidson, Joshua; Tonapi, Krittika; Yadav, Lav; Malkaram, Sridhar; Vajja, Gopinath; Hankins, Gerald; Harris, Robert; Park, Minkyu; Choi, Doil; Stommel, John; Reddy, Umesh K.

2016-01-01

Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes. PMID:27901114

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L.

PubMed

Nimmakayala, Padma; Abburi, Venkata L; Saminathan, Thangasamy; Alaparthi, Suresh B; Almeida, Aldo; Davenport, Brittany; Nadimi, Marjan; Davidson, Joshua; Tonapi, Krittika; Yadav, Lav; Malkaram, Sridhar; Vajja, Gopinath; Hankins, Gerald; Harris, Robert; Park, Minkyu; Choi, Doil; Stommel, John; Reddy, Umesh K

2016-11-30

Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.

Ultrasound analysis of the vertebral artery during non-thrust cervical translatoric spinal manipulation.

PubMed

Creighton, Doug; Kondratek, Melodie; Krauss, John; Huijbregts, Peter; Qu, Harvey

2011-05-01

Cervical translatoric spinal manipulation (TSM) techniques have been suggested as a safer alternative to cervical thrust rotatory techniques. The objective of this study was to determine the effect of three C5-C6 non-thrust TSM techniques on vertebral artery (VA) lumen diameter (LD) and two blood flow velocity parameters. The two-tailed research hypothesis was that the TSM techniques would result in a significant change (increase or decrease) in blood flow velocity and arterial LD at the C5-C6 intertransverse portion of the VA. In a sample of 30 subjects representative of a clinical population, color-coded duplex Doppler diagnostic ultrasound imaging was used to collect data on LD, peak systolic velocity (PSV), and end diastolic velocity with the cervical spine positioned in neutral and in three different manipulation positions. Pair-wise mean differences between measurements at baseline (neutral position) and in all three manipulation positions were analyzed using two-tailed paired t-tests with alpha set at 0·05. Of the 18 paired comparisons, there were four statistically significant differences between measurements in the neutral position and a manipulation position, three concerning LD and one PSV. The three significant differences in LD ranged from 4·6 to 3·2% and were not associated with changes in blood flow velocity. The one significant change in PSV was only 6·6 cm/s. A value that still greatly exceeded the end diastolic velocity. No subject experienced symptoms associated with VA compromise. This study has provided evidence for the safety of the three lower cervical non-thrust TSM techniques on the current population studied. Further study is required on thrust versus non-thrust TSM techniques and on levels other than C5-C6.

The local clinical validation of a new lithium heparin tube with a barrier: BD Vacutainer® Barricor LH Plasma tube.

PubMed

Arslan, Fatma Demet; Karakoyun, Inanc; Basok, Banu Isbilen; Aksit, Merve Zeytinli; Baysoy, Anil; Ozturk, Yasemin Kilic; Guclu, Yusuf Adnan; Duman, Can

2017-10-15

Although serum-providing blood tubes with a barrier are still widely used due to their significant advantages, the use of blood tubes with a barrier to provide plasma is becoming widespread. We compared 22 analytes in a BD Vacutainer® Barricor LH Plasma tube for local clinical validation of this new lithium heparin tube with a barrier. Samples from 44 volunteers were collected in different tubes (Becton Dickinson and Company): Z tube without additive (reference), clot-activator tube with gel (SST), lithium heparin tube without gel (LiH), and lithium heparin tube with barrier (Barricor). Analyte concentrations in different tubes were compared with the reference tube. All tubes were also evaluated according to additional testing (different centrifugation durations, blood-sampling techniques and individual differences). Aspartate aminotransferase (AST), glucose (Glc), potassium (K), lactate dehydrogenase (LD), sodium (Na), and total protein (TP) had a significant bias in Barricor (9.19%, - 3.24%, - 4.88%, 21.60%, - 0.40%, 5.03%, respectively) relative to the reference tube. There was no statistical difference between different centrifugation durations and individual differences for AST, K and LD in LiH and/or Barricor (P > 0.05). There was a significant bias for LD between LiH and Barricor in terms of blood-sampling techniques (21.2% and 12.4%, respectively). Recently, the use of plasma has become prominent due to some of its advantages. In this study, plasma AST, K, LD, Glc and TP levels in Barricor were clinically different in comparison to serum. The results of additional tests showed that higher levels of LD in Barricor did not result from haemolysis, and they might be related to other factors including number of platelets, cellular fragility, or functional environment.

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6.

PubMed

Oparina, Nina Y; Delgado-Vega, Angelica M; Martinez-Bueno, Manuel; Magro-Checa, César; Fernández, Concepción; Castro, Rafaela Ortega; Pons-Estel, Bernardo A; D'Alfonso, Sandra; Sebastiani, Gian Domenico; Witte, Torsten; Lauwerys, Bernard R; Endreffy, Emoke; Kovács, László; Escudero, Alejandro; López-Pedrera, Chary; Vasconcelos, Carlos; da Silva, Berta Martins; Frostegård, Johan; Truedsson, Lennart; Martin, Javier; Raya, Enrique; Ortego-Centeno, Norberto; de Los Angeles Aguirre, Maria; de Ramón Garrido, Enrique; Palma, María-Jesús Castillo; Alarcon-Riquelme, Marta E; Kozyrev, Sergey V

2015-03-01

To perform fine mapping of the PXK locus associated with systemic lupus erythematosus (SLE) and study functional effects that lead to susceptibility to the disease. Linkage disequilibrium (LD) mapping was conducted by using 1251 SNPs (single nucleotide polymorphism) covering a 862 kb genomic region on 3p14.3 comprising the PXK locus in 1467 SLE patients and 2377 controls of European origin. Tag SNPs and genotypes imputed with IMPUTE2 were tested for association by using SNPTEST and PLINK. The expression QTLs data included three independent datasets for lymphoblastoid cells of European donors: HapMap3, MuTHER and the cross-platform eQTL catalogue. Correlation analysis of eQTLs was performed using Vassarstats. Alternative splicing for the PXK gene was analysed on mRNA from PBMCs. Fine mapping revealed long-range LD (>200 kb) extended over the ABHD6, RPP14, PXK, and PDHB genes on 3p14.3. The highly correlated variants tagged an SLE-associated haplotype that was less frequent in the patients compared with the controls (OR=0.89, p=0.00684). A robust correlation between the association with SLE and enhanced expression of ABHD6 gene was revealed, while neither expression, nor splicing alterations associated with SLE susceptibility were detected for PXK. The SNP allele frequencies as well as eQTL pattern analysed in the CEU and CHB HapMap3 populations indicate that the SLE association and the effect on ABHD6 expression are specific to Europeans. These results confirm the genetic association of the locus 3p14.3 with SLE in Europeans and point to the ABHD6 and not PXK, as the major susceptibility gene in the region. We suggest a pathogenic mechanism mediated by the upregulation of ABHD6 in individuals carrying the SLE-risk variants. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Gene Flow between the Korean Peninsula and Its Neighboring Countries

PubMed Central

Cho, Yoon Shin; Oh, Ji Hee; Ryu, Min Hyung; Chung, Hye Won; Seo, Jeong-Sun; Lee, Jong-Eun; Oh, Bermseok; Bhak, Jong; Kim, Hyung-Lae

2010-01-01

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages. PMID:20686617

Predicting Performance on Academic and Non-Academic Tasks: A Comparison of Adolescents with and without Learning Disabilities

ERIC Educational Resources Information Center

Job, Jenelle M.; Klassen, Robert M.

2012-01-01

Previous research suggests that adolescents with learning disabilities (LD) are less accurate in predicting academic performance than normally achieving (NA) adolescents and display a tendency to overestimate their level of performance (e.g., Klassen, 2007). However, no studies have been conducted investigating whether this overestimation is…

A Profile of Interpersonal Conflict Resolution of Children with Learning Disabilities

ERIC Educational Resources Information Center

Agaliotis, Ioannis; Goudiras, Dimitrios

2004-01-01

This study involved a comparison between 30 children with Learning Disabilities (LD) and 30 typically developing peers, regarding their ability to resolve interpersonal conflict problems. It was hypothesized that the groups would show significant differences along the following parameters: (a) understanding of the components of the problems; (b)…

Cognitive Addition: Comparison of Learning Disabled and Academically Normal Children.

ERIC Educational Resources Information Center

Geary, David C.; And Others

To isolate the process deficits underlying a specific learning disability in mathematics achievement, 77 academically normal and 46 learning disabled (LD) students in second, fourth or sixth grade were presented 140 simple addition problems using a true-false reaction time verification paradigm. (The problems were on a video screen controlled by…

Dark nights reverse metabolic disruption caused by dim light at night.

PubMed

Fonken, L K; Weil, Z M; Nelson, R J

2013-06-01

The increasing prevalence of obesity and related metabolic disorders coincides with increasing exposure to light at night. Previous studies report that mice exposed to dim light at night (dLAN) develop symptoms of metabolic syndrome. This study investigated whether mice returned to dark nights after dLAN exposure recover metabolic function. Male Swiss-Webster mice were assigned to either: standard light-dark (LD) conditions for 8 weeks (LD/LD), dLAN for 8 weeks (dLAN/dLAN), LD for 4 weeks followed by 4 weeks of dLAN (LD/dLAN), and dLAN for 4 weeks followed by 4 weeks of LD (dLAN/LD). After 4 weeks in their respective lighting conditions both groups initially placed in dLAN increased body mass gain compared to LD mice. Half of the dLAN mice (dLAN/LD) were then transferred to LD and vice versa (LD/dLAN). Following the transfer dLAN/dLAN and LD/dLAN mice gained more weight than LD/LD and dLAN/LD mice. At the conclusion of the study dLAN/LD mice did not differ from LD/LD mice with respect to weight gain and had lower fat pad mass compared to dLAN/dLAN mice. Compared to all other groups dLAN/dLAN mice decreased glucose tolerance as indicated by an intraperitoneal glucose tolerance test at week 7, indicating that dLAN/LD mice recovered glucose metabolism. dLAN/dLAN mice also increased MAC1 mRNA expression in peripheral fat as compared to both LD/LD and dLAN/LD mice, suggesting peripheral inflammation is induced by dLAN, but not sustained after return to LD. These results suggest that re-exposure to dark nights ameliorates metabolic disruption caused by dLAN exposure. Copyright © 2013 The Obesity Society.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

PubMed

Bizon, Chris; Spiegel, Michael; Chasse, Scott A; Gizer, Ian R; Li, Yun; Malc, Ewa P; Mieczkowski, Piotr A; Sailsbery, Josh K; Wang, Xiaoshu; Ehlers, Cindy L; Wilhelmsen, Kirk C

2014-01-30

The reduction in the cost of sequencing a human genome has led to the use of genotype sampling strategies in order to impute and infer the presence of sequence variants that can then be tested for associations with traits of interest. Low-coverage Whole Genome Sequencing (WGS) is a sampling strategy that overcomes some of the deficiencies seen in fixed content SNP array studies. Linkage-disequilibrium (LD) aware variant callers, such as the program Thunder, may provide a calling rate and accuracy that makes a low-coverage sequencing strategy viable. We examined the performance of an LD-aware variant calling strategy in a population of 708 low-coverage whole genome sequences from a community sample of Native Americans. We assessed variant calling through a comparison of the sequencing results to genotypes measured in 641 of the same subjects using a fixed content first generation exome array. The comparison was made using the variant calling routines GATK Unified Genotyper program and the LD-aware variant caller Thunder. Thunder was found to improve concordance in a coverage dependent fashion, while correctly calling nearly all of the common variants as well as a high percentage of the rare variants present in the sample. Low-coverage WGS is a strategy that appears to collect genetic information intermediate in scope between fixed content genotyping arrays and deep-coverage WGS. Our data suggests that low-coverage WGS is a viable strategy with a greater chance of discovering novel variants and associations than fixed content arrays for large sample association analyses.

AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping

PubMed Central

Campbell, Michael C.; Tishkoff, Sarah A.

2010-01-01

Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. PMID:18593304

GTPase Sar1 regulates the trafficking and secretion of the virulence factor gp63 in Leishmania.

PubMed

Parashar, Smriti; Mukhopadhyay, Amitabha

2017-07-21

Metalloprotease gp63 ( Leishmania donovani gp63 (Ldgp63)) is a critical virulence factor secreted by Leishmania However, how newly synthesized Ldgp63 exits the endoplasmic reticulum (ER) and is secreted by this parasite is unknown. Here, we cloned, expressed, and characterized the GTPase LdSar1 and other COPII components like LdSec23, LdSec24, LdSec13, and LdSec31 from Leishmania to understand their role in ER exit of Ldgp63. Using dominant-positive (LdSar1:H74L) and dominant-negative (LdSar1:T34N) mutants of LdSar1, we found that GTP-bound LdSar1 specifically binds to LdSec23, which binds, in turn, with LdSec24(1-702) to form a prebudding complex. Moreover, LdSec13 specifically interacted with His 6 -LdSec31(1-603), and LdSec31 bound the prebudding complex via LdSec23. Interestingly, dileucine 594/595 and valine 597 residues present in the Ldgp63 C-terminal domain were critical for binding with LdSec24(703-966), and GFP-Ldgp63 L594A/L595A or GFP-Ldgp63 V597S mutants failed to exit from the ER. Moreover, Ldgp63-containing COPII vesicle budding from the ER was inhibited by LdSar1:T34N in an in vitro budding assay, indicating that GTP-bound LdSar1 is required for budding of Ldgp63-containing COPII vesicles. To directly demonstrate the function of LdSar1 in Ldgp63 trafficking, we coexpressed RFP-Ldgp63 along with LdSar1:WT-GFP or LdSar1:T34N-GFP and found that LdSar1:T34N overexpression blocks Ldgp63 trafficking and secretion in Leishmania Finally, we noted significantly compromised survival of LdSar1:T34N-GFP-overexpressing transgenic parasites in macrophages. Taken together, these results indicated that Ldgp63 interacts with the COPII complex via LdSec24 for Ldgp63 ER exit and subsequent secretion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Application of passive sampling in assessing the occurrence and risk of antibiotics and endocrine disrupting chemicals in the Yangtze Estuary, China.

PubMed

Shi, X; Zhou, J L; Zhao, H; Hou, L; Yang, Y

2014-09-01

Polar organic chemical integrative sampler (POCIS) was used in assessing the occurrence and risk of 12 widely used antibiotics and 5 most potent endocrine disrupting chemicals (EDCs) in the Yangtze Estuary, China. During laboratory validation, the kinetics of pollutant uptake by POCIS were linear, and the sampling rates of most compounds were raised by flow rate and salinity, reaching the highest values at salinity 14‰. The sampling rates varied with the target compounds with the EDCs showing the highest values (overall average=0.123Ld(-1)), followed by chloramphenicols (0.100Ld(-1)), macrolides (0.089Ld(-1)), and finally sulfonamides (0.056Ld(-1)). Validation in the Yangtze Estuary in 2013 showed that the field sampling rates were significantly greater for all compounds except bisphenol A, in comparison to laboratory results, and high-frequency spot sampling is critical for fully validating the passive sampler. The field studies show that antibiotics were widely detected in the Yangtze Estuary, with concentrations varying from below quantification to 1613ngL(-1), suggesting their widespread use and persistence in estuarine waters. The dominating pollutants in July were sulfonamides with a total concentration of 258ngL(-1) and in October were macrolides with a total concentration of 350ngL(-1). The calculation of risk quotient suggested that sulfapyridine, sulfaquinoxaline and erythromycin-H2O may have caused medium damage to sensitive organisms such as fish. Copyright © 2014. Published by Elsevier Ltd.

Acute and subacute oral toxicity of periodate salts in rats.

PubMed

Lent, Emily May; Crouse, Lee C B; Eck, William S

2017-02-01

Periodate salts are being developed as potential replacements for perchlorate due to potential health hazards associated with exposure to perchlorate. The aim of this study was to investigate acute and subacute effects of periodate salts in rats. Acute oral toxicity of potassium and sodium periodate was determined using the Sequential Stage-Wise Probit method. The LD 50 for potassium periodate was 732 (95% CI = 539-838, slope = 13.4) and 685 mg/kg (95% CI = 580-809, slope = 10.6) for females and males, respectively. The LD 50 for sodium periodate was 318 (95% CI = 292-347, slope = 24.3) and 741 mg/kg (95% CI = 704-779, slope = 31.2) for females and males, respectively. In the subacute study, rats were administered sodium periodate at five doses (1/16 LD 50 up to LD 50 ) or distilled water for 14-days via oral gavage. Female rats in the 318 mg/kg-day group and male rats in the 185, 370, and 741 mg/kg-day groups exhibited moribundity, kidney toxicity, uremia, and a stress response. BMDL 10 s of 17.2 and 33.7 mg/kg-day were derived for females and males, respectively. Comparison with the NOAEL for perchlorate-induced thyroid toxicity in rats (0.009 mg/kg-day) suggests sodium periodate is less toxic than perchlorate on a subacute basis. Copyright © 2016. Published by Elsevier Inc.

Reversible Nuclear-Lipid-Droplet Morphology Induced by Oleic Acid: A Link to Cellular-Lipid Metabolism

PubMed Central

Lagrutta, Lucía C.; Montero-Villegas, Sandra; Layerenza, Juan P.; Sisti, Martín S.; García de Bravo, Margarita M.

2017-01-01

Neutral lipids—involved in many cellular processes—are stored as lipid droplets (LD), those mainly cytosolic (cLD) along with a small nuclear population (nLD). nLD could be involved in nuclear-lipid homeostasis serving as an endonuclear buffering system that would provide or incorporate lipids and proteins involved in signalling pathways as transcription factors and as enzymes of lipid metabolism and nuclear processes. Our aim was to determine if nLD constituted a dynamic domain. Oleic-acid (OA) added to rat hepatocytes or HepG2 cells in culture produced cellular-phenotypic LD modifications: increases in TAG, CE, C, and PL content and in cLD and nLD numbers and sizes. LD increments were reversed on exclusion of OA and were prevented by inhibition of acyl-CoA synthetase (with Triacsin C) and thus lipid biosynthesis. Under all conditions, nLD corresponded to a small population (2–10%) of total cellular LD. The anabolism triggered by OA, involving morphologic and size changes within the cLD and nLD populations, was reversed by a net balance of catabolism, upon eliminating OA. These catabolic processes included lipolysis and the mobilization of hydrolyzed FA from the LD to cytosolic-oxidation sites. These results would imply that nLD are actively involved in nuclear processes that include lipids. In conclusion, nLD are a dynamic nuclear domain since they are modified by OA through a reversible mechanism in combination with cLD; this process involves acyl-CoA-synthetase activity; ongoing TAG, CE, and PL biosynthesis. Thus, liver nLD and cLD are both dynamic cellular organelles. PMID:28125673

Comparison of Oral Language Usage among English Language Learners Diagnosed with a Learning Disability and Those in General Education

ERIC Educational Resources Information Center

Pray, Lisa

2009-01-01

The investigator compared the linguistic characteristics of Spanish and English language samples taken from English language learners (ELLs) diagnosed with an academic learning disability (LD) and ELLs in general education to determine if the errors and characteristics of their language use differ. There was a statistically significant difference…

Do Learning Difficulties Differentiate Elementary Teachers' Attributional Patterns for Students' Academic Failure? A Comparison between Greek Regular and Special Education Teachers

ERIC Educational Resources Information Center

Vlachou, Anastasia; Eleftheriadou, Dimitra; Metallidou, Panayiota

2014-01-01

This study aimed to (a) investigate whether the presence of learning difficulties (LD) in primary school children differentiates Greek teachers' attributional patterns, emotional responses, expectations and evaluative feedback for the children's academic failures and (b) to examine possible differences between regular and special education…

Young People with Harmful Sexual Behaviour: Do Those with Learning Disabilities Form a Distinct Subgroup?

ERIC Educational Resources Information Center

Almond, Louise; Giles, Susan

2008-01-01

The study examines 102 young people with Learning Disabilities (n = 51) and without a learning disability (NLD; n = 51) to explore ways in which LD young people with harmful sexual behaviours (HSB) should be recognized as a subgroup requiring specialized treatment and intervention. Throughout this comparison of perpetrator, victim and abuse…

Teacher Interpersonal Behavior and Adolescents' Motivation in Mathematics: A Comparison of Learning Disabled, Average, and Talented Students, Chapter 3

ERIC Educational Resources Information Center

Lapointe, Judith M.; Legault, Frederic; Batiste, Seth J.

2005-01-01

This study examined student perceptions of teacher behavior in three motivational variables (self-efficacy beliefs, intrinsic value, and test anxiety in mathematics) for adolescents enrolled in three distinct schooling tracks. Questionnaires were administered to 111 learning disabled (LD), 224 average (AV) and 258 talented students (TA). Some…

Admixture in Hispanic Americans: its impact on ITGAM association and implications for admixture mapping in SLE.

PubMed

Molineros, J E; Kim-Howard, X; Deshmukh, H; Jacob, C O; Harley, J B; Nath, S K

2009-07-01

Systemic Lupus Erythematosus (SLE) disproportionately affects minorities, such as Hispanic Americans (HA). Prevalence of SLE is 3-5 times higher in HA than in European-derived populations and have more active disease at the time of diagnosis, with more serious organ system involvement. HA is an admixed population, it is possible that there is an effect of admixture on the relative risk of the disease. This admixture can create substantial increase of linkage disequilibrium (LD) in both magnitude and range, which can provide a unique opportunity for admixture mapping. The main objectives of this study are to (a) estimate hidden population structure in HA individuals; (b) estimate individual ancestry proportions and its impact on SLE risk; (c) assess impact of admixture on ITGAM association, a recently identified SLE susceptibility gene; and (d) estimate power of admixture mapping in HA. Our dataset contained 1125 individuals, of whom 884 (657 SLE cases and 227 controls) were self-classified as HA. Using 107 unlinked ancestry informative markers (AIMs), we estimated hidden population structure and individual ancestry in HA. Out of 5671 possible pairwise LD, 54% were statistically significant, indicating recent population admixture. The best-fitted model for HA was a four-population model with average ancestry of European (48%), American-Indian (AI) (40%), African (8%) and a fourth population (4%) with unknown ancestry. We also identified significant higher risk associated with AI ancestry (odds ratio (OR)=4.84, P=0.0001, 95% CI (confidence interval)=2.14-10.95) on overall SLE. We showed that ITGAM is associated as a risk factor for SLE (OR=2.06, P=8.74 x 10(-5), 95% CI=1.44-2.97). This association is not affected by population substructure or admixture. We have shown that HA have great potential and are an appropriate population for admixture mapping. As expected, the case-only design is more powerful than case-control design, for any given admixture proportion or ancestry risk ratio.

Dynamics of genome change among Legionella species

PubMed Central

Joseph, Sandeep J.; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S.; Kozak-Muiznieks, Natalia A.; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D.; Dean, Deborah

2016-01-01

Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires’ Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1–17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD–causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence. PMID:27633769

Sensitivity of some nitrogen fixers and the target pest Fusarium oxysporum to fungicide thiram.

PubMed

Osman, Awad G; Sherif, Ashraf M; Elhussein, Adil A; Mohamed, Afrah T

2012-03-01

This study was carried out to investigate the toxic effects of the fungicide thiram (TMTD) against five nitrogen fixers and the thiram target pest Fusarium oxysporum under laboratory conditions. Nitrogen fixing bacteria Falvobacterium showed the highest values of LD(50) and proved to be the most resistant to the fungicide followed by Fusarium oxysporum, while Pseudomonas aurentiaca was the most affected microorganism. LD(50) values for these microorganisms were in 2-5 orders of magnitude lower in comparison with LD(50) value for Fusarium oxysporum. Thiram was most toxic to Pseudomonas aurentiaca followed by Azospirillum. The lowest toxicity index was recorded for Fusarium oxysporum and Flavobacterium. The slope of the curve for Azomonas, Fusarium oxysporum and Flavobacterium is more steep than that of the other curves, suggesting that even a slight increase of the dose of the fungicide can cause a very strong negative effect. Thiram was more selective to Pseudomonas aurentiaca followed by Azospirillum, Rhizobium meliloti and Azomonas. The lowest selectivity index of the fungicide was recorded for Falvobacterium followed by Fusarium oxysporum. The highest safety coefficient of the fungicide was assigned for Flavobacterium, while Pseudomonas aurentiaca showed the lowest value.

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP).

PubMed

Snyder, David A; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase. Copyright © 2015 Elsevier Inc. All rights reserved.

Resin cements formulated with thio-urethanes can strengthen porcelain and increase bond strength to ceramics.

PubMed

Bacchi, Atais; Spazzin, Aloisio Oro; de Oliveira, Gabriel Rodrigues; Pfeifer, Carmem; Cesar, Paulo Francisco

2018-06-01

The use of thio-urethane oligomers has been shown to significantly improve the mechanical properties of resin cements (RCs). The aim of this study was to use thio-urethane-modified RC to potentially reinforce the porcelain-RC structure and to improve the bond strength to zirconia and lithium disilicate. Six oligomers were synthesized by combining thiols - pentaerythritol tetra-3-mercaptopropionate (PETMP, P) or trimethylol-tris-3-mercaptopropionate (TMP, T) - with di-functional isocyanates - 1,6-Hexanediol-diissocyante (HDDI) (aliphatic, AL) or 1,3-bis(1-isocyanato-1-methylethyl)benzene (BDI) (aromatic, AR) or Dicyclohexylmethane 4,4'-Diisocyanate (HMDI) (cyclic, CC). Thio-urethanes (20 wt%) were added to a BisGMA/UDMA/TEGDMA organic matrix. Filler was introduced at 60 wt%. The microshear bond strength (μSBS), Weibull modulus (m), and failure pattern of RCs bonded to zirconia (ZR) and lithium disilicate (LD) ceramics was evaluated. Biaxial flexural test and fractographic analysis of porcelain discs bonded to RCs were also performed. The biaxial flexural strength (σ bf ) and m were calculated in the tensile surfaces of porcelain and RC structures (Z = 0 and Z = -t 2 , respectively). The μSBS was improved with RCs formulated with oligomers P_AL or T_AL bonded to LD and P_AL, P_AR or T_CC bonded to zirconia in comparison to controls. Mixed failures predominated in all groups. σ bf had superior values at Z = 0 with RCs formulated with oligomers P_AL, P_AR, T_AL, or T_CC in comparison to control; σ bf increased with all RCs composed by thio-urethanes at Z = -t 2 . Fractographic analysis revealed all fracture origins at Z = 0. The use of specific thio-urethane oligomers as components of RCs increased both the biaxial flexural strength of the porcelain-RC structure and the μSBS to LD and ZR. The current investigation suggests that it is possible to reinforce the porcelain-RC pair and obtain higher bond strength to LD and ZR with RCs formulated with selected types of thio-urethane oligomers. Copyright © 2018 Elsevier Ltd. All rights reserved.

Accuracy of computer-aided design models of the jaws produced using ultra-low MDCT doses and ASIR and MBIR.

PubMed

Al-Ekrish, Asma'a A; Alfadda, Sara A; Ameen, Wadea; Hörmann, Romed; Puelacher, Wolfgang; Widmann, Gerlig

2018-06-16

To compare the surface of computer-aided design (CAD) models of the maxilla produced using ultra-low MDCT doses combined with filtered backprojection (FBP), adaptive statistical iterative reconstruction (ASIR) and model-based iterative reconstruction (MBIR) reconstruction techniques with that produced from a standard dose/FBP protocol. A cadaveric completely edentulous maxilla was imaged using a standard dose protocol (CTDIvol: 29.4 mGy) and FBP, in addition to 5 low dose test protocols (LD1-5) (CTDIvol: 4.19, 2.64, 0.99, 0.53, and 0.29 mGy) reconstructed with FBP, ASIR 50, ASIR 100, and MBIR. A CAD model from each test protocol was superimposed onto the reference model using the 'Best Fit Alignment' function. Differences between the test and reference models were analyzed as maximum and mean deviations, and root-mean-square of the deviations, and color-coded models were obtained which demonstrated the location, magnitude and direction of the deviations. Based upon the magnitude, size, and distribution of areas of deviations, CAD models from the following protocols were comparable to the reference model: FBP/LD1; ASIR 50/LD1 and LD2; ASIR 100/LD1, LD2, and LD3; MBIR/LD1. The following protocols demonstrated deviations mostly between 1-2 mm or under 1 mm but over large areas, and so their effect on surgical guide accuracy is questionable: FBP/LD2; MBIR/LD2, LD3, LD4, and LD5. The following protocols demonstrated large deviations over large areas and therefore were not comparable to the reference model: FBP/LD3, LD4, and LD5; ASIR 50/LD3, LD4, and LD5; ASIR 100/LD4, and LD5. When MDCT is used for CAD models of the jaws, dose reductions of 86% may be possible with FBP, 91% with ASIR 50, and 97% with ASIR 100. Analysis of the stability and accuracy of CAD/CAM surgical guides as directly related to the jaws is needed to confirm the results.

Fatigue resistance of ultrathin CAD/CAM complete crowns with a simplified cementation process.

PubMed

Magne, Pascal; Carvalho, Adriana O; Bruzi, Greciana; Giannini, Marcelo

2015-10-01

Traditional tooth preparation for complete crowns requires a substantial amount of hard tissue reduction. This is in contrast with the principles of minimally invasive dentistry. An ultrathin complete crown preparation is proposed instead. The purpose of this in vitro study was to assess the fatigue resistance and failure mode of computer-aided design and computer-aided manufacturing (CAD/CAM) ultrathin complete molar crowns placed with self-adhesive cement. Different restorative materials (resin nanoceramic [RNC], feldspathic ceramic [FEL], and lithium disilicate [LD]) were compared. Forty-five extracted molars with a standardized crown preparation were restored with the Cerec 3 CAD/CAM system using FEL, LD, or RNC (n=15). FEL and LD restorations were etched with hydrofluoric acid and silanated. RNC restorations and all preparations were treated with airborne-particle abrasion. All restorations (thickness=0.7 mm) were cemented with RelyX Unicem II Automix cement and submitted to cyclic isometric loading, beginning with a load of 200 N (5000 cycles) and followed by stages of 400, 600, 800, 1000, 1200, and 1400 N at a maximum of 30 000 cycles each. The specimens were loaded until failure or for a maximum of 185 000 cycles. The failure mode was categorized as "catastrophic," "possibly reparable," or "reparable." The groups were compared using life table survival analysis (log rank test at α=.05). Previously published data from the same authors about traditional complete crowns (thickness 1.5 mm) using the same experimental design were included for comparison. All specimens survived the fatigue test until the 600 N step. RNC, LD, and FEL failed at an average load of 1014 N (1 survival), 1123 N (2 survivals), and 987 N (no survivals), and no difference in survival rate was found. No catastrophic failures were reported after the fatigue test. Comparison with previously published data showed that 1.5-mm thick complete crowns demonstrated higher survival rates than the ultrathin restorations, independent of the material. The fatigue resistance of ultrathin complete molar crowns (placed with a simplified cementation process) made of RNC, LD, and FEL was not significantly different. All materials survived the normal range of masticatory forces. All failures were re-restorable. Regular crowns of 1.5 to 2.0 mm thickness may present higher survival rates than ultrathin ones. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.).

PubMed

Ademe, Mulugeta Seyoum; He, Shoupu; Pan, Zhaoe; Sun, Junling; Wang, Qinglian; Qin, Hongde; Liu, Jinhai; Liu, Hui; Yang, Jun; Xu, Dongyong; Yang, Jinlong; Ma, Zhiying; Zhang, Jinbiao; Li, Zhikun; Cai, Zhongmin; Zhang, Xuelin; Zhang, Xin; Huang, Aifen; Yi, Xianda; Zhou, Guanyin; Li, Lin; Zhu, Haiyong; Pang, Baoyin; Wang, Liru; Jia, Yinhua; Du, Xiongming

2017-12-01

Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed significant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at r 2  = 0.1, and decreased to ~1 to 2 cM at r 2  = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 significant (p < 0.01) marker-trait associations, including seven associations for fiber length, ten for fiber micronaire, nine for fiber strength, eight for fiber elongation, five for fiber uniformity index, five for fiber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker-trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identified QTLs/genes. The QTLs identified in this study will potentially facilitate improvement of fiber yield and quality in the future cotton molecular breeding programs.

Fine-mapping and initial characterization of QT interval loci in African Americans.

PubMed

Avery, Christy L; Sethupathy, Praveen; Buyske, Steven; He, Qianchuan; Lin, Dan-Yu; Arking, Dan E; Carty, Cara L; Duggan, David; Fesinmeyer, Megan D; Hindorff, Lucia A; Jeff, Janina M; Klein, Liviu; Patton, Kristen K; Peters, Ulrike; Shohet, Ralph V; Sotoodehnia, Nona; Young, Alicia M; Kooperberg, Charles; Haiman, Christopher A; Mohlke, Karen L; Whitsel, Eric A; North, Kari E

2012-01-01

The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10(-4)): ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10(-5)): one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation.

Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans

PubMed Central

Avery, Christy L.; Sethupathy, Praveen; Buyske, Steven; He, Qianchuan; Lin, Dan-Yu; Arking, Dan E.; Carty, Cara L.; Duggan, David; Fesinmeyer, Megan D.; Hindorff, Lucia A.; Jeff, Janina M.; Klein, Liviu; Patton, Kristen K.; Peters, Ulrike; Shohet, Ralph V.; Sotoodehnia, Nona; Young, Alicia M.; Kooperberg, Charles; Haiman, Christopher A.; Mohlke, Karen L.; Whitsel, Eric A.; North, Kari E.

2012-01-01

The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10−4): ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10−5): one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation. PMID:22912591

RNA interference of chitin synthase genes inhibits chitin biosynthesis and affects larval performance in Leptinotarsa decemlineata (Say).

PubMed

Shi, Ji-Feng; Mu, Li-Li; Chen, Xu; Guo, Wen-Chao; Li, Guo-Qing

2016-01-01

Dietary introduction of bacterially expressed double-stranded RNA (dsRNA) has great potential for management of Leptinotarsa decemlineata . Identification of the most attractive candidate genes for RNA interference (RNAi) is the first step. In the present paper, three complete chitin synthase cDNA sequences ( LdChSAa , LdChSAb and LdChSB ) were cloned. LdChSAa and LdChSAb , two splicing variants of LdChSA gene, were highly expressed in ectodermally-derived epidermal cells forming epidermis, trachea, foregut and hindgut, whereas LdChSB was mainly transcribed in midgut cells. Feeding bacterially expressed ds ChSA (derived from a common fragment of LdChSAa and LdChSAb ), ds ChSAa , ds ChSAb and ds ChSB in the second- and fourth-instar larvae specifically knocked down their target mRNAs. RNAi of LdChSAa + LdChSAb and LdChSAa lowered chitin contents in whole body and integument samples, and thinned tracheal taenidia. The resulting larvae failed to ecdyse, pupate, or emerge as adults. Comparably, knockdown of LdChSAb mainly affected pupal-adult molting. The LdChSAb RNAi pupae did not completely shed the old larval exuviae, which caused failure of adult emergence. In contrast, silencing of LdChSB significantly reduced foliage consumption, decreased chitin content in midgut sample, damaged midgut peritrophic matrix, and retarded larval growth. As a result, the development of the LdChSB RNAi hypomorphs was arrested. Our data reveal that these LdChS s are among the effective candidate genes for an RNAi-based control strategy against L. decemlineata .

Comparison of behavioural activation with guided self-help for treatment of depression in adults with intellectual disabilities: a randomised controlled trial.

PubMed

Jahoda, Andrew; Hastings, Richard; Hatton, Chris; Cooper, Sally-Ann; Dagnan, Dave; Zhang, Ruiqi; McConnachie, Alex; McMeekin, Nicola; Appleton, Kim; Jones, Rob; Scott, Katie; Fulton, Lauren; Knight, Rosie; Knowles, Dawn; Williams, Chris; Briggs, Andrew; MacMahon, Ken; Lynn, Helen; Smith, Ian; Thomas, Gail; Melville, Craig

2017-12-01

Psychological therapies are first-line interventions for depression, but existing provision is not accessible for many adults with intellectual disabilities. We investigated the clinical and cost-effectiveness of a behavioural activation intervention (BeatIt) for people with intellectual disabilities and depression. BeatIt was compared with a guided self-help intervention (StepUp). We did a multicentre, single-blind, randomised, controlled trial with follow-up at 4 months and 12 months after randomisation. Participants aged 18 years or older, with mild to moderate intellectual disabilities and clinically significant depression were recruited from health and social care services in the UK. The primary outcome was the Glasgow Depression Scale for people with a Learning Disability (GDS-LD) score at 12 months. Analyses were done on an intention-to-treat basis. This trial is registered with ISCRTN, number ISRCTN09753005. Between Aug 8, 2013, and Sept 1, 2015, 161 participants were randomly assigned (84 to BeatIt; 77 to StepUp); 141 (88%) participants completed the trial. No group differences were found in the effects of BeatIt and StepUp based on GDS-LD scores at 12 months (12·03 [SD 7·99] GDS-LD points for BeatIt vs 12·43 [SD 7·64] GDS-LD points for StepUp; mean difference 0·26 GDS-LD points [95% CI -2·18 to 2·70]; p=0·833). Within-group improvements in GDS-LD scores occurred in both groups at 12 months (BeatIt, mean change -4·2 GDS-LD points [95% CI -6·0 to -2·4], p<0·0001; StepUp, mean change -4·5 GDS-LD points [-6·2 to -2·7], p<0·0001), with large effect sizes (BeatIt, 0·590 [95% CI 0·337-0·844]; StepUp, 0·627 [0·380-0·873]). BeatIt was not cost-effective when compared with StepUp, although the economic analyses indicated substantial uncertainty. Treatment costs were only approximately 3·6-6·8% of participants' total support costs. No treatment-related or trial-related adverse events were reported. This study is, to our knowledge, the first large randomised controlled trial assessing individual psychological interventions for people with intellectual disabilities and mental health problems. These findings show that there is no evidence that BeatIt is more effective than StepUp; both are active and potentially effective interventions. National Institute for Health Research. Copyright © 2017 Elsevier Ltd. All rights reserved.

926 nm laser operation in Nd:GdNbO4 crystal based on 4F3/2 → 4I9/2 transition

NASA Astrophysics Data System (ADS)

Yan, Renpeng; Li, Xudong; Yao, Wenming; Shen, Yingjie; Zhou, Zhongxiang; Peng, Fang; Zhang, Qingli; Dou, Renqing; Gao, Jing

2018-05-01

926 nm laser operation in a Nd:GdNbO4 crystal based on quasi-three-level 4F3/2 → 4I9/2 transition is reported, for the first time to our best knowledge. An average output power of 393 mW at 926 nm under 879 nm LD pumping is obtained with a slope efficiency of 33.3% and an optical-to-optical efficiency of 26.0%. The slope efficiency with respect to absorbed pump power is estimated to be 47.7%. Comparison between output characters of 926 nm laser under direct and indirect pumping is conducted. The average output power at 926 nm under 808 nm LD pumping reaches 305 mW with an optical-to-optical efficiency of 16.1%.

A comparative study of progressive wear of four dental monolithic, veneered glass-ceramics.

PubMed

Zhang, Zhenzhen; Yi, Yuanping; Wang, Xuesong; Guo, Jiawen; Li, Ding; He, Lin; Zhang, Shaofeng

2017-10-01

This study evaluated the wear performance and wear mechanisms of four dental glass-ceramics, based on the microstructure and mechanical properties in the progressive wear process. Bar (N = 40, n = 10) and disk (N = 32, n = 8) specimens were prepared from (A) lithium disilicate glass-ceramic (LD), (B) leucite reinforced glass-ceramic (LEU), (C) feldspathic glass-ceramic (FEL), and (D) fluorapatite glass-ceramic (FLU). The bar specimens were tested for three-point flexural strength, hardness, fracture toughness and elastic modulus. The disk specimens paired with steatite antagonists were tested in a pin-on-disk tribometer with 10N up to 1000,000 wear cycles. The wear analysis of glass-ceramics was performed using a 3D profilometer after every 200,000 wear cycles. Wear loss of steatite antagonists was calculated by measuring the weight and density using sensitive balance and Archimedes' method. Wear morphologies and microstructures were analyzed by scanning electron microscopy (SEM). The crystalline phase compositions were determined using X-ray diffraction (XRD). One-way analysis of variance (ANOVA) was used to analyze the data. Multiple pair-wise comparison of means was performed by Tukey's post-hoc test. LD showed the highest fracture toughness, flexural strength, elastic modulus and crystallinity, followed by LEU and FEL, and FLU showed the lowest. However, the hardness of LD was lower than all the other three types of ceramics. For steatite antagonists, LD produced the least wear loss of antagonist, followed by LEU and FEL, and FLU had the most wear loss. For glass-ceramic materials, LD exhibited similar wear loss as LEU, but more than FLU and FEL did. Moreover, fracture occurred on the wear surface of FLU. In the progressive wear process, veneering porcelains showed better wear resistance but fluorapatite veneering porcelains appeared fracture surface. Monolithic lithium disilicate glass-ceramics with higher mechanical properties showed more wear loss, however, they did not fracture and produced less wear loss of antagonists. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Comparison of Emotional-Motivational (A-R-D Theory) Personality Characteristics in Learning Disabled, Normal Achieving, and High Achieving Children.

ERIC Educational Resources Information Center

Hufano, Linda D.

The study examined emotional-motivational personality characteristics of 15 learning disabled, 15 normal achieving, and 15 high achieving students (grades 3-5). The study tested the hypothesis derived from the A-R-D (attitude-reinforcer-discriminative) theory of motivation that learning disabled (LD) children differ from normal and high achieving…

A comparison of the adaptations of strains of Lymantria dispar multiple nucleopolyhedrovirus to hosts from spatially isolated populations

Treesearch

V.V. Martemyanov; J.D. Podgwaite; I.A. Belousova; S.V. Pavlushin; J.M. Slavicek; O.A. Baturina; M.R. Kabilov; A.V. Ilyinykh

2017-01-01

The adaptation of pathogens to either their hosts or to environmental conditions is the focus of many current ecological studies. In this work we compared the ability of six spatially-distant Lymantria dispar (gypsy moth) multiple nucleopolyhedrovirus (LdMNPV) strains (three from eastern North America and three from central Asia) to induce acute...

Australian tiger snake (Notechis scutatus) and mexican coral snake (Micruris species) antivenoms prevent death from United States coral snake (Micrurus fulvius fulvius) venom in a mouse model.

PubMed

Wisniewski, Michael S; Hill, Robert E; Havey, Joshua M; Bogdan, Gregory M; Dart, Richard C

2003-01-01

Wyeth-Ayerst has discontinued production of Antivenin (Micrurus fulvius). Currently, there is no other approved coral snake antivenom available in the United States. This study was a randomized, placebo-controlled and blinded determination of the ability of a Mexican Micrurus (coral snake) antivenom and an Australian Notechis (tiger snake) antivenom to prevent lethality from a United States Micrurus fulvius fulvius venom in a mouse model. Venom dosing was based on an LD50 determined for this experiment. Our comparison groups included: (1) M. f. fulvius venom + Micrurus antivenom, (2) M. f. fulvius venom + Notechis antivenom, (3) M. f. fulvius venom + protein control, (4) 0.9% normal saline + protein control, (5) saline + Notechis antivenom, (6) saline + Micrurus antivenom. Venom dose was 5 times the determined LD50. The antivenom amounts were capable of neutralizing 10 times the venom injected (50 times the LD50). The LD50 of M. f. fulvius venom was determined to be 0.85 mg/kg. All mice in both antivenom test groups were protected from lethality for the entire 24-hour observation period. Six of the 7 mice in the venom test group died, with a survival time of 349 +/- 382 minutes (mean +/- s.d.) after the venom injection. All three groups of control mice survived the entire 24-hour observation period. Mexican Micrurus antivenom and Australian Notechis antivenom provide protection from lethality in mice envenomated with a United States M. f. filvius venom.

Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.

PubMed

Wu, Tiee-Jian; Huang, Ying-Hsueh; Li, Lung-An

2005-11-15

Several measures of DNA sequence dissimilarity have been developed. The purpose of this paper is 3-fold. Firstly, we compare the performance of several word-based or alignment-based methods. Secondly, we give a general guideline for choosing the window size and determining the optimal word sizes for several word-based measures at different window sizes. Thirdly, we use a large-scale simulation method to simulate data from the distribution of SK-LD (symmetric Kullback-Leibler discrepancy). These simulated data can be used to estimate the degree of dissimilarity beta between any pair of DNA sequences. Our study shows (1) for whole sequence similiarity/dissimilarity identification the window size taken should be as large as possible, but probably not >3000, as restricted by CPU time in practice, (2) for each measure the optimal word size increases with window size, (3) when the optimal word size is used, SK-LD performance is superior in both simulation and real data analysis, (4) the estimate beta of beta based on SK-LD can be used to filter out quickly a large number of dissimilar sequences and speed alignment-based database search for similar sequences and (5) beta is also applicable in local similarity comparison situations. For example, it can help in selecting oligo probes with high specificity and, therefore, has potential in probe design for microarrays. The algorithm SK-LD, estimate beta and simulation software are implemented in MATLAB code, and are available at http://www.stat.ncku.edu.tw/tjwu

Academic procrastination and feelings toward procrastination in LD and non-LD students: Preliminary insights for future intervention.

PubMed

Hen, Meirav

2018-01-01

Academic procrastination is a prevalent behavior that negatively influences students' performance and well-being. The growing number of students with learning disabilities (LD) in higher education communities leads to the need to study and address academic procrastination in this unique population of students and to develop ways to prevent and intervene. The present study examined the difference in academic procrastination between LD, non-LD, and supported LD college students in Israel. Findings indicated a significant difference between the three groups, both in academic procrastination and in the desire to change this behavior. Interestingly, supported LD students were similar to non-LD students in all parameters of academic procrastination; however, they expressed less desire to change this behavior than unsupported LD students. These findings highlight the effect of general academic support on academic procrastination in LD students. Future studies will need to further explore the specific elements of support that most contribute to the reduction of academic procrastination in LD students. Specific support programs for academic procrastination in LD students who take into account the findings of these future studies can then be developed and studied.

The Effects of Spaceflight on the Rat Circadian Timing System

NASA Technical Reports Server (NTRS)

Fuller, Charles A.; Murakami, Dean M.; Hoban-Higgins, Tana M.; Fuller, Patrick M.; Robinson, Edward L.; Tang, I.-Hsiung

2003-01-01

Two fundamental environmental influences that have shaped the evolution of life on Earth are gravity and the cyclic changes occurring over the 24-hour day. Light levels, temperature, and humidity fluctuate over the course of a day, and organisms have adapted to cope with these variations. The primary adaptation has been the evolution of a biological timing system. Previous studies have suggested that this system, named the circadian (circa - about; dies - a day) timing system (CTS), may be sensitive to changes in gravity. The NASA Neurolab spaceflight provided a unique opportunity to evaluate the effects of microgravity on the mammalian CTS. Our experiment tested the hypotheses that microgravity would affect the period, phasing, and light sensitivity of the CTS. Twenty-four Fisher 344 rats were exposed to 16 days of microgravity on the Neurolab STS-90 mission, and 24 Fisher 344 rats were also studied on Earth as one-G controls. Rats were equipped with biotelemetry transmitters to record body temperature (T(sub b)) and heart rate (HR) continuously while the rats moved freely. In each group, 18 rats were exposed to a 24-hour light-dark (LD 12:12) cycle, and six rats were exposed to constant dim red-light (LL). The ability of light to induce a neuronal activity marker (c-fos) in the circadian pacemaker of the brain, the suprachiasmatic nucleus (SCN), was examined in rats studied on flight days two (FD2) and 14 (FD14), and postflight days two (R+1) and 14 (R+13). The flight rats in LD remained synchronized with the LD cycle. However, their T(sub b), rhythm was markedly phase-delayed relative to the LD cycle. The LD flight rats also had a decreased T(sub b) and a change in the waveform of the T(sub b) rhythm compared to controls. Rats in LL exhibited free-running rhythms of T(sub b), and HR; however, the periods were longer in microgravity. Circadian period returned to preflight values after landing. The internal phase angle between rhythms was different in flight than in one-G. Compared with control rats, the flight rats exhibited no change in HR. Finally, the LD FD2 flight rats demonstrated a reduced sensitivity to light as shown by significantly reduced c-fos expression in the SCN in comparison with controls. These findings constitute the first demonstration that microgravity affects the fundamental properties of the mammalian circadian timing system, specifically by influencing the clock's period, and its ability to maintain temporal organization and phase angle of synchronization to an external LD cycle.

Alcohol responsiveness in laryngeal dystonia: A survey study

PubMed Central

Kirke, Diana N.; Frucht, Steven J.; Simonyan, Kristina

2015-01-01

Laryngeal dystonia (LD) is a task-specific focal dystonia of unknown pathophysiology affecting speech production. We examined the demographics of anecdotally reported alcohol use and its effects on LD symptoms using an online survey based on Research Electronic Data Capture (REDCap™) and National Spasmodic Dysphonia Association’s patient registry. From 641 participants, 531 were selected for data analysis, and 110 were excluded because of unconfirmed diagnosis. A total of 406 patients (76.5%) had LD and 125 (23.5%) had LD and voice tremor (LD/VT). The consumption of alcohol was reported by 374 LD (92.1%) and 109 LD/VT (87.2%) patients. Improvement of voice symptoms after alcohol ingestion was noted by 227 LD (55.9% of all patients) and 73 LD/VT (58.4%), which paralleled the improvement observed by patient’s family and/or friends in 214 LD (57.2%) and 69 LD/VT (63.3%) patients. The benefits lasted 1–3 hours in both groups with the maximum effect after 2 drinks in LD patients (p = 0.002), whereas LD/VT symptoms improved independent of the consumed amount (p = 0.48). Our data suggest that isolated dystonic symptoms, such as in LD, are responsive to alcohol intake and this responsiveness is not attributed to the presence of VT, which is known to have significant benefits from alcohol ingestion. Alcohol may modulate the pathophysiological mechanisms underlying abnormal neurotransmission of γ-aminobutyric acid (GABA) in dystonia and as such provide new avenues for novel therapeutic options in these patients. PMID:25929664

Lyme disease

PubMed Central

Henry, Bonnie; Crabtree, Alexis; Roth, David; Blackman, Doug; Morshed, Muhammad

2012-01-01

Abstract Objective To determine physicians’ level of awareness and knowledge of Lyme disease (LD) in a low-prevalence area and whether physicians’ practices align with current guidelines for treatment of LD. Design A 23-item questionnaire assessing demographic characteristics, general knowledge about LD, laboratory testing for LD, and responses to 3 clinical scenarios. Setting British Columbia (BC). Participants Pediatricians, FPs, and internal medicine specialists who were licensed to practise in BC. Main outcome measures Knowledge of signs and symptoms of LD, beliefs about risk of LD, attitudes toward LD in patients in their practices, and application of accepted practice guidelines for the treatment of LD in clinical scenarios. Results Overall, 80.6% of respondents were FPs. Average knowledge score was 72.5% for FPs and 75.0% for other specialists. Most respondents (75.6% of FPs and 71.8% of other specialists) underestimated the occurrence of erythema migrans (EM), and only 26.1% and 28.3%, respectively, knew that EM alone was diagnostic for LD. A total of 30.5% of FPs and 12.1% of other specialists reported having treated a patient for the disease despite not believing that the patient had LD. Of all the respondents, 62.1% knew that LD was a reportable disease in BC. Respondents’ reports of risk of LD in their areas were appropriately associated with actual risk based on ecological niche. Conclusion Physicians are knowledgeable about the clinical signs and symptoms of LD and aware of the risk of the disease despite being in a low-endemic area. Physicians in BC are comfortable with treating patients empirically for LD. Education is needed to inform physicians that EM is diagnostic and no laboratory testing is indicated before treatment. Raising awareness among physicians that LD is reportable might improve reporting of future cases. PMID:22734172

Adult Leigh disease without failure to thrive.

PubMed

Sakushima, Ken; Tsuji-Akimoto, Sachiko; Niino, Masaaki; Saitoh, Shinji; Yabe, Ichiro; Sasaki, Hidenao

2011-07-01

Most Leigh disease (LD) patients die before reaching adulthood, but there are reports of "adult LD." The clinical features of adult LD were quite different from those in infant or childhood cases. Here, we describe a normally developed patient with adult LD, who presented with spastic paraplegia that was followed several years later by acute encephalopathy. We also conducted a systemic literature search on adult LD and integrated its various manifestations to arrive at a diagnostic procedure for adult LD. A 26-year-old woman presented with acute encephalopathy after spastic paraplegia. On her first admission, she exhibited bilateral basal ganglia lesion on magnetic resonance images and normal serum lactate levels. On second admission, she had acute encephalopathy with lactic acidosis and bilateral basal ganglia and brainstem lesions. A muscle biopsy revealed cytochrome c oxidase deficiency, and a diagnosis of adult LD was made. Despite treatment in the intensive care unit, she died 9 days after admission. A review of the literature describing adult LD revealed that developmental delay, COX deficiency, serum lactate elevation, and basal ganglia lesions occurred less frequently than they did in children with LD. Cranial nerve disturbance, pyramidal signs, and cerebellar dysfunction were the primary symptoms in adult LD. Thus, the many differences between childhood and adult LD may be helpful for diagnosing adult LD.

Investigating on the Methodology Effect When Evaluating Lucid Dream

PubMed Central

Ribeiro, Nicolas; Gounden, Yannick; Quaglino, Véronique

2016-01-01

Lucid dreaming (LD) is a state of consciousness in which the dreamer is aware that he or she is dreaming and can possibly control the content of his or her dream. To investigate the LD prevalence among different samples, researchers have used different types of methodologies. With regard to retrospective self-report questionnaire, two ways of proceeding seem to emerge. In one case, a definition of LD is given to participants (“During LD, one is–while dreaming–aware of the fact that one is dreaming. It is possible to deliberately wake up, to control the dream action, or to observe passively the course of the dream with this awareness”), while in the other instances, participants are presented separate questions targeting specific LD indicators (dream awareness and dream control). In the present study, we measured LD frequency in a sample of French student in order to investigate for possible disparities in LD frequency depending on the type of questionnaire as outlined above. Moreover, we also study links between the prevalence of LD as assessed, respectively, by each questionnaire with various factors such as Vividness of Mental Imagery and Parasomnia. Results revealed no significant difference between LD frequencies across questionnaires. For the questionnaire with definition (DefQuest), 81.05% of participants reported experience of LD once or more. Concerning the questionnaire based on LD indicators (AwarContQuest), 73.38% of participants reported having experienced LD once or more. However, with regard to the correlations analysis, links between LD prevalence and factors such as Vividness of Mental Imagery and Parasomnia, varied across questionnaires. This result is an argument suggesting that researchers should be careful when investigating links between LD and other factors. The type of methodology may influence findings on LD research. Further studies are needed to investigate on the methodology effect in LD research namely on the respective weight of awareness and control. PMID:27625622

Host lipid droplets: An important source of lipids salvaged by the intracellular parasite Toxoplasma gondii

PubMed Central

Romano, Julia D.

2017-01-01

Toxoplasma is an obligate intracellular parasite that replicates in mammalian cells within a parasitophorous vacuole (PV) that does not fuse with any host organelles. One mechanism developed by the parasite for nutrient acquisition is the attraction of host organelles to the PV. Here, we examined the exploitation of host lipid droplets (LD), ubiquitous fat storage organelles, by Toxoplasma. We show that Toxoplasma replication is reduced in host cells that are depleted of LD, or impaired in TAG lipolysis or fatty acid catabolism. In infected cells, the number of host LD and the expression of host LD-associated genes (ADRP, DGAT2), progressively increase until the onset of parasite replication. Throughout infection, the PV are surrounded by host LD. Toxoplasma is capable of accessing lipids stored in host LD and incorporates these lipids into its own membranes and LD. Exogenous addition of oleic acid stimulates LD biogenesis in the host cell and results in the overaccumulation of neutral lipids in very large LD inside the parasite. To access LD-derived lipids, Toxoplasma intercepts and internalizes within the PV host LD, some of which remaining associated with Rab7, which become wrapped by an intravacuolar network of membranes (IVN). Mutant parasites impaired in IVN formation display diminished capacity of lipid uptake from host LD. Moreover, parasites lacking an IVN-localized phospholipase A2 are less proficient in salvaging lipids from host LD in the PV, suggesting a major contribution of the IVN for host LD processing in the PV and, thus lipid content release. Interestingly, gavage of parasites with lipids unveils, for the first time, the presence in Toxoplasma of endocytic-like structures containing lipidic material originating from the PV lumen. This study highlights the reliance of Toxoplasma on host LD for its intracellular development and the parasite’s capability in scavenging neutral lipids from host LD. PMID:28570716

PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs

PubMed Central

Cheng, Zhongshan; Chu, Hin; Fan, Yanhui; Li, Cun; Song, You-Qiang; Zhou, Jie; Yuen, Kwok-Yung

2015-01-01

Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. PMID:26612672

Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

PubMed

Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

2018-06-01

Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.

Comparative Human Health and Environmental Toxicology Review of Seven Candidate Obscurant Smokes for Replacement of M83 Grenade

DTIC Science & Technology

2017-03-01

day; acute oral and dermal LD50 > 2000 mg/kg; inhalation LD50 > 20 mg/L Mixed evidence for carcinogenicity and mutagenicity (B2, 2...subchronic oral LOAEL 5–200 mg/kg/day; acute oral 25 < LD50 < 2000 mg/kg; dermal 50 < LD50 < 2000 mg/kg; inhalation 0.5 < LD50 < 20 mg/L Positive...corroborative evidence for carcinogenicity and mutagenicity; subchronic LOAEL < 5 mg/kg/day; acute oral LD50 ≤ 25 mg/kg; dermal LD50 ≤ 50 mg/kg

Gamma Strength Functions and Level Densities from High-Resolution Proton Scattering under 0°

NASA Astrophysics Data System (ADS)

von Neumann-Cosel, Peter; Bassauer, Sergej; Martin, Dirk; Tamii, Atsushi

2018-05-01

Inelastic proton scattering at energies of a few 100 MeV and forward angles including 0° provides a novel method to measure gamma strength functions (GSF) in nuclei in an energy range of about 5 - 20 MeV. The experiments provide not only the E1 but also the M1 part of the GSF. The latter is poorly known in heavy nuclei. Comparison with gamma decay data (e.g. from the Oslo method) allows to test the generalised Brink-Axel (BA) hypothesis in the energy region of the pygmy dipole resonance (PDR) crucial for the modelling of (n,γ) and (γ,n) reactions in astrophysical reaction networks. From the two test cases studied, 208Pb remains inconclusive in the energy region of the PDR because of large Porter-Thomas fluctuations due to the small level density (LD), while the BA hypothesis seems to hold in case of 96Mo. A fluctuation analysis of the high-resolution data also provides a direct measure of the LD in the energy region of the isovector giant dipole resonance (IVGDR) well above the neutron threshold, where hardly any experimental information is available. This permits an independent test of the decomposition of GSF and LD in Oslo-type experiments.

Evaluation of AgNORs in Oral Potentially Malignant Lesions.

PubMed

Tomazelli, Karin Berria; Modolo, Filipe; Rivero, Elena Riet Correa

2015-01-01

Oral squamous cell carcinoma (OSCC) is usually preceded by detectable mucosal changes, as leukoplakias and erythroplakia. Histologically, these lesions can range from hyperkeratosis and acanthosis to epithelial dysplasia and even OSCC. The aim of this study was to investigate the proliferative activity, using AgNORs quantification proteins, in low- and high-risk oral epithelial dysplasia, OSCC, and nondysplastic epithelium (inflammatory fibrous hyperplasia). The sample was divided into 4 groups: G1: 10 cases of inflammatory fibrous hyperplasia (IFH), G2: 11 cases of low-risk epithelial dysplasia (LD), G3: 10 cases of high-risk epithelial dysplasia (HD), and G4: 11 cases of OSCC. The quantitative analysis was performed using an image processing software in photomicrographs at 1000x magnification. The one-way ANOVA was used for comparison of the mean AgNORs counts between the study groups. The mean AgNORs count was significantly higher (P ≤ 0.01) in OSCC when compared to IFH and the LD; however, it was not statistically different from HD. The mean number of LD was significantly lower than the HD and OSCC, with no difference related to IFH. AgNORs quantification can be an important and cheap method to help in the determination of the degree of epithelial dysplasia and, consequently, in the analysis of their potential for malignant transformation.

Effect of exposure routes on the relationships of lethal toxicity to rats from oral, intravenous, intraperitoneal and intramuscular routes.

PubMed

Ning, Zhong H; Long, Shuang; Zhou, Yuan Y; Peng, Zi Y; Sun, Yi N; Chen, Si W; Su, Li M; Zhao, Yuan H

2015-11-01

The lethal toxicity values (log 1/LD(50)) of 527 aliphatic and aromatic compounds in oral, intravenous, intramuscular and intraperitoneal routes were used to investigate the relationships of log 1/LD(50) from different exposure routes. Regression analysis shows that the log 1/LD(50) values are well correlated between intravenous and intraperitoneal or intramuscular injections. However, the correlations between oral and intravenous or intraperitoneal routes are relatively poor. Comparison of the average residuals indicates that intravenous injection is the most sensitive exposure route and oral administration is the least sensitive exposure route. This is attributed to the difference in kinetic process of toxicity testing. The toxic effect of a chemical can be similar or significantly different between exposure routes, depending on the absorption rates of chemicals into blood. Inclusion of hydrophobic parameter and fractions of ionic forms can improve the correlations between intravenous and intraperitoneal or oral routes, but not between intraperitoneal and oral routes. This is due to the differences of absorption rate in different exposure environments from different routes. Several factors, such as experimental uncertainty, metabolism and toxic kinetics, can affect the correlations between intravenous and intraperitoneal or oral routes. Copyright © 2015 Elsevier Inc. All rights reserved.

Quality of Life in Children and Adolescents With Learning Problems: Development and Validation of the LD/QOL15 Scale.

PubMed

Waber, Deborah P; Boiselle, Ellen C; Forbes, Peter W; Girard, Jonathan M; Sideridis, Georgios D

2018-05-01

Learning problems (LP) can have wider implications than the academic deficits per se. The goal of the present series of studies was to develop a reliable and valid quality-of-life measure targeted to children and adolescents with LP. In Study 1, using a 35-item questionnaire, we surveyed 151 parents/guardians of children referred for assessment of learning disorders. Exploratory factor analysis identified a three-factor model: Academic Performance, School Understanding, and Child/Family Psychological. These factors were validated against standardized measures of academic achievement and psychosocial functioning. The questionnaire was then reduced to 15 items-the LD/QOL15 -and administered to a community sample of 325 parents/guardians of children in Grades 1 to 8 (Study 2). The three-factor model was verified with confirmatory factor analysis. Comparison of general education ( n = 232) and LP ( n = 93) groups within the community sample documented substantial group differences ( p < .0001), with the LP group having higher mean scores. These differences were larger for older students (Grades 5-8) than younger students (Grades 1-4; p < .01). The LD/QOL15 is a brief and reliable measure that is valid to assess quality of life and, potentially, outcomes in children and adolescents with LP.

Executive Functions Predict the Success of Top-Soccer Players

PubMed Central

Vestberg, Torbjörn; Gustafson, Roland; Maurex, Liselotte; Ingvar, Martin; Petrovic, Predrag

2012-01-01

While the importance of physical abilities and motor coordination is non-contested in sport, more focus has recently been turned toward cognitive processes important for different sports. However, this line of studies has often investigated sport-specific cognitive traits, while few studies have focused on general cognitive traits. We explored if measures of general executive functions can predict the success of a soccer player. The present study used standardized neuropsychological assessment tools assessing players' general executive functions including on-line multi-processing such as creativity, response inhibition, and cognitive flexibility. In a first cross-sectional part of the study we compared the results between High Division players (HD), Lower Division players (LD) and a standardized norm group. The result shows that both HD and LD players had significantly better measures of executive functions in comparison to the norm group for both men and women. Moreover, the HD players outperformed the LD players in these tests. In the second prospective part of the study, a partial correlation test showed a significant correlation between the result from the executive test and the numbers of goals and assists the players had scored two seasons later. The results from this study strongly suggest that results in cognitive function tests predict the success of ball sport players. PMID:22496850

Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

PubMed Central

Miller, Joshua M; Poissant, Jocelyn; Malenfant, René M; Hogg, John T; Coltman, David W

2015-01-01

Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D′, and χ′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible. PMID:26380673

Highly reproducible laser beam scanning device for an internal source laser desorption microprobe Fourier transform mass spectrometer

NASA Astrophysics Data System (ADS)

Scott, Jill R.; Tremblay, Paul L.

2002-03-01

Traditionally, mass spectrometry has relied on manipulating the sample target to provide scanning capabilities for laser desorption microprobes. This has been problematic for an internal source laser desorption Fourier transform mass spectrometer (LD-FTMS) because of the high magnetic field (7 Tesla) and geometric constraints of the superconducting magnet bore. To overcome these limitations, we have implemented a unique external laser scanning mechanism for an internal source LD-FTMS. This mechanism provides adjustable resolution enhancement so that the spatial resolution at the target is not limited to that of the stepper motors at the light source (˜5 μm/step). The spatial resolution is now limited by the practical optical diffraction limit of the final focusing lens. The scanning mechanism employs a virtual source that is wavelength independent up to the final focusing lens, which can be controlled remotely to account for focal length dependence on wavelength. A binary index provides an automatic alignment feature. The virtual source is located ˜9 ft from the sample; therefore, it is completely outside of the vacuum system and beyond the 50 G line of the fringing magnetic field. To eliminate reproducibility problems associated with vacuum pump vibrations, we have taken advantage of the magnetic field inherent to the FTMS to utilize Lenz's law for vibrational dampening. The LD-FTMS microprobe has exceptional reproducibility, which enables successive mapping sequences for depth-profiling studies.

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

PubMed Central

Goicoechea, P G; Herrán, A; Durand, J; Bodénès, C; Plomion, C; Kremer, A

2015-01-01

We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the ‘species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory. PMID:25515016

Comparison of aerially-applied Gypchek strains against gypsy moth (Lepidoptera: Lymantriidae) in the presence of an Entomophaga maimaiga epizootic

Treesearch

R.E. Webb; G.B. White; J.D. Podgwaite; V. D' Amico; J. Slavicek; J. Swearingen; B. Onken; K.W. Thorpe

2005-01-01

The standard strain (LDP-226) of Gypchek®, a nucleopolyhedrovirus product registered by the USDA Forest Service against the gypsy moth, Lymantria dispar (L.), was compared against a strain, LdMNPV-203NL (NL = nonliquefying), that was developed for production in cell culture. Both strains were applied by air to U.S. government property in...

The Impact of Executive Function Skills on Writing: A Comparison of Fifth-Grade Students with Learning Disabilities and Students with Typical Development

ERIC Educational Resources Information Center

Nathan, Anne Michelle

2009-01-01

This study explored the relationship between verbal fluency skills and writing skills in developing writers. There were three research questions addressed: (1) Was there a difference between fifth-grade students who have a learning disability (LD) in written language and fifth-grade students with typical development (TD) on the Delis-Kaplan…

Attributional Patterns towards Students with and without Learning Disabilities: A Comparison of Pre- and In-Service Teachers in China

ERIC Educational Resources Information Center

Jiang, Han; Woodcock, Stuart

2018-01-01

This study aims to investigate the differences of attributional responses to students with and without learning disabilities (LD) between pre- and in-service teachers in mainland China. A total of 204 teachers (101 pre-service and 103 in-service teachers) were surveyed using vignettes and Likert scale questions to ascertain their responses to…

Photoperiod-Induced Increases in Bone Mineral Apposition Rate in Siberian Hamsters and the Involvement of Seasonal Leptin Changes

PubMed Central

Kokolski, Marie; Ebling, Francis J.; Henstock, James R.; Anderson, Susan I.

2017-01-01

The adipokine leptin regulates energy balance, appetite, and reproductive maturation. Leptin also acts on bone growth and remodeling, but both osteogenic and anti-osteogenic effects have been reported depending on experimental conditions. Siberian hamsters (Phodopus sungorus) have natural variation in circulating leptin concentrations, where serum leptin is significantly decreased during the short day (SD)-induced winter state. In summer long day (LD) photoperiods, appetite and body adiposity increase with associated central leptin insensitivity. This natural change in leptin secretion was exploited to investigate leptin’s effect on bone growth. Hamsters were injected with calcium-chelating fluorescent dyes to measure bone mineral apposition rate (MAR). Measurements were initially obtained from 5-week and 6-month-old animals maintained in low leptin (SD) or high leptin (LD) states. A further study investigated effects of chronic administration of recombinant mouse leptin to hamsters housed in SD and LD conditions; growth plate thickness and bone density were also assessed. As expected, a reduction in body mass was seen in hamsters exposed to SD, confirming the phenotype change in all studies. Serum leptin concentrations were significantly reduced in SD animals in all studies. MAR was reproducibly and significantly increased in the femurs of SD animals in all studies. Vitamin D and growth plate thickness were significantly increased in SD animals at 6 months. No effect on bone density was observed in any study. Taken together these data suggest that bone growth is associated with the low leptin, winter, lean state. In leptin-treated animals, there was a significant interaction effect of leptin and photoperiod. In comparison to their vehicle counterparts, SD animals had decreased and LD animals had increased MAR, which was not apparent prior to leptin administration. In conclusion, increased MAR was associated with low serum leptin levels in early life and sustained over 6 months, implying that leptin has a negative effect on bone growth in this model. The unexpected finding that MAR increased after peripheral leptin administration in LD suggests that leptin exerts different effects on bone growth dependent on initial leptin status. This adds further weight to the hypothesis that leptin-treated LD animals display central leptin resistance. PMID:29312147

Photoperiod-Induced Increases in Bone Mineral Apposition Rate in Siberian Hamsters and the Involvement of Seasonal Leptin Changes.

PubMed

Kokolski, Marie; Ebling, Francis J; Henstock, James R; Anderson, Susan I

2017-01-01

The adipokine leptin regulates energy balance, appetite, and reproductive maturation. Leptin also acts on bone growth and remodeling, but both osteogenic and anti-osteogenic effects have been reported depending on experimental conditions. Siberian hamsters ( Phodopus sungorus ) have natural variation in circulating leptin concentrations, where serum leptin is significantly decreased during the short day (SD)-induced winter state. In summer long day (LD) photoperiods, appetite and body adiposity increase with associated central leptin insensitivity. This natural change in leptin secretion was exploited to investigate leptin's effect on bone growth. Hamsters were injected with calcium-chelating fluorescent dyes to measure bone mineral apposition rate (MAR). Measurements were initially obtained from 5-week and 6-month-old animals maintained in low leptin (SD) or high leptin (LD) states. A further study investigated effects of chronic administration of recombinant mouse leptin to hamsters housed in SD and LD conditions; growth plate thickness and bone density were also assessed. As expected, a reduction in body mass was seen in hamsters exposed to SD, confirming the phenotype change in all studies. Serum leptin concentrations were significantly reduced in SD animals in all studies. MAR was reproducibly and significantly increased in the femurs of SD animals in all studies. Vitamin D and growth plate thickness were significantly increased in SD animals at 6 months. No effect on bone density was observed in any study. Taken together these data suggest that bone growth is associated with the low leptin, winter, lean state. In leptin-treated animals, there was a significant interaction effect of leptin and photoperiod. In comparison to their vehicle counterparts, SD animals had decreased and LD animals had increased MAR, which was not apparent prior to leptin administration. In conclusion, increased MAR was associated with low serum leptin levels in early life and sustained over 6 months, implying that leptin has a negative effect on bone growth in this model. The unexpected finding that MAR increased after peripheral leptin administration in LD suggests that leptin exerts different effects on bone growth dependent on initial leptin status. This adds further weight to the hypothesis that leptin-treated LD animals display central leptin resistance.

Rapid phase adjustment of melatonin and core body temperature rhythms following a 6-h advance of the light/dark cycle in the horse

PubMed Central

Murphy, Barbara A; Elliott, Jeffrey A; Sessions, Dawn R; Vick, Mandi M; Kennedy, Erin L; Fitzgerald, Barry P

2007-01-01

Background Rapid displacement across multiple time zones results in a conflict between the new cycle of light and dark and the previously entrained program of the internal circadian clock, a phenomenon known as jet lag. In humans, jet lag is often characterized by malaise, appetite loss, fatigue, disturbed sleep and performance deficit, the consequences of which are of particular concern to athletes hoping to perform optimally at an international destination. As a species renowned for its capacity for athletic performance, the consequences of jet lag are also relevant for the horse. However, the duration and severity of jet lag related circadian disruption is presently unknown in this species. We investigated the rates of re-entrainment of serum melatonin and core body temperature (BT) rhythms following an abrupt 6-h phase advance of the LD cycle in the horse. Methods Six healthy, 2 yr old mares entrained to a 12 h light/12 h dark (LD 12:12) natural photoperiod were housed in a light-proofed barn under a lighting schedule that mimicked the external LD cycle. Following baseline sampling on Day 0, an advance shift of the LD cycle was accomplished by ending the subsequent dark period 6 h early. Blood sampling for serum melatonin analysis and BT readings were taken at 3-h intervals for 24 h on alternate days for 11 days. Disturbances to the subsequent melatonin and BT 24-h rhythms were assessed using repeated measures ANOVA and analysis of Cosine curve fitting parameters. Results We demonstrate that the equine melatonin rhythm re-entrains rapidly to a 6-h phase advance of an LD12:12 photocycle. The phase shift in melatonin was fully complete on the first day of the new schedule and rhythm phase and waveform were stable thereafter. In comparison, the advance in the BT rhythm was achieved by the third day, however BT rhythm waveform, especially its mesor, was altered for many days following the LD shift. Conclusion Aside from the temperature rhythm disruption, rapid resynchronization of the melatonin rhythm suggests that the central circadian pacemaker of the horse may possess a particularly robust entrainment response. The consequences for athletic performance remain unknown. PMID:17718919

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers.

PubMed

Pavy, N; Namroud, M-C; Gagnon, F; Isabel, N; Bousquet, J

2012-03-01

In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r(2) value was 0.19 (s.d.=0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r(2)=0.28), and a second group of 38 genes had weaker LD (mean r(2)=0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology

PubMed Central

Lijavetzky, Diego; Cabezas, José Antonio; Ibáñez, Ana; Rodríguez, Virginia; Martínez-Zapater, José M

2007-01-01

Background Single-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibilities for genetic and breeding applications such as cultivar identification, construction of genetic maps, the assessment of genetic diversity, the detection of genotype/phenotype associations, or marker-assisted breeding. In addition, the efficiency of these activities can be improved thanks to the ease with which SNP genotyping can be automated. Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative sequence polymorphisms within and among a reduced number of cultivars. In parallel, the sequence of the grapevine cultivar Pinot Noir is also providing thousands of polymorphisms present in this highly heterozygous genome. Still the general application of those SNPs requires further validation since their use could be restricted to those specific genotypes. Results In order to develop a large SNP set of wide application in grapevine we followed a systematic re-sequencing approach in a group of 11 grape genotypes corresponding to ancient unrelated cultivars as well as wild plants. Using this approach, we have sequenced 230 gene fragments, what represents the analysis of over 1 Mb of grape DNA sequence. This analysis has allowed the discovery of 1573 SNPs with an average of one SNP every 64 bp (one SNP every 47 bp in non-coding regions and every 69 bp in coding regions). Nucleotide diversity in grape (π = 0.0051) was found to be similar to values observed in highly polymorphic plant species such as maize. The average number of haplotypes per gene sequence was estimated as six, with three haplotypes representing over 83% of the analyzed sequences. Short-range linkage disequilibrium (LD) studies within the analyzed sequences indicate the existence of a rapid decay of LD within the selected grapevine genotypes. To validate the use of the detected polymorphisms in genetic mapping, cultivar identification and genetic diversity studies we have used the SNPlex™ genotyping technology in a sample of grapevine genotypes and segregating progenies. Conclusion These results provide accurate values for nucleotide diversity in coding sequences and a first estimate of short-range LD in grapevine. Using SNPlex™ genotyping we have shown the application of a set of discovered SNPs as molecular markers for cultivar identification, linkage mapping and genetic diversity studies. Thus, the combination a highly efficient re-sequencing approach and the SNPlex™ high throughput genotyping technology provide a powerful tool for grapevine genetic analysis. PMID:18021442

Variation resources at UC Santa Cruz.

PubMed

Thomas, Daryl J; Trumbower, Heather; Kern, Andrew D; Rhead, Brooke L; Kuhn, Robert M; Haussler, David; Kent, W James

2007-01-01

The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in the context of other genomic annotations. Primary data from dbSNP is included for many organisms, with added information including genomic alleles and orthologous alleles for closely related organisms. Display filtering and coloring is available by variant type, functional class or other annotations. Annotation of potential errors is highlighted and a genomic alignment of the variant's flanking sequence is displayed. HapMap allele frequencies and linkage disequilibrium (LD) are available for each HapMap population, along with non-human primate alleles. The browsing and analysis tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Reducing Tick-Borne Disease in Alabama: Linking Health Risk Perception with Spatial Analysis Using the NASA Earth Observing System

NASA Technical Reports Server (NTRS)

Hemmings, S.; Renneboog, N.; Firsing, S.; Capilouto, E.; Harden, J.; Hyden, R.; Tipre, M.; Zhang, Y.

2010-01-01

Lyme disease (LD) accounts for most vector-borne disease reports in the U.S., and although its existence in Alabama remains controversial, other tick-borne illnesses (TBI) such as Southern Tick-Associated Rash Illness (STARI) pose a health concern in the state. Phase One of the Marshall Space Flight Center-UAB DEVELOP study of TBI identified the presence of the chain of infection for LD (Ixodes scapularis ticks carrying Borrelia burgdorferi bacteria) and STARI (Amblyomma americanum ticks and an as-yet-unconfirmed agent) in Alabama. Both LD and STARI are associated with the development of erythema migrans rashes around an infected tick bite, and while treatable with oral antibiotics, a review of educational resources available to state residents revealed low levels of prevention information. To improve prevention, recognition, and treatment of TBI in Alabama, Phase Two builds a health communication campaign based on vector habitat mapping and risk perception assessment. NASA Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) satellite imagery identified likely tick habitats using remotely sensed measurements of vegetation vigor (Normalized Difference Vegetation Index) and soil moisture. Likely tick habitats, identified as those containing both high vegetation density and soil moisture, included Oak Mountain State Park, Bankhead National Forest, and Talladega National Forest. To target a high-risk group -- outdoor recreation program participants at Alabama universities -- the study developed a behavior survey instrument based on existing studies of LD risk factors and theoretical constructs from the Social Ecological Model and Health Belief Model. The survey instrument was amended to include geographic variables in the assessment of TBI knowledge, attitudes, and prevention behaviors, and the vector habitat model will be expanded to incorporate additional environmental variables and in situ data. Remotely sensed environmental data combined with risk perception assessments inform an ongoing outreach campaign consisting of stakeholder meetings and educational seminars.

Nursing Students with Learning Disabilities.

ERIC Educational Resources Information Center

Selekman, Janice

2002-01-01

Discusses the following topics: identification and classification of learning disabilities (LD), effects of LD on nursing students, teaching and learning, LD legislation, and academic interventions for nursing students with LD. (SK)

Tick bite and Lyme disease-related emergency department encounters in New Hampshire, 2010-2014.

PubMed

Daly, E R; Fredette, C; Mathewson, A A; Dufault, K; Swenson, D J; Chan, B P

2017-12-01

Lyme disease (LD) is a common tick-borne disease in New Hampshire (NH). While LD is a reportable condition and cases are counted for public health surveillance, many more people receive care for tick bites or diagnoses of LD than are reflected in surveillance data. NH's emergency department (ED) data system was queried for tick bite and LD-related encounters. Chief complaint text was queried for words related to LD or tick bites. International Classification of Diseases 9th Revision (ICD-9) codes were queried for the LD diagnosis code (088.81). Emergency department patient data were matched to reportable disease data to determine the proportion of ED patients reported to the health department as a suspected LD case. Data were analysed to calculate frequencies for key demographic and reporting characteristics. From 2010 to 2014, 13,615 tick bite or LD-related ED encounters were identified in NH, with most due to tick bites (76%). Of 3,256 patients with a LD-related ED encounter, 738 (23%) were reported to the health department as a suspected LD case. The geographic distribution of ED patients was similar to reported LD cases; however, the regions of the state that experienced higher rates of ED encounters were different than the regions that observed higher rates of reported LD cases. Seasonal distribution of ED encounters peaked earlier than reported LD cases with a second peak in the fall. While age and sex distribution was similar among ED patients and reported LD cases, the rates for children 5 years and younger and adults 65 years and older were greater for ED encounters. Patients frequently visit the ED to seek care for tick bites and suspected LD. Results of ED data analyses can be used to target education, in particular for ED providers and the public through timely distribution of evidence-based educational materials and training programmes. © 2017 Blackwell Verlag GmbH.

Effect of Concomitant Medications on the Safety and Efficacy of Extended-Release Carbidopa-Levodopa (IPX066) in Patients With Advanced Parkinson Disease: A Post Hoc Analysis.

PubMed

LeWitt, Peter A; Verhagen Metman, Leo; Rubens, Robert; Khanna, Sarita; Kell, Sherron; Gupta, Suneel

Extended-release (ER) carbidopa-levodopa (CD-LD) (IPX066/RYTARY/NUMIENT) produces improvements in "off" time, "on" time without troublesome dyskinesia, and Unified Parkinson Disease Rating Scale scores compared with immediate-release (IR) CD-LD or IR CD-LD plus entacapone (CLE). Post hoc analyses of 2 ER CD-LD phase 3 trials evaluated whether the efficacy and safety of ER CD-LD relative to the respective active comparators were altered by concomitant medications (dopaminergic agonists, monoamine oxidase B [MAO-B] inhibitors, or amantadine). ADVANCE-PD (n = 393) assessed safety and efficacy of ER CD-LD versus IR CD-LD. ASCEND-PD (n = 91) evaluated ER CD-LD versus CLE. In both studies, IR- and CLE-experienced patients underwent a 6-week, open-label dose-conversion period to ER CD-LD prior to randomization. For analysis, the randomized population was divided into 3 subgroups: dopaminergic agonists, rasagiline or selegiline, and amantadine. For each subgroup, changes from baseline in PD diary measures ("off" time and "on" time with and without troublesome dyskinesia), Unified Parkinson Disease Rating Scale Parts II + III scores, and adverse events were analyzed, comparing ER CD-LD with the active comparator. Concomitant dopaminergic agonist or MAO-B inhibitor use did not diminish the efficacy (improvement in "off" time and "on" time without troublesome dyskinesia) of ER CD-LD compared with IR CD-LD or CLE, whereas the improvement with concomitant amantadine failed to reach significance. Safety and tolerability were similar among the subgroups, and ER CD-LD did not increase troublesome dyskinesia. For patients on oral LD regimens and taking a dopaminergic agonist, and/or a MAO-B inhibitor, changing from an IR to an ER CD-LD formulation provides approximately an additional hour of "good" on time.

Effect of Concomitant Medications on the Safety and Efficacy of Extended-Release Carbidopa-Levodopa (IPX066) in Patients With Advanced Parkinson Disease: A Post Hoc Analysis

PubMed Central

LeWitt, Peter A.; Verhagen Metman, Leo; Rubens, Robert; Khanna, Sarita; Kell, Sherron; Gupta, Suneel

2018-01-01

Objectives Extended-release (ER) carbidopa-levodopa (CD-LD) (IPX066/RYTARY/NUMIENT) produces improvements in “off” time, “on” time without troublesome dyskinesia, and Unified Parkinson Disease Rating Scale scores compared with immediate-release (IR) CD-LD or IR CD-LD plus entacapone (CLE). Post hoc analyses of 2 ER CD-LD phase 3 trials evaluated whether the efficacy and safety of ER CD-LD relative to the respective active comparators were altered by concomitant medications (dopaminergic agonists, monoamine oxidase B [MAO-B] inhibitors, or amantadine). Methods ADVANCE-PD (n = 393) assessed safety and efficacy of ER CD-LD versus IR CD-LD. ASCEND-PD (n = 91) evaluated ER CD-LD versus CLE. In both studies, IR- and CLE-experienced patients underwent a 6-week, open-label dose-conversion period to ER CD-LD prior to randomization. For analysis, the randomized population was divided into 3 subgroups: dopaminergic agonists, rasagiline or selegiline, and amantadine. For each subgroup, changes from baseline in PD diary measures (“off” time and “on” time with and without troublesome dyskinesia), Unified Parkinson Disease Rating Scale Parts II + III scores, and adverse events were analyzed, comparing ER CD-LD with the active comparator. Results and Conclusions Concomitant dopaminergic agonist or MAO-B inhibitor use did not diminish the efficacy (improvement in “off” time and “on” time without troublesome dyskinesia) of ER CD-LD compared with IR CD-LD or CLE, whereas the improvement with concomitant amantadine failed to reach significance. Safety and tolerability were similar among the subgroups, and ER CD-LD did not increase troublesome dyskinesia. For patients on oral LD regimens and taking a dopaminergic agonist, and/or a MAO-B inhibitor, changing from an IR to an ER CD-LD formulation provides approximately an additional hour of “good” on time. PMID:29432286

Resting State EEG in Children With Learning Disabilities: An Independent Component Analysis Approach.

PubMed

Jäncke, Lutz; Alahmadi, Nsreen

2016-01-01

In this study, the neurophysiological underpinnings of learning disabilities (LD) in children are examined using resting state EEG. We were particularly interested in the neurophysiological differences between children with learning disabilities not otherwise specified (LD-NOS), learning disabilities with verbal disabilities (LD-Verbal), and healthy control (HC) children. We applied 2 different approaches to examine the differences between the different groups. First, we calculated theta/beta and theta/alpha ratios in order to quantify the relationship between slow and fast EEG oscillations. Second, we used a recently developed method for analyzing spectral EEG, namely the group independent component analysis (gICA) model. Using these measures, we identified substantial differences between LD and HC children and between LD-NOS and LD-Verbal children in terms of their spectral EEG profiles. We obtained the following findings: (a) theta/beta and theta/alpha ratios were substantially larger in LD than in HC children, with no difference between LD-NOS and LD-Verbal children; (b) there was substantial slowing of EEG oscillations, especially for gICs located in frontal scalp positions, with LD-NOS children demonstrating the strongest slowing; (c) the estimated intracortical sources of these gICs were mostly located in brain areas involved in the control of executive functions, attention, planning, and language; and (d) the LD-Verbal children demonstrated substantial differences in EEG oscillations compared with LD-NOS children, and these differences were localized in language-related brain areas. The general pattern of atypical neurophysiological activation found in LD children suggests that they suffer from neurophysiological dysfunction in brain areas involved with the control of attention, executive functions, planning, and language functions. LD-Verbal children also demonstrate atypical activation, especially in language-related brain areas. These atypical neurophysiological activation patterns might provide a helpful guide for rehabilitation strategies to treat the deficiencies in these children with LD. © EEG and Clinical Neuroscience Society (ECNS) 2015.

Methodological issues concerning the application of reliable laser particle sizing in soils

NASA Astrophysics Data System (ADS)

de Mascellis, R.; Impagliazzo, A.; Basile, A.; Minieri, L.; Orefice, N.; Terribile, F.

2009-04-01

During the past decade, the evolution of technologies has enabled laser diffraction (LD) to become a much widespread means of particle size distribution (PSD), replacing sedimentation and sieve analysis in many scientific fields mainly due to its advantages of versatility, fast measurement and high reproducibility. Despite such developments of the last decade, the soil scientist community has been quite reluctant to replace the good old sedimentation techniques (ST); possibly because of (i) the large complexity of the soil matrix inducing different types of artefacts (aggregates, deflocculating dynamics, etc.), (ii) the difficulties in relating LD results with results obtained through sedimentation techniques and (iii) the limited size range of most LD equipments. More recently LD granulometry is slowly gaining appreciation in soil science also because of some innovations including an enlarged size dynamic range (0,01-2000 m) and the ability to implement more powerful algorithms (e.g. Mie theory). Furthermore, LD PSD can be successfully used in the application of physically based pedo-transfer functions (i.e., Arya and Paris model) for investigations of soil hydraulic properties, due to the direct determination of PSD in terms of volume percentage rather than in terms of mass percentage, thus eliminating the need to adopt the rough approximation of a single value for soil particle density in the prediction process. Most of the recent LD work performed in soil science deals with the comparison with sedimentation techniques and show the general overestimation of the silt fraction following a general underestimation of the clay fraction; these well known results must be related with the different physical principles behind the two techniques. Despite these efforts, it is indeed surprising that little if any work is devoted to more basic methodological issues related to the high sensitivity of LD to the quantity and the quality of the soil samples. Our work aims to both analyse and to suggest technical solutions to address the following key methodological problems: (i) sample representativeness due to the very small amount of soil sample required by LD (e.g. 0,2 g) as compared to ST (e.g. 40 g for densimetry); (ii) PSD reading variability caused by the large number of instantaneous reading on a very small volume of the solution, (iii) the varying soil mineralogy that in turn produce varying refractive indexes affecting PSD results, (iv) the determination of the mass density of the soil samples to compare results with those obtained from ST. Our results, referring to many different soil types (Vertisols, Regosols, Andosols, Calcisols, Luvisols) show that the listed major technical problems can be successfully addressed by the following set of solutions: (i) adequate subsampling in both solid and liquid phases (including a setup of a dilution system); (ii) preliminary study of the PSD variability to reasonably increase the number of readings per each sample; (iii, iv) preliminary sensitivity analysis of both refractive indexes and mass density in accordance to the specific soil mineralogy.

Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs.

PubMed

Huson, Heather J; vonHoldt, Bridgett M; Rimbault, Maud; Byers, Alexandra M; Runstadler, Jonathan A; Parker, Heidi G; Ostrander, Elaine A

2012-02-01

Alaskan sled dogs are a genetically distinct population shaped by generations of selective interbreeding with purebred dogs to create a group of high-performance athletes. As a result of selective breeding strategies, sled dogs present a unique opportunity to employ admixture-mapping techniques to investigate how breed composition and trait selection impact genomic structure. We used admixture mapping to investigate genetic ancestry across the genomes of two classes of sled dogs, sprint and long-distance racers, and combined that with genome-wide association studies (GWAS) to identify regions that correlate with performance-enhancing traits. The sled dog genome is enhanced by differential contributions from four non-admixed breeds (Alaskan Malamute, Siberian Husky, German Shorthaired Pointer, and Borzoi). A principal components analysis (PCA) of 115,000 genome-wide SNPs clearly resolved the sprint and distance populations as distinct genetic groups, with longer blocks of linkage disequilibrium (LD) observed in the distance versus sprint dogs (7.5-10 and 2.5-3.75 kb, respectively). Furthermore, we identified eight regions with the genomic signal from either a selective sweep or an association analysis, corroborated by an excess of ancestry when comparing sprint and distance dogs. A comparison of elite and poor-performing sled dogs identified a single region significantly associated with heat tolerance. Within the region we identified seven SNPs within the myosin heavy chain 9 gene (MYH9) that were significantly associated with heat tolerance in sprint dogs, two of which correspond to conserved promoter and enhancer regions in the human ortholog.

QuickSmart: a basic academic skills intervention for middle school students with learning difficulties.

PubMed

Graham, Lorraine; Bellert, Anne; Thomas, Jenny; Pegg, John

2007-01-01

QuickSmart is a basic academic skills intervention designed for persistently low-achieving students in the middle years of schooling that aims to improve the automaticity of basic skills to improve higher-order processes, such as problem solving and comprehension, as measured on standardized tests. The QuickSmart instructional program consists of three structured, teacher- or teacher aide-directed, 30-minute, small-group lessons each week for approximately 26 weeks. In this study, 42 middle school students experiencing learning difficulties (LD) completed the QuickSmart reading program, and a further 42 students with LD took part in the QuickSmart mathematics program. To investigate the effects of the intervention, comparisons were made between the reading and mathematics progress of the intervention group and a group of 10 high-achieving and 10 average-achieving peers. The results indicated that although the standardized reading comprehension and mathematics scores of QuickSmart students remained below those of comparison students, they improved significantly from pretest to posttest. In contrast, the standardized scores of comparison students were not significantly different from pretest to posttest. On measures of response speed and accuracy gathered using the Cognitive Aptitude Assessment System (CAAS), QuickSmart students were able to narrow the gap between their performance and that of their high- and average-achieving peers. Implications are drawn regarding the importance of interventions that emphasize the automaticity of basic academic skills for students with learning difficulties.

Long Dynamics Simulations of Proteins Using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties

PubMed Central

Li, Xianfeng; Hassan, Sergio A.; Mehler, Ernest L.

2006-01-01

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a Cα RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable early in the simulation, reaching a Cα RMSD of about 2.7 Å and remaining at this value until the end of the simulation; the Cα RMSD of the EW/MD simulation was about 1.5 Å. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP–ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (Cα RMSD of ≈1.0 Å), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a Cα RMSD of ≈1.5 Å at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain–side chain (sc–sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP–ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP–ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein–protein interactions. PMID:15959866

The relation of LD and gender with emotional intelligence in college students.

PubMed

Reiff, H B; Hatzes, N M; Bramel, M H; Gibbon, T

2001-01-01

This study examined the relation of learning disabilities (LD) and gender with emotional intelligence in 128 college students. Fifty-four students with LD (32 men and 22 women) and 74 without LD (34 men and 40 women) attending two colleges and one university participated in the study. Emotional intelligence was assessed using the Emotional Quotient Inventory (EQ-i; BarOn,1997), a self-report instrument designed to measure interpersonal and intrapersonal skills, stress management, adaptability, and general mood. A 2-way multivariate analysis of variance (MANOVA) was performed to examine the main effects of LD and gender and the interaction of the two main effects on the five composites of the EQ-i. Students with LD had fewer credits and lower scholastic aptitude test (SAT) scores, high school grade point averages (GPAs), and college GPAs than students without LD; women students were older and had higher college GPAs than men students. Results of the MANOVA indicated significant main effects of both LD and gender; no significant interaction occurred. Post hoc univariate analyses of the five composites revealed significant differences between students with LD and students without LD on stress management and adaptability, significant differences between men and women students on interpersonal skills, and significant differences of the interaction of LD and gender on interpersonal skills.

QSAR Modeling of Rat Acute Toxicity by Oral Exposure

PubMed Central

Zhu, Hao; Martin, Todd M.; Ye, Lin; Sedykh, Alexander; Young, Douglas M.; Tropsha, Alexander

2009-01-01

Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. In this study, a comprehensive dataset of 7,385 compounds with their most conservative lethal dose (LD50) values has been compiled. A combinatorial QSAR approach has been employed to develop robust and predictive models of acute toxicity in rats caused by oral exposure to chemicals. To enable fair comparison between the predictive power of models generated in this study versus a commercial toxicity predictor, TOPKAT (Toxicity Prediction by Komputer Assisted Technology), a modeling subset of the entire dataset was selected that included all 3,472 compounds used in the TOPKAT’s training set. The remaining 3,913 compounds, which were not present in the TOPKAT training set, were used as the external validation set. QSAR models of five different types were developed for the modeling set. The prediction accuracy for the external validation set was estimated by determination coefficient R2 of linear regression between actual and predicted LD50 values. The use of the applicability domain threshold implemented in most models generally improved the external prediction accuracy but expectedly led to the decrease in chemical space coverage; depending on the applicability domain threshold, R2 ranged from 0.24 to 0.70. Ultimately, several consensus models were developed by averaging the predicted LD50 for every compound using all 5 models. The consensus models afforded higher prediction accuracy for the external validation dataset with the higher coverage as compared to individual constituent models. The validated consensus LD50 models developed in this study can be used as reliable computational predictors of in vivo acute toxicity. PMID:19845371

Effectiveness of Donepezil, Rivastigmine, and (±)Huperzine A in Counteracting the Acute Toxicity of Organophosphorus Nerve Agents: Comparison with Galantamine

PubMed Central

Aracava, Yasco; Pereira, Edna F. R.; Akkerman, Miriam; Adler, Michael

2009-01-01

Galantamine, a centrally acting cholinesterase (ChE) inhibitor and a nicotinic allosteric potentiating ligand used to treat Alzheimer's disease, is an effective and safe antidote against poisoning with nerve agents, including soman. Here, the effectiveness of galantamine was compared with that of the centrally active ChE inhibitors donepezil, rivastigmine, and (±)huperzine A as a pre- and/or post-treatment to counteract the acute toxicity of soman. In the first set of experiments, male prepubertal guinea pigs were treated intramuscularly with one of the test drugs and 30 min later challenged with 1.5 × LD50 soman (42 μg/kg s.c.). All animals that were pretreated with galantamine (6–8 mg/kg), 3 mg/kg donepezil, 6 mg/kg rivastigmine, or 0.3 mg/kg (±)huperzine A survived the soman challenge, provided that they were also post-treated with atropine (10 mg/kg i.m.). However, only galantamine was well tolerated. In subsequent experiments, the effectiveness of specific treatment regimens using 8 mg/kg galantamine, 3 mg/kg donepezil, 6 mg/kg rivastigmine, or 0.3 mg/kg (±)huperzine A was compared in guinea pigs challenged with soman. In the absence of atropine, only galantamine worked as an effective and safe pretreatment in animals challenged with 1.0 × LD50 soman. Galantamine was also the only drug to afford significant protection when given to guinea pigs after 1.0 × LD50 soman. Finally, all test drugs except galantamine reduced the survival of the animals when administered 1 or 3 h after the challenge with 0.6 or 0.7 × LD50 soman. Thus, galantamine emerges as a superior antidotal therapy against the toxicity of soman. PMID:19741148

[The blood coagulation system and microcirculatory disorders in ixodid tick-borne borreliosis caused by Borrelia miyamotoi].

PubMed

Platonov, A E; Sarksyan, D S; Karan, L S; Shipulin, G A; Gordygina, E V; Malinin, O V; Maleev, V V

2015-01-01

To study blood coagulation and microcirculatory disorders as a possible cause of transient dysfunctions of organs (the kidney, liver, heart, lung, etc.) in patients with ixodid tick-borne borreliosis caused by Borrelia miyamotoi (Bmt). SUBJECTS AND METHODS; Twenty-four patients with Lyme disease (LD) and 28 Bmt patients treated at Izhevsk City Hospital (Udmurtia) were examined in the study. Platelet counts and the presence of D-dimers were determined; activated partial thromboplastin time, prothrombin time, thrombin time, fibrinogen and antithrombin III levels, and Factor XIIa-dependent fibrin clot lysis time were measured. Slit lamp microscopy of the conjunctiva was. also carried out. Results. Platelet counts'were less than 150,000 per pL of blood in 43% of the Bmt patients. All the Bmt patients had at least one abnormal coagulation parameter of the eight ones that were tested; 64% of them had marked coagulation disorders with three or more abnormal laboratory findings. In contrast, all the eight parameters were normal in 71% of the LD patients. The other seven LD patients had only one or two abnormal coagulation parameters (p < 0.001 in comparison with Bmt patients). Microscopic examination of eye capillary blood flow revealed pathological findings that included aggregates of erythrocytes and obstructed and/or sinuous capillaries in 22 (79%) of the Bmt patients, but none of the LD patients. A total of 14 Bmt patients had both coagulation and microcirculatory abnormalities. Eleven of them also had transient signs of organ dysfunction. As far as Borrelia secrete no known toxins, we hypothesized that uncovered disorders of blood coagulation and microcirculation in Bmt patients may contribute to organ dysfunction.

Antithrombotic potency of ticagrelor versus clopidogrel in type-2 diabetic patients with cardiovascular disease.

PubMed

Zafar, M Urooj; Baber, Usman; Smith, Donald A; Sartori, Samantha; Contreras, Johanna; Rey-Mendoza, Juan; Linares-Koloffon, Carlos A; Escolar, Gines; Mehran, Roxana; Fuster, Valentin; Badimon, Juan J

2017-10-05

Type-2 Diabetes Mellitus [T2DM] is associated with increased platelet reactivity and hypo-response to antiplatelet drugs. Ticagrelor, with its faster and more potent antiplatelet effects, was shown to reduce adverse events more than clopidogrel in the overall CAD patient population of PLATO trial, but the benefits did not reach statistical significance in the T2DM subgroup. To better understand these findings, we compared the antithrombotic effects of ticagrelor versus with clopidogrel in T2DM patients with cardiovascular disease. In a randomized, 2 treatment-sequence, crossover-design, T2DM patients (n=20, 57±8 years, 60 % male) received a loading-dose [LD] plus one week of daily-therapy [DT] of clopidogrel or ticagrelor. Treatment effects were assessed by measuring thrombus formation (Badimon Chamber) and platelet aggregation (Multiple Electrode Aggregometry (MEA) Analyzer and VerifyNow®) at 2- and 6-hour post-LD and on Day-7 of DT, in comparison with pre-treatment baseline. After 2 weeks of washout, patients switched to the second treatment under identical testing conditions. Ticagrelor significantly reduced thrombus formation versus baseline at 2- and 6-hour post-LD and Day-7 of DT (33 %, 40 % and 31 %, respectively, p<0.01 for all) whereas thrombus reductions with clopidogrel were much lower and significant only at 6-hour post-LD (16 %, 20 % and 17 %, respectively). Antithrombotic effect of ticagrelor at 6-hour was significantly stronger than clopidogrel (p<0.05). Platelet aggregation (MEA and VerifyNow®) was inhibited by both treatments but effects of ticagrelor were significantly stronger at each time-point. Ticagrelor exhibits a faster and more potent antithrombotic effect than clopidogrel in T2DM patients with cardiovascular disease, supporting its use in this population.

Environmental Challenges and Physiological Solutions: Comparative Energetic Daily Rhythms of Field Mice Populations from Different Ecosystems

PubMed Central

Scantlebury, Michael; Haim, Abraham

2012-01-01

Daily and seasonal variations in physiological characteristics of mammals can be considered adaptations to temporal habitat variables. Across different ecosystems, physiological adjustments are expected to be sensitive to different environmental signals such as changes in photoperiod, temperature or water and food availability; the relative importance of a particular signal being dependent on the ecosystem in question. Energy intake, oxygen consumption (VO2) and body temperature (Tb) daily rhythms were compared between two populations of the broad-toothed field mouse Apodemus mystacinus, one from a Mediterranean and another from a sub-Alpine ecosystem. Mice were acclimated to short-day (SD) ‘winter’ and long-day (LD) ‘summer’ photoperiods under different levels of salinity simulating osmotic challenges. Mediterranean mice had higher VO2 values than sub-Alpine mice. In addition, mice exposed to short days had higher VO2 values when given water with a high salinity compared with mice exposed to long days. By comparison, across both populations, increasing salinity resulted in a decreased Tb in SD- but not in LD-mice. Thus, SD-mice may conserve energy by decreasing Tb during (‘winter’) conditions which are expected to be cool, whereas LD-mice might do the opposite and maintain a higher Tb during (‘summer’) conditions which are expected to be warm. LD-mice behaved to reduce energy expenditure, which might be considered a useful trait during ‘summer’ conditions. Overall, increasing salinity was a clear signal for Mediterranean-mice with resultant effects on VO2 and Tb daily rhythms but had less of an effect on sub-Alpine mice, which were more responsive to changes in photoperiod. Results provide an insight into how different populations respond physiologically to various environmental challenges. PMID:23251469

Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure.

PubMed

Zhu, Hao; Martin, Todd M; Ye, Lin; Sedykh, Alexander; Young, Douglas M; Tropsha, Alexander

2009-12-01

Few quantitative structure-activity relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity end points. In this study, a comprehensive data set of 7385 compounds with their most conservative lethal dose (LD(50)) values has been compiled. A combinatorial QSAR approach has been employed to develop robust and predictive models of acute toxicity in rats caused by oral exposure to chemicals. To enable fair comparison between the predictive power of models generated in this study versus a commercial toxicity predictor, TOPKAT (Toxicity Prediction by Komputer Assisted Technology), a modeling subset of the entire data set was selected that included all 3472 compounds used in TOPKAT's training set. The remaining 3913 compounds, which were not present in the TOPKAT training set, were used as the external validation set. QSAR models of five different types were developed for the modeling set. The prediction accuracy for the external validation set was estimated by determination coefficient R(2) of linear regression between actual and predicted LD(50) values. The use of the applicability domain threshold implemented in most models generally improved the external prediction accuracy but expectedly led to the decrease in chemical space coverage; depending on the applicability domain threshold, R(2) ranged from 0.24 to 0.70. Ultimately, several consensus models were developed by averaging the predicted LD(50) for every compound using all five models. The consensus models afforded higher prediction accuracy for the external validation data set with the higher coverage as compared to individual constituent models. The validated consensus LD(50) models developed in this study can be used as reliable computational predictors of in vivo acute toxicity.

A randomized trial comparing live and telemedicine deliveries of an imagery-based behavioral intervention for breast cancer survivors: reducing symptoms and barriers to care.

PubMed

Freeman, Lyn W; White, Rebecca; Ratcliff, Chelsea G; Sutton, Sue; Stewart, Mary; Palmer, J Lynn; Link, Judith; Cohen, Lorenzo

2015-08-01

This multi-site randomized trial evaluates the quality of life (QOL) benefits of an imagery-based group intervention titled 'Envision the Rhythms of Life'(ERL). Breast cancer survivors >6 weeks post-treatment were randomized to attend five weekly 4-h group sessions at a community center with therapist present (live delivery (LD), n = 48), therapist streamed via telemedicine (telemedicine delivery (TD), n = 23), or to a waitlist control (WL) group (n = 47). Weekly individual phone calls to encourage at-home practice began at session one and continued until the 3-month follow-up. Seven self-report measures of QOL were examined at baseline, 1-month and 3-month post-treatments including health-related and breast cancer-specific QOL, fatigue, cognitive function, spirituality, distress, and sleep. The Bonferroni method was used to correct for multiple comparisons, and alpha was adjusted to 0.01. Linear multilevel modeling analyses revealed less fatigue, cognitive dysfunction, and sleep disturbance for LD and TD compared with WL across the follow-up (p's < 0.01). Changes in fatigue, cognitive dysfunction, sleep disturbance, and health-related and breast cancer-related QOL were clinically significant. There were no differences between LD and TD. Both the live and telemedicine delivered ERL intervention resulted in improvements in multiple QOL domains for breast cancer survivors compared with WL. Further, there were no significant differences between LD and TD, suggesting telemedicine delivered ERL intervention may represent an effective and viable option for cancer survivors in remote areas. Copyright © 2014 John Wiley & Sons, Ltd.

Environmental challenges and physiological solutions: comparative energetic daily rhythms of field mice populations from different ecosystems.

PubMed

Scantlebury, Michael; Haim, Abraham

2012-01-01

Daily and seasonal variations in physiological characteristics of mammals can be considered adaptations to temporal habitat variables. Across different ecosystems, physiological adjustments are expected to be sensitive to different environmental signals such as changes in photoperiod, temperature or water and food availability; the relative importance of a particular signal being dependent on the ecosystem in question. Energy intake, oxygen consumption (VO(2)) and body temperature (T(b)) daily rhythms were compared between two populations of the broad-toothed field mouse Apodemus mystacinus, one from a Mediterranean and another from a sub-Alpine ecosystem. Mice were acclimated to short-day (SD) 'winter' and long-day (LD) 'summer' photoperiods under different levels of salinity simulating osmotic challenges. Mediterranean mice had higher VO(2) values than sub-Alpine mice. In addition, mice exposed to short days had higher VO(2) values when given water with a high salinity compared with mice exposed to long days. By comparison, across both populations, increasing salinity resulted in a decreased T(b) in SD- but not in LD-mice. Thus, SD-mice may conserve energy by decreasing T(b) during ('winter') conditions which are expected to be cool, whereas LD-mice might do the opposite and maintain a higher T(b) during ('summer') conditions which are expected to be warm. LD-mice behaved to reduce energy expenditure, which might be considered a useful trait during 'summer' conditions. Overall, increasing salinity was a clear signal for Mediterranean-mice with resultant effects on VO(2) and T(b) daily rhythms but had less of an effect on sub-Alpine mice, which were more responsive to changes in photoperiod. Results provide an insight into how different populations respond physiologically to various environmental challenges.

Comparison of Prasugrel and Ticagrelor Antiplatelet Effects in Korean Patients Presenting With ST-Segment Elevation Myocardial Infarction.

PubMed

Lee, Young Seok; Jin, Cai De; Kim, Moo Hyun; Guo, Long Zhe; Cho, Young-Rak; Park, Kyungil; Park, Jong Sung; Park, Tae-Ho; Kim, Young Dae

2015-01-01

There is insufficient data on the efficacy of prasugrel and ticagrelor in Korean patients with ST-segment elevation myocardial infarction (STEMI). I n the current double-blind, prospective pilot study, 39 patients with STEMI undergoing primary percutaneous coronary intervention were randomized to receive prasugrel 60 mg loading dose (LD) followed by 10 mg daily maintenance dose (n=19), or ticagrelor 180 mg LD followed by 90 mg twice daily maintenance dose (n=20). We assessed platelet reactivity with the VerifyNow and Vasodilator-Stimulated Phosphoprotein (VASP) P2Y12 assays. Compared to baseline platelet reactivity, both prasugrel and ticagrelor groups achieved similar and significantly lower P2Y12 reaction units (PRU) (259 [IQR: 230 to 281] vs. 28 [12 to 55] for prasugrel; 261 [196 to 286] vs. 43 [11 to 61] for ticagrelor), and platelet reactivity indexes (PRI) (51.2% [39.3 to 61.3] vs. 8.1% [6.1 to 14.7] for prasugrel; 47.5% [38.4 to 50.4] vs. 11.2% [7.1 to 15.5] for ticagrelor, all P values <0.001) at 48 h post-LD. Most patients had low platelet reactivity with 95% PRU values <85 and 82% with PRI <16%. Both prasugrel and ticagrelor were effective for platelet inhibition in Korean STEMI patients with almost no patients exhibiting high platelet reactivity at 48 h after the LD. Our finding of a high number of patients with very low platelet reactivity deserves further studies to assess the safety of the drugs (Prasugrel and Ticagrelor in ST-segment Elevation Myocardial Infarction Study, NCT02075125).

Sensitivity of species to chemicals: dose-response characteristics for various test types (LC(50), LR(50) and LD(50)) and modes of action.

PubMed

Hendriks, A Jan; Awkerman, Jill A; de Zwart, Dick; Huijbregts, Mark A J

2013-11-01

While variable sensitivity of model species to common toxicants has been addressed in previous studies, a systematic analysis of inter-species variability for different test types, modes of action and species is as of yet lacking. Hence, the aim of the present study was to identify similarities and differences in contaminant levels affecting cold-blooded and warm-blooded species administered via different routes. To that end, data on lethal water concentrations LC50, tissue residues LR50 and oral doses LD50 were collected from databases, each representing the largest of its kind. LC50 data were multiplied by a bioconcentration factor (BCF) to convert them to internal concentrations that allow for comparison among species. For each endpoint data set, we calculated the mean and standard deviation of species' lethal level per compound. Next, the means and standard deviations were averaged by mode of action. Both the means and standard deviations calculated depended on the number of species tested, which is at odds with quality standard setting procedures. Means calculated from (BCF) LC50, LR50 and LD50 were largely similar, suggesting that different administration routes roughly yield similar internal levels. Levels for compounds interfering biochemically with elementary life processes were about one order of magnitude below that of narcotics disturbing membranes, and neurotoxic pesticides and dioxins induced death in even lower amounts. Standard deviations for LD50 data were similar across modes of action, while variability of LC50 values was lower for narcotics than for substances with a specific mode of action. The study indicates several directions to go for efficient use of available data in risk assessment and reduction of species testing. Copyright © 2013 Elsevier Inc. All rights reserved.

Effectiveness of donepezil, rivastigmine, and (+/-)huperzine A in counteracting the acute toxicity of organophosphorus nerve agents: comparison with galantamine.

PubMed

Aracava, Yasco; Pereira, Edna F R; Akkerman, Miriam; Adler, Michael; Albuquerque, Edson X

2009-12-01

Galantamine, a centrally acting cholinesterase (ChE) inhibitor and a nicotinic allosteric potentiating ligand used to treat Alzheimer's disease, is an effective and safe antidote against poisoning with nerve agents, including soman. Here, the effectiveness of galantamine was compared with that of the centrally active ChE inhibitors donepezil, rivastigmine, and (+/-)huperzine A as a pre- and/or post-treatment to counteract the acute toxicity of soman. In the first set of experiments, male prepubertal guinea pigs were treated intramuscularly with one of the test drugs and 30 min later challenged with 1.5 x LD(50) soman (42 microg/kg s.c.). All animals that were pretreated with galantamine (6-8 mg/kg), 3 mg/kg donepezil, 6 mg/kg rivastigmine, or 0.3 mg/kg (+/-)huperzine A survived the soman challenge, provided that they were also post-treated with atropine (10 mg/kg i.m.). However, only galantamine was well tolerated. In subsequent experiments, the effectiveness of specific treatment regimens using 8 mg/kg galantamine, 3 mg/kg donepezil, 6 mg/kg rivastigmine, or 0.3 mg/kg (+/-)huperzine A was compared in guinea pigs challenged with soman. In the absence of atropine, only galantamine worked as an effective and safe pretreatment in animals challenged with 1.0 x LD(50) soman. Galantamine was also the only drug to afford significant protection when given to guinea pigs after 1.0 x LD(50) soman. Finally, all test drugs except galantamine reduced the survival of the animals when administered 1 or 3 h after the challenge with 0.6 or 0.7 x LD(50) soman. Thus, galantamine emerges as a superior antidotal therapy against the toxicity of soman.

[Oral toxicity at 60-days of sacha inchi oil (Plukenetia volubilis L.) and linseed (Linum usitatissimum L.), and determination of lethal dose 50 in rodents].

PubMed

Gorriti, Arilmi; Arroyo, Jorge; Quispe, Fredy; Cisneros, Braulio; Condorhuamán, Martín; Almora, Yuan; Chumpitaz, Víctor

2010-09-01

To evaluate the oral toxicity at 60 days and to determine the lethal dose 50 (LD 50) of raw sacha inchi (Plukenetia volubilis L.) and linseed (Linum ussitatisimum) oils in Holtzman rats and mice of the strain Balb C57 respectively. For the evaluation of the oral toxicity of repeated doses for 60 days, 24 male Holtzman rats were used, divided in three groups of 8 each, the groups were: physiologic saline solution 4 mL/kg (FSS), sacha inchi oil 0.5 mL/kg (SI05) and linseed oil 0.5 mL/kg (L05), during the experiment the body weight was controlled weekly, and signs of toxicity in the research groups, as well as total cholesterol, HDL, glucose, triglycerides and alkaline phosphatase at days 30 and 60 after initiating the experiment. For the evaluation of the LD50 male mice of the Balb C57 strain were used in groups of 10 animals, and they were administered increasing oral doses of raw oils until reaching 1 mL/kg (37 g/kg). The serum parameters in the rats indicated there is no toxicity at 60 days and that the administration of the oils lowered the levels of cholesterol, triglycerides and increased the HDL in comparison with the control group. The LD50 shows that the raw sacha inchi and linseed oils have doses above 37 g/kg of body weight. Sacha inchi and linseed oils are harmless at 60 days and present a LD50 above the 37 g/kg of animal.

Levetiracetam in adult patients with and without learning disability: focus on behavioral adverse effects.

PubMed

Brodtkorb, Eylert; Klees, Theresa M; Nakken, Karl O; Lossius, Rasmus; Johannessen, Svein I

2004-04-01

Optimal antiepileptic drug treatment in patients with learning disability (LD) represents a particular challenge. These patients are often unable to report toxicity, and side effects may manifest as behavioral problems. The aim of this open study was to compare efficacy and tolerability of levetiracetam (LEV) in patients with LD and those without LD. One hundred eighty-four consecutive adult patients who received LEV were followed for an average of 8.1 months. Fifty-six patients (30%) had LD. Thirty-nine percent of patients with refractory epilepsy (37% with and 40% without LD) had > 50% seizure reduction. Significantly more behavioral side effects (23% vs 10%) and a tendency toward less reported somatic central nervous side effects were found in the LD group. We conclude that LEV is equally effective and well tolerated in both patients with LD and patients without LD. However, behavioral problems are more frequent in patients with LD, whereas the tendency toward seizure increase is not enhanced.

The development of response surface pathway design to reduce animal numbers in toxicity studies

PubMed Central

2014-01-01

Background This study describes the development of Response Surface Pathway (RSP) design, assesses its performance and effectiveness in estimating LD50, and compares RSP with Up and Down Procedures (UDPs) and Random Walk (RW) design. Methods A basic 4-level RSP design was used on 36 male ICR mice given intraperitoneal doses of Yessotoxin. Simulations were performed to optimise the design. A k-adjustment factor was introduced to ensure coverage of the dose window and calculate the dose steps. Instead of using equal numbers of mice on all levels, the number of mice was increased at each design level. Additionally, the binomial outcome variable was changed to multinomial. The performance of the RSP designs and a comparison of UDPs and RW were assessed by simulations. The optimised 4-level RSP design was used on 24 female NMRI mice given Azaspiracid-1 intraperitoneally. Results The in vivo experiment with basic 4-level RSP design estimated the LD50 of Yessotoxin to be 463 μg/kgBW (95% CI: 383–535). By inclusion of the k-adjustment factor with equal or increasing numbers of mice on increasing dose levels, the estimate changed to 481 μg/kgBW (95% CI: 362–566) and 447 μg/kgBW (95% CI: 378–504 μg/kgBW), respectively. The optimised 4-level RSP estimated the LD50 to be 473 μg/kgBW (95% CI: 442–517). A similar increase in power was demonstrated using the optimised RSP design on real Azaspiracid-1 data. The simulations showed that the inclusion of the k-adjustment factor, reduction in sample size by increasing the number of mice on higher design levels and incorporation of a multinomial outcome gave estimates of the LD50 that were as good as those with the basic RSP design. Furthermore, optimised RSP design performed on just three levels reduced the number of animals from 36 to 15 without loss of information, when compared with the 4-level designs. Simulated comparison of the RSP design with UDPs and RW design demonstrated the superiority of RSP. Conclusion Optimised RSP design reduces the number of animals needed. The design converges rapidly on the area of interest and is at least as efficient as both the UDPs and RW design. PMID:24661560

Chernobyl doses. Volume 1. Analysis of forest canopy radiation response from multispectral imagery and the relationship to doses. Technical report, 29 July 1987-30 September 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

McClennan, G.E.; Anno, G.H.; Whicker, F.W.

1994-09-01

This volume of the report Chernobyl Doses presents details of a new, quantitative method for remotely sensing ionizing radiation dose to vegetation. Analysis of Landsat imagery of the area within a few kilometers of the Chernobyl nuclear reactor station provides maps of radiation dose to pine forest canopy resulting from the accident of April 26, 1986. Detection of the first date of significant, persistent deviation from normal of the spectral reflectance signature of pine foliage produces contours of radiation dose in the 20 to 80 Gy range extending up to 4 km from the site of the reactor explosion. Themore » effective duration of exposure for the pine foliage is about 3 weeks. For this exposure time, the LD50 of Pinus sylvestris (Scotch pine) is about 23 Gy. The practical lower dose limit for the remote detection of radiation dose to pine foliage with the Landsat Thematic Mapper is about 5 Gy or 1/4 of the LD50.« less

Genome-wide and fine-resolution association analysis of malaria in West Africa.

PubMed

Jallow, Muminatou; Teo, Yik Ying; Small, Kerrin S; Rockett, Kirk A; Deloukas, Panos; Clark, Taane G; Kivinen, Katja; Bojang, Kalifa A; Conway, David J; Pinder, Margaret; Sirugo, Giorgio; Sisay-Joof, Fatou; Usen, Stanley; Auburn, Sarah; Bumpstead, Suzannah J; Campino, Susana; Coffey, Alison; Dunham, Andrew; Fry, Andrew E; Green, Angela; Gwilliam, Rhian; Hunt, Sarah E; Inouye, Michael; Jeffreys, Anna E; Mendy, Alieu; Palotie, Aarno; Potter, Simon; Ragoussis, Jiannis; Rogers, Jane; Rowlands, Kate; Somaskantharajah, Elilan; Whittaker, Pamela; Widden, Claire; Donnelly, Peter; Howie, Bryan; Marchini, Jonathan; Morris, Andrew; SanJoaquin, Miguel; Achidi, Eric Akum; Agbenyega, Tsiri; Allen, Angela; Amodu, Olukemi; Corran, Patrick; Djimde, Abdoulaye; Dolo, Amagana; Doumbo, Ogobara K; Drakeley, Chris; Dunstan, Sarah; Evans, Jennifer; Farrar, Jeremy; Fernando, Deepika; Hien, Tran Tinh; Horstmann, Rolf D; Ibrahim, Muntaser; Karunaweera, Nadira; Kokwaro, Gilbert; Koram, Kwadwo A; Lemnge, Martha; Makani, Julie; Marsh, Kevin; Michon, Pascal; Modiano, David; Molyneux, Malcolm E; Mueller, Ivo; Parker, Michael; Peshu, Norbert; Plowe, Christopher V; Puijalon, Odile; Reeder, John; Reyburn, Hugh; Riley, Eleanor M; Sakuntabhai, Anavaj; Singhasivanon, Pratap; Sirima, Sodiomon; Tall, Adama; Taylor, Terrie E; Thera, Mahamadou; Troye-Blomberg, Marita; Williams, Thomas N; Wilson, Michael; Kwiatkowski, Dominic P

2009-06-01

We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.

Stroop Color-Word Test: A Screening Measure of Selective Attention to Differentiate LD From Non LD Children.

ERIC Educational Resources Information Center

Lazarus, Philip J.; And Others

1984-01-01

Used the Stroop Color-Word Test to measure selective attention in learning disabled (N=45) and nonLD (N=50) children. Results indicated that LD children have a significant weakness in the process of selective attention compared to the nonLD children. Findings suggested that the Stroop is an effective screening measure. (JAC)

Lipid Droplet Biogenesis and Function in the Endothelium.

PubMed

Kuo, Andrew; Lee, Monica Y; Sessa, William C

2017-04-14

Fatty acids (FA) are transported across the capillary endothelium to parenchymal tissues. However, it is not known how endothelial cells (EC) from large vessels process a postprandial surge of FA. This study was designed to characterize lipid droplet (LD) formation in EC by manipulating pathways leading to the formation and degradation of LD. In addition, several functions of LD-derived FA were assessed. LD were present in EC lining the aorta after the peak in plasma triglycerides initiated by a gavage of olive oil in mice, in vivo. Similarly, in isolated aorta, oleic acid treatment generates LD in EC ex vivo. Cultured EC readily form LD largely via the enzyme DGAT (diacylglycerol O-acyltransferase 1) and degrade LD via ATGL (adipocyte triglyceride lipase) after FA loading. Functionally, LD-derived FA are dynamically regulated and function to protect EC from lipotoxic stress and provide FA for metabolic needs. Our results delineate endothelial LD dynamics for the first time in vivo and in vitro. Moreover, LD formation protects EC from lipotoxic stress, regulates EC glycolysis, and provides a source of FA for adjacent cells in the vessel wall or tissues. © 2017 American Heart Association, Inc.

Severity of Lipodystrophy Is Associated with Decreased Health-Related Quality of Life

PubMed Central

Murri, Rita; Orlando, Gabriella; Giovanardi, Chiara; Squillace, Nicola; Vandelli, Marcella; Beghetto, Barbara; Nardini, Giulia; De Paola, Maria; Esposito, Roberto; Wu, Albert W.

2008-01-01

Abstract The impact of lipodystrophy (LD) on quality of life is high, but it has not been demonstrated in literature. The objective of the study was to assess the impact of LD on the health–related quality of life (HRQOL) in HIV-infected people on highly active antiretroviral therapy (HAART). Patients with LD phenotype defined by the Multicenter AIDS Cohort Study (MACS) were included. Three different methods were used to define LD severity: both patient and physician evaluation using the HIV Outpatient Study (HOPS) severity scales and the Lipodystrophy Case Definition (LDCD). The HRQOL was evaluated by MOS-HIV Health Survey. Four hundred one patients on HAART for a mean of 108 ± 52 months were evaluated for LD at the Metabolic Clinic of Modena and Reggio Emilia University were enrolled from January 2003 to July 2006. According to self-perceived or physician-based HOPS, 106 (26.5%) and 122 (30.4%) patients had severe LD. Females had significantly more severe LD. Few HRQOL scores correlated to LD severity using the physician-based score (both HOPSph and LDCD), while all the HRQOL scores correlated with LD severity when a patient-based score was used (HOPSpt). In multiple linear regression analysis, Mental Health HRQOL score, gender, body mass index, age, body image satisfaction were independent predictors of patient-based (HOPSpt) LD, while none of the HRQOL scores, but female gender, age, waist-to-hip ratio, limb fat, and body image satisfaction were correlated with physician-estimated HOPSph LD severity. HRQOL was strongly correlated with LD severity when a patient-based score was used. For an overall assessment of the impact of LD on HIV-infected people, both patient-based and physician-based measures are required. PMID:18647097

Canine RD3 mutation establishes rod cone dysplasia type 2 (rcd2) as ortholog of human and murine rd3

PubMed Central

Kukekova, Anna V.; Goldstein, Orly; Johnson, Jennifer L.; Richardson, Malcolm A.; Pearce-Kelling, Susan E.; Swaroop, Anand; Friedman, James S.; Aguirre, Gustavo D.; Acland, Gregory M.

2009-01-01

Rod cone dysplasia type 2 (rcd2) is an autosomal recessive disorder that segregates in collie dogs. Linkage disequilibrium and meiotic linkage mapping were combined to take advantage of population structure within this breed, and to fine map rcd2 to a 230 kb candidate region that included the gene C1orf36 responsible for human and murine rd3, and within which all affected dogs were homozygous for one haplotype. In one of three identified canine retinal RD3 splice variants, an insertion was found that cosegregates with rcd2, and is predicted to alter the last 61 codons of the normal open reading frame and further extend the ORF. Thus combined meiotic linkage and LD mapping within a single canine breed can yield critical reduction of the disease interval when appropriate advantage is taken of within breed population structure. This should permit a similar approach to tackle other hereditary traits that segregate in single closed populations. PMID:19130129

Admixture in Hispanic-Americans: Its impact on ITGAM association and implications for admixture mapping in SLE

PubMed Central

Molineros, Julio E.; Kim-Howard, Xana; Deshmukh, Harshal; Jacob, Chaim O.; Harley, John B.; Nath, Swapan K.

2009-01-01

Systemic Lupus Erythematosus (SLE) disproportionately affects minorities, such as Hispanic-Americans. Prevalence of SLE is 3–5 times higher in Hispanic Americans (HA) than European derived populations, and have more active disease at the time of diagnosis, with more serious organ system involvement. HA is an admixed population, it is possible that there is an effect of admixture on the relative risk of disease. This admixture can create substantial increase of linkage disequilibrium (LD) in both magnitude and range, which can provide a unique opportunity for admixture mapping. Main objectives of this study are to (a) estimate hidden population structure in HA individuals; (b) estimate individual ancestry proportions and its impact on SLE risk; (c) assess impact of admixture on ITGAM association, a recently identified SLE susceptibility gene; and (d) estimate power of admixture mapping in HA. Our dataset contained 1,125 individuals, of whom 884 (657 SLE cases and 227 controls) were self classified as HA. Using 107 unlinked ancestry informative markers (AIMs) we estimated hidden population structure and individual ancestry in HA. Out of 5,671 possible pair-wise LD, 54% were statistically significant, indicating recent population admixture. The best fitted model for HA was a four population model with average ancestry of European (48%), American-Indian (40%), African (8%) and a fourth population (4%) with unknown ancestry. We also identified significant higher risk associated with American-Indian ancestry (OR=4.84, P=0.0001, 95%CI=2.14—10.95) on overall SLE. We showed that ITGAM is associated as a risk factor for SLE (OR= 2.06, P=8.74×10−5, 95%CI=1.44–2.97). This association is not affected by population substructure or admixture. We have demonstrated that HA have great potential and are an 3 appropriate population for admixture mapping. As expected, the case-only design is more powerful than case-control design, for any given admixture proportion or ancestry risk ratio. PMID:19387459

Glucose-6-phosphate dehydrogenase and Trypanothione reductase interaction protects Leishmania donovani from metalloid mediated oxidative stress.

PubMed

Ghosh, Ayan Kumar; Saini, Savita; Das, Sushmita; Mandal, Abhishek; Sardar, Abul Hasan; Ansari, Md Yousuf; Abhishek, Kumar; Kumar, Ajay; Singh, Ruby; Verma, Sudha; Equbal, Asif; Ali, Vahab; Das, Pradeep

2017-05-01

Exploration of metabolons as viable drug target is rare in kinetoplastid biology. Here we present a novel protein-protein interaction among Glucose-6-phosphate dehydrogenase (LdG6PDH) and Trypanothione reductase (LdTryR) of Leishmania donovani displaying interconnection between central glucose metabolism and thiol metabolism of this parasite. Digitonin fractionation patterns observed through immunoblotting indicated localisation of both LdG6PDH and LdTryR in cytosol. In-silico and in-vitro interaction observed by size exclusion chromatography, co-purification, pull-down assay and spectrofluorimetric analysis revealed LdG6PDH and LdTryR physically interact with each other in a NADPH dependent manner. Coupled enzymatic assay displayed that NADPH generation was severely impaired by addition of Sb III , As III and Te IV extraneously, which hint towards metalloid driven structural changes of the interacting proteins. Co-purification patterns and pull-down assays also depicted that metalloids (Sb III , As III and Te IV ) hinder the in-vitro interaction of these two enzymes. Surprisingly, metalloids at sub-lethal concentrations induced the in-vivo interaction of LdG6PDH and LdTryR, as analyzed by pull-down assays and fluorescence microscopy signifying protection against metalloid mediated ROS. Inhibition of LdTryR by thioridazine in LdG6PDH -/- parasites resulted in metalloid induced apoptotic death of the parasites due to abrupt fall in reduced thiol content, disrupted NADPH/NADP + homeostasis and lethal oxidative stress. Interestingly, clinical isolates of L.donovani resistant to SAG exhibited enhanced interaction between LdG6PDH and LdTryR and showed cross resistivity towards As III and Te IV . Thus, our findings propose the metabolon of LdG6PDH and LdTryR as an alternate therapeutic target and provide mechanistic insight about metalloid resistance in Visceral Leishmaniasis. Copyright © 2017. Published by Elsevier Inc.

Lucid Dreaming: Intensity, But Not Frequency, Is Inversely Related to Psychopathology

PubMed Central

Aviram, Liat; Soffer-Dudek, Nirit

2018-01-01

Lucid dreaming (LD) is awareness that one is dreaming, during the dream state. However, some define and assess LD relying also on controlling dream events, although control is present only in a subset of lucid dreams. LD has been claimed to represent well-being, and has even been used as a therapeutic agent. Conversely, LD is associated with mixed sleep-wake states, which are related to bizarre cognitions, stress, and psychopathology, and have been construed as arousal permeating and disrupting sleep. We propose that previous conflicting findings regarding relations between LD and both psychopathology and well-being, stem from the non-differentiated assessment of frequency and control. The present study aimed to develop an expansive measure of several LD characteristics (the Frequency and Intensity Lucid Dream questionnaire; FILD), and explore their relations with symptomatology. Undergraduate students (N = 187) self-reported trait LD, psychopathology (depression, anxiety, obsessive-compulsive symptoms, dissociation, and schizotypy), stress, and sleep problems; 2 months later, a subsample (n = 78) reported psychopathology again, and also completed a dream diary each morning for 14 days. Preliminary evidence supports the reliability and validity of the FILD. Items converged into four domains: frequency, intensity (e.g., control, activity, certainty of dreaming), emotional valence, and the use of induction techniques. We report an optimal frequency cutoff score to identify those likely to experience LD within a 2-week period. Whereas LD frequency was unrelated to psychopathology, LD intensity, and positive LD emotions, were inversely associated with several psychopathological symptoms. Use of deliberate induction techniques was positively associated with psychopathology and sleep problems. Additionally, we demonstrated directionality by employing a prospective-longitudinal design, showing that deliberate LD induction predicted an increase in dissociation and schizotypy symptoms across 2 months. We conclude that lucidity should not be considered as necessarily suggestive of well-being; LD may be positive or negative, depending on lucidity characteristics. Additionally, deliberate LD induction may harbor negative long-term risk. PMID:29623062

Effect of low-head lock and dam structures on migration and spawning of American shad and striped bass in the Cape Fear River, North Carolina

USGS Publications Warehouse

Smith, Joseph A.; Hightower, Joseph E.

2012-01-01

Anadromous fish populations within the Cape Fear River, North Carolina, have declined substantially since the late 1800s. Three low-head lock-and-dam (LD) structures on the river (LD-1–3) contributed to this decline by limiting access to upstream spawning habitat. We used egg sampling and sonic telemetry to examine the effects of the LD structures on migration and spawning activity of American shad Alosa sapidissima and striped bassMorone saxatilis. Egg distribution and stage of development suggested that most of the American shad spawning took place downstream from the lowermost structure, LD-1. The predicted mean density of stage-1 American shad eggs at a water temperature of 21°C was 895 eggs/1,000 m3 (95% credible interval [CI] = 800–994) below LD-1; 147 eggs/1,000 m3 (95% CI = 103–197) below LD-2; and 32 eggs/1,000 m3 (95% CI = 17–49) below the uppermost structure, LD-3. The probability of capturing a stage-1 American shad egg was strongly dependent on water temperature and hour of egg collection. Transmitter detections for 20 sonic-tagged American shad and 20 striped bass in 2008 showed that for both species, the majority of fish moved upstream of LD-1; 35% of American shad and 25% of striped bass migrated upstream of LD-3. Based on passage rates at the three LD structures, American shad would be expected to be most abundant downstream of LD-1 and upstream of LD-3. For striped bass, the river section between LD-2 and LD-3 had the highest egg collections and highest predicted proportion of the run. In combination, these results demonstrate that the locking program provides some access to historical spawning habitat, although further improvements in fish passage could benefit both species.

Lucid Dreaming: Intensity, But Not Frequency, Is Inversely Related to Psychopathology.

PubMed

Aviram, Liat; Soffer-Dudek, Nirit

2018-01-01

Lucid dreaming (LD) is awareness that one is dreaming, during the dream state. However, some define and assess LD relying also on controlling dream events, although control is present only in a subset of lucid dreams. LD has been claimed to represent well-being, and has even been used as a therapeutic agent. Conversely, LD is associated with mixed sleep-wake states, which are related to bizarre cognitions, stress, and psychopathology, and have been construed as arousal permeating and disrupting sleep. We propose that previous conflicting findings regarding relations between LD and both psychopathology and well-being, stem from the non-differentiated assessment of frequency and control. The present study aimed to develop an expansive measure of several LD characteristics (the Frequency and Intensity Lucid Dream questionnaire; FILD), and explore their relations with symptomatology. Undergraduate students ( N = 187) self-reported trait LD, psychopathology (depression, anxiety, obsessive-compulsive symptoms, dissociation, and schizotypy), stress, and sleep problems; 2 months later, a subsample ( n = 78) reported psychopathology again, and also completed a dream diary each morning for 14 days. Preliminary evidence supports the reliability and validity of the FILD. Items converged into four domains: frequency, intensity (e.g., control, activity, certainty of dreaming), emotional valence, and the use of induction techniques. We report an optimal frequency cutoff score to identify those likely to experience LD within a 2-week period. Whereas LD frequency was unrelated to psychopathology, LD intensity, and positive LD emotions, were inversely associated with several psychopathological symptoms. Use of deliberate induction techniques was positively associated with psychopathology and sleep problems. Additionally, we demonstrated directionality by employing a prospective-longitudinal design, showing that deliberate LD induction predicted an increase in dissociation and schizotypy symptoms across 2 months. We conclude that lucidity should not be considered as necessarily suggestive of well-being; LD may be positive or negative, depending on lucidity characteristics. Additionally, deliberate LD induction may harbor negative long-term risk.

Investigating quality of life and self-stigma in Hong Kong children with specific learning disabilities.

PubMed

Chan, Yi; Chan, Yim Yuk; Cheng, Sui Lam; Chow, Man Yin; Tsang, Yau Wai; Lee, Clara; Lin, Chung-Ying

2017-09-01

Children with specific learning disabilities (SpLD) are likely to develop self-stigma and have a poor quality of life (QoL) because of their poor academic performance. Although both self-stigma and poor QoL issues are likely to be found in low academic achievers without SpLD, children with SpLD have worse situation because their diagnosis of SpLD suggests that their learning struggles are biological and permanent. Specifically, students' perception of own capabilities may be affected more by the diagnosis of SpLD than their own actual performance. We examined the self-stigma and QoL of children with SpLD in Hong Kong, a region with an academics-focused culture. Children with SpLD (n=49,M age ±SD=9.55±1.21; SpLD group) and typically developing children (n=32,M age ±SD=9.81±1.40; TD group) completed a Kid-KINDL to measure QoL and a Modified Self-Stigma Scale to measure self-stigma. All parents completed a parallel Kid-KINDL to measure QoL of their children. Compared with the TD group, the SpLD group had a higher level of self-stigma (p=0.027) and lower QoL (child-reported Kid-KINDL: p=0.001; parent-reported Kid-KINDL: p<0.001). In the academics-focused environment in Hong Kong, SpLD was associated with impaired QoL and higher self-stigma. Treatments targeting the learning process of children with SpLD may be designed to overcome self-stigma and to improve QoL. In addition, the program may involve parents of the children with SpLD or other people (e.g., the peer of the children with SpLD) for improving their understanding and perceptions of SpLD. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mucuna pruriens for Parkinson's disease: Low-cost preparation method, laboratory measures and pharmacokinetics profile.

PubMed

Cassani, Erica; Cilia, Roberto; Laguna, Janeth; Barichella, Michela; Contin, Manuela; Cereda, Emanuele; Isaias, Ioannis U; Sparvoli, Francesca; Akpalu, Albert; Budu, Kwabena Ofosu; Scarpa, Maria Teresa; Pezzoli, Gianni

2016-06-15

Parkinson's disease (PD) is a progressive neurological condition. Levodopa (LD) is the gold standard therapy for PD patients. Most PD patients in low-income areas cannot afford long-term daily Levodopa therapy. The aim of our study was to investigate if Mucuna pruriens (MP), a legume with high LD content that grows in tropical regions worldwide, might be potential alternative for poor PD patients. We analyzed 25 samples of MP from Africa, Latin America and Asia. We measured the content in LD in various MP preparations (dried, roasted, boiled). LD pharmacokinetics and motor response were recorded in four PD patients, comparing MP vs. LD+Dopa-Decarboxylase Inhibitor (DDCI) formulations. Median LD concentration in dried MP seeds was 5.29%; similar results were obtained in roasted powder samples (5.3%), while boiling reduced LD content up to 70%. Compared to LD+DDCI, MP extract at similar LD dose provided less clinical benefit, with a 3.5-fold lower median AUC. Considering the lack of a DDCI, MP therapy may provide clinical benefit only when content of LD is at least 3.5-fold the standard LD+DDCI. If long-term MP proves to be safe and effective in controlled clinical trials, it may be a sustainable alternative therapy for PD in low-income countries. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

The Effect of Activity with E-Book on Vocabulary and Story Comprehension: A Comparison between Kindergarteners at Risk of Learning Disabilities and Typically Developing Kindergarteners

ERIC Educational Resources Information Center

Shamir, Adina; Korat, Ofra; Shlafer, Inessa

2011-01-01

The purpose of the current study was to investigate the effectiveness of e-book activity for vocabulary acquisition and story comprehension among kindergarteners at risk for learning disabilities (LD) as opposed to typically developing (TD) children. Participants included 136 children aged between five and seven (M = 71.2; SD = 5.64, in months),…

Familial patterns of learning disabilities.

PubMed

Smith, S

1992-12-01

Extended families of 12 young adults (9 LD, 3 non-LD) were given a battery of tests and questionnaires, and 131 persons, ranging in age from 6 to 85, were classified as LD or non-LD on the basis of subtest scores 1 SD below the mean or less on subtests of the PIAT and WRAT achievement tests. Pedigree analysis indicated that LD was strongly familial, with the most probable mode involving a major gene effect, but the type of disability (reading/ math) was not directly inherited. Autoimmune disorders were significantly correlated (P<.005) with LD, especially in families in which LD remained a major handicap into adulthood, a trait that also varied between families. In two of the LD families, adults showed little evidence of the reading/spelling deficits they had shown when tested as children, while adults in other families failed to make gains in reading and spelling.

Weather-Dependent Risk for Legionnaires' Disease, United States.

PubMed

Simmering, Jacob E; Polgreen, Linnea A; Hornick, Douglas B; Sewell, Daniel K; Polgreen, Philip M

2017-11-01

Using the Nationwide Inpatient Sample and US weather data, we estimated the probability of community-acquired pneumonia (CAP) being diagnosed as Legionnaires' disease (LD). LD risk increases when weather is warm and humid. With warm weather, we found a dose-response relationship between relative humidity and the odds for LD. When the mean temperature was 60°-80°F with high humidity (>80.0%), the odds for CAP being diagnosed with LD were 3.1 times higher than with lower levels of humidity (<50.0%). Thus, in some regions (e.g., the Southwest), LD is rarely the cause of hospitalizations. In other regions and seasons (e.g., the mid-Atlantic in summer), LD is much more common. Thus, suspicion for LD should increase when weather is warm and humid. However, when weather is cold, dry, or extremely hot, empirically treating all CAP patients for LD might contribute to excessive antimicrobial drug use at a population level.

Design of laser diode driver with constant current and temperature control system

NASA Astrophysics Data System (ADS)

Wang, Ming-cai; Yang, Kai-yong; Wang, Zhi-guo; Fan, Zhen-fang

2017-10-01

A laser Diode (LD) driver with constant current and temperature control system is designed according to the LD working characteristics. We deeply researched the protection circuit and temperature control circuit based on thermos-electric cooler(TEC) cooling circuit and PID algorithm. The driver could realize constant current output and achieve stable temperature control of LD. Real-time feedback control method was adopted in the temperature control system to make LD work on its best temperature point. The output power variety and output wavelength shift of LD caused by current and temperature instability were decreased. Furthermore, the driving current and working temperature is adjustable according to specific requirements. The experiment result showed that the developed LD driver meets the characteristics of LD.

Validity and usefulness of the Line Drill test for adolescent basketball players: a Bayesian multilevel analysis.

PubMed

Carvalho, Humberto M; Gonçalves, Carlos E; Grosgeorge, Bernard; Paes, Roberto R

2017-01-01

The study examined the validity of the Line Drill test (LD) in male adolescent basketball players (10-15 years). Sensitiveness of the LD to changes in performance across a training and competition season (4 months) was also considered. Age, maturation, body size and LD were measured (n = 57). Sensitiveness of the LD was examined pre- and post-competitive season in a sub-sample (n = 44). The time at each of the four shuttle sprints of the LD (i.e. four stages) was modelled with Bayesian multilevel models. We observed very large correlation of performance at stage 4 (full LD protocol) with stage 3, but lower correlations with the early LD stages. Players' performance by somatic maturity differed substantially only when considering full LD protocol performance. Substantial improvements in all stages of the protocol were observed across the 4-month competitive season. The LD protocol should be shortened by the last full court shuttle sprint, remaining sensitive to training exposure, and independent of maturity status and body size.

Comparison of alternative beef production systems based on forage finishing or grain-forage diets with or without growth promotants: 2. Meat quality, fatty acid composition, and overall palatability.

PubMed

Faucitano, L; Chouinard, P Y; Fortin, J; Mandell, I B; Lafrenière, C; Girard, C L; Berthiaume, R

2008-07-01

Five beef cattle management regimens were evaluated for their effect on meat quality, fatty acid composition, and overall palatability of the longis-simus dorsi (LD) muscle in Angus cross steers. A 98-d growing phase was conducted using grass silage with or without supplementation of growth promotants (Revalor G and Rumensin) or soybean meal. Dietary treatments in the finishing phase were developed with or without supplementation of growth promotants based on exclusive feeding of forages with no grain supplementation, or the feeding of grain:forage (70:30) diets. Growth promotants increased (P < 0.01) shear force and tended (P = 0.06) to increase toughness of the LD muscle due to limited postmortem proteolytic activity (lower myofibrillar fragmentation index value; P = 0.02). Grain feeding increased DM and intramuscular fat content (P = 0.03 and P = 0.05, respectively) in the LD but decreased the sensory panel tenderness score (P = 0.01). Growth promotants increased (P

Relationship Between Radiation Therapy Dose and Outcome in Patients Treated With Neoadjuvant Chemoradiation Therapy and Surgery for Stage IIIA Non-Small Cell Lung Cancer: A Population-Based, Comparative Effectiveness Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sher, David J., E-mail: david_sher@rush.edu; Fidler, Mary Jo; Seder, Christopher W.

Purpose: To compare, using the National Cancer Database, survival, pathologic, and surgical outcomes in patients with stage IIIA non-small cell lung cancer treated with differential doses of neoadjuvant chemoradiation therapy, with the aim to discern whether radiation dose escalation was associated with a comparative effectiveness benefit and/or toxicity risk. Methods and Materials: Patients in the National Cancer Database with stage IIIA non-small cell lung cancer treated with neoadjuvant chemoradiation therapy and surgery between 1998 and 2005 were analyzed. Dose strata were divided between 36 to 45 Gy (low-dose radiation therapy, LD-RT), 45 to 54 Gy (inclusive, standard-dose, SD-RT), and 54 to 74 Gymore » (high-dose, HD-RT). Outcomes included overall survival, residual nodal disease, positive surgical margin status, hospital length of stay, and adverse surgical outcomes (30-day mortality or readmission). Results: The cohort consisted of 1041 patients: 233 (22%) LD-RT, 584 (56%) SD-RT, and 230 (22%) HD-RT. The median, 3-year, and 5-year overall survival outcomes were 34.9 months, 48%, and 37%, respectively. On univariable analysis, patients treated with SD-RT experienced prolonged overall survival (median 38.3 vs 31.8 vs 29.0 months for SD-RT, LD-RT, and HD-RT, respectively, P=.0089), which was confirmed on multivariable analysis (hazard ratios 0.77 and 0.81 vs LD and HD, respectively). Residual nodal disease was seen less often after HD-RT (25.5% vs 31.8% and 37.5% for HD-RT, LD-RT, and SD-RT, respectively, P=.0038). Patients treated with SD-RT had fewer prolonged hospital stays. There were no differences in positive surgical margin status or adverse surgical outcomes between the cohorts. Conclusions: Neoadjuvant chemoradiation therapy between 45 and 54 Gy was associated with superior survival in comparison with doses above and below this threshold. Although this conclusion is limited by selection bias, clear candidates for trimodality therapy do not seem to achieve additional benefit with dose escalation.« less

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

PubMed

N'Diaye, Amidou; Haile, Jemanesh K; Cory, Aron T; Clarke, Fran R; Clarke, John M; Knox, Ron E; Pozniak, Curtis J

2017-01-01

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.

A Genetic Screen for Mutants with Supersized Lipid Droplets in Caenorhabditis elegans

PubMed Central

Li, Shiwei; Xu, Shibin; Ma, Yanli; Wu, Shuang; Feng, Yu; Cui, Qingpo; Chen, Lifeng; Zhou, Shuang; Kong, Yuanyuan; Zhang, Xiaoyu; Yu, Jialei; Wu, Mengdi; Zhang, Shaobing O.

2016-01-01

To identify genes that regulate the dynamics of lipid droplet (LD) size, we have used the genetically tractable model organism Caenorhabditis elegans, whose wild-type LD population displays a steady state of size with an upper limit of 3 μm in diameter. From a saturated forward genetic screen of 6.7 × 105 mutagenized haploid genomes, we isolated 118 mutants with supersized intestinal LDs often reaching 10 μm. These mutants define nine novel complementation groups, in addition to four known genes (maoc-1, dhs-28, daf-22, and prx-10). The nine groups are named drop (lipid droplet abnormal) and categorized into four classes. Class I mutants drop-5 and drop-9, similar to prx-10, are up-regulated in ACS-22-DGAT-2-dependent LD growth, resistant to LD hydrolysis, and defective in peroxisome import. Class II mutants drop-2, drop-3, drop-6, and drop-7 are up-regulated in LD growth, are resistant to LD hydrolysis, but are not defective in peroxisome import. Class III mutants drop-1 and drop-8 are neither up-regulated in LD growth nor resistant to LD hydrolysis, but seemingly up-regulated in LD fusion. Class IV mutant drop-4 is cloned as sams-1 and, different to the other three classes, is ACS-22-independent and hydrolysis-resistant. These four classes of supersized LD mutants should be valuable for mechanistic studies of LD cellular processes including growth, hydrolysis, and fusion. PMID:27261001

Post-hoc analysis showing better clinical response with the loading dose of certolizumab pegol in Japanese patients with active rheumatoid arthritis.

PubMed

Takeuchi, Tsutomu; Yamamoto, Kazuhiko; Yamanaka, Hisashi; Ishiguro, Naoki; Tanaka, Yoshiya; Eguchi, Katsumi; Watanabe, Akira; Origasa, Hideki; Kobayashi, Mariko; Shoji, Toshiharu; Togo, Osamu; Miyasaka, Nobuyuki; Koike, Takao

2016-07-01

To compare the efficacy and safety of certolizumab pegol (CZP) with and without loading dose (LD) in a post-hoc analysis of two Japanese clinical studies. Data from the double-blind trials (DBT) J-RAPID and HIKARI, and their open-label extension (OLE) studies, were used. Patients randomized to CZP 200 mg every 2 weeks (Q2W) groups starting with LD (400 mg Weeks 0/2/4; LD group; J-RAPID: n = 82, HIKARI: n = 116) and patients randomized to placebo groups who subsequently started CZP Q2W without LD in the OLEs (No-LD group; J-RAPID: n = 61, HIKARI: n = 99) were analyzed. Efficacy and pharmacokinetics were assessed during 24 weeks. Adverse events were reported from all studies. In both trials, the LD groups showed more rapid initial ACR20/50/70 kinetics, and maintained higher ACR50/70 responses until 24 weeks, compared with the No-LD groups. Anti-CZP antibody development was less frequent in the LD groups (J-RAPID: 1.2% versus 4.9%; HIKARI: 17.2% versus 27.3%). Similar safety profiles were reported between LD and No-LD groups (any AEs: 281.8 versus 315.7 [J-RAPID], 282.6 versus 321.3 [HIKARI] [incidence rate/100 patient-years]). Despite limitations, including comparing DBT and OLE studies, these results suggest that a CZP LD improves clinical response in active rheumatoid arthritis without altering the safety profile.

Characteristic behaviors of students with LD who have teacher-identified math weaknesses.

PubMed

Bryant, D P; Bryant, B R; Hammill, D D

2000-01-01

Mathematics learning disabilities (LD) have gained increased attention over the last decade from both researchers and practitioners. A large percentage of students receiving learning disability services experience difficulties with mathematics, but little research has examined the specific mathematics behaviors of students with LD who have teacher-identified math weaknesses. This study examines the literature on mathematics LD and identifies specific behaviors from that body of research for the purpose of determining the extent to which those behaviors are observed in students with LD. Data are presented from observations of 391 special education professionals on 1724 students with LD, 870 of whom had identified math weaknesses and 854 of whom did not. Our results validate the existing literature and provide implications for teachers, researchers, and others interested in studying mathematics LD.

Structure and dynamics of the bacterial communities in fermentation of the traditional Chinese post-fermented pu-erh tea revealed by 16S rRNA gene clone library.

PubMed

Zhao, Ming; Xiao, Wei; Ma, Yan; Sun, Tingting; Yuan, Wenxia; Tang, Na; Zhang, Donglian; Wang, Yongxia; Li, Yali; Zhou, Hongjie; Cui, Xiaolong

2013-10-01

Microbes are thought to have key roles in the development of the special properties of post-fermented pu-erh tea (pu-erh shucha), a well-known traditional Chinese tea; however, little is known about the bacteria during the fermentation. In this work, the structure and dynamics of the bacterial community involved in the production of pu-erh shucha were investigated using 16S rRNA gene clone libraries constructed from samples collected on days zero (LD-0), 5 (LD-5), 10 (LD-10), 15 (LD-15) and 20 (LD-20) of the fermentation. A total of 747 sequences with individual clone library containing 115-174 sequences and 4-20 unique operational taxonomic units (OTUs) were obtained. These OTUs were grouped into four phyla (Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria) and further identified as members of 10 families, such as Alcaligenaceae, Bacillaceae, Enterobacteriaceae, etc. The dominant bacteria were Enterobacteriaceae in the raw material (LD-0) and in the initial stages of fermentation (LD-5 and LD-10), which changed to Bacillaceae at the last stages of fermentation (LD-15 and LD-20) at a temperature of 40-60 °C. It is interesting that the dominant OTUs in libraries LD-15 and LD-20 were very closely related to Bacillus coagulans, which is a safe thermoduric probiotic. Together the bacterial diversity and dynamics during a fermentation of pu-erh shucha were demonstrated, and a worthy clue for artificial inoculation of B. coagulans to improve the health benefits of pu-erh shucha or produce probiotic pu-erh tea were provided.

Impact of perioperative liver dysfunction on in-hospital mortality and long-term survival in infective endocarditis patients.

PubMed

Diab, M; Sponholz, C; von Loeffelholz, C; Scheffel, P; Bauer, M; Kortgen, A; Lehmann, T; Färber, G; Pletz, M W; Doenst, T

2017-12-01

Infective endocarditis (IE) is often associated with multiorgan dysfunction and mortality. The impact of perioperative liver dysfunction (LD) on outcome remains unclear and little is known about factors leading to postoperative LD. We performed a retrospective, single-center analysis on 285 patients with left-sided IE without pre-existing chronic liver disease referred to our center between 2007 and 2013 for valve surgery. Sequential organ failure assessment (SOFA) score was used to evaluate organ dysfunction. Chi-square, Cox regression, and multivariate analyses were used for evaluation. Preoperative LD (Bilirubin >20 μmol/L) was present in 68 of 285 patients. New, postoperative LD occurred in 54 patients. Hypoxic hepatitis presented the most common origin of LD, accompanied with high short-term mortality. In-hospital mortality was higher in patients with preoperative and postoperative LD compared to patients without LD (51.5, 24.1, and 10.4%, respectively, p < 0.001). 5-year survival was worse in patients with pre- or postoperative LD compared to patients without LD (20.1, 37.1, and 57.0% respectively). A landmark analysis revealed similar 5-year survival between groups after patient discharge. Quality of life was similar between groups when patients survived the perioperative period. Logistic regression analysis identified duration of cardiopulmonary bypass and S. aureus infection as independent predictors of postoperative LD. Perioperative liver dysfunction in patients with infective endocarditis is an independent predictor of short- and long-term mortalities. After surviving the hospital stay, 5-year prognosis is not different and quality of life is not affected by LD. S. aureus and duration of cardiopulmonary bypass represent risk factors for postoperative LD.

Sero-Diagnosis of Mycobacterium avium Complex Lung Disease Using Serum Immunoglobulin A Antibody against Glycopeptidolipid Antigen in Taiwan

PubMed Central

Wang, Jann-Tay; Jou, Ruwen; Wang, Jann-Yuan; Kobayashi, Kazuo; Lai, Hsin-Chih; Yu, Chong-Jen; Lee, Li-Na; Luh, Kwen-Tay

2013-01-01

Background Lung disease (LD) due to non-tuberculous mycobacteria is an important clinical concern. Mycobacterium avium complex (MAC) is one of the most common causative agents but the diagnosis of MAC-LD remains challenging. Detection of serum IgA antibody against MAC glycopeptidolipid (GPL) has recently been shown to improve the diagnosis of MAC-LD, but has yet to be validated worldwide. Methods This prospective study was conducted in a tertiary referral center in northern Taiwan and enrolled patients with MAC-LD, MAC contamination, other lung diseases, and control subjects. Serum immunoglobulin A (IgA) antibody against MAC-GPL was detected in the participants and its specificity and sensitivity was assessed. Results There were 56 patients with MAC-LD, 11 with MAC contamination, 13 M. kansasii-LD, 26 LD due to rapidly-growing mycobacteria (RGM), 48 pulmonary tuberculosis, and 42 household contacts of patients with TB. Patients with MAC-LD were older and 32% of them had an underlying co-morbidity. By logistic regression, serum MAC-GPL IgA level was an independent predictor of MAC-LD among the study subjects and those with culture-positive specimens for MAC. By the receiver operating characteristic curve, serum MAC-GPL IgA had a good power to discriminate MAC-LD from MAC contamination. Under the optimal cut-off value of 0.73 U/mL, its sensitivity and specificity were 60% and 91%, respectively. Among MAC-LD patients, presence of co-morbidity was associated with MAC-GPL <0.73 U/ml in logistic regression analysis. Conclusions Measurement of serum anti-MAC-GPL IgA level is useful for the diagnosis of MAC-LD. However, its implement in clinical practice for immuno-compromised hosts needs careful consideration. PMID:24260398

Lumbar Drains Decrease the Risk of Postoperative Cerebrospinal Fluid Leak Following Endonasal Endoscopic Surgery for Suprasellar Meningiomas in Patients With High Body Mass Index.

PubMed

Cohen, Salomon; Jones, Samuel H; Dhandapani, Sivashanmugam; Negm, Hazem M; Anand, Vijay K; Schwartz, Theodore H

2018-01-01

Postoperative cerebrospinal fluid (CSF) leak is a persistent, albeit much less prominent, complication following endonasal endoscopic surgery. The pathology with highest risk is suprasellar meningiomas. A postoperative lumbar drain (LD) is used to decrease the risk of CSF leak but is not universally accepted. To compare the rates of postoperative CSF leak between patients with and without LD who underwent endonasal endoscopic surgical resection of suprasellar meningiomas. A consecutive series of newly diagnosed suprasellar meningiomas was drawn from a prospectively acquired database of endonasal endoscopic surgeries at our institution. An intraoperative, preresection LD was placed and left open at 5 cc/h for ∼48 h. In a subset of patients, the LD could not be placed. Rates of postoperative CSF leak were compared between patients with and without an LD. Twenty-five patients underwent endonasal endoscopic surgical resection of suprasellar meningiomas. An LD could not be placed in 2 patients. There were 2 postoperative CSF leaks (8%), both of which occurred in the patients who did not have an LD (P = .0033). The average body mass index (BMI) of the patients in whom the LD could not be placed was 39.1 kg/m2, compared with 27.6 kg/m2 for those in whom the LD could be placed (P = .009). In the subgroup of obese patients (BMI > 30 kg/m2), LD placement was protective against postoperative CSF leak (P = .022). The inability to place an LD in patients with obesity is a risk factor for postoperative CSF leak. An LD may be useful to prevent postoperative CSF leak, particularly in patients with elevated BMI. Copyright © 2017 by the Congress of Neurological Surgeons

The P450 enzyme Shade mediates the hydroxylation of ecdysone to 20-hydroxyecdysone in the Colorado potato beetle, Leptinotarsa decemlineata.

PubMed

Kong, Y; Liu, X-P; Wan, P-J; Shi, X-Q; Guo, W-C; Li, G-Q

2014-10-01

Ecdysone 20-monooxygenase (E20MO), a cytochrome P450 monooxygenase (CYP314A1), catalyses the conversion of ecdysone (E) to 20-hydroxyecdysone (20E). We report here the cloning and characterization of the Halloween gene Shade (Shd) encoding E20MO in the Colorado potato beetle, Leptinotarsa decemlineata. LdSHD has five conserved motifs typical of insect P450s, ie the Helix-C, Helix-I, Helix-K, PxxFxPE/DRF (PERF) and heme-binding motifs. LdShd was expressed in developing eggs, the first to fourth instars, wandering larvae, pupae and adults, with statistically significant fluctuations. Its mRNA was ubiquitously distributed in the head, thorax and abdomen. The recombinant LdSHD protein expressed in Spodoptera frugiperda 9 (Sf9) cells catalysed the conversion of E to 20E. Dietary introduction of double-stranded RNA (dsRNA) of LdShd into the second instar larvae successfully knocked down the LdShd expression level, decreased the mRNA level of the ecdysone receptor (LdEcR) gene, caused larval lethality, delayed development and affected pupation. Moreover, ingestion of LdShd-dsRNA by the fourth instars also down-regulated LdShd and LdEcR expression, reduced the 20E titre, and negatively influenced pupation. Introduction of 20E and a nonsteroidal ecdysteroid agonist halofenozide into the LdShd-dsRNA-ingested second instars, and of halofenozide into the LdShd-dsRNA-ingested fourth instars almost completely relieved the negative effects on larval performance. Thus, LdSHD functions to regulate metamorphotic processes by converting E to 20E in a coleopteran insect species Le. decemlineata. © 2014 The Royal Entomological Society.

Effect of taping on foot kinematics in persons with chronic ankle instability.

PubMed

Deschamps, Kevin; Dingenen, Bart; Pans, Femke; Van Bavel, Isabelle; Matricali, Giovanni Arnoldo; Staes, Filip

2016-07-01

To investigate differences in rigid-foot and multi-segmental foot kinematics between healthy (control) and chronic ankle instability (CAI) participants during running and to evaluate the effect of low-Dye (LD) and high-Dye (HD) taping on foot kinematics of CAI subjects. Cross-sectional, comparative study. Kinematic data of 12 controls and 15 CAI participants were collected by a 3D motion analysis system during running. CAI participants performed barefoot (CAI_BF) running trials as well as trials with taping. A rigid Plug-in gait Model and the Rizzoli 3D Multi-Segment Foot Model were used. Groups were compared using one-dimensional statistical parametric mapping. An increased inversion, a decreased dorsiflexion between the foot and tibia and a decreased external foot progression angle were found during terminal swing and early stance in the CAI_BF group. With respect to the taped conditions, post-hoc SPM{t} calculations highlighted a more dorsiflexed rearfoot (38-46% running cycle) in the CAI_HD compared to the CAI_LD, and a more inverted Mid-Met angle (6-24% running cycle) in the CAI_LD compared to the CAI_BF condition. This study revealed significant differences in rigid foot and multi-segmental foot kinematics between all groups. As high-dye taping embraces shank-rearfoot and forefoot, it seems to have better therapeutic features with respect to low-dye taping as the latter created a more inverted forefoot which may not be recommended in this population. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Corpus Callosum Diffusion and Language Lateralization in Patients with Brain Tumors: A DTI and fMRI Study.

PubMed

Tantillo, Gabriella; Peck, Kyung K; Arevalo-Perez, Julio; Lyo, John K; Chou, Joanne F; Young, Robert J; Brennan, Nicole Petrovich; Holodny, Andrei I

2016-01-01

Examining how left-hemisphere brain tumors might impact both the microstructure of the corpus callosum (CC) as measured by fractional anisotropy (FA) values in diffusion tensor imaging (DTI) as well as cortical language lateralization measured with functional MRI (fMRI). fMRI tasks (phonemic fluency and verb generation) were performed in order to detect activation in Broca's and Wernicke's area. Twenty patients with left-hemisphere brain tumors were investigated. fMRI results were divided into left dominant (LD), right dominant (RD), or codominant (CD) for language function. DTI was performed to generate FA maps in the anterior and posterior CC. FA values were correlated with the degree of language dominance. Patients who were LD or RD for language in Broca's area had lower FA in the anterior CC than those who were CD for language (median for CD = .72, LD = .66, RD = .65, P < .09). Lateralized versus CD group level analysis also showed that CD patients had higher FA in the anterior CC than patients who displayed strong lateralization in either hemisphere (median for CD = .72, lateralized = .65, P < .05). Our preliminary observations indicate that the greater FA in CD patients may reflect a more directional microstructure for the CC in this region, suggesting a greater need for interhemispheric transfer of information. Because brain tumors can cause compensatory codominance, our findings may suggest a mechanism by which interhemispheric transfer is facilitated during plasticity in the presence of a tumor. Copyright © 2015 by the American Society of Neuroimaging.

A YAC contig of the human CC chemokine genes clustered on chromosome 17q11.2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naruse, Kuniko; Nomiyama, Hisayuki; Miura, Retsu

1996-06-01

CC chemokines are cytokines that attract and activate leukocytes. The human genes for the CC chemokines are clustered on chromosome 17. To elucidate the genomic organization of the CC chemokine genes, we constructed a YAC contig comprising 34 clones. The contig was shown to contain all 10 CC chemokine genes reported so far, except for one gene whose nucleotide sequence is not available. The contig also contains 4 CC chemokine-like genes, which were deposited in GenBank as ESTs and are here referred to as NCC-1, NCC-2, NCC-3, and NCC-4. Within the contig, the CC chemokine genes were localized in twomore » regions. In addition, the CC chemokine genes were localized in two regions. In addition, the CC chemokine genes were more precisely mapped on chromosome 17q11.2 using a somatic cell hybrid cell DNA panel containing various portions of human chromosome 17. Interestingly, a reciprocal translocation t(Y;17) breakpoint, contained in the hybrid cell line Y1741, lay between the two chromosome 17 chemokine gene regions covered by our YAC contig. From these results, the order and the orientation of CC chemokine genes on chromosome 17 were determined as follows: centromere-neurofibromatosis 1-(MCP-3, MCP-1, NCC-1, I-309)-Y1741 breakpoint-RANTES-(LD78{gamma}, AT744.2, LD78{beta})-(NCC-3, NCC-2, AT744.1, LD78{alpha})-NCC-4-retinoic acid receptor {alpha}-telomere. 22 refs., 1 fig., 2 tabs.« less

Comparative study of the fungicide Benomyl toxicity on some plant growth promoting bacteria and some fungi in pure cultures.

PubMed

Elslahi, Randa H; Osman, Awad G; Sherif, Ashraf M; Elhussein, Adil A

2014-03-01

Six laboratory experiments were carried out to investigate the effect of the fungicide Benomyl on pure cultures of some plant growth promoting bacteria (PGPB) and some fungi. The highest LD50 was recorded for Bacillus circulans and proved to be the most resistant to the fungicide, followed by Azospirillum braziliense, while Penicillium sp. was the most affected microorganism. LD50 values for the affected microorganisms were in 21-240 orders of magnitude lower in comparison with the LD50 value for Azospirillum braziliense. The results indicate a strong selectivity for Benomyl against Rhizobium meliloti and Penicillium sp. when compared to other microorganisms tested. The highest safety coefficient was recorded for Bacillus circulans followed by Azospirillum braziliense, while Rhizobium meliloti, showed the lowest safety coefficient value compared to other bacteria. The lowest toxicity index was recorded for Bacillus circulans and Azospirillum braziliense. The slope of the curves for Bacillus sp. and Rhizobium meliloti was steeper than that of the other curves, suggesting that even a slight increase of the dose of the fungicide can cause a very strong negative effect. In conclusion, Benomyl could be applied without restriction when using inocula based on growth promoting bacteria such as symbiotic nitrogen fixers (Rhizobium meliloti), non-symbiotic nitrogen fixers (Azospirillum braziliense) or potassium solibilizers (Bacillus circulans), given that the fungicide is applied within the range of the recommended field dose.

Activity-rest stimulation protocol improves cardiac assistance in dynamic cardiomyoplasty.

PubMed

Rigatelli, Gianluca; Carraro, Ugo; Barbiero, Mario; Zanchetta, Mario; Dimopoulos, Konstantinos; Cobelli, Franco; Riccardi, Riccardo; Rigatelli, Giorgio

2002-03-01

No data have ever been published regarding cardiac assistance in demand dynamic cardiomyoplasty (DDCMP). We tested the efficacy of the Doppler flow wire in measuring beat-to-beat aortic flow velocity and evaluating cardiac assistance in demand cardiomyoplasty patients. The technique was tested in seven patients (M/F=6/1; age=57.1+/-6.2 years; atrial fibrillation/sinus rhythm=1/6; NYHA=1.4+/-0.5). Measurements were done using a 0.018inch peripheral Doppler flow wire advanced through a 5F arterial femoral sheath. Three 1-min periods with the stimulator off and three 1-min periods with clinical stimulation were recorded. We measured peak aortic flow velocity in all beats. Latissimus dorsi (LD) mechanogram was simultaneously recorded. Comparison between pre-operative and follow-up data showed significantly higher values of tetanic fusion frequency (TFF) and ejection fraction at follow-up, whereas mean NYHA class was significantly lower. Statistical analysis showed an increase in aortic flow velocity not only in assisted versus rest period, but also in assisted versus unassisted beats (8.42+/-6.98% and 7.55+/-3.07%). A linear correlation was found between the increase in flow velocity and LD wrap TFF (r(2)=0.53). In DDCMP, systolic assistance is significant and correlated to LD speed of contraction; demand stimulation protocol maintains muscle properties and increases muscle performance.

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

PubMed Central

Brorsson, C.; Hansen, N. T.; Lage, K.; Bergholdt, R.; Brunak, S.; Pociot, F.

2009-01-01

Aim To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)-DRB1, -DQA1, -DQB1 genes. Methods We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein–protein interaction (ppi) networks to identify disease-associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein modules were statistically evaluated using permutation. Results A total of 151 genes could be mapped to nodes within the protein interaction network and their interaction partners were identified. Five protein interaction modules reached statistical significance using this approach. The identified proteins are well known in the pathogenesis of T1D, but the modules also contain additional candidates that have been implicated in β-cell development and diabetic complications. Conclusions The extensive LD within the MHC region makes it important to develop new methods for analysing genotyping data for identification of additional risk genes for T1D. Combining genetic data with knowledge about functional pathways provides new insight into mechanisms underlying T1D. PMID:19143816

Comparison of 3.0 T magnetic resonance imaging and X-ray mammography in the measurement of ductal carcinoma in situ: a comparison with histopathology.

PubMed

Pickles, Martin D; Gibbs, Peter; Hubbard, Anne; Rahman, Ayesha; Wieczorek, Joanna; Turnbull, Lindsay W

2015-04-01

To determine if MRI data obtained at 3.0 T can more accurately report the size of DCIS as compared to radiographic mammography, as a whole cohort and when subdivided by lesion characteristics. Thirty-nine participants underwent X-ray mammography and MRI prior to breast surgery for DCIS. Longest diameter (LD) measurements were recorded for each imaging modality and compared to histopathological LD via a logarithmic transformed Bland-Altman agreement plot methodology resulting in dimensionless mean difference and 95% limits of agreement (LoA). Data from 39 patients with a median age of 55 years (range 38-78 years) underwent analysis. Mastectomy was undertaken in 21 cases, while breast conserving surgery was performed in 18 subjects. Histopathological analysis revealed one low grade, nine intermediate grade, and 21 high grade lesions. The mean±standard deviation LD measurements for histopathology, X-ray mammography and MRI were 50.6±34.2 mm, 30.7±23.1 mm and 49.6±26.8 mm respectively. Bland-Altman agreement plot analysis for the whole cohort revealed not only a smaller logarithmic mean difference between MRI and histopathology (0.086), but also narrower 95% LoA (-0.941 to 1.113) compared with X-ray mammography and histopathology (mean difference -0.658, 95% LoA -3.503 to 2.187). When the level of agreement was assessed between clinically relevant subgroups additional significant differences were noted based on grade, hormonal receptor status, invasion, necrosis, mircocalcifications and growth pattern. MRI provides a more accurate estimation of DCIS size than X-ray mammography. MRI's superior ability was not only noted in general, but also for clinical relevant subdivisions such as grade and the presence or absence of necrosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

β-Propeller Blades as Ancestral Peptides in Protein Evolution

PubMed Central

Kopec, Klaus O.; Lupas, Andrei N.

2013-01-01

Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world. PMID:24143202

Heterologous co-expression of a yeast diacylglycerol acyltransferase (ScDGA1) and a plant oleosin (AtOLEO3) as an efficient tool for enhancing triacylglycerol accumulation in the marine diatom Phaeodactylum tricornutum.

PubMed

Zulu, Nodumo Nokulunga; Popko, Jennifer; Zienkiewicz, Krzysztof; Tarazona, Pablo; Herrfurth, Cornelia; Feussner, Ivo

2017-01-01

Microalgae are promising alternate and renewable sources for producing valuable products such as biofuel and essential fatty acids. Although this is the case, there are still challenges impeding on the effective commercial production of microalgal products. For instance, their product yield is still too low. Therefore, this study was oriented towards enhancing triacylglycerol (TAG) accumulation in the diatom Phaeodactylum tricornutum (strain Pt4). To achieve this, a type 2 acyl-CoA:diacylglycerol acyltransferase from yeast ( ScDGA1 ) and the lipid droplet (LD) stabilizing oleosin protein 3 from Arabidopsis thaliana ( AtOLEO3 ) were expressed in Pt4. The individual expression of ScDGA1 and AtOLEO3 in Pt4 resulted in a 2.3- and 1.4-fold increase in TAG levels, respectively, in comparison to the wild type. The co-expression of both, ScDGA1 and AtOLEO3 , was accompanied by a 3.6-fold increase in TAG content. On the cellular level, the lines co-expressing ScDGA1 and AtOLEO3 showed the presence of the larger and increased numbers of lipid droplets when compared to transformants expressing single genes and an empty vector. Under nitrogen stress, TAG productivity was further increased twofold in comparison to nitrogen-replete conditions. While TAG accumulation was enhanced in the analyzed transformants, the fatty acid composition remained unchanged neither in the total lipid nor in the TAG profile. The co-expression of two genes was shown to be a more effective strategy for enhancing TAG accumulation in P. tricornutum strain Pt4 than a single gene strategy. For the first time in a diatom, a LD protein from a vascular plant, oleosin, was shown to have an impact on TAG accumulation and on LD organization.

Comparison of low density and high density pedicle screw instrumentation in Lenke 1 adolescent idiopathic scoliosis.

PubMed

Shen, Mingkui; Jiang, Honghui; Luo, Ming; Wang, Wengang; Li, Ning; Wang, Lulu; Xia, Lei

2017-08-02

The correlation between implant density and deformity correction has not yet led to a precise conclusion in adolescent idiopathic scoliosis (AIS). The aim of this study was to evaluate the effects of low density (LD) and high density (HD) pedicle screw instrumentation in terms of the clinical, radiological and Scoliosis Research Society (SRS)-22 outcomes in Lenke 1 AIS. We retrospectively reviewed 62 consecutive Lenke 1 AIS patients who underwent posterior spinal arthrodesis using all-pedicle screw instrumentation with a minimum follow-up of 24 months. The implant density was defined as the number of screws per spinal level fused. Patients were then divided into two groups according to the average implant density for the entire study. The LD group (n = 28) had fewer than 1.61 screws per level, while the HD group (n = 34) had more than 1.61 screws per level. The radiographs were analysed preoperatively, postoperatively and at final follow-up. The perioperative and SRS-22 outcomes were also assessed. Independent sample t tests were used between the two groups. Comparisons between the two groups showed no significant differences in the correction of the main thoracic curve and thoracic kyphosis, blood transfusion, hospital stay, and SRS-22 scores. Compared with the HD group, there was a decreased operating time (278.4 vs. 331.0 min, p = 0.004) and decreased blood loss (823.6 vs. 1010.9 ml, p = 0.048), pedicle screws needed (15.1 vs. 19.6, p < 0.001), and implant costs ($10,191.0 vs. $13,577.3, p = 0.003) in the LD group. Both low density and high density pedicle screw instrumentation achieved satisfactory deformity correction in Lenke 1 AIS patients. However, the operating time and blood loss were reduced, and the implant costs were decreased with the use of low screw density constructs.

Global, broad, or specific cognitive differences? Using a MIMIC model to examine differences in CHC abilities in children with learning disabilities.

PubMed

Niileksela, Christopher R; Reynolds, Matthew R

2014-01-01

This study was designed to better understand the relations between learning disabilities and different levels of latent cognitive abilities, including general intelligence (g), broad cognitive abilities, and specific abilities based on the Cattell-Horn-Carroll theory of intelligence (CHC theory). Data from the Differential Ability Scales-Second Edition (DAS-II) were used to create a multiple-indicator multiple cause model to examine the latent mean differences in cognitive abilities between children with and without learning disabilities in reading (LD reading), math (LD math), and reading and writing(LD reading and writing). Statistically significant differences were found in the g factor between the norm group and the LD groups. After controlling for differences in g, the LD reading and LD reading and writing groups showed relatively lower latent processing speed, and the LD math group showed relatively higher latent comprehension-knowledge. There were also some differences in some specific cognitive abilities, including lower scores in spatial relations and numerical facility for the LD math group, and lower scores in visual memory for the LD reading and writing group. These specific mean differences were above and beyond any differences in the latent cognitive factor means.

Novel Small-Molecule Antibacterial Agents

DTIC Science & Technology

2014-07-01

post-exposure protection of mice against 5 LD50 BoNTA. HAB also showed significant 4-hour-post-exposure protection of zebrafish against 5 LD50 BoNTA...protection of mice against 5 LD50 BoNTA. HAB also showed significant 4-hour-post-exposure protection of zebrafish against 5 LD50 BoNTA. Our kinetics...significant 4-hour-post-exposure protection of zebrafish against 5 LD50 BoNTA. Our kinetics and affinity analyses using the surface plasmon resonance

Genetic Validation of Leishmania donovani Lysyl-tRNA Synthetase Shows that It Is Indispensable for Parasite Growth and Infectivity

PubMed Central

Chadha, Sanya; Mallampudi, N. Arjunreddy; Mohapatra, Debendra K.

2017-01-01

ABSTRACT Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis. Increasing resistance and severe side effects of existing drugs have led to the need to identify new chemotherapeutic targets. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and are required for protein synthesis. aaRSs are known drug targets for bacterial and fungal pathogens. Here, we have characterized and evaluated the essentiality of L. donovani lysyl-tRNA synthetase (LdLysRS). Two different coding sequences for lysyl-tRNA synthetases are annotated in the Leishmania genome database. LdLysRS-1 (LdBPK_150270.1), located on chromosome 15, is closer to apicomplexans and eukaryotes, whereas LdLysRS-2 (LdBPK_300130.1), present on chromosome 30, is closer to bacteria. In the present study, we have characterized LdLysRS-1. Recombinant LdLysRS-1 displayed aminoacylation activity, and the protein localized to the cytosol. The LdLysRS-1 heterozygous mutants had a restrictive growth phenotype and attenuated infectivity. LdLysRS-1 appears to be an essential gene, as a chromosomal knockout of LdLysRS-1 could be generated when the gene was provided on a rescuing plasmid. Cladosporin, a fungal secondary metabolite and a known inhibitor of LysRS, was more potent against promastigotes (50% inhibitory concentration [IC50], 4.19 µM) and intracellular amastigotes (IC50, 1.09 µM) than were isomers of cladosporin (3-epi-isocladosporin and isocladosporin). These compounds exhibited low toxicity to mammalian cells. The specificity of inhibition of parasite growth caused by these inhibitors was further assessed using LdLysRS-1 heterozygous mutant strains and rescue mutant promastigotes. These inhibitors inhibited the aminoacylation activity of recombinant LdLysRS. Our data provide a framework for the development of a new class of drugs against this parasite. IMPORTANCE Aminoacyl-tRNA synthetases are housekeeping enzymes essential for protein translation, providing charged tRNAs for the proper construction of peptide chains. These enzymes provide raw materials for protein translation and also ensure fidelity of translation. L. donovani is a protozoan parasite that causes visceral leishmaniasis. It is a continuously proliferating parasite that depends heavily on efficient protein translation. Lysyl-tRNA synthetase is one of the aaRSs which charges lysine to its cognate tRNA. Two different coding sequences for lysyl-tRNA synthetases (LdLysRS) are present in this parasite. LdLysRS-1 is closer to apicomplexans and eukaryotes, whereas LdLysRS-2 is closer to bacteria. Here, we have characterized LdLysRS-1 of L. donovani. LdLysRS-1 appears to be an essential gene, as the chromosomal null mutants did not survive. The heterozygous mutants showed slower growth kinetics and exhibited attenuated virulence. This study also provides a platform to explore LdLysRS-1 as a potential drug target. PMID:28875178

Genetic Validation of Leishmania donovani Lysyl-tRNA Synthetase Shows that It Is Indispensable for Parasite Growth and Infectivity.

PubMed

Chadha, Sanya; Mallampudi, N Arjunreddy; Mohapatra, Debendra K; Madhubala, Rentala

2017-01-01

Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis. Increasing resistance and severe side effects of existing drugs have led to the need to identify new chemotherapeutic targets. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and are required for protein synthesis. aaRSs are known drug targets for bacterial and fungal pathogens. Here, we have characterized and evaluated the essentiality of L. donovani lysyl-tRNA synthetase ( Ld LysRS). Two different coding sequences for lysyl-tRNA synthetases are annotated in the Leishmania genome database. Ld LysRS-1 (LdBPK_150270.1), located on chromosome 15, is closer to apicomplexans and eukaryotes, whereas Ld LysRS-2 (LdBPK_300130.1), present on chromosome 30, is closer to bacteria. In the present study, we have characterized Ld LysRS-1. Recombinant Ld LysRS-1 displayed aminoacylation activity, and the protein localized to the cytosol. The Ld LysRS-1 heterozygous mutants had a restrictive growth phenotype and attenuated infectivity. Ld LysRS-1 appears to be an essential gene, as a chromosomal knockout of Ld LysRS-1 could be generated when the gene was provided on a rescuing plasmid. Cladosporin, a fungal secondary metabolite and a known inhibitor of LysRS, was more potent against promastigotes (50% inhibitory concentration [IC 50 ], 4.19 µM) and intracellular amastigotes (IC 50 , 1.09 µM) than were isomers of cladosporin (3-epi-isocladosporin and isocladosporin). These compounds exhibited low toxicity to mammalian cells. The specificity of inhibition of parasite growth caused by these inhibitors was further assessed using Ld LysRS-1 heterozygous mutant strains and rescue mutant promastigotes. These inhibitors inhibited the aminoacylation activity of recombinant Ld LysRS. Our data provide a framework for the development of a new class of drugs against this parasite. IMPORTANCE Aminoacyl-tRNA synthetases are housekeeping enzymes essential for protein translation, providing charged tRNAs for the proper construction of peptide chains. These enzymes provide raw materials for protein translation and also ensure fidelity of translation. L. donovani is a protozoan parasite that causes visceral leishmaniasis. It is a continuously proliferating parasite that depends heavily on efficient protein translation. Lysyl-tRNA synthetase is one of the aaRSs which charges lysine to its cognate tRNA. Two different coding sequences for lysyl-tRNA synthetases ( Ld LysRS) are present in this parasite. Ld LysRS-1 is closer to apicomplexans and eukaryotes, whereas Ld LysRS-2 is closer to bacteria. Here, we have characterized Ld LysRS-1 of L. donovani . Ld LysRS-1 appears to be an essential gene, as the chromosomal null mutants did not survive. The heterozygous mutants showed slower growth kinetics and exhibited attenuated virulence. This study also provides a platform to explore Ld LysRS-1 as a potential drug target.

Legionnaires' Disease Outbreak at a Resort in Cozumel, Mexico

PubMed Central

Hampton, Lee M.; Garrison, Laurel; Kattan, Jessica; Brown, Ellen; Kozak-Muiznieks, Natalia A.; Lucas, Claressa; Fields, Barry; Fitzpatrick, Nicole; Sapian, Luis; Martin-Escobar, Teresa; Waterman, Stephen; Hicks, Lauri A.; Alpuche-Aranda, Celia; Lopez-Gatell, Hugo

2016-01-01

Background. A Legionnaires' disease (LD) outbreak at a resort on Cozumel Island in Mexico was investigated by a joint Mexico-United States team in 2010. This is the first reported LD outbreak in Mexico, where LD is not a reportable disease. Methods. Reports of LD among travelers were solicited from US health departments and the European Working Group for Legionella Infections. Records from the resort and Cozumel Island health facilities were searched for possible LD cases. In April 2010, the resort was searched for possible Legionella exposure sources. The temperature and total chlorine of the water at 38 sites in the resort were measured, and samples from those sites were tested for Legionella. Results. Nine travelers became ill with laboratory-confirmed LD within 2 weeks of staying at the resort between May 2008 and April 2010. The resort and its potable water system were the only common exposures. No possible LD cases were identified among resort workers. Legionellae were found to have extensively colonized the resort's potable water system. Legionellae matching a case isolate were found in the resort's potable water system. Conclusions. Medical providers should test for LD when treating community-acquired pneumonia that is severe or affecting patients who traveled in the 2 weeks before the onset of symptoms. When an LD outbreak is detected, the source should be identified and then aggressively remediated. Because LD can occur in tropical and temperate areas, all countries should consider making LD a reportable disease if they have not already done so. PMID:27704023

Legionnaires' Disease Outbreak at a Resort in Cozumel, Mexico.

PubMed

Hampton, Lee M; Garrison, Laurel; Kattan, Jessica; Brown, Ellen; Kozak-Muiznieks, Natalia A; Lucas, Claressa; Fields, Barry; Fitzpatrick, Nicole; Sapian, Luis; Martin-Escobar, Teresa; Waterman, Stephen; Hicks, Lauri A; Alpuche-Aranda, Celia; Lopez-Gatell, Hugo

2016-09-01

Background.  A Legionnaires' disease (LD) outbreak at a resort on Cozumel Island in Mexico was investigated by a joint Mexico-United States team in 2010. This is the first reported LD outbreak in Mexico, where LD is not a reportable disease. Methods.  Reports of LD among travelers were solicited from US health departments and the European Working Group for Legionella Infections. Records from the resort and Cozumel Island health facilities were searched for possible LD cases. In April 2010, the resort was searched for possible Legionella exposure sources. The temperature and total chlorine of the water at 38 sites in the resort were measured, and samples from those sites were tested for Legionella . Results.  Nine travelers became ill with laboratory-confirmed LD within 2 weeks of staying at the resort between May 2008 and April 2010. The resort and its potable water system were the only common exposures. No possible LD cases were identified among resort workers. Legionellae were found to have extensively colonized the resort's potable water system. Legionellae matching a case isolate were found in the resort's potable water system. Conclusions.  Medical providers should test for LD when treating community-acquired pneumonia that is severe or affecting patients who traveled in the 2 weeks before the onset of symptoms. When an LD outbreak is detected, the source should be identified and then aggressively remediated. Because LD can occur in tropical and temperate areas, all countries should consider making LD a reportable disease if they have not already done so.

Post-hoc analysis showing better clinical response with the loading dose of certolizumab pegol in Japanese patients with active rheumatoid arthritis

PubMed Central

Takeuchi, Tsutomu; Yamamoto, Kazuhiko; Yamanaka, Hisashi; Ishiguro, Naoki; Tanaka, Yoshiya; Eguchi, Katsumi; Watanabe, Akira; Origasa, Hideki; Kobayashi, Mariko; Shoji, Toshiharu; Togo, Osamu; Miyasaka, Nobuyuki; Koike, Takao

2016-01-01

Abstract Objectives: To compare the efficacy and safety of certolizumab pegol (CZP) with and without loading dose (LD) in a post-hoc analysis of two Japanese clinical studies. Methods: Data from the double-blind trials (DBT) J-RAPID and HIKARI, and their open-label extension (OLE) studies, were used. Patients randomized to CZP 200 mg every 2 weeks (Q2W) groups starting with LD (400 mg Weeks 0/2/4; LD group; J-RAPID: n = 82, HIKARI: n = 116) and patients randomized to placebo groups who subsequently started CZP Q2W without LD in the OLEs (No-LD group; J-RAPID: n = 61, HIKARI: n = 99) were analyzed. Efficacy and pharmacokinetics were assessed during 24 weeks. Adverse events were reported from all studies. Results: In both trials, the LD groups showed more rapid initial ACR20/50/70 kinetics, and maintained higher ACR50/70 responses until 24 weeks, compared with the No-LD groups. Anti-CZP antibody development was less frequent in the LD groups (J-RAPID: 1.2% versus 4.9%; HIKARI: 17.2% versus 27.3%). Similar safety profiles were reported between LD and No-LD groups (any AEs: 281.8 versus 315.7 [J-RAPID], 282.6 versus 321.3 [HIKARI] [incidence rate/100 patient-years]). Conclusions: Despite limitations, including comparing DBT and OLE studies, these results suggest that a CZP LD improves clinical response in active rheumatoid arthritis without altering the safety profile. PMID:26472043

Differential Roles of Cell Death-inducing DNA Fragmentation Factor-α-like Effector (CIDE) Proteins in Promoting Lipid Droplet Fusion and Growth in Subpopulations of Hepatocytes*♦

PubMed Central

Xu, Wenyi; Wu, Lizhen; Yu, Miao; Chen, Feng-Jung; Arshad, Muhammad; Xia, Xiayu; Ren, Hao; Yu, Jinhai; Xu, Li; Xu, Dijin; Li, John Zhong; Li, Peng; Zhou, Linkang

2016-01-01

Lipid droplets (LDs) are dynamic subcellular organelles whose growth is closely linked to obesity and hepatic steatosis. Cell death-inducing DNA fragmentation factor-α-like effector (CIDE) proteins, including Cidea, Cideb, and Cidec (also called Fsp27), play important roles in lipid metabolism. Cidea and Cidec are LD-associated proteins that promote atypical LD fusion in adipocytes. Here, we find that CIDE proteins are all localized to LD-LD contact sites (LDCSs) and promote lipid transfer, LD fusion, and growth in hepatocytes. We have identified two types of hepatocytes, one with small LDs (small LD-containing hepatocytes, SLHs) and one with large LDs (large LD-containing hepatocytes, LLHs) in the liver. Cideb is localized to LDCSs and promotes lipid exchange and LD fusion in both SLHs and LLHs, whereas Cidea and Cidec are specifically localized to the LDCSs and promote lipid exchange and LD fusion in LLHs. Cideb-deficient SLHs have reduced LD sizes and lower lipid exchange activities. Fasting dramatically induces the expression of Cidea/Cidec and increases the percentage of LLHs in the liver. The majority of the hepatocytes from the liver of obese mice are Cidea/Cidec-positive LLHs. Knocking down Cidea or Cidec significantly reduced lipid storage in the livers of obese animals. Our data reveal that CIDE proteins play differential roles in promoting LD fusion and lipid storage; Cideb promotes lipid storage under normal diet conditions, whereas Cidea and Cidec are responsible for liver steatosis under fasting and obese conditions. PMID:26733203

Fast and Accurate Approximation to Significance Tests in Genome-Wide Association Studies

PubMed Central

Zhang, Yu; Liu, Jun S.

2011-01-01

Genome-wide association studies commonly involve simultaneous tests of millions of single nucleotide polymorphisms (SNP) for disease association. The SNPs in nearby genomic regions, however, are often highly correlated due to linkage disequilibrium (LD, a genetic term for correlation). Simple Bonferonni correction for multiple comparisons is therefore too conservative. Permutation tests, which are often employed in practice, are both computationally expensive for genome-wide studies and limited in their scopes. We present an accurate and computationally efficient method, based on Poisson de-clumping heuristics, for approximating genome-wide significance of SNP associations. Compared with permutation tests and other multiple comparison adjustment approaches, our method computes the most accurate and robust p-value adjustments for millions of correlated comparisons within seconds. We demonstrate analytically that the accuracy and the efficiency of our method are nearly independent of the sample size, the number of SNPs, and the scale of p-values to be adjusted. In addition, our method can be easily adopted to estimate false discovery rate. When applied to genome-wide SNP datasets, we observed highly variable p-value adjustment results evaluated from different genomic regions. The variation in adjustments along the genome, however, are well conserved between the European and the African populations. The p-value adjustments are significantly correlated with LD among SNPs, recombination rates, and SNP densities. Given the large variability of sequence features in the genome, we further discuss a novel approach of using SNP-specific (local) thresholds to detect genome-wide significant associations. This article has supplementary material online. PMID:22140288

Cytotoxic activity of plants of family zygophyllaceae and euphorbiaceae.

PubMed

Dastagir, Ghulam; Hussain, Farrukh

2014-07-01

The methanolic and n-hexane extracts of studied plants showed significant toxicity to brine shrimps. The methanolic extract of Fagonia cretica had highest LD50 (117.72) value, while Peganum harmala showed low LD50 value (41.70) compared to n-hexane extract. The methanolic and n-hexane extracts of Tribulus terrestris showed similar LD50 values. The methanolic extract of Chrozophora tinctoria showed low LD50 value than the n-hexane extract. The methanolic extract of Ricinus communis showed highest LD50 value while the n-hexane extract showed lowest LD50 value. The LD50 value less than 100 was obtained for n-hexane extracts of Fagonia cretica, Peganum harmala and Ricinus communis. The n-hexane extracts of these plants also showed the highest toxicity as compare to methanolic extracts. The chemical constituents detected in the present investigation might be responsible for cytotoxic activity.

7 CFR 1737.32 - Loan Design (LD).

Code of Federal Regulations, 2012 CFR

2012-01-01

... Studies-Area Coverage Survey and Loan Design § 1737.32 Loan Design (LD). (a) A loan application requires supporting data collectively called a “Loan Design.” The LD contains a forecast of service requirements and a... 7 Agriculture 11 2012-01-01 2012-01-01 false Loan Design (LD). 1737.32 Section 1737.32 Agriculture...

7 CFR 1737.32 - Loan Design (LD).

Code of Federal Regulations, 2013 CFR

2013-01-01

... Studies-Area Coverage Survey and Loan Design § 1737.32 Loan Design (LD). (a) A loan application requires supporting data collectively called a “Loan Design.” The LD contains a forecast of service requirements and a... 7 Agriculture 11 2013-01-01 2013-01-01 false Loan Design (LD). 1737.32 Section 1737.32 Agriculture...

7 CFR 1737.32 - Loan Design (LD).

Code of Federal Regulations, 2010 CFR

2010-01-01

... Studies-Area Coverage Survey and Loan Design § 1737.32 Loan Design (LD). (a) A loan application requires supporting data collectively called a “Loan Design.” The LD contains a forecast of service requirements and a... 7 Agriculture 11 2010-01-01 2010-01-01 false Loan Design (LD). 1737.32 Section 1737.32 Agriculture...

7 CFR 1737.32 - Loan Design (LD).

Code of Federal Regulations, 2011 CFR

2011-01-01

... Studies-Area Coverage Survey and Loan Design § 1737.32 Loan Design (LD). (a) A loan application requires supporting data collectively called a “Loan Design.” The LD contains a forecast of service requirements and a... 7 Agriculture 11 2011-01-01 2011-01-01 false Loan Design (LD). 1737.32 Section 1737.32 Agriculture...

7 CFR 1737.32 - Loan Design (LD).

Code of Federal Regulations, 2014 CFR

2014-01-01

... Studies-Area Coverage Survey and Loan Design § 1737.32 Loan Design (LD). (a) A loan application requires supporting data collectively called a “Loan Design.” The LD contains a forecast of service requirements and a... 7 Agriculture 11 2014-01-01 2014-01-01 false Loan Design (LD). 1737.32 Section 1737.32 Agriculture...

Effect of CAI on Achievement of LD Students in English

ERIC Educational Resources Information Center

Sivaram, R. T.; Ramar, R.

2014-01-01

The present experimental study was undertaken with three objectives in view, (i) to identify students with language learning disabilities (ii) to develop CAI software to teach LD students through computer-assisted instruction and (iii) to measure the effectiveness of CAI with special reference to LD students. Two matched groups of LD students were…

Experimental investigation of flow characteristics around four square-cylinder arrays at subcritical Reynolds numbers

NASA Astrophysics Data System (ADS)

Liu, Mingyue; Xiao, Longfei; Yang, Lijun

2015-09-01

The Deep Draft Semi-Submersible (DDS) concepts are known for their favourable vertical motion performance. However, the DDS may experience critical Vortex-Induced Motion (VIM) stemming from the fluctuating forces on the columns. In order to investigate the current-induced excitation forces of VIM, an experimental study of flow characteristics around four square-section cylinders in a square configuration is presented. A number of column spacing ratios and array attack angles were considered to investigate the parametric influences. The results comprise flow patterns, drag and lift forces, as well as Strouhal numbers. It is shown that both the drag and lift forces acting on the cylinders are slightly different between the various L/D values, and the fluctuating forces peak at L/D = 4.14. The lift force of downstream cylinders reaches its maximum at around α = 15°. Furthermore, the flow around circular-section-cylinder arrays is also discussed in comparison with that of square cylinders.

Comparative investigation of Umbellularia californica and Laurus nobilis leaf essential oils and identification of constituents active against Aedes aegypti.

PubMed

Tabanca, Nurhayat; Avonto, Cristina; Wang, Mei; Parcher, Jon F; Ali, Abbas; Demirci, Betul; Raman, Vijayasankar; Khan, Ikhlas A

2013-12-18

Umbellularia californica (California bay laurel) and Laurus nobilis (Mediterranean bay laurel) leaves may be mistaken or used as a substitute on the market due to their morphological similarity. In this study, a comparison of anatomical and chemical features and biological activity of both plants is presented. L. nobilis essential oil biting deterrent and larvicidal activity were negligible. On the other hand, U. californica leaf oil showed biting deterrent activity against Aedes aegypti . The identified active repellents was thymol, along with (-)-umbellulone, 1,8-cineole, and (-)-α-terpineol. U. californica essential oil also demonstrated good larvicidal activity against 1-day-old Ae. aegypti larvae with a LD50 value of 52.6 ppm. Thymol (LD50 = 17.6 ppm), p-cymene, (-)-umbellulone, and methyleugenol were the primary larvicidal in this oil. Umbellulone was found as the principal compound (37%) of U. californica essential oil, but was not present in L. nobilis essential oil. Umbellulone mosquito activity is here reported for the first time.

Muscle fibre characteristics, enzyme activity and meat colour of wild boar (Sus scrofa s. L.) muscle with 2n=36 compared to those of phenotypically similar crossbreeds (2n=37 and 2n=38).

PubMed

Skewes, Oscar; Cádiz, Patricia; Merino, Victoria; Islas, Armando; Morales, Rodrigo

2014-10-01

The aim of the present study was to evaluate European wild boar (Sus scrofa s. L.) of chromosomal number 2n=36 in comparison with phenotypically similar crossbreeds (2n=37 and 2n=38) with respect to the muscle fibre characteristics and enzyme activity as well as meat colour in the longissimus dorsi (LD) and semimembranosus (SM) muscles. Differences in the proportion of IIA fibre in the LD muscle between karyotypes 2n=37 and 2n=38 were found. The 2n=36 group showed a lower muscle fibre cross-section area than the 2n=38 karyotype. The meat colour of the 2n=36 karyotype group was redder than 2n=37 and 2n=38. The muscle fibre cross-section area might explain the differences in colour of the meat of wild boar. Copyright © 2014 Elsevier Ltd. All rights reserved.

Anti-cobra venom activity of plant Andrographis paniculata and its comparison with polyvalent anti-snake venom

PubMed Central

Premendran, S. Jhon; Salwe, Kartik J.; Pathak, Swanand; Brahmane, Ranjana; Manimekalai, K.

2011-01-01

Background: To investigate the anti-cobra venom effect of alcoholic extract of Andrographis paniculata. Materials and Methods: After calculating the LD99 of snake venom, the venom-neutralizing ability of plant extract at the dose 1 g/kg and 2 g/kg was determined using in vitro and in vivo methods. The alleviation in the mean survival time of the animals were used to infer the antivenom property of the drug after challenging with LD99 of snake venom. Results: The ethanolic extract of plant A. paniculata significantly increases mean survival time and the protection fold, but could not protect animals from death when used alone. The higher dose, i.e., 2 g/kg was found better than that of the lower. ASV was found more effective than the plant extract. When ASV was given along with plant extract, it potentiates its effect. Conclusion: The observation demonstrates the anti-cobra venom activity of ethanolic extract of A. paniculata which is comparable with ASV. PMID:22346236

Aerogenic vaccination with a Burkholderia mallei auxotroph protects against aerosol-initiated glanders in mice.

PubMed

Ulrich, Ricky L; Amemiya, Kei; Waag, David M; Roy, Chad J; DeShazer, David

2005-03-14

Burkholderia mallei is an obligate mammalian pathogen that causes the zoonotic disease glanders. Two live attenuated B. mallei strains, a capsule mutant and a branched-chain amino acid auxotroph, were evaluated for use as vaccines against aerosol-initiated glanders in mice. Animals were aerogenically vaccinated and serum samples were obtained before aerosol challenge with a high-dose (>300 times the LD50) of B. mallei ATCC 23344. Mice vaccinated with the capsule mutant developed a Th2-like Ig subclass antibody response and none survived beyond 5 days. In comparison, the auxotrophic mutant elicited a Th1-like Ig subclass antibody response and 25% of the animals survived for 1 month postchallenge. After a low-dose (5 times the LD50) aerosol challenge, the survival rates of auxotroph-vaccinated and unvaccinated animals were 50 and 0%, respectively. Thus, live attenuated strains that promote a Th1-like Ig response may serve as promising vaccine candidates against aerosol infection with B. mallei.

Measuring lexical diversity in narrative discourse of people with aphasia.

PubMed

Fergadiotis, Gerasimos; Wright, Heather H; West, Thomas M

2013-05-01

A microlinguistic content analysis for assessing lexical semantics in people with aphasia (PWA) is lexical diversity (LD). Sophisticated techniques have been developed to measure LD. However, validity evidence for these methodologies when applied to the discourse of PWA is lacking. The purpose of this study was to evaluate four measures of LD to determine how effective they were at measuring LD in PWA. Four measures of LD were applied to short discourse samples produced by 101 PWA: (a) the Measure of Textual Lexical Diversity (MTLD; McCarthy, 2005), (b) the Moving-Average Type-Token Ratio (MATTR; Covington, 2007), (c) D (McKee, Malvern, & Richards, 2000), and (d) the Hypergeometric Distribution (HD-D; McCarthy & Jarvis, 2007). LD was estimated using each method, and the scores were subjected to a series of analyses (e.g., curve-fitting, analysis of variance, confirmatory factor analysis). Results from the confirmatory factor analysis suggested that MTLD and MATTR reflect LD and little of anything else. Further, two indices (HD-D and D) were found to be equivalent, suggesting that either one can be used when samples are >50 tokens. MTLD and MATTR yielded the strongest evidence for producing unbiased LD scores, suggesting that they may be the best measures for capturing LD in PWA.

Prospective evaluation of RT-PCR on sputum versus culture, urinary antigens and serology for Legionnaire's disease diagnosis.

PubMed

Botelho-Nevers, Elisabeth; Grattard, Florence; Viallon, Alain; Allegra, Séverine; Jarraud, Sophie; Verhoeven, Paul; Marcuccilli, Adrien; Lucht, Fréderic; Pozzetto, Bruno; Berthelot, Philippe

2016-08-01

Legionnaires' disease (LD) is a severe disease associated with community and hospital-acquired pneumonia, frequently under diagnosed. The main aim of our study was to determine the value of PCR for the diagnosis of LD in routine clinical practice. In a prospective study, from March 2007 to April 2010, the value of PCR on non-invasive respiratory specimens (NIRS) was compared to those of the other available tools for LD diagnosis in patients hospitalized for pneumonia. Among 254 consecutive cases of pneumonia included, 24 cases were LD (19 confirmed and 5 probable) representing the first documented microbiological etiology. Molecular diagnosis of LD was performed on NIRS by using 16S rRNA PCR, and secondarily mip PCR, with no discrepant results between the 2 methods: it was found positive in 14 cases and led to identify 2 supplementary probable cases of LD. Based on clinical and at least 2 positive LD tests, PCR yielded a better diagnostic value than antigen urinary test (12 vs 10 cases). These results revealed that molecular diagnosis of LD on NIRS is reliable and may contribute to better identify cases of LD. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Improved Bioavailability of Levodopa Using Floatable Spray-Coated Microcapsules for the Management of Parkinson's Disease.

PubMed

Baek, Jong-Suep; Tee, Jie Kai; Pang, Yi Yun; Tan, Ern Yu; Lim, Kah Leong; Ho, Han Kiat; Loo, Say Chye Joachim

2018-06-01

Oral administration of levodopa (LD) is the gold standard in managing Parkinson's disease (PD). Although LD is the most effective drug in treating PD, chronic administration of LD induces levodopa-induced dyskinesia. A continuous and sustained provision of LD to the brain could, therefore, reduce peak-dose dyskinesia. In commercial oral formulations, LD is co-administrated with an AADC inhibitor (carbidopa) and a COMT inhibitor (entacapone) to enhance its bioavailability. Nevertheless, patients are known to take up to five tablets a day because of poor sustained-releasing capabilities that lead to fluctuations in plasma concentrations. To achieve a prolonged release of LD with the aim of improving its bioavailability, floatable spray-coated microcapsules containing all three PD drugs were developed. This gastro-retentive delivery system showed sustained release of all PD drugs, at similar release kinetics. Pharmacokinetics study was conducted and this newly developed formulation showed a more plateaued delivery of LD that is void of the plasma concentration fluctuations observed for the control (commercial formulation). At the same time, measurements of LD and dopamine of mice administered with this formulation showed enhanced bioavailability of LD. This study highlights a floatable, sustained-releasing delivery system in achieving improved pharmacokinetics data compared to a commercial formulation.

Quantitative Analysis of Lipid Droplet Fusion: Inefficient Steady State Fusion but Rapid Stimulation by Chemical Fusogens

PubMed Central

Murphy, Samantha; Martin, Sally; Parton, Robert G.

2010-01-01

Lipid droplets (LDs) are dynamic cytoplasmic organelles containing neutral lipids and bounded by a phospholipid monolayer. Previous studies have suggested that LDs can undergo constitutive homotypic fusion, a process linked to the inhibitory effects of fatty acids on glucose transporter trafficking. Using strict quantitative criteria for LD fusion together with refined light microscopic methods and real-time analysis, we now show that LDs in diverse cell types show low constitutive fusogenic activity under normal growth conditions. To investigate the possible modulation of LD fusion, we screened for agents that can trigger fusion. A number of pharmacological agents caused homotypic fusion of lipid droplets in a variety of cell types. This provided a novel cell system to study rapid regulated fusion between homotypic phospholipid monolayers. LD fusion involved an initial step in which the two adjacent membranes became continuous (<10 s), followed by the slower merging (100 s) of the neutral lipid cores to produce a single spherical LD. These fusion events were accompanied by changes to the LD surface organization. Measurements of LDs undergoing homotypic fusion showed that fused LDs maintained their initial volume, with a corresponding decrease in surface area suggesting rapid removal of membrane from the fused LD. This study provides estimates for the level of constitutive LD fusion in cells and questions the role of LD fusion in vivo. In addition, it highlights the extent of LD restructuring which occurs when homotypic LD fusion is triggered in a variety of cell types. PMID:21203462

Risk factors of learning disabilities in Chinese children in Wuhan.

PubMed

Yao, Bin; Wu, Han-Rong

2003-12-01

To investigate prevalence rate of learning disabilities (LD) in Chinese children, and to explore related risk factors, and to provide theoretical basis for preventing such disabilities. One thousand and one hundred fifty one children were randomly selected in primary schools. According to criteria set by ICD-10, 118 children diagnosed as LD were classified into the study group. Four hundred and ninety one children were classified into the normal control group. Five hundred and forty two children were classified into the excellent control group. The study instruments included PRS (The pupil rating scale revised screening for learning disabilities), Conners' children behavior check-list taken by parents and YG-WR character check-list. The prevalence rate of LD in Chinese children was 10.3%. Significant differences were observed between LD and normally learning children, and between the LD group and the excellent group, in terms of scores of Conners' behavior check-list (P < 0.05). The study further showed that individual differences in character between the LD group and the control groups still existed even after controlling individual differences in age, IQ, and gender. Some possible causal explanations contributing to LD were improper teaching by parents, low educational level of the parents, and children's characteristics and social relationships. These data underscore the fact that LD is a serious national public health problem in China. LD is resulted from a number of factors. Good studying and living environments should be created for LD children.

The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes.

PubMed

Porto-Neto, Laercio R; Kijas, James W; Reverter, Antonio

2014-03-24

The extent of linkage disequilibrium (LD) between molecular markers impacts genome-wide association studies and implementation of genomic selection. The availability of high-density single nucleotide polymorphism (SNP) genotyping platforms makes it possible to investigate LD at an unprecedented resolution. In this work, we characterised LD decay in breeds of beef cattle of taurine, indicine and composite origins and explored its variation across autosomes and the X chromosome. In each breed, LD decayed rapidly and r2 was less than 0.2 for marker pairs separated by 50 kb. The LD decay curves clustered into three groups of similar LD decay that distinguished the three main cattle types. At short distances between markers (<10 kb), taurine breeds showed higher LD (r2=0.45) than their indicine (r2=0.25) and composite (r2=0.32) counterparts. This higher LD in taurine breeds was attributed to a smaller effective population size and a stronger bottleneck during breed formation. Using all SNPs on only the X chromosome, the three cattle types could still be distinguished. However for taurine breeds, the LD decay on the X chromosome was much faster and the background level much lower than for indicine breeds and composite populations. When using only SNPs that were polymorphic in all breeds, the analysis of the X chromosome mimicked that of the autosomes. The pattern of LD mirrored some aspects of the history of breed populations and showed a sharp decay with increasing physical distance between markers. We conclude that the availability of the HD chip can be used to detect association signals that remained hidden when using lower density genotyping platforms, since LD dropped below 0.2 at distances of 50 kb.

Physiological roles of trehalose in Leptinotarsa larvae revealed by RNA interference of trehalose-6-phosphate synthase and trehalase genes.

PubMed

Shi, Ji-Feng; Xu, Qing-Yu; Sun, Qiang-Kun; Meng, Qing-Wei; Mu, Li-Li; Guo, Wen-Chao; Li, Guo-Qing

2016-10-01

Trehalose is proposed to serve multiple physiological roles in insects. However, its importance remains largely unconfirmed. In the present paper, we knocked down either a trehalose biosynthesis gene (trehalose-6-phosphate synthase, LdTPS) or each of three degradation genes (soluble trehalases LdTRE1a, LdTRE1b or membrane-bound LdTRE2) in Leptinotarsa decemlineata by RNA interference (RNAi). Knockdown of LdTPS decreased trehalose content and caused larval and pupal lethality. The LdTPS RNAi survivors consumed a greater amount of foliage, obtained a heavier body mass, accumulated more glycogen, lipid and proline, and had a smaller amount of chitin compared with the controls. Ingestion of trehalose but not glucose rescued the food consumption increase and larval mass rise, increased survivorship, and recovered glycogen, lipid and chitin to the normal levels. In contrast, silencing of LdTRE1a increased trehalose content and resulted in larval and pupal lethality. The surviving LdTRE1a RNAi hypomorphs fed a smaller quantity of food, had a lighter body weight, depleted lipid and several glucogenic amino acids, and contained a smaller amount of chitin. Neither trehalose nor glucose ingestion rescued these LdTRE1a RNAi defects. Silencing of LdTRE1b caused little effects. Knockdown of LdTRE2 caused larval death, increased trehalose contents in several tissues and diminished glycogen in the brain-corpora cardiaca-corpora allata complex (BCC). Feeding glucose but not trehalose partially rescued the high mortality rate and recovered glycogen content in the BCC. It seems that trehalose is involved in feeding regulation, sugar absorption, brain energy supply and chitin biosynthesis in L. decemlineata larvae. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lyme Disease: Emergency Department Considerations.

PubMed

Applegren, Nathan D; Kraus, Chadd K

2017-06-01

Lyme disease (LD) is the most common vector-borne illness in North America. Reported cases of LD have increased from approximately 10,000 cases annually in 1991 to >25,000 cases in 2014. Greater recognition, enhanced surveillance, and public education have contributed to the increased prevalence, as have geographic expansion and the number of infected ticks. Cases are reported primarily in the Northeastern United States, Wisconsin, and Minnesota, with children having the highest incidence of LD among all age groups. The increased incidence and prevalence of LD in the United States makes it increasingly more common for patients to present to the emergency department (ED) for tick bites and LD-related chief complaints, such as the characteristic erythema migrans skin manifestation. We sought to review the etiology of LD, describe its clinical presentations and sequela, and provide a practical classification and approach to ED management of patients with LD-related presentations. In this review, ED considerations for LD are presented and clinical presentations and management of the disease at different stages is discussed. Delayed sequelae that have significant morbidity, including Lyme carditis and Lyme neuroborreliosis, are discussed. Diagnostic tests and management are described in detail. The increasing prevalence and growing geographic reach of Lyme disease makes it critically important for emergency physicians to consider the diagnosis in patients presenting with symptoms suggestive of LD and to initiate appropriate treatment to minimize the potential of delayed sequelae. Special consideration should be made for the epidemiology of LD and a high clinical suspicion should be present for patients in endemic areas or with known exposures to ticks. Emergency physicians can play a critical role in the recognition, diagnosis, and treatment of LD. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential Roles of Cell Death-inducing DNA Fragmentation Factor-α-like Effector (CIDE) Proteins in Promoting Lipid Droplet Fusion and Growth in Subpopulations of Hepatocytes.

PubMed

Xu, Wenyi; Wu, Lizhen; Yu, Miao; Chen, Feng-Jung; Arshad, Muhammad; Xia, Xiayu; Ren, Hao; Yu, Jinhai; Xu, Li; Xu, Dijin; Li, John Zhong; Li, Peng; Zhou, Linkang

2016-02-26

Lipid droplets (LDs) are dynamic subcellular organelles whose growth is closely linked to obesity and hepatic steatosis. Cell death-inducing DNA fragmentation factor-α-like effector (CIDE) proteins, including Cidea, Cideb, and Cidec (also called Fsp27), play important roles in lipid metabolism. Cidea and Cidec are LD-associated proteins that promote atypical LD fusion in adipocytes. Here, we find that CIDE proteins are all localized to LD-LD contact sites (LDCSs) and promote lipid transfer, LD fusion, and growth in hepatocytes. We have identified two types of hepatocytes, one with small LDs (small LD-containing hepatocytes, SLHs) and one with large LDs (large LD-containing hepatocytes, LLHs) in the liver. Cideb is localized to LDCSs and promotes lipid exchange and LD fusion in both SLHs and LLHs, whereas Cidea and Cidec are specifically localized to the LDCSs and promote lipid exchange and LD fusion in LLHs. Cideb-deficient SLHs have reduced LD sizes and lower lipid exchange activities. Fasting dramatically induces the expression of Cidea/Cidec and increases the percentage of LLHs in the liver. The majority of the hepatocytes from the liver of obese mice are Cidea/Cidec-positive LLHs. Knocking down Cidea or Cidec significantly reduced lipid storage in the livers of obese animals. Our data reveal that CIDE proteins play differential roles in promoting LD fusion and lipid storage; Cideb promotes lipid storage under normal diet conditions, whereas Cidea and Cidec are responsible for liver steatosis under fasting and obese conditions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterizing Lyme Disease Surveillance in an Endemic State.

PubMed

Rutz, H J; Wee, S B; Feldman, K A

2018-03-01

Lyme disease (LD) is the most common vector-borne disease in Maryland and the United States. Surveillance for LD is valuable for understanding the burden of the disease, particularly to assess whether the disease is spreading and to appreciate who is affected. However, not all cases of LD in Maryland are reported, and surveillance practices vary across each of Maryland's 24 local health departments (LHDs). To better understand this variability and to systematically characterize the surveillance process, we surveyed Maryland's LHDs regarding LD surveillance. The Maryland Local Health Department Lyme Disease Surveillance Survey has been administered annually since 2011. Questions asked each year included whether all LD reports are investigated or only a subset, and how many reports are not entered into the surveillance database. Since 2011, Maryland has lost surveillance personnel for LD. Each year from 2009 to 2012, a median 3598 (range 2462 to 5722) reports were not entered into the surveillance database and hence not investigated. These reports represent 43-55% of all reports received for the year. Over time, more LHDs chose to streamline their LD investigation approach by investigating only those reports that met the criteria for laboratory evidence of infection: in 2008, 5 (21%) LHDs investigated only a subset of LD reports; by 2013, this increased to 15 (63%). There is wide variability across LHDs in how LD investigations are conducted. Maryland LHDs have experienced a loss of LD surveillance personnel with a concomitant increase in the number of LHDs adopting a streamlined approach to investigating cases. These findings underscore the tremendous burden of LD on the public health agencies and highlight the need for alternative approaches that can both reduce burden and preserve surveillance data quality. © 2016 Blackwell Verlag GmbH.

Activation of a Ca(2+)-dependent protein kinase involves intramolecular binding of a calmodulin-like regulatory domain

NASA Technical Reports Server (NTRS)

Huang, J. F.; Teyton, L.; Harper, J. F.; Evans, M. L. (Principal Investigator)

1996-01-01

Ca(2+)-dependent protein kinases (CDPKs) are regulated by a C-terminal calmodulin-like domain (CaM-LD). The CaM-LD is connected to the kinase by a short junction sequence which contains a pseudosubstrate autoinhibitor. To understand how the CaM-LD regulates a CDPK, a recombinant CDPK (isoform CPK-1 from Arabidopsis, accession no. L14771) was made as a fusion protein in Escherichia coli. We show here that a truncated CDPK lacking a CaM-LD (e.g. mutant delta NC-26H) can be activated by exogenous calmodulin or an isolated CaM-LD (Kact approximately 2 microM). We propose that Ca2+ activation of a CDPK normally occurs through intramolecular binding of the CaM-LD to the junction. When the junction and CaM-LD are made as two separate polypeptides, the CaM-LD can bind the junction in a Ca(2+)-dependent fashion with a dissociation constant (KD) of 6 x 10(-6) M, as determined by kinetic binding analyses. When the junction and CaM-LD are tethered in a single polypeptide (e.g. in protein JC-1), their ability to engage in bimolecular binding is suppressed (e.g. the tethered CaM-LD cannot bind a separate junction). A mutation which disrupts the putative CaM-LD binding sequence (e.g. substitution LRV-1444 to DLPG) appears to block intramolecular binding, as indicated by the restored ability of a tethered CaM-LD to engage in bimolecular binding. This mutation, in the context of a full-length enzyme (mutant KJM46H), appears to block Ca2+ activation. Thus, a disruption of intramolecular binding correlates with a disruption of the Ca2+ activation mechanism. CDPKs provide the first example of a member of the calmodulin superfamily where a target binding sequence is located within the same polypeptide.

Interaction between cysteine synthase and serine O-acetyltransferase proteins and their stage specific expression in Leishmania donovani.

PubMed

Singh, Kuljit; Singh, Krishn Pratap; Equbal, Asif; Suman, Shashi S; Zaidi, Amir; Garg, Gaurav; Pandey, Krishna; Das, Pradeep; Ali, Vahab

2016-12-01

Leishmania possess a unique trypanothione redox metabolism with undebated roles in protection from oxidative damage and drug resistance. The biosynthesis of trypanothione depends on l-cysteine bioavailability which is regulated by cysteine biosynthesis pathway. The de novo cysteine biosynthesis pathway is comprised of serine O-acetyltransferase (SAT) and cysteine synthase (CS) enzymes which sequentially mediate two consecutive steps of cysteine biosynthesis, and is absent in mammalian host. However, despite the apparent dependency of redox metabolism on cysteine biosynthesis pathway, the role of SAT and CS in redox homeostasis has been unexplored in Leishmania parasites. Herein, we have characterized CS and SAT to investigate their interaction and relative abundance of these proteins in promastigote vs. amastigote growth stages of L. donovani. CS and SAT genes of L. donovani (LdCS and LdSAT) were cloned, expressed, and fusion proteins purified to homogeneity with affinity column chromatography. Purified LdCS contains PLP as cofactor and showed optimum enzymatic activity at pH 7.5. Enzyme kinetics showed that LdCS catalyses the synthesis of cysteine using O-acetylserine and sulfide with a K m of 15.86 mM and 0.17 mM, respectively. Digitonin fractionation and indirect immunofluorescence microscopy showed that LdCS and LdSAT are localized in the cytoplasm of promastigotes. Size exclusion chromatography, co-purification, pull down and immuno-precipitation assays demonstrated a stable complex formation between LdCS and LdSAT proteins. Furthermore, LdCS and LdSAT proteins expression/activity was upregulated in amastigote growth stage of the parasite. Thus, the stage specific differential expression of LdCS and LdSAT suggests that it may have a role in the redox homeostasis of Leishmania. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Dream characteristics in a Brazilian sample: an online survey focusing on lucid dreaming

PubMed Central

Mota-Rolim, Sérgio A.; Targino, Zé H.; Souza, Bryan C.; Blanco, Wilfredo; Araujo, John F.; Ribeiro, Sidarta

2013-01-01

During sleep, humans experience the offline images and sensations that we call dreams, which are typically emotional and lacking in rational judgment of their bizarreness. However, during lucid dreaming (LD), subjects know that they are dreaming, and may control oneiric content. Dreaming and LD features have been studied in North Americans, Europeans and Asians, but not among Brazilians, the largest population in Latin America. Here we investigated dreams and LD characteristics in a Brazilian sample (n = 3,427; median age = 25 years) through an online survey. The subjects reported recalling dreams at least once a week (76%), and that dreams typically depicted actions (93%), known people (92%), sounds/voices (78%), and colored images (76%). The oneiric content was associated with plans for the upcoming days (37%), memories of the previous day (13%), or unrelated to the dreamer (30%). Nightmares usually depicted anxiety/fear (65%), being stalked (48%), or other unpleasant sensations (47%). These data corroborate Freudian notion of day residue in dreams, and suggest that dreams and nightmares are simulations of life situations that are related to our psychobiological integrity. Regarding LD, we observed that 77% of the subjects experienced LD at least once in life (44% up to 10 episodes ever), and for 48% LD subjectively lasted less than 1 min. LD frequency correlated weakly with dream recall frequency (r = 0.20, p < 0.01), and LD control was rare (29%). LD occurrence was facilitated when subjects did not need to wake up early (38%), a situation that increases rapid eye movement sleep (REMS) duration, or when subjects were under stress (30%), which increases REMS transitions into waking. These results indicate that LD is relatively ubiquitous but rare, unstable, difficult to control, and facilitated by increases in REMS duration and transitions to wake state. Together with LD incidence in USA, Europe and Asia, our data from Latin America strengthen the notion that LD is a general phenomenon of the human species. PMID:24368900

Dream characteristics in a Brazilian sample: an online survey focusing on lucid dreaming.

PubMed

Mota-Rolim, Sérgio A; Targino, Zé H; Souza, Bryan C; Blanco, Wilfredo; Araujo, John F; Ribeiro, Sidarta

2013-01-01

During sleep, humans experience the offline images and sensations that we call dreams, which are typically emotional and lacking in rational judgment of their bizarreness. However, during lucid dreaming (LD), subjects know that they are dreaming, and may control oneiric content. Dreaming and LD features have been studied in North Americans, Europeans and Asians, but not among Brazilians, the largest population in Latin America. Here we investigated dreams and LD characteristics in a Brazilian sample (n = 3,427; median age = 25 years) through an online survey. The subjects reported recalling dreams at least once a week (76%), and that dreams typically depicted actions (93%), known people (92%), sounds/voices (78%), and colored images (76%). The oneiric content was associated with plans for the upcoming days (37%), memories of the previous day (13%), or unrelated to the dreamer (30%). Nightmares usually depicted anxiety/fear (65%), being stalked (48%), or other unpleasant sensations (47%). These data corroborate Freudian notion of day residue in dreams, and suggest that dreams and nightmares are simulations of life situations that are related to our psychobiological integrity. Regarding LD, we observed that 77% of the subjects experienced LD at least once in life (44% up to 10 episodes ever), and for 48% LD subjectively lasted less than 1 min. LD frequency correlated weakly with dream recall frequency (r = 0.20, p < 0.01), and LD control was rare (29%). LD occurrence was facilitated when subjects did not need to wake up early (38%), a situation that increases rapid eye movement sleep (REMS) duration, or when subjects were under stress (30%), which increases REMS transitions into waking. These results indicate that LD is relatively ubiquitous but rare, unstable, difficult to control, and facilitated by increases in REMS duration and transitions to wake state. Together with LD incidence in USA, Europe and Asia, our data from Latin America strengthen the notion that LD is a general phenomenon of the human species.

Characterisation of the dynamic behaviour of lipid droplets in the early mouse embryo using adaptive harmonic generation microscopy.

PubMed

Watanabe, Tomoko; Thayil, Anisha; Jesacher, Alexander; Grieve, Kate; Debarre, Delphine; Wilson, Tony; Booth, Martin; Srinivas, Shankar

2010-06-03

Lipid droplets (LD) are organelles with an important role in normal metabolism and disease. The lipid content of embryos has a major impact on viability and development. LD in Drosophila embryos and cultured cell lines have been shown to move and fuse in a microtubule dependent manner. Due to limitations in current imaging technology, little is known about the behaviour of LD in the mammalian embryo. Harmonic generation microscopy (HGM) allows one to image LD without the use of exogenous labels. Adaptive optics can be used to correct aberrations that would otherwise degrade the quality and information content of images. We have built a harmonic generation microscope with adaptive optics to characterise early mouse embryogenesis. At fertilization, LD are small and uniformly distributed, but in the implanting blastocyst, LD are larger and enriched in the invading giant cells of the trophectoderm. Time-lapse studies reveal that LD move continuously and collide but do not fuse, instead forming aggregates that subsequently behave as single units. Using specific inhibitors, we show that the velocity and dynamic behaviour of LD is dependent not only on microtubules as in other systems, but also on microfilaments. We explore the limits within which HGM can be used to study living embryos without compromising viability and make the counterintuitive finding that 16 J of energy delivered continuously over a period of minutes can be less deleterious than an order of magnitude lower energy delivered dis-continuously over a period of hours. LD in pre-implantation mouse embryos show a previously unappreciated complexity of behaviour that is dependent not only on microtubules, but also microfilaments. Unlike LD in other systems, LD in the mouse embryo do not fuse but form aggregates. This study establishes HGM with adaptive optics as a powerful tool for the study of LD biology and provides insights into the photo-toxic effects of imaging embryos.

Immunization with Live Attenuated Leishmania donovani Centrin−/− Parasites Is Efficacious in Asymptomatic Infection

PubMed Central

Ismail, Nevien; Kaul, Amit; Bhattacharya, Parna; Gannavaram, Sreenivas; Nakhasi, Hira L.

2017-01-01

Currently, there is no vaccine against visceral leishmaniasis (VL). Toward developing an effective vaccine, we have reported extensively on the immunogenicity of live attenuated LdCentrin−/− mutants in naive animal models. In VL endemic areas, asymptomatic carriers outnumber symptomatic cases of VL and are considered to be a reservoir of infection. Vaccination of asymptomatic cases represents a viable strategy to eliminate VL. Immunological correlates of protection thus derived might have limited applicability in conditions where the immunized host has prior exposure to virulent infection. To examine whether LdCen−/− parasites can induce protective immunity in experimental hosts that have low-level parasitemia from a previous exposure mimicking an asymptomatic condition, we infected C57Bl/6 mice with wild-type Leishmania donovani parasites expressing LLO epitope (LdWTLLO 103, i.v.). After 3 weeks, the mice with low levels of parasitemia were immunized with LdCen−/− parasites expressing 2W epitope (LdCen−/−2W 3 × 106 i.v.) to characterize the immune responses in the same host. Antigen experienced CD4+ T cells from the asymptomatic (LdWTLLO infected) LdCen−/−2W immunized, and other control groups were enriched using LLO- and 2W-specific tetramers, followed by Flow cytometric analysis. Our analysis showed that comparable CD4+ T cell proliferation and CD4+ memory T cell responses (TCM) represented by CD62Lhi, CCR7+, and IL-7R+ T cell populations were induced with LdCen−/−2W in both asymptomatic and naive animals that received LdCen−/− immunization. Upon restimulation with peptide, TCM cells differentiated into effector T cells and there was no significant difference in the recall response in animals with asymptomatic infection. Following virulent challenge, comparable reduction in splenic parasite burden was observed in both asymptomatic and naive LdCen−/− immunized animals concomitant with the development of multifunctional CD4+ and CD8+ T cells. Further, LdCen−/−2W immunization resulted in complete clearance of the preexisting asymptomatic infection (LdWTLLO). Our results demonstrate that LdCen−/−2W immunization could be efficacious for use in asymptomatic VL individuals. Further, immunization with LdCen−/− could help in reducing the parasite burden in the asymptomatic cases and aid in controlling the VL in endemic areas. PMID:29312315

Breed-Specific Ancestry Studies and Genome-Wide Association Analysis Highlight an Association Between the MYH9 Gene and Heat Tolerance in Alaskan Sprint Racing Sled Dogs

PubMed Central

Huson, Heather J.; vonHoldt, Bridgett M.; Rimbault, Maud; Byers, Alexandra M.; Runstadler, Jonathan A.; Parker, Heidi G.; Ostrander, Elaine A.

2012-01-01

Alaskan sled dogs are a genetically distinct population shaped by generations of selective interbreeding with purebred dogs to create a group of high performance athletes. As a result of selective breeding strategies, sled dogs present a unique opportunity to employ admixture-mapping techniques to investigate how breed composition and trait selection impact genomic structure. We used admixture mapping to investigate genetic ancestry across the genomes of two classes of sled dogs, sprint and long distance racers, and combined that with genome wide association studies (GWAS) to identify regions correlating with performance enhancing traits. The sled dog genome is enhanced by differential contributions from four non-admixed breeds (Alaskan Malamute, Siberian Husky, German Shorthaired Pointer, and Borzoi). A principle components analysis (PCA) of 115,000 genome-wide SNPs clearly resolved the sprint and distance populations as distinct genetic groups, with longer blocks of linkage disequilibrium (LD) observed in the distance versus sprint dogs (7.5–10 and 2.5–3.75 kb, respectively). Further, we identified eight regions with the genomic signal either from a selective sweep or an association analysis, corroborated by an excess of ancestry when comparing sprint and distance dogs. A comparison of elite and poor performing sled dogs identified a single region significantly association with heat tolerance. Within the region we identified seven SNPs within the myosin heavy chain 9 gene (MYH9) that were significantly associated with heat tolerance in sprint dogs, two of which correspond to conserved promoter and enhancer regions in the human ortholog. PMID:22105876

A Comparison of Two Skip Entry Guidance Algorithms

NASA Technical Reports Server (NTRS)

Rea, Jeremy R.; Putnam, Zachary R.

2007-01-01

The Orion capsule vehicle will have a Lift-to-Drag ratio (L/D) of 0.3-0.35. For an Apollo-like direct entry into the Earth's atmosphere from a lunar return trajectory, this L/D will give the vehicle a maximum range of about 2500 nm and a maximum crossrange of 216 nm. In order to y longer ranges, the vehicle lift must be used to loft the trajectory such that the aerodynamic forces are decreased. A Skip-Trajectory results if the vehicle leaves the sensible atmosphere and a second entry occurs downrange of the atmospheric exit point. The Orion capsule is required to have landing site access (either on land or in water) inside the Continental United States (CONUS) for lunar returns anytime during the lunar month. This requirement means the vehicle must be capable of flying ranges of at least 5500 nm. For the L/D of the vehicle, this is only possible with the use of a guided Skip-Trajectory. A skip entry guidance algorithm is necessary to achieve this requirement. Two skip entry guidance algorithms have been developed: the Numerical Skip Entry Guidance (NSEG) algorithm was developed at NASA/JSC and PredGuid was developed at Draper Laboratory. A comparison of these two algorithms will be presented in this paper. Each algorithm has been implemented in a high-fidelity, 6 degree-of-freedom simulation called the Advanced NASA Technology Architecture for Exploration Studies (ANTARES). NASA and Draper engineers have completed several monte carlo analyses in order to compare the performance of each algorithm in various stress states. Each algorithm has been tested for entry-to-target ranges to include direct entries and skip entries of varying length. Dispersions have been included on the initial entry interface state, vehicle mass properties, vehicle aerodynamics, atmosphere, and Reaction Control System (RCS). Performance criteria include miss distance to the target, RCS fuel usage, maximum g-loads and heat rates for the first and second entry, total heat load, and control system saturation. The comparison of the performance criteria has led to a down select and guidance merger that will take the best ideas from each algorithm to create one skip entry guidance algorithm for the Orion vehicle.

Learning Disability Identification Criteria and Reporting in Empirical Research: A Review of 2001-2013

ERIC Educational Resources Information Center

Williams, Jacob L.; Miciak, Jeremy; McFarland, Laura; Wexler, Jade

2016-01-01

This review documents the learning disabilities (LD) identification criteria and procedures utilized in empirical research including students with LD published from 2001 to 2013 in three journals dedicated to the study of LD. Results reveal several troublesome findings related to transparency in reporting and the coherence of the LD construct.…

Genomic analysis of five Lymantria dispar nucleopolyhedrovirus isolates and biological activity against different host strains of Lymantria dispar

USDA-ARS?s Scientific Manuscript database

To evaluate genetic diversity of Lymantria dispar nucleopolyhedrovirus (LdMNPV) at the genomic level, five isolates of LdMNPV from North America, Europe, and Asia were selected for complete genome sequence determination and analysis. These isolates consist of LdMNPV-2161 from Korea; LdMNPV-3029, a ...

Intervention Effects for Students with Comorbid Forms of Learning Disability: Understanding the Needs of Nonresponders

ERIC Educational Resources Information Center

Fuchs, Lynn S.; Fuchs, Douglas; Compton, Donald L.

2013-01-01

In this article, we considered evidence from our intervention research programs on whether students with learning disability (LD) in reading and mathematics (comorbid LD) respond differently to intervention, compared to students with reading LD alone (RD) or to students with mathematics LD alone (MD). The goal was to gain insight into whether…

Metrics for comparison of crystallographic maps

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

2014-10-01

Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

Static behaviour of 3x3 pile group in sand under lateral loading

NASA Astrophysics Data System (ADS)

SureshKumar, R.; BharathKumar, R.; MohanKumar, L.; Visuvasam, J.; Sairam, V.

2017-11-01

This paper presents the static lateral load behaviour of single pile in comparison with 3x3 pile group in sand. The piled raft system is modelled using PLAXIS3D. Parametric studies of varying length to diameter (L/D) and spacing of piles in a group and diameter of piles (S/D) have been performed. The behaviour of group piles in terms of static lateral load capacity and group efficiency has been discussed.

Multiple animal studies for medical chemical defense program in soldier/patient decontamination and drug development on task order 86-25: Evaluation of the effectiveness of two ROHM and HAAS candidate decontamination systems against percutaneous application of undiluted TGD, Gd, VX HD, and L on the laboratory albino rabbit. Final report, 1 September 1986-1 February 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joiner, R.L.; Keys, W.B.; Harroff, H.H.

1988-02-18

A task was assigned to Battelle's Medical Research and Evaluation Facility(MREF) to evaluate the effectiveness of two candidate decontamination systems when compared to the standard dual component M258A1 decontamination system currently fielded by the U.S. Army. The chemical surety material (CSM) used in the evaluation were the organophosphates Soman (GD), polymer thickened GD (TGD), and VX, and the vesicants sulfur mustard (HD) and Lewisite (LS). The efficacies of the two candidate decontamination systems were evaluated in such a manner as to determine the LD50 and protective ratio (PR) for each decontaminant against each organophosphate CSM as compared to the standardmore » M258A1 decontamination system LD50. The PR constituted a comparison for each candidate system against the M258A1 standard. In the vesicant phase of the screen, the efficacies of the candidate systems were evaluated in a side-by-side comparison to the M258A1 decontamination system to determine whether the candidates were as good as or better than the standard dual component system.« less

[Effect of light regimens on the age dynamics of estrous function and serum prolactin level in rats].

PubMed

Vinogradova, I A; Chernova, I V

2006-01-01

The effect of different light regimens (standard 12 h. light : 12 h. darkness LD; 24-hour constant light LL, light deprivation DD, natural light regimen of the North-West of Russia NL) on the age dynamics of estrous function and on the serum prolactin in female LIO rats has been studied for two years. The rats were maintained at the one of above-mentioned regimes from the age of 25 days. The cytological monitoring of the estrous cycle was conducted every three months. The level of prolactin was studied at the age of 6, 12, 18 and 24 months. It has been found out that the regimen of constant light (LL) and the spring-summer period lead to earlier maturation, premature age-related changes of the rats' estrous cycle and to the increase of the level of serum prolactin in comparison with those in rats kept at the LD regimen. Light deprivation (DD) leads to the opposite changes. It has been noted that the exposure to constant light during the whole year is accompanied by more expressed and earlier developed age-related changes of estrous cycle in comparison with the natural light of the North-West of Russia with its peculiar year photoperiodicity (short day in autumn-winter period and white nights in spring-summer period).

Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

PubMed Central

Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93–96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13–89%)/functional allelic diversity (18–77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54–0.68) and extended LD decay (400–500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding. PMID:25873920

Comparing physiographic maps with different categorisations

NASA Astrophysics Data System (ADS)

Zawadzka, J.; Mayr, T.; Bellamy, P.; Corstanje, R.

2015-02-01

This paper addresses the need for a robust map comparison method suitable for finding similarities between thematic maps with different forms of categorisations. In our case, the requirement was to establish the information content of newly derived physiographic maps with regards to set of reference maps for a study area in England and Wales. Physiographic maps were derived from the 90 m resolution SRTM DEM, using a suite of existing and new digital landform mapping methods with the overarching purpose of enhancing the physiographic unit component of the Soil and Terrain database (SOTER). Reference maps were seven soil and landscape datasets mapped at scales ranging from 1:200,000 to 1:5,000,000. A review of commonly used statistical methods for categorical comparisons was performed and of these, the Cramer's V statistic was identified as the most appropriate for comparison of maps with different legends. Interpretation of multiple Cramer's V values resulting from one-by-one comparisons of the physiographic and baseline maps was facilitated by multi-dimensional scaling and calculation of average distances between the maps. The method allowed for finding similarities and dissimilarities amongst physiographic maps and baseline maps and informed the recommendation of the most suitable methodology for terrain analysis in the context of soil mapping.

Dynamic stability analysis for a self-mixing interferometry system.

PubMed

Fan, Yuanlong; Yu, Yanguang; Xi, Jiangtao; Guo, Qinghua

2014-11-17

A self-mixing interferometry (SMI) system is a laser diode (LD) with an external cavity formed by a moving external target. The behavior of an SMI system is governed by the injection current J to the LD and the parameters associated with the external cavity mainly including optical feedback factor C, the initial external cavity length (L₀) and the light phase (ϕ₀) which is mapped to the movement of the target. In this paper, we investigate the dynamic behavior of an SMI system by using the Lang-Kobayashi model. The stability boundary of such system is presented in the plane of (C, ϕ₀), from which a critical C (denoted as C(critical)) is derived. Both simulations and experiments show that the stability can be enhanced by increasing either L₀ or J. Furthermore, three regions on the plane of (C, ϕ₀) are proposed to characterize the behavior of an SMI system, including stable, semi-stable and unstable regions. We found that the existing SMI model is only valid for the stable region, and the semi-stable region has potential applications on sensing and measurement but needs re-modeling the system by considering the bandwidth of the detection components.

Genome-Wide Association Mapping of Acid Soil Resistance in Barley (Hordeum vulgare L.)

PubMed Central

Zhou, Gaofeng; Broughton, Sue; Zhang, Xiao-Qi; Ma, Yanling; Zhou, Meixue; Li, Chengdao

2016-01-01

Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) have been used to detect QTLs underlying complex traits in major crops. In this study, we collected 218 barley (Hordeum vulgare L.) lines including wild barley and cultivated barley from China, Canada, Australia, and Europe. A total of 408 polymorphic markers were used for population structure and LD analysis. GWAS for acid soil resistance were performed on the population using a general linkage model (GLM) and a mixed linkage model (MLM), respectively. A total of 22 QTLs (quantitative trait loci) were detected with the GLM and MLM analyses. Two QTLs, close to markers bPb-1959 (133.1 cM) and bPb-8013 (86.7 cM), localized on chromosome 1H and 4H respectively, were consistently detected in two different trials with both the GLM and MLM analyses. Furthermore, bPb-8013, the closest marker to the major Al3+ resistance gene HvAACT1 in barley, was identified to be QTL5. The QTLs could be used in marker-assisted selection to identify and pyramid different loci for improved acid soil resistance in barley. PMID:27064793

Imaging fluorescence detected linear dichroism of plant cell walls in laser scanning confocal microscope.

PubMed

Steinbach, Gábor; Pomozi, István; Zsiros, Ottó; Páy, Anikó; Horváth, Gábor V; Garab, Gyozo

2008-03-01

Anisotropy carries important information on the molecular organization of biological samples. Its determination requires a combination of microscopy and polarization spectroscopy tools. The authors constructed differential polarization (DP) attachments to a laser scanning microscope in order to determine physical quantities related to the anisotropic distribution of molecules in microscopic samples; here the authors focus on fluorescence-detected linear dichroism (FDLD). By modulating the linear polarization of the laser beam between two orthogonally polarized states and by using a demodulation circuit, the authors determine the associated transmitted and fluorescence intensity-difference signals, which serve the basis for LD (linear dichroism) and FDLD, respectively. The authors demonstrate on sections of Convallaria majalis root tissue stained with Acridin Orange that while (nonconfocal) LD images remain smeared and weak, FDLD images recorded in confocal mode reveal strong anisotropy of the cell wall. FDLD imaging is suitable for mapping the anisotropic distribution of transition dipoles in 3 dimensions. A mathematical model is proposed to account for the fiber-laminate ultrastructure of the cell wall and for the intercalation of the dye molecules in complex, highly anisotropic architecture. Copyright 2007 International Society for Analytical Cytology.

Functional identification of a Lippia dulcis bornyl diphosphate synthase that contains a duplicated, inhibitory arginine-rich motif.

PubMed

Hurd, Matthew C; Kwon, Moonhyuk; Ro, Dae-Kyun

2017-08-26

Lippia dulcis (Aztec sweet herb) contains the potent natural sweetener hernandulcin, a sesquiterpene ketone found in the leaves and flowers. Utilizing the leaves for agricultural application is challenging due to the presence of the bitter-tasting and toxic monoterpene, camphor. To unlock the commercial potential of L. dulcis leaves, the first step of camphor biosynthesis by a bornyl diphosphate synthase needs to be elucidated. Two putative monoterpene synthases (LdTPS3 and LdTPS9) were isolated from L. dulcis leaf cDNA. To elucidate their catalytic functions, E. coli-produced recombinant enzymes with truncations of their chloroplast transit peptides were assayed with geranyl diphosphate (GPP). In vitro enzyme assays showed that LdTPS3 encodes bornyl diphosphate synthase (thus named LdBPPS) while LdTPS9 encodes linalool synthase. Interestingly, the N-terminus of LdBPPS possesses two arginine-rich (RRX 8 W) motifs, and enzyme assays showed that the presence of both RRX 8 W motifs completely inhibits the catalytic activity of LdBPPS. Only after the removal of the putative chloroplast transit peptide and the first RRX 8 W, LdBPPS could react with GPP to produce bornyl diphosphate. LdBPPS is distantly related to the known bornyl diphosphate synthase from sage in a phylogenetic analysis, indicating a converged evolution of camphor biosynthesis in sage and L. dulcis. The discovery of LdBPPS opens up the possibility of engineering L. dulcis to remove the undesirable product, camphor. Copyright © 2017 Elsevier Inc. All rights reserved.

Aggressiveness, violence, homicidality, homicide, and Lyme disease

PubMed Central

Bransfield, Robert C

2018-01-01

Background No study has previously analyzed aggressiveness, homicide, and Lyme disease (LD). Materials and methods Retrospective LD chart reviews analyzed aggressiveness, compared 50 homicidal with 50 non-homicidal patients, and analyzed homicides. Results Most aggression with LD was impulsive, sometimes provoked by intrusive symptoms, sensory stimulation or frustration and was invariably bizarre and senseless. About 9.6% of LD patients were homicidal with the average diagnosis delay of 9 years. Postinfection findings associated with homicidality that separated from the non-homicidal group within the 95% confidence interval included suicidality, sudden abrupt mood swings, explosive anger, paranoia, anhedonia, hypervigilance, exaggerated startle, disinhibition, nightmares, depersonalization, intrusive aggressive images, dissociative episodes, derealization, intrusive sexual images, marital/family problems, legal problems, substance abuse, depression, panic disorder, memory impairments, neuropathy, cranial nerve symptoms, and decreased libido. Seven LD homicides included predatory aggression, poor impulse control, and psychosis. Some patients have selective hyperacusis to mouth sounds, which I propose may be the result of brain dysfunction causing a disinhibition of a primitive fear of oral predation. Conclusion LD and the immune, biochemical, neurotransmitter, and the neural circuit reactions to it can cause impairments associated with violence. Many LD patients have no aggressiveness tendencies or only mild degrees of low frustration tolerance and irritability and pose no danger; however, a lesser number experience explosive anger, a lesser number experience homicidal thoughts and impulses, and much lesser number commit homicides. Since such large numbers are affected by LD, this small percent can be highly significant. Much of the violence associated with LD can be avoided with better prevention, diagnosis, and treatment of LD. PMID:29576731

Influence of low concentration acid treatment on lithium disilicate core/veneer ceramic bond strength

PubMed Central

Garcia, Rudan P.; Conti, Paulo CR.; Pereira, Jefferson R.; Valle, Accácio Ld.

2013-01-01

Objective: This study evaluated the influence of low concentration acid treatment on the shear bond strength between lithium disilicate (LD) infrastructure and veneering porcelain. The surface morphology characteristic after this acid treatment was also examined. Study Design: LD reinforced ceramic cylinders (n=10) (IPS e.max Press, Ivoclar-Vivadent, Schaan, Liechtenstein) were treated (LD-treated) with a low concentration acid solution (Invex Liquid – Ivoclar-Vivadent, Schaan, Liechtenstein) or not treated with the acid solution (LD-untreated). They were veneered with a glass ceramic (IPS e.max Ceram, Ivoclar-Vivadent, Schaan, Liechtenstein). A metal ceramic group (CoCr) was tested as control. Shear bond strength (SBS) was conducted using a universal testing machine at 0.5 mm/min. Surface morphology characteristics after acid treatment were analyzed using scanning electron microscopy. Results: The acid treatment at low concentrations did not influence the SBS of the LD/veneering porcelain interface. The CoCr group showed the significant higher SBS value (35.59 ± 5.97 MPa), followed by LD-untreated group (27.76 ± 3.59 MPa) and LD-treated (27.02 ± 4.79 MPa). The fracture modes were predominantly adhesive for CoCr group and cohesive within the infrastructure for DL groups. Scanning Electron Microscopy (SEM) analysis showed no morphological differences between treated and untreated LD surfaces. Conclusions: Low concentration acid treatment did not improved SBS of veneering ceramic to LD and did not cause morphological changes on the LD surface. Key words:Lithium disilicate, glass ceramics, acid etching, shear bond strength, scanning electron microscopy. PMID:24455073

Neurobiology and clinical implications of lucid dreaming.

PubMed

Mota-Rolim, Sérgio A; Araujo, John F

2013-11-01

Several lines of evidence converge to the idea that rapid eye movement sleep (REMS) is a good model to foster our understanding of psychosis. Both REMS and psychosis course with internally generated perceptions and lack of rational judgment, which is attributed to a hyperlimbic activity along with hypofrontality. Interestingly, some individuals can become aware of dreaming during REMS, a particular experience known as lucid dreaming (LD), whose neurobiological basis is still controversial. Since the frontal lobe plays a role in self-consciousness, working memory and attention, here we hypothesize that LD is associated with increased frontal activity during REMS. A possible way to test this hypothesis is to check whether transcranial magnetic or electric stimulation of the frontal region during REMS triggers LD. We further suggest that psychosis and LD are opposite phenomena: LD as a physiological awakening while dreaming due to frontal activity, and psychosis as a pathological intrusion of dream features during wake state due to hypofrontality. We further suggest that LD research may have three main clinical implications. First, LD could be important to the study of consciousness, including its pathologies and other altered states. Second, LD could be used as a therapy for recurrent nightmares, a common symptom of depression and post-traumatic stress disorder. Finally, LD may allow for motor imagery during dreaming with possible improvement of physical rehabilitation. In all, we believe that LD research may clarify multiple aspects of brain functioning in its physiological, altered and pathological states. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

[A comparative study on characterizations of genetic recombination hotspots in PPARG gene between Kirgiz and Uyghur ethnic groups in Xinjiang].

PubMed

Zohra, Rozi; Song, M S; Iliham, Nizam; Dolikun, Mamatyusupu

2016-08-16

To investigate the characterizations of genetic recombination hotspots and linkage disequilibrium (LD) patterns in peroxisome proliferative activated receptor gamma (PPARG) gene in Kirgiz and Uyghur ethnic groups. Blood samples were collected from 100 Kirgiz (50 healthy controls and 50 patients with type 2 diabetes mellitus) residents in Halajun County, Artux City, Kizilsu Kirgiz Autonomous Prefecture, Xinjiang in August 2013, and 50 healthy Uyghur residents in Hotan Prefecture of Xinjiang Uygur Autonomous Region in May 2012.Thirty-one tagSNPs in PPARG gene were genotyped using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) method.The recombination hotspots and LD patterns within the PPARG gene were estimated by analyzing the SNP genotying data using the Hotspot Fisher program and Haploview software, respectively. Eighteen tagSNPs (rs1151999, rs1175540, rs1875796, rs1899951, rs2292101, rs2921190, rs2938397, rs2959272, rs2959273, rs2972162, rs3856806, rs4135247, rs4135275, rs709151, rs4135354, rs6805419, rs17036700 and rs4135304) were same with relatively higher recombination rates between the patients with type 2 diabetes mellitus (T2DM) and healthy controls of Kirgiz ethnic group, and healthy controls of Uyghur ethnic group.Five haplotype blocks with LD coefficient D' value of 1, indicating no genetic recombination occurred within the region, were observed in the healthy controls of Kirgiz ethnic groups, whereas five haplotype blocks with LD coefficient D' value less than 1 were observed in the Kirgiz patients with T2DM, indicating historical recombination events occurred within the region.Four haplotype blocks with LD coefficient D' value of 1 were observed in the Uyghur healthy controls, indicating no genetic recombination occurred within the region.There were significantly different recombination hotspot profiles between the Kirgiz, Uyghur, Utah residents with Northern and Western European ancestry (CEU), Yoruban in Ibadan, Nigeria (YRI) and Han Chinese in Beijing (CHB) and Japanese in Tokyo (JPT) samples.There are six recombination hotspots in the HapMap profile of genetic recombination.The last 5 SNPs within the PPARG gene were shown with lower recombination rates in the Kirgiz, whereas no recombination hotspot was found in the Uyghur. Variable recombination rates may be present in certain chromosome region between patients and healthy controls within the same or between the different ethnic groups.There may be presence of recombination hotspots of ethnic specificity and with variable recombination rates.

Predictive value of late decelerations for fetal acidemia in unselective low-risk pregnancies.

PubMed

Sameshima, Hiroshi; Ikenoue, Tsuyomu

2005-01-01

We evaluated the clinical significance of late decelerations (LD) of intrapartum fetal heart rate (FHR) monitoring to detect low pH (< 7.1) in low-risk pregnancies. We selected two secondary and two tertiary-level institutions where 10,030 women delivered. Among them, 5522 were low-risk pregnancies. The last 2 hours of FHR patterns before delivery were interpreted according to the guidelines of the National Institute of Child Health and Human Development. The correlation between the incidence of LD (occasional, < 50%; recurrent, > or = 50%) and severity (reduced baseline FHR accelerations and variability) of LD, and low pH (< 7.1) were evaluated. Statistical analyses included a contingency table with chi2 and the Fisher test, and one-way analysis of variance with the Bonferroni/Dunn test. In the 5522 low-risk pregnancies, 301 showed occasional LD and 99 showed recurrent LD. Blood gases and pH values deteriorated as the incidence of LD increased and as baseline accelerations or variability was decreased. Positive predictive value for low pH (< 7.1) was exponentially elevated from 0% at no deceleration, 1% in occasional LD, and > 50% in recurrent LD with no baseline FHR accelerations and reduced variability. In low-risk pregnancies, information on LD combined with acceleration and baseline variability enables us to predict the potential incidence of fetal acidemia.

[Clinical correlation of hypnagogic hypersynchrony during sleep in normal children and those with learning disability].

PubMed

Olmos G de Alba, G; Fraire-Martínez, M I; Valenzuela-Romero, R

One of the electroencephalographic (EEG) patterns that can be mistaken for paroxysmal clinical activity, when not taken into account and especially in children, is hypnagogic hypersynchrony (HH). This consists in generalised, paroxysmal, synchronic, symmetrical, slow, high voltage waves lasting 2 8 seconds, which appear in drowsiness and in stage I. It was observed that this pattern often appeared in children with learning disability (LD). AIMS. To correlate clinical data with the presence of HH during sleep in normal children and those with LD. We assessed 180 children between the ages of 6 12 years with normal neurological development, 130 of which suffered LD and 50 who did not have LD. EEG was performed with sleep deprivation, following the International Federation of Clinical Neurophysiology guidelines. The presence or absence of HH, together with its characteristics, was assessed. Of the children with LD, 35.38% displayed HH and of the children without LD, only 4% displayed HH. Since the characteristics of HH in the children with LD were different to previous descriptions, we put forward criteria with which to evaluate those differences. HH appeared more often in children with LD than in normal children. Qualitative, quantitative (p< 0.05) and morphological changes were found in the paroxysmal activity of HH during the stages of sleep in children with LD.

Friendship Predictors of Global Self-Worth and Domain-Specific Self-Concepts in University Students with and without Learning Disability

ERIC Educational Resources Information Center

Shany, Michal; Wiener, Judith; Assido, Michal

2013-01-01

This study investigated the association among friendship, global self-worth, and domain-specific self-concepts in 102 university students with and without learning disabilities (LD). Students with LD reported lower global self-worth and academic self-concept than students without LD, and this difference was greater for women. Students with LD also…

Model-based risk assessment and public health analysis to prevent Lyme disease

PubMed Central

Sabounchi, Nasim S.; Roome, Amanda; Spathis, Rita; Garruto, Ralph M.

2017-01-01

The number of Lyme disease (LD) cases in the northeastern United States has been dramatically increasing with over 300 000 new cases each year. This is due to numerous factors interacting over time including low public awareness of LD, risk behaviours and clothing choices, ecological and climatic factors, an increase in rodents within ecologically fragmented peri-urban built environments and an increase in tick density and infectivity in such environments. We have used a system dynamics (SD) approach to develop a simulation tool to evaluate the significance of risk factors in replicating historical trends of LD cases, and to investigate the influence of different interventions, such as increasing awareness, controlling clothing risk and reducing mouse populations, in reducing LD risk. The model accurately replicates historical trends of LD cases. Among several interventions tested using the simulation model, increasing public awareness most significantly reduces the number of LD cases. This model provides recommendations for LD prevention, including further educational programmes to raise awareness and control behavioural risk. This model has the potential to be used by the public health community to assess the risk of exposure to LD. PMID:29291075

Tunable single frequency fiber laser based on FP-LD injection locking.

PubMed

Zhang, Aiqin; Feng, Xinhuan; Wan, Minggui; Li, Zhaohui; Guan, Bai-ou

2013-05-20

We propose and demonstrate a tunable single frequency fiber laser based on Fabry Pérot laser diode (FP-LD) injection locking. The single frequency operation principle is based on the fact that the output from a FP-LD injection locked by a multi-longitudinal-mode (MLM) light can have fewer longitudinal-modes number and narrower linewidth. By inserting a FP-LD in a fiber ring laser cavity, single frequency operation can be possibly achieved when stable laser oscillation established after many roundtrips through the FP-LD. Wavelength switchable single frequency lasing can be achieved by adjusting the tunable optical filter (TOF) in the cavity to coincide with different mode of the FP-LD. By adjustment of the drive current of the FP-LD, the lasing modes would shift and wavelength tunable operation can be obtained. In experiment, a wavelength tunable range of 32.4 nm has been obtained by adjustment of the drive current of the FP-LD and a tunable filter in the ring cavity. Each wavelength has a side-mode suppression ratio (SMSR) of at least 41 dB and a linewidth of about 13 kHz.

Liver injury correlates with biomarkers of autoimmunity and disease activity and represents an organ system involvement in patients with systemic lupus erythematosus

PubMed Central

Liu, Yuxin; Yu, Jianghong; Oaks, Zachary; Marchena-Mendez, Ivan; Francis, Lisa; Bonilla, Eduardo; Aleksiejuk, Phillip; Patel, Jessica; Banki, Katalin; Landas, Steve K.; Perl, Andras

2015-01-01

Liver disease (LD), defined as ≥2-fold elevation of aspartate aminotransferase (AST) or alanine aminotransferase (ALT), was examined in a longitudinal study of systemic lupus erythematosus (SLE) patients. Among 435 patients, 90 (20.7%) had LD with a greater prevalence in males (15/39; 38.5%) than females (75/396; 18.9%; p = 0.01). SLE disease activity index (SLEDAI) was greater in LD patients (7.8 ± 0.7) relative to those without (5.8 ± 0.3; p = 0.0025). Anti-smooth muscle antibodies, anti-DNA antibodies, hypocomplementemia, proteinuria, leucopenia, thrombocytopenia, and anti-phospholipid syndrome were increased in LD. An absence of LD was noted in patients receiving rapamycin relative to azathioprine, cyclosporine A, or cyclophosphamide. An absence of LD was also noted in patients treated with N-acetylcysteine. LFTs were normalized and SLEDAI was diminished with increased prednisone use in 76/90 LD patients over 12.1 ± 2.6 months. Thus, LD is attributed to autoimmunity and disease activity, it responds to prednisone, and it is potentially preventable by rapamycin or N-acetylcysteine treatment. PMID:26160213

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyn, Rodney K.; Department of Chemistry, University of Ottawa, Ottawa; Kennedy, David C.

Research highlights: {yields} Hepatitis C virus uses lipid droplets (LD) onto which HCV core proteins bind. {yields} HCV core proteins on LDs facilitate viral particle assembly. {yields} We used a novel combination of CARS, two-photon fluorescence, and DIC microscopies. {yields} Particle tracking experiments show that core slowly affects LD localization. {yields} Particle tracking measured the change in speed and directionality of LD movement. -- Abstract: The hepatitis C virus (HCV) is a global health problem, with limited treatment options and no vaccine available. HCV uses components of the host cell to proliferate, including lipid droplets (LD) onto which HCV coremore » proteins bind and facilitate viral particle assembly. We have measured the dynamics of HCV core protein-mediated changes in LDs and rates of LD movement on microtubules using a combination of coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), and differential interference contrast (DIC) microscopies. Results show that the HCV core protein induces rapid increases in LD size. Particle tracking experiments show that HCV core protein slowly affects LD localization by controlling the directionality of LD movement on microtubules. These dynamic processes ultimately aid HCV in propagating and the molecules and interactions involved represent novel targets for potential therapeutic intervention.« less

Bidirectional Lipid Droplet Velocities Are Controlled by Differential Binding Strengths of HCV Core DII Protein

PubMed Central

Lyn, Rodney K.; Hope, Graham; Sherratt, Allison R.; McLauchlan, John; Pezacki, John Paul

2013-01-01

Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein’s lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV. PMID:24223760

Impact of endurance exercise on levodopa-associated cortisol release and force increase in patients with Parkinson's disease.

PubMed

Müller, Thomas; Muhlack, Siegfried

2008-06-01

Levodopa (LD) application improves motor symptoms and reduces cortisol levels in patients with Parkinson's disease (PD). Endurance exercise enhances cortisol release in proportion to the intensity of the effort and thus may counteract the LD associated cortisol decrease. We measured levels of cortisol and LD over an 1-h long interval following administration of soluble 200 mg LD/50 mg benserazide with concomitant maximal grip strength assessment in 16 PD patients under cued conditions during rest and endurance exercise. The motor response, the plasma levels of cortisol and LD did not significantly differ between both conditions. Cortisol concentrations significantly decreased even during exercise. Grip strength only significantly went up during rest. Endurance exercise did not counteract the LD associated decreased cortisol release. Since cortisol improves muscle function, the lack of increase in maximal grip strength following LD administration during exercise may contribute to reduced exercise capacity, which is reported by PD patients.

Subsonic Longitudinal Performance Coefficient Extraction from Shuttle Flight Data: an Accuracy Assessment for Determination of Data Base Updates

NASA Technical Reports Server (NTRS)

Findlay, J. T.; Kelly, G. M.; Mcconnell, J. G.; Compton, H. R.

1983-01-01

Longitudinal performance comparisons between flight derived and predicted values are presented for the first five NASA Space Shuttle Columbia flights. Though subsonic comparisons are emphasized, comparisons during the transonic and low supersonic regions of flight are included. Computed air data information based on the remotely sensed atmospheric measurements as well as in situ Orbiter Air Data System (ADS) measurements were incorporated. Each air data source provides for comparisons versus the predicted values from the LaRC data base. Principally, L/D, C sub L, and C sub D, comparisons are presented, though some pitching moment results are included. Similarities in flight conditions and spacecraft configuration during the first five flights are discussed. Contributions from the various elements of the data base are presented and the overall differences observed between the flight and predicted values are discussed in terms of expected variations. A discussion on potential data base updates is presented based on the results from the five flights to date.

Photophysical properties of a laser dye (LD-473) in different solvents

NASA Astrophysics Data System (ADS)

Ibnaouf, K. H.; Alhathlool, R.; Ali, M. K. M.

2018-06-01

In this paper, we investigated the spectroscopic properties the 1, 2, 3, 8-tetrahydrofuran, 2, 3, 8-(LD-473) dissolved in seven types of solvents with different concentrations. The absorption, emission, fluorescence and its quantum yield and Stokes shift of LD-473 were measured. The amplified spontaneous emission (ASE) spectra of LD-473 have been obtained using a transverse laser cavity configuration, where the LD-473 was pumped by laser pulses from the third harmonic of an Nd: YAG laser (355 nm). LD-473 in non-polar solvents exhibits dual ASEs around 445 and 470 nm, whereas the corresponding fluorescence spectrum shows only one peak around 437 nm. The peak at 470 nm is due to the combination of two excited molecules and the solvent between them.

Mucuna pruriens and Its Major Constituent L-DOPA Recover Spermatogenic Loss by Combating ROS, Loss of Mitochondrial Membrane Potential and Apoptosis

PubMed Central

Singh, Akhand Pratap; Sarkar, Saumya; Tripathi, Muktanand; Rajender, Singh

2013-01-01

Background The Ayurvedic medicinal system claims Mucuna pruriens (MP) to possess pro-male fertility, aphrodisiac and adaptogenic properties. Some scientific evidence also supports its pro-male fertility properties; however, the mechanism of its action is not yet clear. The present study aimed at demonstrating spermatogenic restorative efficacy of MP and its major constituent L-DOPA (LD), and finding the possible mechanism of action thereof in a rat model. Methodology/Findings Ethinyl estradiol (EE) was administered at a rate of 3 mg/kg body weight (BW)/day for a period of 14 days to generate a rat model with compromised spermatogenesis. MP and LD were administered in two separate groups of these animals starting 15th day for a period of 56 days, and the results were compared with an auto-recovery (AR) group. Sperm count and motility, testis histo-architecture, level of reactive oxygen species (ROS), mitochondrial membrane potential (MMP), apoptosis, peripheral hormone levels and testicular germ cell populations were analysed, in all experimental groups. We observed efficient and quick recovery of spermatogenesis in MP and LD groups in comparison to the auto-recovery group. The treatment regulated ROS level, apoptosis, and mitochondrial membrane potential (MMP), recovered the hypothalamic-pituitary-gonadal axis and the number of testicular germ cells, ultimately leading to increased sperm count and motility. Conclusion/Significance M. pruriens efficiently recovers the spermatogenic loss induced due to EE administration. The recovery is mediated by reduction in ROS level, restoration of MMP, regulation of apoptosis and eventual increase in the number of germ cells and regulation of apoptosis. The present study simplified the complexity of mechanism involved and provided meaningful insights into MP/LD mediated correction of spermatogenic impairment caused by estrogens exposure. This is the first study demonstrating that L-DOPA largely accounts for pro-spermatogenic properties of M. pruriens. The manuscript bears CDRI communication number 8374. PMID:23349947

Mucuna pruriens and its major constituent L-DOPA recover spermatogenic loss by combating ROS, loss of mitochondrial membrane potential and apoptosis.

PubMed

Singh, Akhand Pratap; Sarkar, Saumya; Tripathi, Muktanand; Rajender, Singh

2013-01-01

The Ayurvedic medicinal system claims Mucuna pruriens (MP) to possess pro-male fertility, aphrodisiac and adaptogenic properties. Some scientific evidence also supports its pro-male fertility properties; however, the mechanism of its action is not yet clear. The present study aimed at demonstrating spermatogenic restorative efficacy of MP and its major constituent L-DOPA (LD), and finding the possible mechanism of action thereof in a rat model. Ethinyl estradiol (EE) was administered at a rate of 3 mg/kg body weight (BW)/day for a period of 14 days to generate a rat model with compromised spermatogenesis. MP and LD were administered in two separate groups of these animals starting 15(th) day for a period of 56 days, and the results were compared with an auto-recovery (AR) group. Sperm count and motility, testis histo-architecture, level of reactive oxygen species (ROS), mitochondrial membrane potential (MMP), apoptosis, peripheral hormone levels and testicular germ cell populations were analysed, in all experimental groups. We observed efficient and quick recovery of spermatogenesis in MP and LD groups in comparison to the auto-recovery group. The treatment regulated ROS level, apoptosis, and mitochondrial membrane potential (MMP), recovered the hypothalamic-pituitary-gonadal axis and the number of testicular germ cells, ultimately leading to increased sperm count and motility. M. pruriens efficiently recovers the spermatogenic loss induced due to EE administration. The recovery is mediated by reduction in ROS level, restoration of MMP, regulation of apoptosis and eventual increase in the number of germ cells and regulation of apoptosis. The present study simplified the complexity of mechanism involved and provided meaningful insights into MP/LD mediated correction of spermatogenic impairment caused by estrogens exposure. This is the first study demonstrating that L-DOPA largely accounts for pro-spermatogenic properties of M. pruriens. The manuscript bears CDRI communication number 8374.

The Toxicology of Perfluorodecanoic Acid in Rodents,

DTIC Science & Technology

Perfluoro -n-decanoic acid or nonadecafluoro-n-decanoic acid (NDFDA) is a straight chain, perfluorinated , ten-carbon acid. Experiments were conducted...to determine the LD50 and to evaluate survival times of rats after single intraperitoneal (IP) injections of NDFDA or of Fluorooctanoic acid ( PFOA ...experimental animals. With NDFDA, the LD50/14 days was 63.6 mg/kg, and the LD50/30 days was 41.4 mg/kg. With PFOA , there was no mortality after the 5th day following injection, and both the LD50/14 and LD50/30 were 188.7 mg/kg.

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

PubMed Central

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod. PMID:22428056

Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers

PubMed Central

2010-01-01

Background The information provided by dense genome-wide markers using high throughput technology is of considerable potential in human disease studies and livestock breeding programs. Genome-wide association studies relate individual single nucleotide polymorphisms (SNP) from dense SNP panels to individual measurements of complex traits, with the underlying assumption being that any association is caused by linkage disequilibrium (LD) between SNP and quantitative trait loci (QTL) affecting the trait. Often SNP are in genomic regions of no trait variation. Whole genome Bayesian models are an effective way of incorporating this and other important prior information into modelling. However a full Bayesian analysis is often not feasible due to the large computational time involved. Results This article proposes an expectation-maximization (EM) algorithm called emBayesB which allows only a proportion of SNP to be in LD with QTL and incorporates prior information about the distribution of SNP effects. The posterior probability of being in LD with at least one QTL is calculated for each SNP along with estimates of the hyperparameters for the mixture prior. A simulated example of genomic selection from an international workshop is used to demonstrate the features of the EM algorithm. The accuracy of prediction is comparable to a full Bayesian analysis but the EM algorithm is considerably faster. The EM algorithm was accurate in locating QTL which explained more than 1% of the total genetic variation. A computational algorithm for very large SNP panels is described. Conclusions emBayesB is a fast and accurate EM algorithm for implementing genomic selection and predicting complex traits by mapping QTL in genome-wide dense SNP marker data. Its accuracy is similar to Bayesian methods but it takes only a fraction of the time. PMID:20969788

Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers.

PubMed

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.

Comparing strategies for selection of low-density SNPs for imputation-mediated genomic prediction in U. S. Holsteins.

PubMed

He, Jun; Xu, Jiaqi; Wu, Xiao-Lin; Bauck, Stewart; Lee, Jungjae; Morota, Gota; Kachman, Stephen D; Spangler, Matthew L

2018-04-01

SNP chips are commonly used for genotyping animals in genomic selection but strategies for selecting low-density (LD) SNPs for imputation-mediated genomic selection have not been addressed adequately. The main purpose of the present study was to compare the performance of eight LD (6K) SNP panels, each selected by a different strategy exploiting a combination of three major factors: evenly-spaced SNPs, increased minor allele frequencies, and SNP-trait associations either for single traits independently or for all the three traits jointly. The imputation accuracies from 6K to 80K SNP genotypes were between 96.2 and 98.2%. Genomic prediction accuracies obtained using imputed 80K genotypes were between 0.817 and 0.821 for daughter pregnancy rate, between 0.838 and 0.844 for fat yield, and between 0.850 and 0.863 for milk yield. The two SNP panels optimized on the three major factors had the highest genomic prediction accuracy (0.821-0.863), and these accuracies were very close to those obtained using observed 80K genotypes (0.825-0.868). Further exploration of the underlying relationships showed that genomic prediction accuracies did not respond linearly to imputation accuracies, but were significantly affected by genotype (imputation) errors of SNPs in association with the traits to be predicted. SNPs optimal for map coverage and MAF were favorable for obtaining accurate imputation of genotypes whereas trait-associated SNPs improved genomic prediction accuracies. Thus, optimal LD SNP panels were the ones that combined both strengths. The present results have practical implications on the design of LD SNP chips for imputation-enabled genomic prediction.

Addition of seaweed (Laminaria digitata) extracts containing laminarin and fucoidan to porcine diets: influence on the quality and shelf-life of fresh pork.

PubMed

Moroney, N C; O'Grady, M N; O'Doherty, J V; Kerry, J P

2012-12-01

A seaweed extract containing laminarin (L) and fucoidan (F) (L/F) was manufactured from brown seaweed (Laminaria digitata) in spray-dried (L/F-SD) and wet (L/F-WS) forms. The effect of supplementation of pig diets with L/F-SD and L/F-WS (L, 500 mg/kg feed; F, 420 mg/kg feed) for 21 days pre-slaughter, on quality indices of fresh M. longissimus dorsi (LD) steaks was examined. Susceptibility of porcine liver, heart, kidney and lung tissue homogenates to iron-induced (1mM FeSO₄) lipid oxidation was also investigated. Dietary supplementation with L/F did not increase plasma total antioxidant status (TAS). In LD steaks stored in modified atmosphere packs (80% O₂:20% CO₂) (MAP) for up to 15 days at 4 °C, muscle pH, surface colour (CIE 'L*' lightness, 'a*' redness and 'b*' yellowness values) and microbiology (psychrotrophic and mesophilic counts, log CFU/g pork) were unaffected by dietary L/F. In general, levels of lipid oxidation (TBARS, mg MDA (malondialdehyde)/kg pork) followed the order: C>LF-SD>L/F-WS. A statistically significant reduction in lipid oxidation (P<0.05) was observed in LD steaks from 75% of pigs (n=6) fed with L/F-WS compared to controls. Iron-induced lipid oxidation increased in liver, heart, kidney and lung tissue homogenates over the 24h storage period and dietary L/F-WS reduced lipid oxidation to the greatest extent in liver tissue homogenates. Results demonstrate potential for the incorporation of marine-derived bioactive antioxidant components into muscle foods via the animal's diet. Copyright © 2012 Elsevier Ltd. All rights reserved.

Answers for Parents of the Child with Learning Disabilities. Showing and Telling It Like It Is!

ERIC Educational Resources Information Center

McCurley, Arlene Bell

The guidebook for parents of learning disabled (LD) children provides answers to questions such as the following: What is a learning disability? How does an LD child behave? What should parents who suspect their child has a learning disability do? Can an LD child succeed in school? How should parents discipline an LD child? How can parents manage…

An Examination of Variability in Identification of Learning Disabled Students according to Selected Discrepancy Formulas over a Three Year Period.

ERIC Educational Resources Information Center

White, Warren J.; And Others

Cumulative files on 276 students (grades 2-12) identified as learning disabled (LD) were analyzed in the project designed to investigate effects of LD selection formulas and the influence of various LD services. Analyses revealed that few (3-5%) of the students were identified as LD by formulas demanding a substantial IQ achievement discrepancy; a…

Hope, Optimism and Loneliness among First-Year College Students with Learning Disabilities: A Brief Longitudinal Study

ERIC Educational Resources Information Center

Rosenstreich, Eyal; Feldman, David B.; Davidson, Oranit B.; Maza, Etai; Margalit, Malka

2015-01-01

The goals of the study were to examine personal resources and social distress during the first month in college among students with learning disabilities (LD) and to compare their experiences with non-LD peer. The sample consisted of 335 first-year undergraduate students falling into two groups: 85 students with LD and 250 non-LD students.…

Interaction of frataxin, an iron binding protein, with IscU of Fe-S clusters biogenesis pathway and its upregulation in AmpB resistant Leishmania donovani.

PubMed

Zaidi, Amir; Singh, Krishn Pratap; Anwar, Shadab; Suman, Shashi S; Equbal, Asif; Singh, Kuljit; Dikhit, Manas R; Bimal, Sanjeeva; Pandey, Krishna; Das, Pradeep; Ali, Vahab

2015-08-01

Leishmania donovani is a unicellular protozoon parasite that causes visceral leishmaniasis (VL), which is a fatal disease if left untreated. Certain Fe-S proteins of the TCA cycle and respiratory chain have been found in the Leishmania parasite but the precise mechanisms for their biogenesis and the maturation of Fe-S clusters remains unknown. Fe-S clusters are ubiquitous cofactors of proteins that perform critical cellular functions. The clusters are biosynthesized by the mitochondrial Iron-Sulphur Cluster (ISC) machinery with core protein components that include the catalytic cysteine desulphurase IscS, the scaffold proteins IscU and IscA, and frataxin as an iron carrier/donor. However, no information regarding frataxin, its regulation, or its role in drug resistance is available for the Leishmania parasite. In this study, we characterized Ld-frataxin to investigate its role in the ISC machinery of L. donovani. We expressed and purified the recombinant Ld-frataxin protein and observed its interaction with Ld-IscU by co-purification and pull-down assay. Furthermore, we observed that the cysteine desulphurase activity of the purified Ld-IscS protein was stimulated in the presence of Ld-frataxin and Ld-IscU, particularly in the presence of iron; neither Ld-frataxin nor Ld-IscU alone had significant effects on Ld-IscS activity. Interestingly, RT-PCR and western blotting showed that Ld-frataxin is upregulated in AmpB-resistant isolates compared to sensitive strains, which may support higher Fe-S protein activity in AmpB-resistant L. donovani. Additionally, Ld-frataxin was localized in the mitochondria, as revealed by digitonin fractionation and indirect immunofluorescence. Thus, our results suggest the role of Ld-frataxin as an iron binding/carrier protein for Fe-S cluster biogenesis that physically interacts with other core components of the ISC machinery within the mitochondria. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

The STEM and CTE Pipeline for Community College Students with Learning Disabilities

NASA Astrophysics Data System (ADS)

Morgan, Micaela Victoria Cesario

The technological nature of the world we live in has produced a need for a workforce that is technologically savvy and possesses 21st century skills and abilities. Given that students with a learning disability (LD) may be an untapped source of science, technology, engineering, and mathematics (STEM) or career and technical education (CTE) potential, it is important to understand 1) whether LD students are capable of pursuing STEM and CTE fields and 2) what will aid them in successfully pursuing those fields. The two studies presented aim to answer those questions through a latent profile and latent class analysis. The results from the first study indicated that there are two STEM capable profiles of LD students: High-STEM and CTE Capability or Low-STEM Capability. It was found that female LD students were significantly more likely to be in the High-STEM and CTE Capability profile (.75, p < .05) by 2.11 times and that African-American LD students were significantly more likely to be found in the Low-STEM Capability profile (-1.31, p < .10). It was also more prevalent for LD students to pursue either STEM or CTE at the 2-year college regardless of what profile they resided in. Understanding a students' STEM or CTE capability can play a role in how they prepare and plan for their future. For the second study it was found that LD students could be categorized into three engagement classes: Highly Engaged LD Students, Moderately Engaged LD Students, and Poorly Engaged LD Students. Again, gender played a role in students' classification and it was found that female students were significantly more likely to be in the Moderately Engaged class (.22, p < .05). Results from this study also indicate that the 2-year pathway is the most traversed by LD students. LD students who were engaged in their IEP process, possess self-determination, and are able to utilize accommodations were more successful in pursuing a STEM and CTE field. Implications for postsecondary institutions will be discussed.

Contrasting results from GWAS and QTL mapping on wing length in great reed warblers.

PubMed

Hansson, Bengt; Sigeman, Hanna; Stervander, Martin; Tarka, Maja; Ponnikas, Suvi; Strandh, Maria; Westerdahl, Helena; Hasselquist, Dennis

2018-04-15

A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p-values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi- vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations. © 2018 John Wiley & Sons Ltd.

Genetics of Sputum Gene Expression in Chronic Obstructive Pulmonary Disease

PubMed Central

Qiu, Weiliang; Cho, Michael H.; Riley, John H.; Anderson, Wayne H.; Singh, Dave; Bakke, Per; Gulsvik, Amund; Litonjua, Augusto A.; Lomas, David A.; Crapo, James D.; Beaty, Terri H.; Celli, Bartolome R.; Rennard, Stephen; Tal-Singer, Ruth; Fox, Steven M.; Silverman, Edwin K.; Hersh, Craig P.

2011-01-01

Previous expression quantitative trait loci (eQTL) studies have performed genetic association studies for gene expression, but most of these studies examined lymphoblastoid cell lines from non-diseased individuals. We examined the genetics of gene expression in a relevant disease tissue from chronic obstructive pulmonary disease (COPD) patients to identify functional effects of known susceptibility genes and to find novel disease genes. By combining gene expression profiling on induced sputum samples from 131 COPD cases from the ECLIPSE Study with genomewide single nucleotide polymorphism (SNP) data, we found 4315 significant cis-eQTL SNP-probe set associations (3309 unique SNPs). The 3309 SNPs were tested for association with COPD in a genomewide association study (GWAS) dataset, which included 2940 COPD cases and 1380 controls. Adjusting for 3309 tests (p<1.5e-5), the two SNPs which were significantly associated with COPD were located in two separate genes in a known COPD locus on chromosome 15: CHRNA5 and IREB2. Detailed analysis of chromosome 15 demonstrated additional eQTLs for IREB2 mapping to that gene. eQTL SNPs for CHRNA5 mapped to multiple linkage disequilibrium (LD) bins. The eQTLs for IREB2 and CHRNA5 were not in LD. Seventy-four additional eQTL SNPs were associated with COPD at p<0.01. These were genotyped in two COPD populations, finding replicated associations with a SNP in PSORS1C1, in the HLA-C region on chromosome 6. Integrative analysis of GWAS and gene expression data from relevant tissue from diseased subjects has located potential functional variants in two known COPD genes and has identified a novel COPD susceptibility locus. PMID:21949713

Genetic Variation and Association Mapping of Seed-Related Traits in Cultivated Peanut (Arachis hypogaea L.) Using Single-Locus Simple Sequence Repeat Markers.

PubMed

Zhao, Jiaojiao; Huang, Li; Ren, Xiaoping; Pandey, Manish K; Wu, Bei; Chen, Yuning; Zhou, Xiaojing; Chen, Weigang; Xia, Youlin; Li, Zeqing; Luo, Huaiyong; Lei, Yong; Varshney, Rajeev K; Liao, Boshou; Jiang, Huifang

2017-01-01

Cultivated peanut ( Arachis hypogaea L.) is an allotetraploid (AABB, 2 n = 4 x = 40), valued for its edible oil and digestible protein. Seed size and weight are important agronomical traits significantly influence the yield and nutritional composition of peanut. However, the genetic basis of seed-related traits remains ambiguous. Association mapping is a powerful approach for quickly and efficiently exploring the genetic basis of important traits in plants. In this study, a total of 104 peanut accessions were used to identify molecular markers associated with seed-related traits using 554 single-locus simple sequence repeat (SSR) markers. Most of the accessions had no or weak relationship in the peanut panel. The linkage disequilibrium (LD) decayed with the genetic distance of 1cM at the genome level and the LD of B subgenome decayed faster than that of the A subgenome. Large phenotypic variation was observed for four seed-related traits in the association panel. Using mixed linear model with population structure and kinship, a total of 30 significant SSR markers were detected to be associated with four seed-related traits ( P < 1.81 × 10 -3 ) in different environments, which explained 11.22-32.30% of the phenotypic variation for each trait. The marker AHGA44686 was simultaneously and repeatedly associated with seed length and hundred-seed weight in multiple environments with large phenotypic variance (26.23 ∼ 32.30%). The favorable alleles of associated markers for each seed-related trait and the optimal combination of favorable alleles of associated markers were identified to significantly enhance trait performance, revealing a potential of utilization of these associated markers in peanut breeding program.

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs.

PubMed

Laucou, Valérie; Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Hausmann, Ludger; Ibáñez, Javier; Le Paslier, Marie-Christine; Maghradze, David; Martinez-Zapater, José Miguel; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

PubMed Central

Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Maghradze, David; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine. PMID:29420602

A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

PubMed Central

McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Penedo, M. Cecilia T.; Røed, Knut H.; Ryder, Oliver A.; Swinburne, June E.; Tozaki, Teruaki; Valberg, Stephanie J.; Vaudin, Mark; Lindblad-Toh, Kerstin

2012-01-01

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species. PMID:22253606

Automated image analysis method for detecting and quantifying macrovesicular steatosis in hematoxylin and eosin-stained histology images of human livers.

PubMed

Nativ, Nir I; Chen, Alvin I; Yarmush, Gabriel; Henry, Scot D; Lefkowitch, Jay H; Klein, Kenneth M; Maguire, Timothy J; Schloss, Rene; Guarrera, James V; Berthiaume, Francois; Yarmush, Martin L

2014-02-01

Large-droplet macrovesicular steatosis (ld-MaS) in more than 30% of liver graft hepatocytes is a major risk factor for liver transplantation. An accurate assessment of the ld-MaS percentage is crucial for determining liver graft transplantability, which is currently based on pathologists' evaluations of hematoxylin and eosin (H&E)-stained liver histology specimens, with the predominant criteria being the relative size of the lipid droplets (LDs) and their propensity to displace a hepatocyte's nucleus to the cell periphery. Automated image analysis systems aimed at objectively and reproducibly quantifying ld-MaS do not accurately differentiate large LDs from small-droplet macrovesicular steatosis and do not take into account LD-mediated nuclear displacement; this leads to a poor correlation with pathologists' assessments. Here we present an improved image analysis method that incorporates nuclear displacement as a key image feature for segmenting and classifying ld-MaS from H&E-stained liver histology slides. 52,000 LDs in 54 digital images from 9 patients were analyzed, and the performance of the proposed method was compared against the performance of current image analysis methods and the ld-MaS percentage evaluations of 2 trained pathologists from different centers. We show that combining nuclear displacement and LD size information significantly improves the separation between large and small macrovesicular LDs (specificity = 93.7%, sensitivity = 99.3%) and the correlation with pathologists' ld-MaS percentage assessments (linear regression coefficient of determination = 0.97). This performance vastly exceeds that of other automated image analyzers, which typically underestimate or overestimate pathologists' ld-MaS scores. This work demonstrates the potential of automated ld-MaS analysis in monitoring the steatotic state of livers. The image analysis principles demonstrated here may help to standardize ld-MaS scores among centers and ultimately help in the process of determining liver graft transplantability. © 2013 American Association for the Study of Liver Diseases.

LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis.

PubMed

Zheng, Jie; Erzurumluoglu, A Mesut; Elsworth, Benjamin L; Kemp, John P; Howe, Laurence; Haycock, Philip C; Hemani, Gibran; Tansey, Katherine; Laurin, Charles; Pourcain, Beate St; Warrington, Nicole M; Finucane, Hilary K; Price, Alkes L; Bulik-Sullivan, Brendan K; Anttila, Verneri; Paternoster, Lavinia; Gaunt, Tom R; Evans, David M; Neale, Benjamin M

2017-01-15

LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously. In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies. The web interface and instructions for using LD Hub are available at http://ldsc.broadinstitute.org/ CONTACT: jie.zheng@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

The effect of low-density diets on broiler breeder performance during the laying period and on embryonic development of their offspring.

PubMed

Enting, H; Kruip, T A M; Verstegen, M W A; van der Aar, P J

2007-05-01

The effect of low-density diets on bird performance, egg composition, and embryonic development was studied with 2,100 female and 210 male Cobb broiler breeders from 25 to 60 wk of age. The experiment included 5 treatments. These included a control group with a normal density diet (ND, 2,800 kcal of AME/kg). Treatments 2 (LD11) and 3 (LD21) had a 11 and 21% lower nutrient density. Treatment 4 (LD11(OP)) had a 11% less dense diet, which was obtained by inclusion of other feed ingredients. In these 4 treatments similar diets were given during the rearing and the laying period. Treatment 5 combined LD12 in the rearing period and ND diets during the laying period (LD12-ND). Egg composition and embryonic development were measured in eggs of ND and LD21 birds at 29 and 41 wk of age. During the laying period from wk 25 to 60, live weights did not differ among treatments, except that birds fed LD11(OP) had lower live weights. A significantly higher rate of lay was provided by LD11 compared with ND. Egg weights were significantly higher when low-density diets were fed, particularly in LD11(OP). Percentage of fertile eggs did not differ among treatments. Compared with the other treatments, LD11(OP) provided a significantly lower hatchability. We found that LD21 resulted in a better development of the area vitellina externa and heart and embryo weight at 29 wk of age. It was concluded that this was related to a higher egg weight and egg white proportion. This suggests that the amount of egg white in eggs of hens fed ND was limiting for embryonic development, particularly in eggs of young broiler breeders.

Field-evolved resistance to λ-cyhalothrin in the lady beetle Eriopis connexa.

PubMed

Costa, P M G; Torres, J B; Rondelli, V M; Lira, R

2018-06-01

Natural enemies are exposed to insecticide sprays for herbivorous species and may evolve field resistance to insecticides. Natural enemies selected for resistance in the field, however, are welcome for pest control. The susceptibility of 20 populations of Eriopis connexa from various crop ecosystems to λ-cyhalothrin was tested. Three bioassays were conducted: (i) topical treatment with lethal dose (LD)50 previously determined for populations considered standard for susceptibility (LD50S) and for resistance (LD50R) to λ-cyhalothrin at technical grade; (ii) dose-mortality assay to calculate the LD for populations exhibiting significant survival to the LD50R; and (iii) determination of survival when exposed to dried residues at field rates. Among the 20 tested populations, seven populations did not survive or survival rates were lower than 10% when treated with LD50R; three populations survived >20%, but lower than 50%; while ten populations exhibited equal or greater survival rates compared with the 50% expected survival for the LD50R. Thus, these ten populations were subjected to dose-mortality response, and the LD50 values varied from 0.046 to 5.44 µg a.i./insect with resistance ratio of 8.52- to 884.08-folds. Adults from these ten populations that were ranked as resistant according to the LD50R exhibited survival from 44.5 to 100% exposed to the lowest and from 38.8 to 100% exposed to the highest field rates of λ-cyhalothrin, respectively. Otherwise, the remaining ten populations ranked as susceptible according to the LD50R showed survival from 3.3 to 56% exposed to the lowest and from 0 to 17.7% exposed to the highest field rates of λ-cyhalothrin, respectively. Therefore, 50% of the tested E. connexa populations exhibited field-evolved resistance to λ-cyhalothrin and the use of a discriminatory LD50 for resistance matched the survival obtained when exposed to the insecticide field rates.

Tolerance of house fly, Musca domestica L. (Diptera: Muscidae) to dichlorvos (76% EC) an insecticide used for fly control in the tsunami-hit coastal villages of southern India.

PubMed

Srinivasan, R; Jambulingam, P; Gunasekaran, K; Boopathidoss, P S

2008-02-01

The Directorate of Public Health (DPH), Tamil Nadu, in southern India employed spraying of dichlorvos (76% EC) for quick elimination of fly concentrations in the tsunami-hit coastal villages at the concentration of 304g (a.i.)/10,000m(2). However, nuisance of house flies remained high particularly in temporary shelters and centralized relief kitchens. Susceptibility of house fly, Musca domestica to dichlorvos was determined in the laboratory to provide information for an effective management of this pest. Various concentrations of dichlorvos (76% EC) viz., 0.1, 0.2, 0.4, 0.6 and 0.8microg (a.i.) per fly, were tested using topical application against F(1) progenies of house flies collected 12 months after insecticide applications from different habitats in the tsunami-hit coastal villages. Fly mortality was recorded at 24h post treatment. Parallel controls were maintained for comparison. Mortality of the house flies varied between 17.5% and 100% and increased with an increase in dosage of the insecticide. Mortality was >80% at 0.6 and 0.8microg (a.i.) per fly. The LD(50) of dichlorvos tested against flies collected from different villages varied from 0.218microg (a.i.) to 0.235microg (a.i.) per fly and the LD(90) varied from 0.574microg (a.i.) to 0.639microg (a.i.) per fly. House flies collected from a rural village, Thirukanur that had never been exposed for insecticide treatment in the past one decade, when tested, the mortality varied between 92.5% and 100% and increased with concentration of dichlorvos. Mortality was >90% from 0.2microg (a.i.) per fly and the LD(50) was 0.0399microg (a.i.)/fly, while the LD(90) was 0.1604microg (a.i.)/fly. The LD(90) values of the flies collected from the tsunami-hit villages were 3.5-3.9 times higher than that of the flies collected from Thirukanur. Fly abundance remained high in tsunami-hit villages with no marked reduction, suggesting that the flies had developed tolerance to dichlorvos. It is suggested that for an effective management of these resistant populations changing insecticides, application of unrelated insecticide, together with an appropriate environmental sanitation measure is necessary to keep the population under check.

Social competence and collaborative guided inquiry science activities: Experiences of students with learning disabilities

NASA Astrophysics Data System (ADS)

Taylor, Jennifer Anne

This thesis presents a qualitative investigation of the effects of social competence on the participation of students with learning disabilities (LD) in the science learning processes associated with collaborative, guided inquiry learning. An inclusive Grade 2 classroom provided the setting for the study. Detailed classroom observations were the primary source of data. In addition, the researcher conducted two interviews with the teacher, and collected samples of students' written work. The purpose of the research was to investigate: (a) How do teachers and peers mediate the participation of students with LD in collaborative, guided inquiry science activities, (b) What learning processes do students with LD participate in during collaborative, guided inquiry science activities, and (c) What components of social competence support and constrain the participation of students with LD during collaborative, guided inquiry science activities? The findings of the study suggest five key ideas for research and teaching in collaborative, guided inquiry science in inclusive classrooms. First, using a variety of collaborative learning formats (whole-class, small-group, and pairs) creates more opportunities for the successful participation of diverse students with LD. Second, creating an inclusive community where students feel accepted and valued may enhance the academic and social success of students with LD. Third, careful selection of partners for students with LD is important for a positive learning experience. Students with LD should be partnered with academically successful, socially competent peers; also, this study suggested that students with LD experience more success working collaboratively in pairs rather than in small groups. Fourth, a variety of strategies are needed to promote active participation and positive social interactions for students with and without LD during collaborative, guided inquiry learning. Fifth, adopting a general approach to teaching collaborative inquiry that crosses curriculum borders may enhance success of inclusive teaching practices.

Negatively-charged residues in the polar carboxy-terminal region in FSP27 are indispensable for expanding lipid droplets.

PubMed

Tamori, Yoshikazu; Tateya, Sanshiro; Ijuin, Takeshi; Nishimoto, Yuki; Nakajima, Shinsuke; Ogawa, Wataru

2016-03-01

FSP27 has an important role in large lipid droplet (LD) formation because it exchanges lipids at the contact site between LDs. In the present study, we clarify that the amino-terminal domain of FSP27 (amino acids 1-130) is dispensable for LD enlargement, although it accelerates LD growth. LD expansion depends on the carboxy-terminal domain of FSP27 (amino acids 131-239). Especially, the negative charge of the acidic residues (D215, E218, E219 and E220) in the polar carboxy-terminal region (amino acids 202-239) is essential for the enlargement of LD. We propose that the carboxy-terminal domain of FSP27 has a crucial role in LD expansion, whereas the amino-terminal domain only has a supportive role. © 2016 Federation of European Biochemical Societies.

Postsecondary Students with Specific Learning Disabilities and with Attention Deficit Hyperactivity Disorder Should Not Be Considered as a Unified Group for Research or Practice

ERIC Educational Resources Information Center

Budd, Jillian; Fichten, Catherine S.; Jorgensen, Mary; Havel, Alice; Flanagan, Tara

2016-01-01

Objective: To examine similarities and differences among college/university students with ADHD, LD, and comorbid ADHD and LD on variables related to academic performance. Method: Students who self-reported ADHD (n = 42), LD (n = 72), or comorbid ADHD and LD (n = 42), completed an online questionnaire which evaluated grades, parental education,…

Assessment of antiradiation drug effectiveness to fission neutron irradiation. Annual report No. 1, April-August 1981

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sigdestad, C.P.

1981-09-01

This report deals with the assays of various compounds for their toxicity of anti-radiation efficacy following exposure to either Co-60 or fission neutron irradiation. The compounds reported herein include WR 347, WR 2721, WR 3689, WR 44923, WR 109342, WR 151327, WR 16843, and WR 176542. The end-points measured in the radiation studies were LD50(6) and LD50(30). The compounds and their dose modification factors (DMF) for the neutron LD50(6) following i.p. administration, were, in descending order of effectiveness: WR 151327 (1.42), WR 347 (1.37), WR 3689 (1.34) WR 44923 (1.34), WR 2721 (1.26), WR 168643 (1.24), and WR 176542 (1.23).more » The corresponding LD50(30)'s for fission neutron irradiation following i.p. administration, were: WR 168643 (1.67), WR 3689 (1.52), WR 151327 (1.45), WR 44923 (1.39), WR 347 (1.22), WR 2721 (1.21), and WR 176542 (1.18). For low LET Co-60 gamma irradiation the LD50(6) and LD50(30) were determined for WR 347 following i.p. administration. The DMF's obtained were: LD50(6) (1.4), LD50(30) (1.5).« less

PGRP-LD mediates A. stephensi vector competency by regulating homeostasis of microbiota-induced peritrophic matrix synthesis

PubMed Central

Song, Xiumei; Wang, Mengfei; Dong, Li

2018-01-01

Peptidoglycan recognition proteins (PGRPs) and commensal microbes mediate pathogen infection outcomes in insect disease vectors. Although PGRP-LD is retained in multiple vectors, its role in host defense remains elusive. Here we report that Anopheles stephensi PGRP-LD protects the vector from malaria parasite infection by regulating gut homeostasis. Specifically, knock down of PGRP-LD (dsLD) increased susceptibility to Plasmodium berghei infection, decreased the abundance of gut microbiota and changed their spatial distribution. This outcome resulted from a change in the structural integrity of the peritrophic matrix (PM), which is a chitinous and proteinaceous barrier that lines the midgut lumen. Reduction of microbiota in dsLD mosquitoes due to the upregulation of immune effectors led to dysregulation of PM genes and PM fragmentation. Elimination of gut microbiota in antibiotic treated mosquitoes (Abx) led to PM loss and increased vectorial competence. Recolonization of Abx mosquitoes with indigenous Enterobacter sp. restored PM integrity and decreased mosquito vectorial capacity. Silencing PGRP-LD in mosquitoes without PM didn’t influence their vector competence. Our results indicate that PGPR-LD protects the gut microbiota by preventing hyper-immunity, which in turn promotes PM structurally integrity. The intact PM plays a key role in limiting P. berghei infection. PMID:29489896

Progranulin is increased in human and murine lipodystrophy.

PubMed

Miehle, Konstanze; Ebert, Thomas; Kralisch, Susan; Hoffmann, Annett; Kratzsch, Jürgen; Schlögl, Haiko; Stumvoll, Michael; Fasshauer, Mathias

2016-10-01

Lipodystrophies (LD) are genetic or acquired disorders sharing the symptom of partial or complete adipose tissue deficiency and a dysregulation of adipokines including leptin and adiponectin. Progranulin, an adipokine with proinflammatory and insulin resistance-inducing characteristics, has not been investigated in LD so far. Circulating progranulin was determined in LD patients (N=37) and in age-, gender-, and body mass index-matched healthy control subjects (N=37). Additionally, we investigated progranulin expression in an LD mouse model as compared to wild-type mice. Moreover, we elucidated circulating progranulin before and during metreleptin supplementation in 10 patients with LD. Median [interquartile range] circulating progranulin was increased in patients with LD (82.9 [25.9] μg/l) as compared to controls (73.6 [22.8] μg/l) (p=0.005). C-reactive protein (CRP) remained an independent and positive predictor of progranulin in multivariate analysis. Progranulin mRNA was significantly upregulated in all adipose tissue depots, i.e. visceral, subcutaneous, and brown adipose tissue, and in muscle of LD animals versus wild-type mice. Progranulin levels did not significantly change during metreleptin supplementation. Progranulin serum concentration is increased in patients with LD, and shows an independent and positive correlation with CRP. Different adipose tissue depots and muscle might be potential origins of elevated progranulin. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evaluation of anaerobic digestates from different feedstocks as growth media for Tetradesmus obliquus, Botryococcus braunii, Phaeodactylum tricornutum and Arthrospira maxima.

PubMed

Massa, Marina; Buono, Silvia; Langellotti, Antonio Luca; Castaldo, Luigi; Martello, Anna; Paduano, Antonello; Sacchi, Raffaele; Fogliano, Vincenzo

2017-05-25

In this paper, two freshwater microalgae (Tetradesmus obliquus and Botryococcus braunii), a marine diatom (Phaeodactylum tricornutum) and a photosynthetic cyanobacterium (Arthrospira maxima) were investigated for their ability to grow on liquid digestates (LDs). Three LDs were obtained from anaerobic digestion of different organic wastes: zootechnical (ZW LD), vegetable biomass (VW LD) and the organic fraction of municipal solid wastes (MW LD). All the strains showed the same growth performance on VW LD as on the respective standard media (SM), while ZW LD was efficient only for growth of T. obliquus and B. braunii. MW LD was the poorest growth medium for all the strains. Data on nutrient removal efficiency showed that A. maxima and T. obliquus made the best use of NH 4 + -N with removal values ranging between 98.9-99.8%, while P. tricornutum and B. braunii showed values of 79.0 and 88.5% respectively. Applying repeated batch cultivation in photobioreactors, the biochemical composition of A. maxima and T. obliquus biomass grown on ZW LD and VW LD, showed an increase of lipid, carbohydrates and ash in both microalgae. Biomass biochemical profiles suggest possible applications in feed, chemicals and energy sectors. Copyright © 2016 Elsevier B.V. All rights reserved.

Altitude engine test of a turbofan exhaust gas mixer to conserve fuel

NASA Technical Reports Server (NTRS)

Cullom, R. R.; Johnsen, R. L.

1977-01-01

A comparison of the specific fuel consumption was made with and without an internal mixer installed in a low bypass ratio, confluent flow turbofan engine. Tests were conducted at several Mach numbers and altitudes for core to fan stream total temperature ratios of 2.0 and 2.5 and mixing lengths of L/D = 0.95 and 1.74. For these test conditions, the specific fuel consumption improvement varied from 2.5 to 4.0 percent.

[Chemotherapeutic effectiveness of a new derivative of 5-alkyl-3N-furanones in experimental staphylococcal infection].

PubMed

Tomnikov, A Iu; Shub, G M

1990-02-01

High chemotherapeutic efficacy of the compound 1929, a new derivative of 5-alkyl-3H-furanones was shown in albino mice with experimental staphylococcal infection caused by intraperitoneal administration to the animals. The efficacy was found to be higher than that of furagin used for comparison. The average therapeutic dose (AD50) of the compound for intraperitoneal administration amounted to 40 mg/kg while the average lethal dose (LD50) was 3000 mg/kg.

Correlations by the entrainment theory of thermodynamic effects for developed cavitation in venturis and comparisons with ogive data

NASA Technical Reports Server (NTRS)

Billet, M. L.; Holl, J. W.; Weir, D. S.

1975-01-01

A semi-empirical entrainment theory was employed to correlate the measured temperature depression, Delta T, in a developed cavity for a venturi. This theory correlates Delta t in terms of the dimensionless numbers of Nusselt, Reynolds, Froude, Weber and Peclet, and dimensionless cavity length, L/D. These correlations are then compared with similar correlations for zero and quarter caliber ogives. In addition, cavitation number data for both limited and developed cavitation in venturis are presented.

Design of high precision temperature control system for TO packaged LD

NASA Astrophysics Data System (ADS)

Liang, Enji; Luo, Baoke; Zhuang, Bin; He, Zhengquan

2017-10-01

Temperature is an important factor affecting the performance of TO package LD. In order to ensure the safe and stable operation of LD, a temperature control circuit for LD based on PID technology is designed. The MAX1978 and an external PID circuit are used to form a control circuit that drives the thermoelectric cooler (TEC) to achieve control of temperature and the external load can be changed. The system circuit has low power consumption, high integration and high precision,and the circuit can achieve precise control of the LD temperature. Experiment results show that the circuit can achieve effective and stable control of the laser temperature.