Insulin receptors internalize by a rapid, saturable pathway requiring receptor autophosphorylation and an intact juxtamembrane region

PubMed Central

1991-01-01

The effect of receptor occupancy on insulin receptor endocytosis was examined in CHO cells expressing normal human insulin receptors (CHO/IR), autophosphorylation- and internalization-deficient receptors (CHO/IRA1018), and receptors which undergo autophosphorylation but lack a sequence required for internalization (CHO/IR delta 960). The rate of [125I]insulin internalization in CHO/IR cells at 37 degrees C was rapid at physiological concentrations, but decreased markedly in the presence of increasing unlabeled insulin (ED50 = 1-3 nM insulin, or 75,000 occupied receptors/cell). In contrast, [125I]insulin internalization by CHO/IRA1018 and CHO/IR delta 960 cells was slow and was not inhibited by unlabeled insulin. At saturating insulin concentrations, the rate of internalization by wild-type and mutant receptors was similar. Moreover, depletion of intracellular potassium, which has been shown to disrupt coated pit formation, inhibited the rapid internalization of [125I]insulin at physiological insulin concentrations by CHO/IR cells, but had little or no effect on [125I]insulin uptake by CHO/IR delta 960 and CHO/IRA1018 cells or wild-type cells at high insulin concentrations. These data suggest that the insulin-stimulated entry of the insulin receptor into a rapid, coated pit-mediated internalization pathway is saturable and requires receptor autophosphorylation and an intact juxtamembrane region. Furthermore, CHO cells also contain a constitutive nonsaturable pathway which does not require receptor autophosphorylation or an intact juxtamembrane region; this second pathway is unaffected by depletion of intracellular potassium, and therefore may be independent of coated pits. Our data suggest that the ligand-stimulated internalization of the insulin receptor may require specific saturable interactions between the receptor and components of the endocytic system. PMID:1757462

SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes

PubMed Central

Mix, Heiko; Lobanov, Alexey V.; Gladyshev, Vadim N.

2007-01-01

Expression of selenocysteine (Sec)-containing proteins requires the presence of a cis-acting mRNA structure, called selenocysteine insertion sequence (SECIS) element. In bacteria, this structure is located in the coding region immediately downstream of the Sec-encoding UGA codon, whereas in eukaryotes a completely different SECIS element has evolved in the 3′-untranslated region. Here, we report that SECIS elements in the coding regions of selenoprotein mRNAs support Sec insertion in higher eukaryotes. Comprehensive computational analysis of all available viral genomes revealed a SECIS element within the ORF of a naturally occurring selenoprotein homolog of glutathione peroxidase 4 in fowlpox virus. The fowlpox SECIS element supported Sec insertion when expressed in mammalian cells as part of the coding region of viral or mammalian selenoproteins. In addition, readthrough at UGA was observed when the viral SECIS element was located upstream of the Sec codon. We also demonstrate successful de novo design of a functional SECIS element in the coding region of a mammalian selenoprotein. Our data provide evidence that the location of the SECIS element in the untranslated region is not a functional necessity but rather is an evolutionary adaptation to enable a more efficient synthesis of selenoproteins. PMID:17169995

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.

PubMed

Lazzarato, F; Franceschinis, G; Botta, M; Cordero, F; Calogero, R A

2004-11-01

RRE allows the extraction of non-coding regions surrounding a coding sequence [i.e. gene upstream region, 5'-untranslated region (5'-UTR), introns, 3'-UTR, downstream region] from annotated genomic datasets available at NCBI. RRE parser and web-based interface are accessible at http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html

Implementation of the International Code of Marketing of Breastmilk Substitutes in the Eastern Mediterranean Region.

PubMed

Al Jawaldeh, Ayoub; Sayed, Ghada

2018-04-05

Optimal breastfeeding practices and appropriate complementary feeding improve child health, survival and development. The countries of the Eastern Mediterranean Region have made significant strides in formulation and implementation of legislation to protect and promote breastfeeding based on The International Code of Marketing of Breast-milk Substitutes (the Code) and subsequent relevant World Health Assembly resolutions. To assess the implementation of the Code in the Region. Assessment was conducted by the World Health Organization (WHO) Regional Office for the Eastern Mediterranean using a WHO standard questionnaire. Seventeen countries in the Region have enacted legislation to protect breastfeeding. Only 6 countries have comprehensive legislation or other legal measures reflecting all or most provisions of the Code; 4 countries have legal measures incorporating many provisions of the Code; 7 countries have legal measures that contain a few provisions of the Code; 4 countries are currently studying the issue; and only 1 country has no measures in place. Further analysis of the legislation found that the text of articles in the laws fully reflected the Code articles in only 6 countries. Most countries need to revisit and amend existing national legislation to implement fully the Code and relevant World Health Assembly resolutions, supported by systematic monitoring and reporting. Copyright © World Health Organization (WHO) 2018. Some rights reserved. This work is available under the CC BY-NC-SA 3.0 IGO license (https://creativecommons.org/licenses/by-nc-sa/3.0/igo).

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

PubMed

Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

2011-09-23

Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

PubMed Central

Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

2011-01-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

PubMed

Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

2011-04-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

Regional metabolism of Met-enkephalin and cholecystokinin on intact ratbrain slices: characterization of specific peptidases.

PubMed

Konkoy, C S; Davis, T P

1995-12-01

The metabolism of Met-enkephalin and cholecystokinin (CCK) 8-(sulfated) by intact microslices was studied in rat brain regions. Incubation of brain slices with Met-enkephalin (400 microM) resulted in a linear rate of disappearance of parent peptide and appearance of metabolic fragments whose rate of accumulation was specific to brain region. The degradative rate (pmol/min/mg of protein) of Met-enkephalin was high in caudate-putamen (5,160 +/- 120) and lower in nucleus accumbens (3,630 +/- 110) and frontal cortex (3,180 +/- 120). Inhibition of aminopeptidases decreased Met-enkephalin degradation (50-97% vs. control) in frontal cortex but was less effective in caudate-putamen (20-34%). Tyr-Gly-Gly and Phe-Met were recovered in caudate-putamen and nucleus accumbens, whereas negligible quantities of these fragments were recovered from frontal cortex. Phosphoramidon, an inhibitor of neutral endopeptidase 24.11, decreased Met-enkephalin degradation in caudate-putamen (14%) but had no effect on that in frontal cortex. A cocktail of bestatin or leuhistin (inhibitors of aminopeptidases), phosphoramidon, and captopril (an inhibitor of angiotensin converting enzyme) protected Met-enkephalin from degradation (recovery > 95%) in caudate-putamen. CCK 8-(sulfated) degradation on slices from caudate-putamen, nucleus accumbens, and frontal cortex was not altered by inhibitors of neutral endopeptidase 24.11, metalloendopeptidase 24.15, angiotensin converting enzyme, or thiol proteases. Inhibitors of either aminopeptidases or serine proteases produced small reductions (13-30%) in CCK degradation in each region. These data provide evidence for regional and structural specificity in terminating the actions of neuropeptides.

Aboveground Biomass Variability Across Intact and Degraded Forests in the Brazilian Amazon

NASA Technical Reports Server (NTRS)

Longo, Marcos; Keller, Michael; Dos-Santos, Maiza N.; Leitold, Veronika; Pinage, Ekena R.; Baccini, Alessandro; Saatchi, Sassan; Nogueira, Euler M.; Batistella, Mateus; Morton, Douglas C.

2016-01-01

Deforestation rates have declined in the Brazilian Amazon since 2005, yet degradation from logging, re, and fragmentation has continued in frontier forests. In this study we quantified the aboveground carbon density (ACD) in intact and degraded forests using the largest data set of integrated forest inventory plots (n 359) and airborne lidar data (18,000 ha) assembled to date for the Brazilian Amazon. We developed statistical models relating inventory ACD estimates to lidar metrics that explained70 of the variance across forest types. Airborne lidar-ACD estimates for intact forests ranged between 5.0 +/- 2.5 and 31.9 +/- 10.8 kg C m(exp -2). Degradation carbon losses were large and persistent. Sites that burned multiple times within a decade lost up to 15.0 +/- 0.7 kg C m(-2)(94%) of ACD. Forests that burned nearly15 years ago had between 4.1 +/- 0.5 and 6.8 +/- 0.3 kg C m(exp -2) (22-40%) less ACD than intact forests. Even for low-impact logging disturbances, ACD was between 0.7 +/- 0.3 and 4.4 +/- 0.4 kg C m(exp -2)(4-21%) lower than unlogged forests. Comparing biomass estimates from airborne lidar to existing biomass maps, we found that regional and pan-tropical products consistently overestimated ACD in degraded forests, under-estimated ACD in intact forests, and showed little sensitivity to res and logging. Fine-scale heterogeneity in ACD across intact and degraded forests highlights the benefits of airborne lidar for carbon mapping. Differences between airborne lidar and regional biomass maps underscore the need to improve and update biomass estimates for dynamic land use frontiers, to better characterize deforestation and degradation carbon emissions for regional carbon budgets and Reduce Emissions from Deforestation and forest Degradation(REDD+).

Ipsilateral intact fibula as a predictor of tibial plafond fracture pattern and severity.

PubMed

Luk, Pamela C; Charlton, Timothy P; Lee, Jackson; Thordarson, David B

2013-10-01

The objective of this study was to determine whether there is a difference in fracture pattern and severity of comminution between tibial plafond fractures with and without associated fibular fractures using computed tomography (CT). We hypothesized that the presence of an intact fibula was predictive of increased tibial plafond fracture severity. This was a case control, radiographic review performed at a single level I university trauma center. Between November 2007 and July 2011, 104 patients with 107 operatively treated tibial pilon fractures and preoperative CT scans were identified: 70 patients with 71 tibial plafond fractures had associated fibular fractures, and 34 patients with 36 tibial plafond fractures had intact fibulas. Four criteria were compared between the 2 groups: AO/OTA classification of distal tibia fractures, Topliss coronal and sagittal fracture pattern classification, plafond region of greatest comminution, and degree of proximal extension of fracture line. The intact fibula group had greater percentages of AO/OTA classification B2 type (5.5 vs 0, P = .046) and B3 type (52.8 vs 28.2, P = .013). Conversely, the percentage of AO/OTA classification C3 type was greater in the fractured fibula group (53.5 vs 30.6, P = .025). Evaluation using the Topliss sagittal and coronal classifications revealed no difference between the 2 groups (P = .226). Central and lateral regions of the plafond were the most common areas of comminution in fractured fibula pilons (32% and 31%, respectively). The lateral region of the plafond was the most common area of comminution in intact fibula pilon fractures (42%). There was no statistically significant difference (P = .71) in degree of proximal extension of fracture line between the 2 groups. Tibial plafond fractures with intact fibulas were more commonly associated with AO/OTA classification B-type patterns, whereas those with fractured fibulas were more commonly associated with C-type patterns. An intact fibula

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

PubMed Central

Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.

2016-01-01

Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

Negligible impact of rare autoimmune-locus coding-region variants on missing heritability.

PubMed

Hunt, Karen A; Mistry, Vanisha; Bockett, Nicholas A; Ahmad, Tariq; Ban, Maria; Barker, Jonathan N; Barrett, Jeffrey C; Blackburn, Hannah; Brand, Oliver; Burren, Oliver; Capon, Francesca; Compston, Alastair; Gough, Stephen C L; Jostins, Luke; Kong, Yong; Lee, James C; Lek, Monkol; MacArthur, Daniel G; Mansfield, John C; Mathew, Christopher G; Mein, Charles A; Mirza, Muddassar; Nutland, Sarah; Onengut-Gumuscu, Suna; Papouli, Efterpi; Parkes, Miles; Rich, Stephen S; Sawcer, Steven; Satsangi, Jack; Simmonds, Matthew J; Trembath, Richard C; Walker, Neil M; Wozniak, Eva; Todd, John A; Simpson, Michael A; Plagnol, Vincent; van Heel, David A

2013-06-13

Genome-wide association studies (GWAS) have identified common variants of modest-effect size at hundreds of loci for common autoimmune diseases; however, a substantial fraction of heritability remains unexplained, to which rare variants may contribute. To discover rare variants and test them for association with a phenotype, most studies re-sequence a small initial sample size and then genotype the discovered variants in a larger sample set. This approach fails to analyse a large fraction of the rare variants present in the entire sample set. Here we perform simultaneous amplicon-sequencing-based variant discovery and genotyping for coding exons of 25 GWAS risk genes in 41,911 UK residents of white European origin, comprising 24,892 subjects with six autoimmune disease phenotypes and 17,019 controls, and show that rare coding-region variants at known loci have a negligible role in common autoimmune disease susceptibility. These results do not support the rare-variant synthetic genome-wide-association hypothesis (in which unobserved rare causal variants lead to association detected at common tag variants). Many known autoimmune disease risk loci contain multiple, independently associated, common and low-frequency variants, and so genes at these loci are a priori stronger candidates for harbouring rare coding-region variants than other genes. Our data indicate that the missing heritability for common autoimmune diseases may not be attributable to the rare coding-region variant portion of the allelic spectrum, but perhaps, as others have proposed, may be a result of many common-variant loci of weak effect.

A search for intact lava tubes on the Moon: Possible lunar base habitats

NASA Technical Reports Server (NTRS)

Coombs, Cassandra R.; Hawke, B. Ray

1992-01-01

We have surveyed lunar sinuous rilles and other volcanic features in an effort to locate intact lava tubes that could be used to house an advanced lunar base. Criteria were established for identifying intact tube segments. Sixty-seven tube candidates within 20 rilles were identified on the lunar nearside. The rilles, located in four mare regions, varied in size and sinuosity. We identified four rilles that exhibited particularly strong evidence for the existence of intact lava tube segments. These are located in the following areas: (1) south of Gruithuisen K, (2) in the Marius Hills region, (3) in the southeastern Mare Serenitatis, and (4) in the eastern Mare Serenitatis. We rated each of the 67 probable tube segments for lunar base suitability based on its dimensions, stability, location, and access to lunar resources. Nine tube segments associated with three separate rilles are considered prime candidates for use as part of an advanced lunar base.

Comparison of Intact PTH and Bio-Intact PTH Assays Among Non-Dialysis Dependent Chronic Kidney Disease Patients.

PubMed

Einbinder, Yael; Benchetrit, Sydney; Golan, Eliezer; Zitman-Gal, Tali

2017-09-01

The third-generation bio-intact parathyroid hormone (PTH) (1-84) assay was designed to overcome problems associated with the detection of C-terminal fragments by the second-generation intact PTH assay. The two assays have been compared primarily among dialysis populations. The present study evaluated the correlations and differences between these two PTH assays among patients with chronic kidney disease (CKD) stages 3 to 5 not yet on dialysis. Blood samples were collected from 98 patients with CKD stages 3 to 5. PTH concentrations were measured simultaneously by using the second-generation - PTH intact-STAT and third-generation bio-intact 1-84 PTH assays. Other serum biomarkers of bone mineral disorders were also assessed. CKD stage was calculated by using the CKD-Epidemiology Collaboration (EPI) formula. Serum bio-intact PTH concentrations were strongly correlated but significantly lower than the intact PTH concentrations (r=0.963, P<0.0001). This finding was consistent among CKD stages 3 to 5. PTH concentrations by both assays (intact and bio-intact PTH) positively correlated with urea (r=0.523, r=0.504; P=0.002, respectively), phosphorus (r=0.532, r=0.521; P<0.0001, respectively) and negatively correlated with blood calcium (r=-0.435, r=-0.476; P<0.0001, respectively), 25(OH) vitamin D, (r=-0.319, r=-0.353; respectively, P<0.0001) and the estimated glomerular filtration rate (r=-0.717, r=-0.688; P<0.0001, respectively). Among patients with CKD stages 3 to 5 not on dialysis, the bio-intact PTH assay detected significantly lower PTH concentrations compared with intact PTH assay. Additional studies that correlate the diagnosis and management of CKD mineral and bone disorders with bone histomorphometric findings are needed to determine whether bio-intact PTH assay results are better surrogate markers in these early stages of CKD. © The Korean Society for Laboratory Medicine

Recollections of Parent Characteristics and Attachment Patterns for College Women of Intact vs. Non-Intact Families

ERIC Educational Resources Information Center

Kilmann, Peter R.; Carranza, Laura V.; Vendemia, Jennifer M. C.

2006-01-01

This study contrasted offsprings' attachment patterns and recollections of parent characteristics in two college samples: 147 females from intact biological parents and 157 females of parental divorce. Secure females from intact or non-intact families rated parents positively, while insecure females rated parents as absent, distant, and demanding.…

Spatially rearranged object parts can facilitate perception of intact whole objects.

PubMed

Cacciamani, Laura; Ayars, Alisabeth A; Peterson, Mary A

2014-01-01

The familiarity of an object depends on the spatial arrangement of its parts; when the parts are spatially rearranged, they form a novel, unrecognizable configuration. Yet the same collection of parts comprises both the familiar and novel configuration. Is it possible that the collection of familiar parts activates a representation of the intact familiar configuration even when they are spatially rearranged? We presented novel configurations as primes before test displays that assayed effects on figure-ground perception from memories of intact familiar objects. In our test displays, two equal-area regions shared a central border; one region depicted a portion of a familiar object. Previous research with such displays has shown that participants are more likely to perceive the region depicting a familiar object as the figure and the abutting region as its ground when the familiar object is depicted in its upright orientation rather than upside down. The novel primes comprised either the same or a different collection of parts as the familiar object in the test display (part-rearranged and control primes, respectively). We found that participants were more likely to perceive the familiar region as figure in upright vs. inverted displays following part-rearranged primes but not control primes. Thus, priming with a novel configuration comprising the same familiar parts as the upcoming figure-ground display facilitated orientation-dependent effects of object memories on figure assignment. Similar results were obtained when the spatially rearranged collection of parts was suggested on the groundside of the prime's border, suggesting that familiar parts in novel configurations access the representation of their corresponding intact whole object before figure assignment. These data demonstrate that familiar parts access memories of familiar objects even when they are arranged in a novel configuration.

Spatially rearranged object parts can facilitate perception of intact whole objects

PubMed Central

Cacciamani, Laura; Ayars, Alisabeth A.; Peterson, Mary A.

2014-01-01

The familiarity of an object depends on the spatial arrangement of its parts; when the parts are spatially rearranged, they form a novel, unrecognizable configuration. Yet the same collection of parts comprises both the familiar and novel configuration. Is it possible that the collection of familiar parts activates a representation of the intact familiar configuration even when they are spatially rearranged? We presented novel configurations as primes before test displays that assayed effects on figure-ground perception from memories of intact familiar objects. In our test displays, two equal-area regions shared a central border; one region depicted a portion of a familiar object. Previous research with such displays has shown that participants are more likely to perceive the region depicting a familiar object as the figure and the abutting region as its ground when the familiar object is depicted in its upright orientation rather than upside down. The novel primes comprised either the same or a different collection of parts as the familiar object in the test display (part-rearranged and control primes, respectively). We found that participants were more likely to perceive the familiar region as figure in upright vs. inverted displays following part-rearranged primes but not control primes. Thus, priming with a novel configuration comprising the same familiar parts as the upcoming figure-ground display facilitated orientation-dependent effects of object memories on figure assignment. Similar results were obtained when the spatially rearranged collection of parts was suggested on the groundside of the prime's border, suggesting that familiar parts in novel configurations access the representation of their corresponding intact whole object before figure assignment. These data demonstrate that familiar parts access memories of familiar objects even when they are arranged in a novel configuration. PMID:24904495

East Asian mtDNA haplogroup determination in Koreans: haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis.

PubMed

Lee, Hwan Young; Yoo, Ji-Eun; Park, Myung Jin; Chung, Ukhee; Kim, Chong-Youl; Shin, Kyoung-Jin

2006-11-01

The present study analyzed 21 coding region SNP markers and one deletion motif for the determination of East Asian mitochondrial DNA (mtDNA) haplogroups by designing three multiplex systems which apply single base extension methods. Using two multiplex systems, all 593 Korean mtDNAs were allocated into 15 haplogroups: M, D, D4, D5, G, M7, M8, M9, M10, M11, R, R9, B, A, and N9. As the D4 haplotypes occurred most frequently in Koreans, the third multiplex system was used to further define D4 subhaplogroups: D4a, D4b, D4e, D4g, D4h, and D4j. This method allowed the complementation of coding region information with control region mutation motifs and the resultant findings also suggest reliable control region mutation motifs for the assignment of East Asian mtDNA haplogroups. These three multiplex systems produce good results in degraded samples as they contain small PCR products (101-154 bp) for single base extension reactions. SNP scoring was performed in 101 old skeletal remains using these three systems to prove their utility in degraded samples. The sequence analysis of mtDNA control region with high incidence of haplogroup-specific mutations and the selective scoring of highly informative coding region SNPs using the three multiplex systems are useful tools for most applications involving East Asian mtDNA haplogroup determination and haplogroup-directed stringent quality control.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

PubMed Central

Pujar, Shashikant; O’Leary, Nuala A; Farrell, Catherine M; Mudge, Jonathan M; Wallin, Craig; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bult, Carol J; Frankish, Adam; Pruitt, Kim D

2018-01-01

Abstract The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. PMID:29126148

Regional and temporal variations in coding of hospital diagnoses referring to upper gastrointestinal and oesophageal bleeding in Germany.

PubMed

Langner, Ingo; Mikolajczyk, Rafael; Garbe, Edeltraut

2011-08-17

Health insurance claims data are increasingly used for health services research in Germany. Hospital diagnoses in these data are coded according to the International Classification of Diseases, German modification (ICD-10-GM). Due to the historical division into West and East Germany, different coding practices might persist in both former parts. Additionally, the introduction of Diagnosis Related Groups (DRGs) in Germany in 2003/2004 might have changed the coding. The aim of this study was to investigate regional and temporal variations in coding of hospitalisation diagnoses in Germany. We analysed hospitalisation diagnoses for oesophageal bleeding (OB) and upper gastrointestinal bleeding (UGIB) from the official German Hospital Statistics provided by the Federal Statistical Office. Bleeding diagnoses were classified as "specific" (origin of bleeding provided) or "unspecific" (origin of bleeding not provided) coding. We studied regional (former East versus West Germany) differences in incidence of hospitalisations with specific or unspecific coding for OB and UGIB and temporal variations between 2000 and 2005. For each year, incidence ratios of hospitalisations for former East versus West Germany were estimated with log-linear regression models adjusting for age, gender and population density. Significant differences in specific and unspecific coding between East and West Germany and over time were found for both, OB and UGIB hospitalisation diagnoses, respectively. For example in 2002, incidence ratios of hospitalisations for East versus West Germany were 1.24 (95% CI 1.16-1.32) for specific and 0.67 (95% CI 0.60-0.74) for unspecific OB diagnoses and 1.43 (95% CI 1.36-1.51) for specific and 0.83 (95% CI 0.80-0.87) for unspecific UGIB. Regional differences nearly disappeared and time trends were less marked when using combined specific and unspecific diagnoses of OB or UGIB, respectively. During the study period, there were substantial regional and temporal

Positive Youth Development, Life Satisfaction, and Problem Behaviors of Adolescents in Intact and Non-Intact Families in Hong Kong

PubMed Central

Shek, Daniel T. L.; Leung, Hildie

2013-01-01

This study investigated whether Chinese adolescents living in intact and non-intact families differed in their positive development, life satisfaction, and risk behavior. A total of 3,328 Secondary 1 students responded to measures of positive youth development (such as resilience and psychosocial competencies), life satisfaction, and risk behavior (substance abuse, delinquency, Internet addiction, consumption of pornographic materials, self-harm, and behavioral intention to engage in problem behavior). Findings revealed that adolescents growing up in intact families reported higher levels of positive developmental outcomes and life satisfaction as compared with adolescents from non-intact families. Adolescents in non-intact families also reported higher levels of risk behaviors than those growing up in intact families. PMID:24400264

Positive youth development, life satisfaction, and problem behaviors of adolescents in intact and non-intact families in Hong Kong.

PubMed

Shek, Daniel T L; Leung, Hildie

2013-01-01

This study investigated whether Chinese adolescents living in intact and non-intact families differed in their positive development, life satisfaction, and risk behavior. A total of 3,328 Secondary 1 students responded to measures of positive youth development (such as resilience and psychosocial competencies), life satisfaction, and risk behavior (substance abuse, delinquency, Internet addiction, consumption of pornographic materials, self-harm, and behavioral intention to engage in problem behavior). Findings revealed that adolescents growing up in intact families reported higher levels of positive developmental outcomes and life satisfaction as compared with adolescents from non-intact families. Adolescents in non-intact families also reported higher levels of risk behaviors than those growing up in intact families.

Body condition and habitat use by Hermann's tortoises in burnt and intact habitats

PubMed Central

Lecq, S.; Ballouard, J.-M.; Caron, S.; Livoreil, B.; Seynaeve, V.; Matthieu, L.-A.; Bonnet, X.

2014-01-01

In Mediterranean regions, fires threaten terrestrial tortoises. Nevertheless, varying proportions of adults survive fire; these surviving individuals can play a central role for population recovery. The regions devastated by fire often include important habitat of Hermann's tortoises (Testudo hermanni hermanni), so assessing the ability of survivors to persist is essential for conserving the species. Body-condition indices provide an integrative estimate of how well individuals cope with environmental variations and impacts, including fires. Between 2002 and 2009, we monitored Hermann's tortoises in intact and burnt habitats in southeastern France. In summer 2003, a strong fire ravaged half of the surveyed zone, providing an opportunity to compare body condition of tortoises between intact and burnt areas over time. Six years later, the impact of fire on vegetation was still marked; large trees were abundant in the intact area, whereas open shrub vegetation prevailed in the burnt area. In both areas, the mean body condition of tortoises fluctuated over time; however, there were no differences between the two areas. A radio-tracking experiment demonstrated that individuals from each area were residents, and not vagrants commuting between areas. We also assessed changes in body condition and microhabitat use in radio-tracked individuals. We found no significant differences between the tortoises living in the burnt and intact areas, despite subtle differences in habitat use. In conclusion: (i) surviving tortoises in an area ravaged by fire can maintain their body condition like individuals living in an intact area, and thus, individuals from burnt areas should not be translocated to supposedly better areas; and (ii) depopulated burnt areas are likely to be appropriate for population-augmentation programmes. PMID:27293640

Exploratory investigations of hypervelocity intact capture spectroscopy

NASA Technical Reports Server (NTRS)

Tsou, P.; Griffiths, D. J.

1993-01-01

The ability to capture hypervelocity projectiles intact opens a new technique available for hypervelocity research. A determination of the reactions taking place between the projectile and the capture medium during the process of intact capture is extremely important to an understanding of the intact capture phenomenon, to improving the capture technique, and to developing a theory describing the phenomenon. The intact capture of hypervelocity projectiles by underdense media generates spectra, characteristic of the material species of projectile and capture medium involved. Initial exploratory results into real-time characterization of hypervelocity intact capture techniques by spectroscopy include ultra-violet and visible spectra obtained by use of reflecting gratings, transmitting gratings, and prisms, and recorded by photographic and electronic means. Spectrometry proved to be a valuable real-time diagnostic tool for hypervelocity intact capture events, offering understanding of the interactions of the projectile and the capture medium during the initial period and providing information not obtainable by other characterizations. Preliminary results and analyses of spectra produced by the intact capture of hypervelocity aluminum spheres in polyethylene (PE), polystyrene (PS), and polyurethane (PU) foams are presented. Included are tentative emission species identifications, as well as gray body temperatures produced in the intact capture process.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

PubMed

Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

2018-01-04

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda.

PubMed

Goz, Eli; Mioduser, Oriah; Diament, Alon; Tuller, Tamir

2017-08-01

Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes, respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to Escherichia coli tRNA pool and the fact that it can change during the bacteriophage life cycle.An analysis of additional aspects related to the expression of viral genes, such as mRNA folding and more complex/longer regulatory signals in the coding regions, is also reported. The reported conclusions are likely to be relevant also to additional viruses. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Intact glycopeptide characterization using mass spectrometry.

PubMed

Cao, Li; Qu, Yi; Zhang, Zhaorui; Wang, Zhe; Prytkova, Iya; Wu, Si

2016-05-01

Glycosylation is one of the most prominent and extensively studied protein post-translational modifications. However, traditional proteomic studies at the peptide level (bottom-up) rarely characterize intact glycopeptides (glycosylated peptides without removing glycans), so no glycoprotein heterogeneity information is retained. Intact glycopeptide characterization, on the other hand, provides opportunities to simultaneously elucidate the glycan structure and the glycosylation site needed to reveal the actual biological function of protein glycosylation. Recently, significant improvements have been made in the characterization of intact glycopeptides, ranging from enrichment and separation, mass spectroscopy (MS) detection, to bioinformatics analysis. In this review, we recapitulated currently available intact glycopeptide characterization methods with respect to their advantages and limitations as well as their potential applications.

A gridded global data set of soil, intact regolith, and sedimentary deposit thicknesses for regional and global land surface modeling

DOE PAGES

Pelletier, Jon D.; Broxton, Patrick D.; Hazenberg, Pieter; ...

2016-01-22

Earth’s terrestrial near-subsurface environment can be divided into relatively porous layers of soil, intact regolith, and sedimentary deposits above unweathered bedrock. Variations in the thicknesses of these layers control the hydrologic and biogeochemical responses of landscapes. Currently, Earth System Models approximate the thickness of these relatively permeable layers above bedrock as uniform globally, despite the fact that their thicknesses vary systematically with topography, climate, and geology. To meet the need for more realistic input data for models, we developed a high-resolution gridded global data set of the average thicknesses of soil, intact regolith, and sedimentary deposits within each 30 arcsecmore » (~ 1 km) pixel using the best available data for topography, climate, and geology as input. Our data set partitions the global land surface into upland hillslope, upland valley bottom, and lowland landscape components and uses models optimized for each landform type to estimate the thicknesses of each subsurface layer. On hillslopes, the data set is calibrated and validated using independent data sets of measured soil thicknesses from the U.S. and Europe and on lowlands using depth to bedrock observations from groundwater wells in the U.S. As a result, we anticipate that the data set will prove useful as an input to regional and global hydrological and ecosystems models.« less

A gridded global data set of soil, intact regolith, and sedimentary deposit thicknesses for regional and global land surface modeling

NASA Astrophysics Data System (ADS)

Pelletier, Jon D.; Broxton, Patrick D.; Hazenberg, Pieter; Zeng, Xubin; Troch, Peter A.; Niu, Guo-Yue; Williams, Zachary; Brunke, Michael A.; Gochis, David

2016-03-01

Earth's terrestrial near-subsurface environment can be divided into relatively porous layers of soil, intact regolith, and sedimentary deposits above unweathered bedrock. Variations in the thicknesses of these layers control the hydrologic and biogeochemical responses of landscapes. Currently, Earth System Models approximate the thickness of these relatively permeable layers above bedrock as uniform globally, despite the fact that their thicknesses vary systematically with topography, climate, and geology. To meet the need for more realistic input data for models, we developed a high-resolution gridded global data set of the average thicknesses of soil, intact regolith, and sedimentary deposits within each 30 arcsec (˜1 km) pixel using the best available data for topography, climate, and geology as input. Our data set partitions the global land surface into upland hillslope, upland valley bottom, and lowland landscape components and uses models optimized for each landform type to estimate the thicknesses of each subsurface layer. On hillslopes, the data set is calibrated and validated using independent data sets of measured soil thicknesses from the U.S. and Europe and on lowlands using depth to bedrock observations from groundwater wells in the U.S. We anticipate that the data set will prove useful as an input to regional and global hydrological and ecosystems models. This article was corrected on 2 FEB 2016. See the end of the full text for details.

50 CFR 622.381 - Landing fish intact.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing fish intact. 622.381 Section 622... Migratory Pelagic Resources (Gulf of Mexico and South Atlantic) § 622.381 Landing fish intact. (a) Cobia... head and fins intact. Such fish may be eviscerated, gilled, and scaled, but must otherwise be...

50 CFR 622.381 - Landing fish intact.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing fish intact. 622.381 Section 622... Migratory Pelagic Resources (Gulf of Mexico and South Atlantic) § 622.381 Landing fish intact. (a) Cobia... head and fins intact. Such fish may be eviscerated, gilled, and scaled, but must otherwise be...

50 CFR 622.276 - Landing fish intact.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing fish intact. 622.276 Section 622... Wahoo Fishery Off the Atlantic States § 622.276 Landing fish intact. (a) Dolphin and wahoo in or from the Atlantic EEZ must be maintained with head and fins intact. Such fish may be eviscerated, gilled...

50 CFR 622.276 - Landing fish intact.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing fish intact. 622.276 Section 622... Wahoo Fishery Off the Atlantic States § 622.276 Landing fish intact. (a) Dolphin and wahoo in or from the Atlantic EEZ must be maintained with head and fins intact. Such fish may be eviscerated, gilled...

Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.

50 CFR 622.38 - Landing fish intact.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 12 2012-10-01 2012-10-01 false Landing fish intact. 622.38 Section 622... § 622.38 Landing fish intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that fish on that vessel in the EEZ are maintained intact and, if taken from the EEZ, are...

50 CFR 622.38 - Landing fish intact.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Landing fish intact. 622.38 Section 622... § 622.38 Landing fish intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that fish on that vessel in the EEZ are maintained intact and, if taken from the EEZ, are...

Identification of coding and non-coding mutational hotspots in cancer genomes.

PubMed

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

Threats to intact tropical peatlands and opportunities for their conservation.

PubMed

Roucoux, K H; Lawson, I T; Baker, T R; Del Castillo Torres, D; Draper, F C; Lähteenoja, O; Gilmore, M P; Honorio Coronado, E N; Kelly, T J; Mitchard, E T A; Vriesendorp, C F

2017-12-01

Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services and maintain their resilience to future environmental change. We explored threats to and opportunities for conserving remaining intact tropical peatlands; thus, we excluded peatlands of Indonesia and Malaysia, where extensive deforestation, drainage, and conversion to plantations means conservation in this region can protect only small fragments of the original ecosystem. We focused on a case study, the Pastaza-Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and is representative of peatland vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. There remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land-use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection does not include the most carbon-dense (domed pole forest) areas. New carbon-based conservation instruments (e.g., REDD+, Green Climate Fund), developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and elsewhere, such as those in New Guinea and Central Africa which remain, for the moment, broadly beyond the frontier of commercial development. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

PubMed Central

Kress, W. John; Erickson, David L.

2007-01-01

Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. PMID:17551588

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

PubMed

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Development of Second Generation Intact Stability Criteria

DTIC Science & Technology

2011-12-01

the intact stability performance of ships, have motivated the development of the second generation intact stability criteria by the IMO Subcommittee on...primary modes of stability failures which are being addressed. The second generation intact stability criteria are planned to have a multitiered structure...and 2 vulnerability criteria that are used as a preliminary design process check of dynamic stability failure risk. This report describes the U.S

Forest Loss in Protected Areas and Intact Forest Landscapes: A Global Analysis

PubMed Central

Heino, Matias; Kummu, Matti; Makkonen, Marika; Mulligan, Mark; Verburg, Peter H.; Jalava, Mika; Räsänen, Timo A.

2015-01-01

In spite of the high importance of forests, global forest loss has remained alarmingly high during the last decades. Forest loss at a global scale has been unveiled with increasingly finer spatial resolution, but the forest extent and loss in protected areas (PAs) and in large intact forest landscapes (IFLs) have not so far been systematically assessed. Moreover, the impact of protection on preserving the IFLs is not well understood. In this study we conducted a consistent assessment of the global forest loss in PAs and IFLs over the period 2000–2012. We used recently published global remote sensing based spatial forest cover change data, being a uniform and consistent dataset over space and time, together with global datasets on PAs’ and IFLs’ locations. Our analyses revealed that on a global scale 3% of the protected forest, 2.5% of the intact forest, and 1.5% of the protected intact forest were lost during the study period. These forest loss rates are relatively high compared to global total forest loss of 5% for the same time period. The variation in forest losses and in protection effect was large among geographical regions and countries. In some regions the loss in protected forests exceeded 5% (e.g. in Australia and Oceania, and North America) and the relative forest loss was higher inside protected areas than outside those areas (e.g. in Mongolia and parts of Africa, Central Asia, and Europe). At the same time, protection was found to prevent forest loss in several countries (e.g. in South America and Southeast Asia). Globally, high area-weighted forest loss rates of protected and intact forests were associated with high gross domestic product and in the case of protected forests also with high proportions of agricultural land. Our findings reinforce the need for improved understanding of the reasons for the high forest losses in PAs and IFLs and strategies to prevent further losses. PMID:26466348

In silico screening of the chicken genome for overlaps between genomic regions: microRNA genes, coding and non-coding transcriptional units, QTL, and genetic variations.

PubMed

Zorc, Minja; Kunej, Tanja

2016-05-01

MicroRNAs (miRNAs) are a class of non-coding RNAs involved in posttranscriptional regulation of target genes. Regulation requires complementarity between target mRNA and the mature miRNA seed region, responsible for their recognition and binding. It has been estimated that each miRNA targets approximately 200 genes, and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals. In our previous study, we collected polymorphisms within miRNA genes in chicken. In the present study, we identified miRNA-related genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery. Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases: miRNA SNiPer, Ensembl, miRBase, NCBI Blast, and QTLdb. Out of 740 known pre-miRNA genes, 263 (35.5 %) contain polymorphisms; among them, 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are gga-miR-6662, containing 23 single nucleotide polymorphisms (SNPs) within the pre-miRNA region, including five consecutive SNPs, and gga-miR-6688, containing ten polymorphisms including three consecutive polymorphisms. Several miRNA-related genomic hotspots have been revealed in chicken genome; polymorphic miRNA genes are located within protein-coding and/or non-coding transcription units and quantitative trait loci (QTL) associated with production traits. The present study includes the first description of an exonic miRNA in a chicken genome, an overlap between the miRNA gene and the exon of the protein-coding gene (gga-miR-6578/HADHB), and the first report of a missense polymorphism located within a mature miRNA seed region. Identified miRNA-related genomic hotspots in chicken can serve researchers as a

Regional TEC model under quiet geomagnetic conditions and low-to-moderate solar activity based on CODE GIMs

NASA Astrophysics Data System (ADS)

Feng, Jiandi; Jiang, Weiping; Wang, Zhengtao; Zhao, Zhenzhen; Nie, Linjuan

2017-08-01

Global empirical total electron content (TEC) models based on TEC maps effectively describe the average behavior of the ionosphere. However, the accuracy of these global models for a certain region may not be ideal. Due to the number and distribution of the International GNSS Service (IGS) stations, the accuracy of TEC maps is geographically different. The modeling database derived from the global TEC maps with different accuracy is likely one of the main reasons that limits the accuracy of the new models. Moreover, many anomalies in the ionosphere are geographic or geomagnetic dependent, and as such the accuracy of global models can deteriorate if these anomalies are not fully incorporated into the modeling approach. For regional models built in small areas, these influences on modeling are immensely weakened. Thus, the regional TEC models may better reflect the temporal and spatial variations of TEC. In our previous work (Feng et al., 2016), a regional TEC model TECM-NEC is proposed for northeast China. However, this model is only directed against the typical region of Mid-latitude Summer Nighttime Anomaly (MSNA) occurrence, which is meaningless in other regions without MSNA. Following the technique of TECM-NEC model, this study proposes another regional empirical TEC model for other regions in mid-latitudes. Taking a small area BeiJing-TianJin-Tangshan (JJT) region (37.5°-42.5° N, 115°-120° E) in China as an example, a regional empirical TEC model (TECM-JJT) is proposed using the TEC grid data from January 1, 1999 to June 30, 2015 provided by the Center for Orbit Determination in Europe (CODE) under quiet geomagnetic conditions. The TECM-JJT model fits the input CODE TEC data with a bias of 0.11TECU and a root mean square error of 3.26TECU. Result shows that the regional model TECM-JJT is consistent with CODE TEC data and GPS-TEC data.

Reduced adaptability, but no fundamental disruption, of norm-based face-coding mechanisms in cognitively able children and adolescents with autism.

PubMed

Rhodes, Gillian; Ewing, Louise; Jeffery, Linda; Avard, Eleni; Taylor, Libby

2014-09-01

Faces are adaptively coded relative to visual norms that are updated by experience. This coding is compromised in autism and the broader autism phenotype, suggesting that atypical adaptive coding of faces may be an endophenotype for autism. Here we investigate the nature of this atypicality, asking whether adaptive face-coding mechanisms are fundamentally altered, or simply less responsive to experience, in autism. We measured adaptive coding, using face identity aftereffects, in cognitively able children and adolescents with autism and neurotypical age- and ability-matched participants. We asked whether these aftereffects increase with adaptor identity strength as in neurotypical populations, or whether they show a different pattern indicating a more fundamental alteration in face-coding mechanisms. As expected, face identity aftereffects were reduced in the autism group, but they nevertheless increased with adaptor strength, like those of our neurotypical participants, consistent with norm-based coding of face identity. Moreover, their aftereffects correlated positively with face recognition ability, consistent with an intact functional role for adaptive coding in face recognition ability. We conclude that adaptive norm-based face-coding mechanisms are basically intact in autism, but are less readily calibrated by experience. Copyright © 2014 Elsevier Ltd. All rights reserved.

GUMAP: A GUPIXWIN-compatible code for extracting regional spectra from nuclear microbeam list mode files

NASA Astrophysics Data System (ADS)

Russell, John L.; Campbell, John L.; Boyd, Nicholas I.; Dias, Johnny F.

2018-02-01

The newly developed GUMAP software creates element maps from OMDAQ list mode files, displays these maps individually or collectively, and facilitates on-screen definitions of specified regions from which a PIXE spectrum can be built. These include a free-hand region defined by moving the cursor. The regional charge is entered automatically into the spectrum file in a new GUPIXWIN-compatible format, enabling a GUPIXWIN analysis of the spectrum. The code defaults to the OMDAQ dead time treatment but also facilitates two other methods for dead time correction in sample regions with count rates different from the average.

Immunohistochemical and histomorphometric evaluation of vascular distribution in intact canine cranial cruciate ligament.

PubMed

Hayashi, Kei; Bhandal, Jitender; Kim, Sun Young; Rodriguez, Carlos O; Entwistle, Rachel; Naydan, Diane; Kapatkin, Amy; Stover, Susan M

2011-02-01

To (1) describe vascular distribution in the grossly intact canine cranial cruciate ligament (CCL) using immunohistochemical techniques specific to 2 components of blood vessels (factor VIII for endothelial cells, laminin for basement membrane); and (2) compare the vascularity in different areas of interest (craniomedial versus caudolateral bands; core versus epiligamentous regions; and proximal versus middle versus distal portions) in the intact normal canine CCL. In vitro study. Large, mature dogs (n=7) of breeds prone to CCL disease that were euthanatized for nonorthopedic conditions. Intact CCL were collected from fresh canine cadavers free from stifle pathology. CCL tissue was processed for immunohistochemistry and stained for factor VIII and laminin. Vascular density was determined by histomorphometric analysis. Specific vascular staining was sparsely identified throughout the CCL; however, the proximal portion of the CCL appears to have a greater number of vessels than the middle or distal portion of the ligament. The CCL is a hypovascular tissue and its vascular distribution is not homogeneous. © Copyright 2010 by The American College of Veterinary Surgeons.

Global forest loss disproportionately erodes biodiversity in intact landscapes.

PubMed

Betts, Matthew G; Wolf, Christopher; Ripple, William J; Phalan, Ben; Millers, Kimberley A; Duarte, Adam; Butchart, Stuart H M; Levi, Taal

2017-07-27

Global biodiversity loss is a critical environmental crisis, yet the lack of spatial data on biodiversity threats has hindered conservation strategies. Theory predicts that abrupt biodiversity declines are most likely to occur when habitat availability is reduced to very low levels in the landscape (10-30%). Alternatively, recent evidence indicates that biodiversity is best conserved by minimizing human intrusion into intact and relatively unfragmented landscapes. Here we use recently available forest loss data to test deforestation effects on International Union for Conservation of Nature Red List categories of extinction risk for 19,432 vertebrate species worldwide. As expected, deforestation substantially increased the odds of a species being listed as threatened, undergoing recent upgrading to a higher threat category and exhibiting declining populations. More importantly, we show that these risks were disproportionately high in relatively intact landscapes; even minimal deforestation has had severe consequences for vertebrate biodiversity. We found little support for the alternative hypothesis that forest loss is most detrimental in already fragmented landscapes. Spatial analysis revealed high-risk hot spots in Borneo, the central Amazon and the Congo Basin. In these regions, our model predicts that 121-219 species will become threatened under current rates of forest loss over the next 30 years. Given that only 17.9% of these high-risk areas are formally protected and only 8.9% have strict protection, new large-scale conservation efforts to protect intact forests are necessary to slow deforestation rates and to avert a new wave of global extinctions.

46 CFR 28.570 - Intact righting energy.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of this...

46 CFR 28.570 - Intact righting energy.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of this...

46 CFR 28.570 - Intact righting energy.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of this...

46 CFR 28.570 - Intact righting energy.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of this...

46 CFR 28.570 - Intact righting energy.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of this...

Small Particles Intact Capture Experiment (SPICE)

NASA Technical Reports Server (NTRS)

Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

1994-01-01

The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

Two-stage sparse coding of region covariance via Log-Euclidean kernels to detect saliency.

PubMed

Zhang, Ying-Ying; Yang, Cai; Zhang, Ping

2017-05-01

In this paper, we present a novel bottom-up saliency detection algorithm from the perspective of covariance matrices on a Riemannian manifold. Each superpixel is described by a region covariance matrix on Riemannian Manifolds. We carry out a two-stage sparse coding scheme via Log-Euclidean kernels to extract salient objects efficiently. In the first stage, given background dictionary on image borders, sparse coding of each region covariance via Log-Euclidean kernels is performed. The reconstruction error on the background dictionary is regarded as the initial saliency of each superpixel. In the second stage, an improvement of the initial result is achieved by calculating reconstruction errors of the superpixels on foreground dictionary, which is extracted from the first stage saliency map. The sparse coding in the second stage is similar to the first stage, but is able to effectively highlight the salient objects uniformly from the background. Finally, three post-processing methods-highlight-inhibition function, context-based saliency weighting, and the graph cut-are adopted to further refine the saliency map. Experiments on four public benchmark datasets show that the proposed algorithm outperforms the state-of-the-art methods in terms of precision, recall and mean absolute error, and demonstrate the robustness and efficiency of the proposed method. Copyright © 2017 Elsevier Ltd. All rights reserved.

Neuropeptide metabolism on intact, regional brain slices: effect of dopaminergic agents on substance P, cholecystokinin and Met-enkephalin degradation.

PubMed

Waters, S M; Konkoy, C S; Davis, T P

1995-08-01

Neuroleptic drugs have been shown to affect the level and messenger ribonucleic acid of specific neuropeptides. The effect of subchronically administered neuroleptics on neuropeptide metabolism, however, has not been systematically characterized. In the present study, the effect of neuroleptics and other dopaminergic compounds on substance P (SP), cholecystokinin and met-enkephalin degradation was determined on intact, regional, rat brain slices. After 7-day administration of haloperidol (1 mg/kg) or chlorpromazine (20 mg/kg), SP degradation was decreased in caudate-putamen and nucleus accumbens. After administration of the dopaminergic agonist apomorphine (5 mg/kg, b.i.d.), SP degradation was increased in the nucleus accumbens. The dopamine D2-receptor antagonist sulpiride (100 mg/kg, b.i.d.) produced no effect on SP degradation. Met-enkephalin degradation was decreased after haloperidol administration in both frontal cortex and caudate-putamen and unaffected by apomorphine administration. The metabolism of cholecystokinin was not affected by neuroleptic treatment. Studies performed with specific peptidase inhibitors suggested that neutral endopeptidase 24.11, metalloendopeptidase 24.15 and aminopeptidases degrade SP on caudate-putamen and nucleus accumbens slices. Therefore, alterations in these peptidases may be responsible for the change noted in SP degradation after dopaminergic compound administration. These metabolic changes noted after neuroleptic administration may therefore contribute to neuroleptic-induced alterations in regional peptide levels.

Structural and molecular interrogation of intact biological systems

PubMed Central

Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

2014-01-01

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection.

PubMed

Mendes-Junior, C T; Castelli, E C; Meyer, D; Simões, A L; Donadi, E A

2013-12-01

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

PubMed Central

Ferlaino, Michael; Rogers, Mark F.; Shihab, Hashem A.; Mort, Matthew; Cooper, David N.; Gaunt, Tom R.; Campbell, Colin

2018-01-01

Background Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. Results We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. Conclusions FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome. PMID:28985712

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

PubMed

Ferlaino, Michael; Rogers, Mark F; Shihab, Hashem A; Mort, Matthew; Cooper, David N; Gaunt, Tom R; Campbell, Colin

2017-10-06

Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.

Airway compliance and dynamics explain the apparent discrepancy in length adaptation between intact airways and smooth muscle strips.

PubMed

Dowie, Jackson; Ansell, Thomas K; Noble, Peter B; Donovan, Graham M

2016-01-01

Length adaptation is a phenomenon observed in airway smooth muscle (ASM) wherein over time there is a shift in the length-tension curve. There is potential for length adaptation to play an important role in airway constriction and airway hyper-responsiveness in asthma. Recent results by Ansell et al., 2015 (JAP 2014 10.1152/japplphysiol.00724.2014) have cast doubt on this role by testing for length adaptation using an intact airway preparation, rather than strips of ASM. Using this technique they found no evidence for length adaptation in intact airways. Here we attempt to resolve this apparent discrepancy by constructing a minimal mathematical model of the intact airway, including ASM which follows the classic length-tension curve and undergoes length adaptation. This allows us to show that (1) no evidence of length adaptation should be expected in large, cartilaginous, intact airways; (2) even in highly compliant peripheral airways, or at more compliant regions of the pressure-volume curve of large airways, the effect of length adaptation would be modest and at best marginally detectable in intact airways; (3) the key parameters which control the appearance of length adaptation in intact airways are airway compliance and the relaxation timescale. The results of this mathematical simulation suggest that length adaptation observed at the level of the isolated ASM may not clearly manifest in the normal intact airway. Copyright © 2015 Elsevier B.V. All rights reserved.

50 CFR 622.38 - Landing fish intact.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Landing fish intact. 622.38 Section 622.38... Landing fish intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that fish... specified in paragraphs (c) and (d) of this section. Such fish may be eviscerated, gilled, and scaled, but...

Pharmacokinetics of erythropoietin in intact and anephric dogs

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

Fu, J.S.; Lertora, J.J.; Brookins, J.

1988-06-01

The present studies were performed to determine the pharmacokinetic parameters of erythropoietin in intact and anephric dogs by use of unlabeled crude native erythropoietin (nEp) and iodine 125-labeled purified recombinant erythropoietin (rEp) given by intravenous infusion for 15 minutes. Sephadex G-75 gel filtration was used to confirm that the 125I-rEp molecule remained iodinated in dog plasma during the 24-hour period of these studies. The plasma disappearance of erythropoietin conformed to a biexponential equation for both nEp and 125I-rEp, with the central compartment being larger than the peripheral compartment. The mean distribution half-life of 75.3 +/- 21.2 minutes for nEp wasmore » significantly (p less than 0.05) longer than that of 125I-rEp (23.7 +/- 5.0 minutes) in intact dogs. The intercompartmental clearance (CIic) for nEp (0.018 +/- 0.006 L/kg/hr) was significantly smaller than that of 125I-rEp (0.068 +/- 0.018 L/kg/hr) in intact dogs (p less than 0.05). There were no significant differences in apparent volume of distribution, elimination half-life, and elimination clearance (CIe) for nEp and rEp in intact dogs. The mean elimination half-life for 125I-rEp in intact dogs (9.0 +/- 0.6 hours) and anephric dogs (13.8 +/- 1.4 hours) was significantly different (p less than 0.05). The CIe for 125I-rEp in anephric dogs (0.008 +/- 0.001 L/kg/hr) was significantly (p less than 0.05) smaller than that of 125I-rEp in intact dogs (0.011 +/- 0.001 L/kg/hr). There were no significant differences in apparent volume of distribution, distribution half-life, and CIic for 125I-rEp in intact and anephric dogs.« less

The sensitivity in the IR spectrum of the intact and pathological tissues by laser biophotometry.

PubMed

Ravariu, Cristian; Bondarciuc, Ala

2014-03-01

In this paper, we use the laser biophotometry for in vivo investigations, searching the most sensitive interactions of the near-infrared spectrum with different tissues. The experimental methods are based on the average reflection coefficient (ARC) measurements. For healthy persons, ARC is the average of five values provided by the biophotometer. The probe is applied on dry skin with minimum pilosity, in five regions: left-right shank, left-right forearm, and epigastrium. For the pathological tissues, the emitting terminal is moved over the suspected area, controlling the reflection coefficient level, till a minimum value occurs, as ARC-Pathological. Then, the probe is moved on the symmetrical healthy region of the body to read the complementary coefficient from intact tissue, ARC-Intact, from the same patient. The experimental results show an ARC range between 67 and 59 mW for intact tissues and a lower range, up to 58-42 mW, for pathological tissues. The method is efficient only in those pathological processes accompanied by variable skin depigmentation, water retention, inflammation, thrombosis, or swelling. Frequently, the ARC ranges are overlapping for some diseases. This induces uncertain diagnosis. Therefore, a statistical algorithm is adopted for a differential diagnosis. The laser biophotometry provides a quantitative biometric parameter, ARC, suitable for fast diagnosis in the internal and emergency medicine. These laser biophotometry measurements are representatives for the Romanian clinical trials.

Intact EAV-HP Endogenous Retrovirus in Sonnerat's Jungle Fowl

PubMed Central

Sacco, M. A.; Howes, K.; Venugopal, K.

2001-01-01

The EAV-HP group of chicken endogenous retrovirus elements was previously shown to be defective, with large deletions of the pol gene. In this report, we demonstrate that genomes of other Gallus species also maintain EAV-HP elements with similar deletions. The chicken EAV-HP1 locus was detected in both red (Gallus gallus gallus) and Sonnerat's (Gallus sonneratii) jungle fowl with identical integration sites, indicating that these elements had integrated before separation of the Gallus species. Furthermore, we demonstrate for the first time that the G. sonneratii genome carries EAV-HP elements with intact pol regions. PMID:11160706

The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin.

PubMed Central

Li, M; Dyda, F; Benhar, I; Pastan, I; Davies, D R

1995-01-01

Domain III of Pseudomonas aeruginosa exotoxin A catalyses the transfer of ADP-ribose from NAD to a modified histidine residue of elongation factor 2 in eukaryotic cells, thus inactivating elongation factor 2. This domain III is inactive in the intact toxin but is active in the isolated form. We report here the 2.5-A crystal structure of this isolated domain crystallized in the presence of NAD and compare it with the corresponding structure in the intact Pseudomonas aeruginosa exotoxin A. We observe a significant conformational difference in the active site region from Arg-458 to Asp-463. Contacts with part of domain II in the intact toxin prevent the adoption of the isolated domain conformation and provide a structural explanation for the observed inactivity. Additional electron density in the active site region corresponds to separate AMP and nicotinamide and indicates that the NAD has been hydrolyzed. The structure has been compared with the catalytic domain of the diphtheria toxin, which was crystallized with ApUp. Images Fig. 1 PMID:7568123

46 CFR 178.325 - Intact stability requirements-monohull sailing vessels.

Code of Federal Regulations, 2014 CFR

2014-10-01

... simplified stability proof test detailed in § 178.330 of this part, in the presence of a Coast Guard marine... 46 Shipping 7 2014-10-01 2014-10-01 false Intact stability requirements-monohull sailing vessels... PASSENGER VESSELS (UNDER 100 GROSS TONS) INTACT STABILITY AND SEAWORTHINESS Intact Stability Standards § 178...

46 CFR 178.325 - Intact stability requirements-monohull sailing vessels.

Code of Federal Regulations, 2012 CFR

2012-10-01

... simplified stability proof test detailed in § 178.330 of this part, in the presence of a Coast Guard marine... 46 Shipping 7 2012-10-01 2012-10-01 false Intact stability requirements-monohull sailing vessels... PASSENGER VESSELS (UNDER 100 GROSS TONS) INTACT STABILITY AND SEAWORTHINESS Intact Stability Standards § 178...

46 CFR 178.325 - Intact stability requirements-monohull sailing vessels.

Code of Federal Regulations, 2013 CFR

2013-10-01

... simplified stability proof test detailed in § 178.330 of this part, in the presence of a Coast Guard marine... 46 Shipping 7 2013-10-01 2013-10-01 false Intact stability requirements-monohull sailing vessels... PASSENGER VESSELS (UNDER 100 GROSS TONS) INTACT STABILITY AND SEAWORTHINESS Intact Stability Standards § 178...

Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). Hanford Environmental Dose Reconstruction Project

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

Ramsdell, J.V. Jr.; Simonen, C.A.; Burk, K.W.

1994-02-01

The purpose of the Hanford Environmental Dose Reconstruction (HEDR) Project is to estimate radiation doses that individuals may have received from operations at the Hanford Site since 1944. This report deals specifically with the atmospheric transport model, Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). RATCHET is a major rework of the MESOILT2 model used in the first phase of the HEDR Project; only the bookkeeping framework escaped major changes. Changes to the code include (1) significant changes in the representation of atmospheric processes and (2) incorporation of Monte Carlo methods for representing uncertainty in input data, model parameters,more » and coefficients. To a large extent, the revisions to the model are based on recommendations of a peer working group that met in March 1991. Technical bases for other portions of the atmospheric transport model are addressed in two other documents. This report has three major sections: a description of the model, a user`s guide, and a programmer`s guide. These sections discuss RATCHET from three different perspectives. The first provides a technical description of the code with emphasis on details such as the representation of the model domain, the data required by the model, and the equations used to make the model calculations. The technical description is followed by a user`s guide to the model with emphasis on running the code. The user`s guide contains information about the model input and output. The third section is a programmer`s guide to the code. It discusses the hardware and software required to run the code. The programmer`s guide also discusses program structure and each of the program elements.« less

Functional Effects of Genetic Polymorphisms in the N-acetyltransferase 1 Coding and 3′ Untranslated Regions

PubMed Central

Zhu, Yuanqi; States, J. Christopher; Wang, Yang; Hein, David W.

2011-01-01

BACKGROUND The functional effects of N-acetyltransferase 1 (NAT1) polymorphisms and haplotypes are poorly understood, compromising the validity of associations reported with diseases including birth defects and numerous cancers. METHODS We investigated the effects of genetic polymorphisms within the NAT1 coding region and the 3′-untranslated region (3′-UTR) and their associated haplotypes on N- and O-acetyltransferase catalytic activities, and NAT1 mRNA and protein levels following recombinant expression in COS-1 cells. RESULTS 1088T>A (rs1057126; 3′-UTR) and 1095C>A (rs15561; 3′-UTR) each slightly reduced NAT1 catalytic activity and NAT1 mRNA and protein levels. A 9-base pair (TAATAATAA) deletion between nucleotides 1065-1090 (3′-UTR) reduced NAT1 catalytic activity and NAT1 mRNA and protein levels. In contrast, a 445G>A (rs4987076; V149I), 459G>A (rs4986990; T153T), 640T>G (rs4986783; S214A) coding region haplotype present in NAT1*11 increased NAT1 catalytic activity and NAT1 protein, but not NAT1 mRNA levels. A combination of the 9-base pair (TAATAATAA) deletion and the 445G>A, 459G>A, 640T>G coding region haplotypes, both present in NAT1*11, appeared to neutralize the opposing effects on NAT1 protein and catalytic activity, resulting in levels of NAT1 protein and catalytic activity that did not differ significantly from the NAT1*4 reference. CONCLUSIONS Since 1095C>A (3′-UTR) is the sole polymorphism present in NAT1*3, our data suggests that NAT1*3 is not functionally equivalent to the NAT1*4 reference. Furthermore, our findings provide biological support for reported associations of 1088T>A and 1095C>A polymorphisms with birth defects. PMID:21290563

50 CFR 622.10 - Landing fish intact--general.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing fish intact--general. 622.10... ATLANTIC General Provisions § 622.10 Landing fish intact—-general. This section contains requirements for landing fish intact that are broadly applicable to finfish in the Gulf EEZ and Caribbean EEZ, as specified...

50 CFR 622.10 - Landing fish intact--general.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing fish intact--general. 622.10... ATLANTIC General Provisions § 622.10 Landing fish intact—-general. This section contains requirements for landing fish intact that are broadly applicable to finfish in the Gulf EEZ and Caribbean EEZ, as specified...

The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

PubMed Central

Oh, Chang Seok; Lee, Soong Deok; Kim, Yi-Suk; Shin, Dong Hoon

2015-01-01

Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods. PMID:26345190

Development of an Efficient Entire-Capsid-Coding-Region Amplification Method for Direct Detection of Poliovirus from Stool Extracts

PubMed Central

Kilpatrick, David R.; Nakamura, Tomofumi; Burns, Cara C.; Bukbuk, David; Oderinde, Soji B.; Oberste, M. Steven; Kew, Olen M.; Pallansch, Mark A.; Shimizu, Hiroyuki

2014-01-01

Laboratory diagnosis has played a critical role in the Global Polio Eradication Initiative since 1988, by isolating and identifying poliovirus (PV) from stool specimens by using cell culture as a highly sensitive system to detect PV. In the present study, we aimed to develop a molecular method to detect PV directly from stool extracts, with a high efficiency comparable to that of cell culture. We developed a method to efficiently amplify the entire capsid coding region of human enteroviruses (EVs) including PV. cDNAs of the entire capsid coding region (3.9 kb) were obtained from as few as 50 copies of PV genomes. PV was detected from the cDNAs with an improved PV-specific real-time reverse transcription-PCR system and nucleotide sequence analysis of the VP1 coding region. For assay validation, we analyzed 84 stool extracts that were positive for PV in cell culture and detected PV genomes from 100% of the extracts (84/84 samples) with this method in combination with a PV-specific extraction method. PV could be detected in 2/4 stool extract samples that were negative for PV in cell culture. In PV-positive samples, EV species C viruses were also detected with high frequency (27% [23/86 samples]). This method would be useful for direct detection of PV from stool extracts without using cell culture. PMID:25339406

Autism Spectrum Disorder and intact executive functioning.

PubMed

Ferrara, R; Ansermet, F; Massoni, F; Petrone, L; Onofri, E; Ricci, P; Archer, T; Ricci, S

2016-01-01

Earliest notions concerning autism (Autism Spectrum Disorders, ASD) describe the disturbance in executive functioning. Despite altered definition, executive functioning, expressed as higher cognitive skills required complex behaviors linked to the prefrontal cortex, are defective in autism. Specific difficulties in children presenting autism or verbal disabilities at executive functioning levels have been identified. Nevertheless, the developmental deficit of executive functioning in autism is highly diversified with huge individual variation and may even be absent. The aim of the present study to examine the current standing of intact executive functioning intact in ASD. Analysis of ASD populations, whether high-functioning, Asperger's or autism Broad Phenotype, studied over a range of executive functions including response inhibition, planning, cognitive flexibility, cognitive inhibition, and alerting networks indicates an absence of damage/impairment compared to the typically-developed normal control subjects. These findings of intact executive functioning in ASD subjects provide a strong foundation on which to construct applications for growth environments and the rehabilitation of autistic subjects.

Reprint of "Two-stage sparse coding of region covariance via Log-Euclidean kernels to detect saliency".

PubMed

Zhang, Ying-Ying; Yang, Cai; Zhang, Ping

2017-08-01

In this paper, we present a novel bottom-up saliency detection algorithm from the perspective of covariance matrices on a Riemannian manifold. Each superpixel is described by a region covariance matrix on Riemannian Manifolds. We carry out a two-stage sparse coding scheme via Log-Euclidean kernels to extract salient objects efficiently. In the first stage, given background dictionary on image borders, sparse coding of each region covariance via Log-Euclidean kernels is performed. The reconstruction error on the background dictionary is regarded as the initial saliency of each superpixel. In the second stage, an improvement of the initial result is achieved by calculating reconstruction errors of the superpixels on foreground dictionary, which is extracted from the first stage saliency map. The sparse coding in the second stage is similar to the first stage, but is able to effectively highlight the salient objects uniformly from the background. Finally, three post-processing methods-highlight-inhibition function, context-based saliency weighting, and the graph cut-are adopted to further refine the saliency map. Experiments on four public benchmark datasets show that the proposed algorithm outperforms the state-of-the-art methods in terms of precision, recall and mean absolute error, and demonstrate the robustness and efficiency of the proposed method. Copyright © 2017 Elsevier Ltd. All rights reserved.

78 FR 18321 - International Code Council: The Update Process for the International Codes and Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-26

... for Residential Construction in High Wind Regions. ICC 700: National Green Building Standard The..., coordinated, and necessary to regulate the built environment. Federal agencies frequently use these codes and... International Codes and Standards consist of the following: ICC Codes International Building Code. International...

Online Hydrophobic Interaction Chromatography-Mass Spectrometry for the Analysis of Intact Monoclonal Antibodies.

PubMed

Chen, Bifan; Lin, Ziqing; Alpert, Andrew J; Fu, Cexiong; Zhang, Qunying; Pritts, Wayne A; Ge, Ying

2018-06-19

Therapeutic monoclonal antibodies (mAbs) are an important class of drugs for a wide spectrum of human diseases. Liquid chromatography (LC) coupled to mass spectrometry (MS) is one of the techniques in the forefront for comprehensive characterization of analytical attributes of mAbs. Among various protein chromatography modes, hydrophobic interaction chromatography (HIC) is a popular offline nondenaturing separation technique utilized to purify and analyze mAbs, typically with the use of non-MS-compatible mobile phases. Herein we demonstrate for the first time, the application of direct HIC-MS and HIC-tandem MS (MS/MS) with electron capture dissociation (ECD) for analyzing intact mAbs on quadrupole-time-of-flight (Q-TOF) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, respectively. Our method allows for rapid determination of relative hydrophobicity, intact masses, and glycosylation profiles of mAbs as well as sequence and structural characterization of the complementarity-determining regions in an online configuration.

On fuzzy semantic similarity measure for DNA coding.

PubMed

Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin

2016-02-01

A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

Measurement of intact-core length of atomizing liquid jets by image deconvolution

NASA Technical Reports Server (NTRS)

Woodward, Roger; Burch, Robert; Kuo, Kenneth; Cheung, Fan-Bill

1993-01-01

The investigation of liquid jet breakup and spray development is critical to the understanding of combustion phenomena in liquid propellant rocket engines. Much work has been done to characterize low-speed liquid jet breakup and dilute sprays, but atomizing jets and dense sprays have yielded few quantitative measurements due to their high liquid load fractions and hence their optical opacity. Focus was on a characteristic of the primary breakup process of round liquid jets, namely the length of the intact-liquid core. The specific application considered is that of shear-coaxial-type rocket engine injectors in which liquid oxygen is injected through the center post while high velocity gaseous hydrogen is injected through a concentric annulus, providing a shear force to the liquid jet surface. Real-time x ray radiography, capable of imaging through the dense two-phase region surrounding the liquid core, is used to make the measurements. The intact-liquid-core length data were obtained and interpreted using two conceptually different methods to illustrate the effects of chamber pressure, gas-to-liquid momentum ratio, and cavitation.

Measurement of intact-core length of atomizing liquid jets by image deconvolution

NASA Astrophysics Data System (ADS)

Woodward, Roger; Burch, Robert; Kuo, Kenneth; Cheung, Fan-Bill

1993-11-01

The investigation of liquid jet breakup and spray development is critical to the understanding of combustion phenomena in liquid propellant rocket engines. Much work has been done to characterize low-speed liquid jet breakup and dilute sprays, but atomizing jets and dense sprays have yielded few quantitative measurements due to their high liquid load fractions and hence their optical opacity. Focus was on a characteristic of the primary breakup process of round liquid jets, namely the length of the intact-liquid core. The specific application considered is that of shear-coaxial-type rocket engine injectors in which liquid oxygen is injected through the center post while high velocity gaseous hydrogen is injected through a concentric annulus, providing a shear force to the liquid jet surface. Real-time x ray radiography, capable of imaging through the dense two-phase region surrounding the liquid core, is used to make the measurements. The intact-liquid-core length data were obtained and interpreted using two conceptually different methods to illustrate the effects of chamber pressure, gas-to-liquid momentum ratio, and cavitation.

Astrocyte activation and wound healing in intact-skull mouse after focal brain injury.

PubMed

Suzuki, Takayuki; Sakata, Honami; Kato, Chiaki; Connor, John A; Morita, Mitsuhiro

2012-12-01

Localised brain tissue damage activates surrounding astrocytes, which significantly influences subsequent long-term pathological processes. Most existing focal brain injury models in rodents employ craniotomy to localise mechanical insults. However, the craniotomy procedure itself induces gliosis. To investigate perilesional astrocyte activation under conditions in which the skull is intact, we created focal brain injuries using light exposure through a cranial window made by thinning the skull without inducing gliosis. The lesion size was maximal at ~ 12 h and showed substantial recovery over the subsequent 30 days. Two distinct types of perilesional reactive astrocyte, identified by GFAP upregulation and hypertrophy, were found. In proximal regions the reactive astrocytes proliferated and expressed nestin, whereas in regions distal to the injury core the astrocytes showed increased GFAP expression but did not proliferate, lacked nestin expression, and displayed different morphology. Simply making the window did not induce any of these changes. There were also significant numbers of neurons in the recovering cortical tissue. In the recovery region, reactive astrocytes radially extended processes which appeared to influence the shapes of neuronal nuclei. The proximal reactive astrocytes also formed a cell layer which appeared to serve as a protective barrier, blocking the spread of IgG deposition and migration of microglia from the lesion core to surrounding tissue. The recovery was preceded by perilesional accumulation of leukocytes expressing vascular endothelial growth factor. These results suggest that, under intact skull conditions, focal brain injury is followed by perilesional reactive astrocyte activities that foster cortical tissue protection and recovery. © 2012 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Development of an efficient entire-capsid-coding-region amplification method for direct detection of poliovirus from stool extracts.

PubMed

Arita, Minetaro; Kilpatrick, David R; Nakamura, Tomofumi; Burns, Cara C; Bukbuk, David; Oderinde, Soji B; Oberste, M Steven; Kew, Olen M; Pallansch, Mark A; Shimizu, Hiroyuki

2015-01-01

Laboratory diagnosis has played a critical role in the Global Polio Eradication Initiative since 1988, by isolating and identifying poliovirus (PV) from stool specimens by using cell culture as a highly sensitive system to detect PV. In the present study, we aimed to develop a molecular method to detect PV directly from stool extracts, with a high efficiency comparable to that of cell culture. We developed a method to efficiently amplify the entire capsid coding region of human enteroviruses (EVs) including PV. cDNAs of the entire capsid coding region (3.9 kb) were obtained from as few as 50 copies of PV genomes. PV was detected from the cDNAs with an improved PV-specific real-time reverse transcription-PCR system and nucleotide sequence analysis of the VP1 coding region. For assay validation, we analyzed 84 stool extracts that were positive for PV in cell culture and detected PV genomes from 100% of the extracts (84/84 samples) with this method in combination with a PV-specific extraction method. PV could be detected in 2/4 stool extract samples that were negative for PV in cell culture. In PV-positive samples, EV species C viruses were also detected with high frequency (27% [23/86 samples]). This method would be useful for direct detection of PV from stool extracts without using cell culture. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

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

Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S.

1995-10-09

In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains amore » functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.« less

Methodology for fast detection of false sharing in threaded scientific codes

DOEpatents

Chung, I-Hsin; Cong, Guojing; Murata, Hiroki; Negishi, Yasushi; Wen, Hui-Fang

2014-11-25

A profiling tool identifies a code region with a false sharing potential. A static analysis tool classifies variables and arrays in the identified code region. A mapping detection library correlates memory access instructions in the identified code region with variables and arrays in the identified code region while a processor is running the identified code region. The mapping detection library identifies one or more instructions at risk, in the identified code region, which are subject to an analysis by a false sharing detection library. A false sharing detection library performs a run-time analysis of the one or more instructions at risk while the processor is re-running the identified code region. The false sharing detection library determines, based on the performed run-time analysis, whether two different portions of the cache memory line are accessed by the generated binary code.

Polyomavirus BK non-coding control region rearrangements in health and disease.

PubMed

Sharma, Preety M; Gupta, Gaurav; Vats, Abhay; Shapiro, Ron; Randhawa, Parmjeet S

2007-08-01

BK virus is an increasingly recognized pathogen in transplanted patients. DNA sequencing of this virus shows considerable genomic variability. To understand the clinical significance of rearrangements in the non-coding control region (NCCR) of BK virus (BKV), we report a meta-analysis of 507 sequences, including 40 sequences generated in our own laboratory, for associations between rearrangements and disease, tissue tropism, geographic origin, and viral genotype. NCCR rearrangements were less frequent in (a) asymptomatic BKV viruria compared to patients viral nephropathy (1.7% vs. 22.5%), and (b) viral genotype 1 compared to other genotypes (2.4% vs. 11.2%). Rearrangements were commoner in malignancy (78.6%), and Norwegians (45.7%), and less common in East Indians (0%), and Japanese (4.3%). A surprising number of rearranged sequences were reported from mononuclear cells of healthy subjects, whereas most plasma sequences were archetypal. This difference could not be related to potential recombinase activity in lymphocytes, as consensus recombination signal sequences could not be found in the NCCR region. NCCR rearrangements are neither required nor a sufficient condition to produce clinical disease. BKV nephropathy and hemorrhagic cystitis are not associated with any unique NCCR configuration or nucleotide sequence.

Aberrant functional connectivity in Papez circuit correlates with memory performance in cognitively intact middle-aged APOE4 carriers.

PubMed

Li, Wenjun; Antuono, Piero G; Xie, Chunming; Chen, Gang; Jones, Jennifer L; Ward, B Douglas; Singh, Suraj P; Franczak, Malgorzata B; Goveas, Joseph S; Li, Shi-Jiang

2014-08-01

The main objective of this study is to detect the early changes in resting-state Papez circuit functional connectivity using the hippocampus as the seed, and to determine the associations between altered functional connectivity (FC) and the episodic memory performance in cognitively intact middle-aged apolipoprotein E4 (APOE4) carriers who are at risk of Alzheimer's disease (AD). Forty-six cognitively intact, middle-aged participants, including 20 APOE4 carriers and 26 age-, sex-, and education-matched noncarriers were studied. The resting-state FC of the hippocampus (HFC) was compared between APOE4 carriers and noncarriers. APOE4 carriers showed significantly decreased FC in brain areas that involve learning and memory functions, including the frontal, cingulate, thalamus and basal ganglia regions. Multiple linear regression analysis showed significant correlations between HFC and the episodic memory performance. Conjunction analysis between neural correlates of memory and altered HFC showed the overlapping regions, especially the subcortical regions such as thalamus, caudate nucleus, and cingulate cortices involved in the Papez circuit. Thus, changes in connectivity in the Papez circuit may be used as an early risk detection for AD. Copyright © 2014. Published by Elsevier Ltd.

Identification of two allelic IgG1 C(H) coding regions (Cgamma1) of cat.

PubMed

Kanai, T H; Ueda, S; Nakamura, T

2000-01-31

Two types of cDNA encoding IgG1 heavy chain (gamma1) were isolated from a single domestic short-hair cat. Sequence analysis indicated a higher level of similarity of these Cgamma1 sequences to human Cgamma1 sequence (76.9 and 77.0%) than to mouse sequence (70.0 and 69.7%) at the nucleotide level. Predicted primary structures of both the feline Cgamma1 genes, designated as Cgamma1a and Cgamma1b, were similar to that of human Cgamma1 gene, for instance, as to the size of constant domains, the presence of six conserved cysteine residues involved in formation of the domain structure, and the location of a conserved N-linked glycosylation site. Sequence comparison between the two alleles showed that 7 out of 10 nucleotide differences were within the C(H)3 domain coding region, all leading to nonsynonymous changes in amino acid residues. Partial sequence analysis of genomic clones showed three nucleotide substitutions between the two Cgamma1 alleles in the intron between the CH2 and C(H)3 domain coding regions. In 12 domestic short-hair cats used in this study, the frequency of Cgamma1a allele (62.5%) was higher than that of the Cgamma1b allele (37.5%).

A-to-I editing of coding and non-coding RNAs by ADARs

PubMed Central

Nishikura, Kazuko

2016-01-01

Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. This A-to-I editing occurs not only in protein-coding regions of mRNAs, but also frequently in non-coding regions that contain inverted Alu repeats. Editing of coding sequences can result in the expression of functionally altered proteins that are not encoded in the genome, whereas the significance of Alu editing remains largely unknown. Certain microRNA (miRNA) precursors are also edited, leading to reduced expression or altered function of mature miRNAs. Conversely, recent studies indicate that ADAR1 forms a complex with Dicer to promote miRNA processing, revealing a new function of ADAR1 in the regulation of RNA interference. PMID:26648264

TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.

PubMed

Xu, Yan; Chen, Yan; Li, Daliang; Liu, Qing; Xuan, Zhenyu; Li, Wen-Hong

2017-02-01

MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.

46 CFR 178.325 - Intact stability requirements-monohull sailing vessels.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 7 2011-10-01 2011-10-01 false Intact stability requirements-monohull sailing vessels....325 Intact stability requirements—monohull sailing vessels. (a) As permitted by § 178.310(c) of this part, a monohull sailing vessel may demonstrate compliance with paragraphs (b) or (c) of this section...

46 CFR 178.320 - Intact stability requirements-non-sailing vessels.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 7 2011-10-01 2011-10-01 false Intact stability requirements-non-sailing vessels. 178.320 Section 178.320 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SMALL PASSENGER... Intact stability requirements—non-sailing vessels. (a) As permitted by § 178.310(c) of this part, the...

Parafoveal letter-position coding in reading.

PubMed

Snell, Joshua; Bertrand, Daisy; Grainger, Jonathan

2018-05-01

The masked-priming lexical decision task has been the paradigm of choice for investigating how readers code for letter identity and position. Insight into the temporal integration of information between prime and target words has pointed out, among other things, that readers do not code for the absolute position of letters. This conception has spurred various accounts of the word recognition process, but the results at present do not favor one account in particular. Thus, employing a new strategy, the present study moves out of the arena of temporal- and into the arena of spatial information integration. We present two lexical decision experiments that tested how the processing of six-letter target words is influenced by simultaneously presented flanking stimuli (each stimulus was presented for 150 ms). We manipulated the orthographic relatedness between the targets and flankers, in terms of both letter identity (same/different letters based on the target's outer/inner letters) and letter position (intact/reversed order of letters and of flankers, contiguous/noncontiguous flankers). Target processing was strongly facilitated by same-letter flankers, and this facilitatory effect was modulated by both letter/flanker order and contiguity. However, when the flankers consisted of the target's inner-positioned letters alone, letter order no longer mattered. These findings suggest that readers may code for the relative position of letters using words' edges as spatial points of reference. We conclude that the flanker paradigm provides a fruitful means to investigate letter-position coding in the fovea and parafovea.

Transient Ejector Analysis (TEA) code user's guide

NASA Technical Reports Server (NTRS)

Drummond, Colin K.

1993-01-01

A FORTRAN computer program for the semi analytic prediction of unsteady thrust augmenting ejector performance has been developed, based on a theoretical analysis for ejectors. That analysis blends classic self-similar turbulent jet descriptions with control-volume mixing region elements. Division of the ejector into an inlet, diffuser, and mixing region allowed flexibility in the modeling of the physics for each region. In particular, the inlet and diffuser analyses are simplified by a quasi-steady-analysis, justified by the assumption that pressure is the forcing function in those regions. Only the mixing region is assumed to be dominated by viscous effects. The present work provides an overview of the code structure, a description of the required input and output data file formats, and the results for a test case. Since there are limitations to the code for applications outside the bounds of the test case, the user should consider TEA as a research code (not as a production code), designed specifically as an implementation of the proposed ejector theory. Program error flags are discussed, and some diagnostic routines are presented.

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice.

PubMed

Schmouth, Jean-François; Castellarin, Mauro; Laprise, Stéphanie; Banks, Kathleen G; Bonaguro, Russell J; McInerny, Simone C; Borretta, Lisa; Amirabbasi, Mahsa; Korecki, Andrea J; Portales-Casamar, Elodie; Wilson, Gary; Dreolini, Lisa; Jones, Steven J M; Wasserman, Wyeth W; Goldowitz, Daniel; Holt, Robert A; Simpson, Elizabeth M

2013-10-14

The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome') strategy to expand our understanding of human gene regulation in vivo. In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear. We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.

3DFEMWATER/3DLEWASTE: NUMERICAL CODES FOR DELINEATING WELLHEAD PROTECTION AREAS IN AGRICULTURAL REGIONS BASED ON THE ASSIMILATIVE CAPACITY CRITERION

EPA Science Inventory

Two related numerical codes, 3DFEMWATER and 3DLEWASTE, are presented sed to delineate wellhead protection areas in agricultural regions using the assimilative capacity criterion. DFEMWATER (Three-dimensional Finite Element Model of Water Flow Through Saturated-Unsaturated Media) ...

Xenopus egg cytoplasm with intact actin.

PubMed

Field, Christine M; Nguyen, Phuong A; Ishihara, Keisuke; Groen, Aaron C; Mitchison, Timothy J

2014-01-01

We report optimized methods for preparing Xenopus egg extracts without cytochalasin D, that we term "actin-intact egg extract." These are undiluted egg cytoplasm that contains abundant organelles, and glycogen which supplies energy, and represents the least perturbed cell-free cytoplasm preparation we know of. We used this system to probe cell cycle regulation of actin and myosin-II dynamics (Field et al., 2011), and to reconstitute the large, interphase asters that organize early Xenopus embryos (Mitchison et al., 2012; Wühr, Tan, Parker, Detrich, & Mitchison, 2010). Actin-intact Xenopus egg extracts are useful for analysis of actin dynamics, and interaction of actin with other cytoplasmic systems, in a cell-free system that closely mimics egg physiology, and more generally for probing the biochemistry and biophysics of the egg, zygote, and early embryo. Detailed protocols are provided along with assays used to check cell cycle state and tips for handling and storing undiluted egg extracts. © 2014 Elsevier Inc. All rights reserved.

Prediction of valid acidity in intact apples with Fourier transform near infrared spectroscopy.

PubMed

Liu, Yan-De; Ying, Yi-Bin; Fu, Xia-Ping

2005-03-01

To develop nondestructive acidity prediction for intact Fuji apples, the potential of Fourier transform near infrared (FT-NIR) method with fiber optics in interactance mode was investigated. Interactance in the 800 nm to 2619 nm region was measured for intact apples, harvested from early to late maturity stages. Spectral data were analyzed by two multivariate calibration techniques including partial least squares (PLS) and principal component regression (PCR) methods. A total of 120 Fuji apples were tested and 80 of them were used to form a calibration data set. The influences of different data preprocessing and spectra treatments were also quantified. Calibration models based on smoothing spectra were slightly worse than that based on derivative spectra, and the best result was obtained when the segment length was 5 nm and the gap size was 10 points. Depending on data preprocessing and PLS method, the best prediction model yielded correlation coefficient of determination (r2) of 0.759, low root mean square error of prediction (RMSEP) of 0.0677, low root mean square error of calibration (RMSEC) of 0.0562. The results indicated the feasibility of FT-NIR spectral analysis for predicting apple valid acidity in a nondestructive way.

Prediction of valid acidity in intact apples with Fourier transform near infrared spectroscopy*

PubMed Central

Liu, Yan-de; Ying, Yi-bin; Fu, Xia-ping

2005-01-01

To develop nondestructive acidity prediction for intact Fuji apples, the potential of Fourier transform near infrared (FT-NIR) method with fiber optics in interactance mode was investigated. Interactance in the 800 nm to 2619 nm region was measured for intact apples, harvested from early to late maturity stages. Spectral data were analyzed by two multivariate calibration techniques including partial least squares (PLS) and principal component regression (PCR) methods. A total of 120 Fuji apples were tested and 80 of them were used to form a calibration data set. The influences of different data preprocessing and spectra treatments were also quantified. Calibration models based on smoothing spectra were slightly worse than that based on derivative spectra, and the best result was obtained when the segment length was 5 nm and the gap size was 10 points. Depending on data preprocessing and PLS method, the best prediction model yielded correlation coefficient of determination (r 2) of 0.759, low root mean square error of prediction (RMSEP) of 0.0677, low root mean square error of calibration (RMSEC) of 0.0562. The results indicated the feasibility of FT-NIR spectral analysis for predicting apple valid acidity in a nondestructive way. PMID:15682498

A Comparison of Bacterial Composition in Diabetic Ulcers and Contralateral Intact Skin

PubMed Central

Gontcharova, Viktoria; Youn, Eunseog; Sun, Yan; Wolcott, Randall D; Dowd, Scot E

2010-01-01

An extensive portion of the healthcare budget is allocated to chronic human infection. Chronic wounds in particular are a major contributor to this financial burden. Little is known about the types of bacteria which may contribute to the chronicity, biofilm and overall bioburden of the wound itself. In this study we compare the bacteriology of wounds and associated intact skin. Wound and paired intact skin swabs (from a contralateral location) were collected. The bacterial diversity was determined using bacterial Tag-encoded FLX amplicon pyrosequencing (bTEFAP). Diversity analysis showed intact skin to be significantly more diverse than wounds on both the species and genus levels (3% and 5% divergence). Furthermore, wounds show heightened levels of anaerobic bacteria, like Peptoniphilus, Finegoldia, and Anaerococcus, and other detrimental genera such as Corynebacterium and Staphylococcus. Although some of these and other bacterial genera were found to be common between intact skin and wounds, notable opportunistic wound pathogens were found at lower levels in intact skin. Principal Component Analysis demonstrated a clear separability of the two groups. The findings of the study not only greatly support the hypothesis of differing bacterial composition of intact skin and wounds, but also contribute additional insight into the ecology of skin and wound microflora. The increased diversity and lowered levels of opportunistic pathogens found in skin make the system highly distinguishable from wounds. PMID:20461221

Modified madigan prostatectomy: a procedure preserved prostatic urethra intact.

PubMed

Lu, Jun; Ye, Zhangqun; Hu, Weilie

2005-01-01

A total of 92 patients with benign prostatic hyperplasia (BPH) were subjected to modified Madigan prostatectomy (MPC) for a much satisfactory effect in open prostatectomy surgery. Exposing anterior prostatic urethra near the bladder neck and conjunct cystotomy modified the MPC procedure. This modified procedure preserved prostatic urethra intact and could also deal with intracystic lesions at the same time. The intact of prostatic urethra was kept completely or largely in 86 cases. The amount of blood loss during modified procedure was less. The mean operative time was 105 min. Seventy patients had been followed up for 3-24 months. The postoperative average Qmax was 19. 2 ml/s. The cystourethrography revealed that the urethra and bladder neck were intact in 10 patients postoperatively. Furthermore, the prostatic urethra was obviously wider after modified MPC. The modified MPC can reduce the occurrence of urethra injury and enlarge the MPC indications. The modified technique is easy to perform with less complications and much satisfactory clinical result.

Arraying of intact liposomes into chemically functionalized microwells.

PubMed

Kalyankar, Nikhil D; Sharma, Manoj K; Vaidya, Shyam V; Calhoun, David; Maldarelli, Charles; Couzis, Alexander; Gilchrist, Lane

2006-06-06

Here, we describe a protocol to bind individual, intact phospholipid bilayer liposomes, which are on the order of 1 microm in diameter, in microwells etched in a regular array on a silicon oxide substrate. The diameter of the wells is on the order of the liposome diameter, so only one liposome is located in each well. The background of the silicon oxide surface is functionalized with a PEG oligomer using the contact printing of a PEG silane to present a surface that resists the adsorption of proteins, lipid material, and liposomes. The interiors of the wells are functionalized with an aminosilane to facilitate the conjugation of biotin, which is then bound to Neutravidin. The avidin-coated well interiors bind the liposomes whose surfaces contain biotinylated lipids. The specific binding of the liposomes to the surface using the biotin-avidin linkage, together with the resistant nature of the background and the physical confinement of the wells, allows the liposomes to remain intact and to not unravel, rupture, and fuse onto the surface. We demonstrate this intact arraying using confocal laser scanning microscopy of fluorophores specifically tagging the microwells, the lipid bilayer, and the aqueous interior of the liposome.

Involvement of the N-terminal region in alpha-crystallin-lens membrane recognition

NASA Technical Reports Server (NTRS)

Ifeanyi, F.; Takemoto, L.; Spooner, B. S. (Principal Investigator)

1991-01-01

Previous studies have demonstrated that alpha-crystallin binds specifically, in a saturable manner, to lens membrane. To determine the region of the alpha-crystallin molecule that might be involved in this binding, native alpha-crystallin from the bovine lens has been treated by limited digestion with trypsin, to produce alpha-A molecules with an intact C-terminal region, and a nicked N-terminal region. Compared to intact alpha-crystallin, trypsin-treated alpha-crystallin binds less avidly to lens membrane, suggesting that the N-terminal region of the alpha-A molecule may play a key role in the recognition between lens membrane and crystallin.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria.

PubMed

Ilag, Leopold L; Videler, Hortense; McKay, Adam R; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H; Robinson, Carol V

2005-06-07

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria

PubMed Central

Ilag, Leopold L.; Videler, Hortense; McKay, Adam R.; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H.; Robinson, Carol V.

2005-01-01

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus. PMID:15923259

A comparison of cosmological hydrodynamic codes

NASA Technical Reports Server (NTRS)

Kang, Hyesung; Ostriker, Jeremiah P.; Cen, Renyue; Ryu, Dongsu; Hernquist, Lars; Evrard, August E.; Bryan, Greg L.; Norman, Michael L.

1994-01-01

We present a detailed comparison of the simulation results of various hydrodynamic codes. Starting with identical initial conditions based on the cold dark matter scenario for the growth of structure, with parameters h = 0.5 Omega = Omega(sub b) = 1, and sigma(sub 8) = 1, we integrate from redshift z = 20 to z = O to determine the physical state within a representative volume of size L(exp 3) where L = 64 h(exp -1) Mpc. Five indenpendent codes are compared: three of them Eulerian mesh-based and two variants of the smooth particle hydrodynamics 'SPH' Lagrangian approach. The Eulerian codes were run at N(exp 3) = (32(exp 3), 64(exp 3), 128(exp 3), and 256(exp 3)) cells, the SPH codes at N(exp 3) = 32(exp 3) and 64(exp 3) particles. Results were then rebinned to a 16(exp 3) grid with the exception that the rebinned data should converge, by all techniques, to a common and correct result as N approaches infinity. We find that global averages of various physical quantities do, as expected, tend to converge in the rebinned model, but that uncertainites in even primitive quantities such as (T), (rho(exp 2))(exp 1/2) persists at the 3%-17% level achieve comparable and satisfactory accuracy for comparable computer time in their treatment of the high-density, high-temeprature regions as measured in the rebinned data; the variance among the five codes (at highest resolution) for the mean temperature (as weighted by rho(exp 2) is only 4.5%. Examined at high resolution we suspect that the density resolution is better in the SPH codes and the thermal accuracy in low-density regions better in the Eulerian codes. In the low-density, low-temperature regions the SPH codes have poor accuracy due to statiscal effects, and the Jameson code gives the temperatures which are too high, due to overuse of artificial viscosity in these high Mach number regions. Overall the comparison allows us to better estimate errors; it points to ways of improving this current generation ofhydrodynamic

Quantifying the ultrastructure of carotid arteries using high-resolution micro-diffusion tensor imaging—comparison of intact versus open cut tissue

NASA Astrophysics Data System (ADS)

Salman Shahid, Syed; Gaul, Robert T.; Kerskens, Christian; Flamini, Vittoria; Lally, Caitríona

2017-12-01

Diffusion magnetic resonance imaging (dMRI) can provide insights into the microstructure of intact arterial tissue. The current study employed high magnetic field MRI to obtain ultra-high resolution dMRI at an isotropic voxel resolution of 117 µm3 in less than 2 h of scan time. A parameter selective single shell (128 directions) diffusion-encoding scheme based on Stejskel-Tanner sequence with echo-planar imaging (EPI) readout was used. EPI segmentation was used to reduce the echo time (TE) and to minimise the susceptibility-induced artefacts. The study utilised the dMRI analysis with diffusion tensor imaging (DTI) framework to investigate structural heterogeneity in intact arterial tissue and to quantify variations in tissue composition when the tissue is cut open and flattened. For intact arterial samples, the region of interest base comparison showed significant differences in fractional anisotropy and mean diffusivity across the media layer (p  <  0.05). For open cut flat samples, DTI based directionally invariant indices did not show significant differences across the media layer. For intact samples, fibre tractography based indices such as calculated helical angle and fibre dispersion showed near circumferential alignment and a high degree of fibre dispersion, respectively. This study demonstrates the feasibility of fast dMRI acquisition with ultra-high spatial and angular resolution at 7 T. Using the optimised sequence parameters, this study shows that DTI based markers are sensitive to local structural changes in intact arterial tissue samples and these markers may have clinical relevance in the diagnosis of atherosclerosis and aneurysm.

Second-generation sequencing of entire mitochondrial coding-regions (∼15.4 kb) holds promise for study of the phylogeny and taxonomy of human body lice and head lice.

PubMed

Xiong, H; Campelo, D; Pollack, R J; Raoult, D; Shao, R; Alem, M; Ali, J; Bilcha, K; Barker, S C

2014-08-01

The Illumina Hiseq platform was used to sequence the entire mitochondrial coding-regions of 20 body lice, Pediculus humanus Linnaeus, and head lice, P. capitis De Geer (Phthiraptera: Pediculidae), from eight towns and cities in five countries: Ethiopia, France, China, Australia and the U.S.A. These data (∼310 kb) were used to see how much more informative entire mitochondrial coding-region sequences were than partial mitochondrial coding-region sequences, and thus to guide the design of future studies of the phylogeny, origin, evolution and taxonomy of body lice and head lice. Phylogenies were compared from entire coding-region sequences (∼15.4 kb), entire cox1 (∼1.5 kb), partial cox1 (∼700 bp) and partial cytb (∼600 bp) sequences. On the one hand, phylogenies from entire mitochondrial coding-region sequences (∼15.4 kb) were much more informative than phylogenies from entire cox1 sequences (∼1.5 kb) and partial gene sequences (∼600 to ∼700 bp). For example, 19 branches had > 95% bootstrap support in our maximum likelihood tree from the entire mitochondrial coding-regions (∼15.4 kb) whereas the tree from 700 bp cox1 had only two branches with bootstrap support > 95%. Yet, by contrast, partial cytb (∼600 bp) and partial cox1 (∼486 bp) sequences were sufficient to genotype lice to Clade A, B or C. The sequences of the mitochondrial genomes of the P. humanus, P. capitis and P. schaeffi Fahrenholz studied are in NCBI GenBank under the accession numbers KC660761-800, KC685631-6330, KC241882-97, EU219988-95, HM241895-8 and JX080388-407. © 2014 The Royal Entomological Society.

Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation

PubMed Central

Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; Frigard, Vianney; Poulain, Damien; van der Werf, Sylvie

2014-01-01

Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. PMID:25268971

Tidal stretches do not modulate responsiveness of intact airways in vitro

PubMed Central

Szabo, Thomas L.; Suki, Béla; Lutchen, Kenneth R.

2010-01-01

Studies on isolated tracheal airway smooth muscle (ASM) strips have shown that length/force fluctuations, similar to those likely occurring during breathing, will mitigate ASM contractility. These studies conjecture that, solely by reducing length oscillations on a healthy, intact airway, one can create airway hyperresponsiveness, but this has never been explicitly tested. The intact airway has additional complexities of geometry and structure that may impact its relevance to isolated ASM strips. We examined the role of transmural pressure (Ptm) fluctuations of physiological amplitudes on the responsiveness of an intact airway. We developed an integrated system utilizing ultrasound imaging to provide real-time measurements of luminal radius and wall thickness over the full length of an intact airway (generation 10 and below) during Ptm oscillations. First, airway constriction dynamics to cumulative acetylcholine (ACh) doses (10−7 to 10−3 M) were measured during static and dynamic Ptm protocols. Regardless of the breathing pattern, the Ptm oscillation protocols were ineffective in reducing the net level of constriction for any ACh dose, compared with the static control (P = 0.225–0.793). Next, Ptm oscillations of increasing peak-to-peak amplitude were applied subsequent to constricting intact airways under static conditions (5.0-cmH2O Ptm) with a moderate ACh dose (10−5 M). Peak-to-peak Ptm oscillations ≤5.0 cmH2O resulted in no statistically significant bronchodilatory response (P = 0.429 and 0.490). Larger oscillations (10 cmH2O, peak to peak) produced modest dilation of 4.3% (P = 0.009). The lack of modulation of airway responsiveness by Ptm oscillations in intact, healthy airways suggests that ASM level mechanisms alone may not be the sole determinant of airway responsiveness. PMID:20431023

Mechanism of autoregulation in the intact kidney.

DOT National Transportation Integrated Search

1963-12-01

The mechanism of renal autoregulation is unclear. The subject of the present investigation is the mechanism of autoregulation of blood flow in the intact kidney. The left kidney of the anesthetized dog was exposed via a flank approach. Renal venous o...

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

Self-etching adhesive on intact enamel, with and without pre-etching.

PubMed

Devarasa, G M; Subba Reddy, V V; Chaitra, N L; Swarna, Y M

2012-05-01

Bond strengths of composite resin to enamel using self-etch adhesive (SEA) Clearfil SE bond system on intact enamel and enamel pre-etched with phosphoric acid were compared. The objective was to determine if the pre-etching would increase the bond strengths of the SEA systems to intact enamel and to evaluate the effect of pre-etching on bond formation of self-etch adhesives on intact enamel. Labial surfaces of 40 caries free permanent upper central and lateral incisors were cleaned, sectioned of their roots. All specimens were mounted on acrylic block and divided randomly into four groups. In two groups the application of self-etch adhesive, Clearfil SE bond was carried as per manufacturer's instructions, composite cylinders were built, whereas in the other two groups, 37% phosphoric acid etching was done before the application of self-etching adhesives. Then the resin tags were analyzed using scanning electron microscope and shear bond strength was measured using Instron universal testing machine. When phosphoric acid was used, there was significant increase in the depth of penetration of resin tags and in the Shear Bond Strength of composite to enamel. The results indicate that out of both treatment groups, pre-etching the intact enamel with 37% phosphoric acid resulted in formation of longer resin tags and higher depth of penetration of resin tags of the Clearfil SE bond, and attaining higher bond strength of the Clearfil SE bond to intact enamel. Copyright © 2011 Wiley Periodicals, Inc.

Numerical modeling of heat transfer and pasteurizing value during thermal processing of intact egg.

PubMed

Abbasnezhad, Behzad; Hamdami, Nasser; Monteau, Jean-Yves; Vatankhah, Hamed

2016-01-01

Thermal Pasteurization of Eggs, as a widely used nutritive food, has been simulated. A three-dimensional numerical model, computational fluid dynamics codes of heat transfer equations using heat natural convection, and conduction mechanisms, based on finite element method, was developed to study the effect of air cell size and eggshell thickness. The model, confirmed by comparing experimental and numerical results, was able to predict the temperature profiles, the slowest heating zone, and the required heating time during pasteurization of intact eggs. The results showed that the air cell acted as a heat insulator. Increasing the air cell volume resulted in decreasing of the heat transfer rate, and the increasing the required time of pasteurization (up to 14%). The findings show that the effect on thermal pasteurization of the eggshell thickness was not considerable in comparison to the air cell volume.

Synonymous deoptimization of the foot-and-mouth disease virus P1 coding region causes attenuation in vivo while inducing a strong neutralizing antibody response

USDA-ARS?s Scientific Manuscript database

Codon bias deoptimization has been previously used to successfully attenuate human pathogens including polio, respiratory syncytial and influenza viruses. We have applied a similar technology to deoptimize the capsid coding region (P1 region) of the cDNA infectious clone of foot-and-mouth disease vi...

Coded Cooperation for Multiway Relaying in Wireless Sensor Networks.

PubMed

Si, Zhongwei; Ma, Junyang; Thobaben, Ragnar

2015-06-29

Wireless sensor networks have been considered as an enabling technology for constructing smart cities. One important feature of wireless sensor networks is that the sensor nodes collaborate in some manner for communications. In this manuscript, we focus on the model of multiway relaying with full data exchange where each user wants to transmit and receive data to and from all other users in the network. We derive the capacity region for this specific model and propose a coding strategy through coset encoding. To obtain good performance with practical codes, we choose spatially-coupled LDPC (SC-LDPC) codes for the coded cooperation. In particular, for the message broadcasting from the relay, we construct multi-edge-type (MET) SC-LDPC codes by repeatedly applying coset encoding. Due to the capacity-achieving property of the SC-LDPC codes, we prove that the capacity region can theoretically be achieved by the proposed MET SC-LDPC codes. Numerical results with finite node degrees are provided, which show that the achievable rates approach the boundary of the capacity region in both binary erasure channels and additive white Gaussian channels.

Coded-aperture imaging of the Galactic center region at gamma-ray energies

NASA Technical Reports Server (NTRS)

Cook, Walter R.; Grunsfeld, John M.; Heindl, William A.; Palmer, David M.; Prince, Thomas A.

1991-01-01

The first coded-aperture images of the Galactic center region at energies above 30 keV have revealed two strong gamma-ray sources. One source has been identified with the X-ray source IE 1740.7 - 2942, located 0.8 deg away from the nucleus. If this source is at the distance of the Galactic center, it is one of the most luminous objects in the galaxy at energies from 35 to 200 keV. The second source is consistent in location with the X-ray source GX 354 + 0 (MXB 1728-34). In addition, gamma-ray flux from the location of GX 1 + 4 was marginally detected at a level consistent with other post-1980 measurements. No significant hard X-ray or gamma-ray flux was detected from the direction of the Galactic nucleus or from the direction of the recently discovered gamma-ray source GRS 1758-258.

The θ-γ neural code.

PubMed

Lisman, John E; Jensen, Ole

2013-03-20

Theta and gamma frequency oscillations occur in the same brain regions and interact with each other, a process called cross-frequency coupling. Here, we review evidence for the following hypothesis: that the dual oscillations form a code for representing multiple items in an ordered way. This form of coding has been most clearly demonstrated in the hippocampus, where different spatial information is represented in different gamma subcycles of a theta cycle. Other experiments have tested the functional importance of oscillations and their coupling. These involve correlation of oscillatory properties with memory states, correlation with memory performance, and effects of disrupting oscillations on memory. Recent work suggests that this coding scheme coordinates communication between brain regions and is involved in sensory as well as memory processes. Copyright © 2013 Elsevier Inc. All rights reserved.

HYDROCARBON VAPOR DIFFUSION IN INTACT CORE SLEEVES

EPA Science Inventory

The diffusion of 2,2,4-trimethylpentane (TMP) and 2,2,5-trimethylhexane (TMH) vapors put of residually contaminated sandy soil from the U.S. Environmental Protection Agency (EPA) field research site at Traverse City, Michigan, was measured and modeled. The headspace of an intact ...

Source Selection Simulation: Intact Team Training on Picking a Provider

DTIC Science & Technology

2015-06-01

seat of a new $100 million stealth fighter before giving her flight simulation time. The ar- gument for source-selection simulation ( SSS ) training is...dynamic is the creation of the SSS Tool. Drawing on his success in using a similar tool in contingency contracting, Long decided we should use a Web...of SSS intact team training. On Sept. 30–Oct. 3, 2014, Professors Long and Elsesser de- livered DAU’s first-ever Intact Team SSS Training to Eglin’s

Detection of Intact Lava Tubes at Marius Hills on the Moon by SELENE (Kaguya) Lunar Radar Sounder

NASA Astrophysics Data System (ADS)

Kaku, T.; Haruyama, J.; Miyake, W.; Kumamoto, A.; Ishiyama, K.; Nishibori, T.; Yamamoto, K.; Crites, Sarah T.; Michikami, T.; Yokota, Y.; Sood, R.; Melosh, H. J.; Chappaz, L.; Howell, K. C.

2017-10-01

Intact lunar lava tubes offer a pristine environment to conduct scientific examination of the Moon's composition and potentially serve as secure shelters for humans and instruments. We investigated the SELENE Lunar Radar Sounder (LRS) data at locations close to the Marius Hills Hole (MHH), a skylight potentially leading to an intact lava tube, and found a distinctive echo pattern exhibiting a precipitous decrease in echo power, subsequently followed by a large second echo peak that may be evidence for the existence of a lava tube. The search area was further expanded to 13.00-15.00°N, 301.85-304.01°E around the MHH, and similar LRS echo patterns were observed at several locations. Most of the locations are in regions of underground mass deficit suggested by GRAIL gravity data analysis. Some of the observed echo patterns are along rille A, where the MHH was discovered, or on the southwest underground extension of the rille.

Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups.

PubMed

Herrnstadt, Corinna; Elson, Joanna L; Fahy, Eoin; Preston, Gwen; Turnbull, Douglass M; Anderson, Christen; Ghosh, Soumitra S; Olefsky, Jerrold M; Beal, M Flint; Davis, Robert E; Howell, Neil

2002-05-01

The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups. Another important result is that there were numerous instances both of parallel mutations at the same site and of reversion (i.e., homoplasy). It is likely that homoplasy in the coding region will confound evolutionary analysis of small sequence sets. By a linkage-disequilibrium approach, additional evidence for the absence of human mtDNA recombination is presented here.

46 CFR 174.045 - Intact stability requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 7 2013-10-01 2013-10-01 false Intact stability requirements. 174.045 Section 174.045 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SUBDIVISION AND STABILITY SPECIAL RULES PERTAINING TO SPECIFIC VESSEL TYPES Special Rules Pertaining to Mobile Offshore Drilling Units § 174.045...

46 CFR 174.045 - Intact stability requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Intact stability requirements. 174.045 Section 174.045 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SUBDIVISION AND STABILITY SPECIAL RULES PERTAINING TO SPECIFIC VESSEL TYPES Special Rules Pertaining to Mobile Offshore Drilling Units § 174.045...

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016

PubMed Central

Kyalo, David; Amratia, Punam; Mundia, Clara W.; Mbogo, Charles M.; Coetzee, Maureen; Snow, Robert W.

2017-01-01

Background: Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods: We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results: The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion: We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016.

PubMed

Kyalo, David; Amratia, Punam; Mundia, Clara W; Mbogo, Charles M; Coetzee, Maureen; Snow, Robert W

2017-01-01

Background : Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods : We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results : The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion : We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

Visual speech alters the discrimination and identification of non-intact auditory speech in children with hearing loss.

PubMed

Jerger, Susan; Damian, Markus F; McAlpine, Rachel P; Abdi, Hervé

2017-03-01

Understanding spoken language is an audiovisual event that depends critically on the ability to discriminate and identify phonemes yet we have little evidence about the role of early auditory experience and visual speech on the development of these fundamental perceptual skills. Objectives of this research were to determine 1) how visual speech influences phoneme discrimination and identification; 2) whether visual speech influences these two processes in a like manner, such that discrimination predicts identification; and 3) how the degree of hearing loss affects this relationship. Such evidence is crucial for developing effective intervention strategies to mitigate the effects of hearing loss on language development. Participants were 58 children with early-onset sensorineural hearing loss (CHL, 53% girls, M = 9;4 yrs) and 58 children with normal hearing (CNH, 53% girls, M = 9;4 yrs). Test items were consonant-vowel (CV) syllables and nonwords with intact visual speech coupled to non-intact auditory speech (excised onsets) as, for example, an intact consonant/rhyme in the visual track (Baa or Baz) coupled to non-intact onset/rhyme in the auditory track (/-B/aa or/-B/az). The items started with an easy-to-speechread/B/or difficult-to-speechread/G/onset and were presented in the auditory (static face) vs. audiovisual (dynamic face) modes. We assessed discrimination for intact vs. non-intact different pairs (e.g., Baa:/-B/aa). We predicted that visual speech would cause the non-intact onset to be perceived as intact and would therefore generate more same-as opposed to different-responses in the audiovisual than auditory mode. We assessed identification by repetition of nonwords with non-intact onsets (e.g.,/-B/az). We predicted that visual speech would cause the non-intact onset to be perceived as intact and would therefore generate more Baz-as opposed to az- responses in the audiovisual than auditory mode. Performance in the audiovisual mode showed more same

Visual Speech Alters the Discrimination and Identification of Non-Intact Auditory Speech in Children with Hearing Loss

PubMed Central

Jerger, Susan; Damian, Markus F.; McAlpine, Rachel P.; Abdi, Hervé

2017-01-01

Objectives Understanding spoken language is an audiovisual event that depends critically on the ability to discriminate and identify phonemes yet we have little evidence about the role of early auditory experience and visual speech on the development of these fundamental perceptual skills. Objectives of this research were to determine 1) how visual speech influences phoneme discrimination and identification; 2) whether visual speech influences these two processes in a like manner, such that discrimination predicts identification; and 3) how the degree of hearing loss affects this relationship. Such evidence is crucial for developing effective intervention strategies to mitigate the effects of hearing loss on language development. Methods Participants were 58 children with early-onset sensorineural hearing loss (CHL, 53% girls, M = 9;4 yrs) and 58 children with normal hearing (CNH, 53% girls, M = 9;4 yrs). Test items were consonant-vowel (CV) syllables and nonwords with intact visual speech coupled to non-intact auditory speech (excised onsets) as, for example, an intact consonant/rhyme in the visual track (Baa or Baz) coupled to non-intact onset/rhyme in the auditory track (/–B/aa or /–B/az). The items started with an easy-to-speechread /B/ or difficult-to-speechread /G/ onset and were presented in the auditory (static face) vs. audiovisual (dynamic face) modes. We assessed discrimination for intact vs. non-intact different pairs (e.g., Baa:/–B/aa). We predicted that visual speech would cause the non-intact onset to be perceived as intact and would therefore generate more same—as opposed to different—responses in the audiovisual than auditory mode. We assessed identification by repetition of nonwords with non-intact onsets (e.g., /–B/az). We predicted that visual speech would cause the non-intact onset to be perceived as intact and would therefore generate more Baz—as opposed to az— responses in the audiovisual than auditory mode. Results

Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice.

PubMed

Rozhdestvensky, Timofey S; Robeck, Thomas; Galiveti, Chenna R; Raabe, Carsten A; Seeger, Birte; Wolters, Anna; Gubar, Leonid V; Brosius, Jürgen; Skryabin, Boris V

2016-02-05

Prader-Willi syndrome (PWS) is a neurogenetic disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. The PWS-critical region (PWScr) contains an array of non-protein coding IPW-A exons hosting intronic SNORD116 snoRNA genes. Deletion of PWScr is associated with PWS in humans and growth retardation in mice exhibiting ~15% postnatal lethality in C57BL/6 background. Here we analysed a knock-in mouse containing a 5'HPRT-LoxP-Neo(R) cassette (5'LoxP) inserted upstream of the PWScr. When the insertion was inherited maternally in a paternal PWScr-deletion mouse model (PWScr(p-/m5'LoxP)), we observed compensation of growth retardation and postnatal lethality. Genomic methylation pattern and expression of protein-coding genes remained unaltered at the PWS-locus of PWScr(p-/m5'LoxP) mice. Interestingly, ubiquitous Snord116 and IPW-A exon transcription from the originally silent maternal chromosome was detected. In situ hybridization indicated that PWScr(p-/m5'LoxP) mice expressed Snord116 in brain areas similar to wild type animals. Our results suggest that the lack of PWScr RNA expression in certain brain areas could be a primary cause of the growth retardation phenotype in mice. We propose that activation of disease-associated genes on imprinted regions could lead to general therapeutic strategies in associated diseases.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

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

Ansong, Charles; Tolic, Nikola; Purvine, Samuel O.

Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. For example systems biology-oriented genome scale modeling efforts greatly benefit from accurate annotation of protein-coding genes to develop proper functioning models. However, determining protein-coding genes for most new genomes is almost completely performed by inference, using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. With the ability to directly measure peptides arising from expressed proteins, mass spectrometry-based proteomics approaches can be used to augment and verify codingmore » regions of a genomic sequence and importantly detect post-translational processing events. In this study we utilized “shotgun” proteomics to guide accurate primary genome annotation of the bacterial pathogen Salmonella Typhimurium 14028 to facilitate a systems-level understanding of Salmonella biology. The data provides protein-level experimental confirmation for 44% of predicted protein-coding genes, suggests revisions to 48 genes assigned incorrect translational start sites, and uncovers 13 non-annotated genes missed by gene prediction programs. We also present a comprehensive analysis of post-translational processing events in Salmonella, revealing a wide range of complex chemical modifications (70 distinct modifications) and confirming more than 130 signal peptide and N-terminal methionine cleavage events in Salmonella. This study highlights several ways in which proteomics data applied during the primary stages of annotation can improve the quality of genome annotations, especially with regards to the annotation of mature protein products.« less

The Multilevel Mixed Intact Group Analysis: A Mixed Method to Seek, Detect, Describe, and Explain Differences Among Intact Groups

ERIC Educational Resources Information Center

Schoonenboom, Judith

2016-01-01

Educational innovations often involve intact subgroups, such as school classes or university departments. In small-scale educational evaluation research, typically involving 1 to 20 subgroups, differences among these subgroups are often neglected. This article presents a mixed method from a qualitative perspective, in which differences among…

Structural determination of intact proteins using mass spectrometry

DOEpatents

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

Pseudomonas aeruginosa infections of intact skin.

PubMed

Agger, W A; Mardan, A

1995-02-01

Pseudomonas aeruginosa infections of healthy skin are uncommon. We report four cases of P. aeruginosa infections of intact skin. These cases illustrate the clinical spectrum of these cutaneous infections: localized, mild epidermal infections (the green nail syndrome and webbed space infections), moderately serious infections (cutaneous folliculitis and otitis externa), and, in immunocompromised patients, extremely serious infections (malignant otitis externa, perirectal infection, and ecthyma gangrenosum).

How can we conserve intact tropical peatlands?

NASA Astrophysics Data System (ADS)

Lawson, Ian; Roucoux, Katherine

2017-04-01

The scientific community has, for more than three decades, been expressing increasing alarm about the fate of peatlands in parts of Indonesia and Malaysia, where extensive land-use conversion and drainage for rice and oil palm have greatly compromised peatland hydrology, ecology, biological richness, and carbon storage. The discourse in the literature on these peatlands is now moving on from attempts to preserve the last remaining fragments of peat-swamp forest, towards discussion of how best to restore damaged ecosystems, and whether it is possible to manage plantations more 'sustainably'. It is becoming increasingly clear, however, that peatlands occur quite widely in other parts of the lowland tropics, including parts of Amazonia and the Congo Basin, and many of these peatlands can reasonably be described as 'intact': although few if any parts of the tropics are totally unaffected by human actions, the hydrology and functional ecology of these systems appear to be close to a 'natural' state. The question then arises as to what should be done with the knowledge of their existence. Here we analyse the arguments in favour of protecting intact peatlands, and the potential conflicts with other priorities such as economic development and social justice. We evaluate alternative mechanisms for protecting intact peatlands, focusing on the particular issues raised by peatlands as opposed to other kinds of tropical ecosystem. We identify ways in which natural science agendas can help to inform these arguments, using our own contributions in palaeoecology and carbon mapping as examples. Finally, we argue for a radical reconsideration of research agendas in tropical peatlands, highlighting the potential contribution of methodologies borrowed from the social sciences and humanities.

Calcium Signaling in Intact Dorsal Root Ganglia

PubMed Central

Gemes, Geza; Rigaud, Marcel; Koopmeiners, Andrew S.; Poroli, Mark J.; Zoga, Vasiliki; Hogan, Quinn H.

2013-01-01

Background Ca2+ is the dominant second messenger in primary sensory neurons. In addition, disrupted Ca2+ signaling is a prominent feature in pain models involving peripheral nerve injury. Standard cytoplasmic Ca2+ recording techniques use high K+ or field stimulation and dissociated neurons. To compare findings in intact dorsal root ganglia, we used a method of simultaneous electrophysiologic and microfluorimetric recording. Methods Dissociated neurons were loaded by bath-applied Fura-2-AM and subjected to field stimulation. Alternatively, we adapted a technique in which neuronal somata of intact ganglia were loaded with Fura-2 through an intracellular microelectrode that provided simultaneous membrane potential recording during activation by action potentials (APs) conducted from attached dorsal roots. Results Field stimulation at levels necessary to activate neurons generated bath pH changes through electrolysis and failed to predictably drive neurons with AP trains. In the intact ganglion technique, single APs produced measurable Ca2+ transients that were fourfold larger in presumed nociceptive C-type neurons than in nonnociceptive Aβ-type neurons. Unitary Ca2+ transients summated during AP trains, forming transients with amplitudes that were highly dependent on stimulation frequency. Each neuron was tuned to a preferred frequency at which transient amplitude was maximal. Transients predominantly exhibited monoexponential recovery and had sustained plateaus during recovery only with trains of more than 100 APs. Nerve injury decreased Ca2+ transients in C-type neurons, but increased transients in Aβ-type neurons. Conclusions Refined observation of Ca2+ signaling is possible through natural activation by conducted APs in undissociated sensory neurons and reveals features distinct to neuronal types and injury state. PMID:20526180

Strategies for Characterization of Low-Abundant Intact or Truncated Low-Molecular-Weight Proteins From Human Plasma.

PubMed

Cai, Tanxi; Yang, Fuquan

2017-01-01

Low-molecular-weight region (LMW, MW≤30kDa) of human serum/plasma proteins, including small intact proteins, truncated fragments of larger proteins, along with some other small components, has been associated with the ongoing physiological and pathological events, and thereby represent a treasure trove of diagnostic molecules. Great progress in the mining of novel biomarkers from this diagnostic treasure trove for disease diagnosis and health monitoring has been achieved based on serum samples from healthy individuals and patients and powerful new approaches in biochemistry and systems biology. However, cumulative evidence indicates that many potential LMW protein biomarkers might still have escaped from detection due to their low abundance, the dynamic complexity of serum/plasma, and the limited efficiency of characterization approaches. Here, we provide an overview of the current state of knowledge with respect to strategies for the characterization of low-abundant LMW proteins (small intact or truncated proteins) from human serum/plasma, involving prefractionation or enrichment methods to reduce dynamic range and mass spectrometry-based characterization of low-abundant LMW proteins. © 2017 Elsevier Inc. All rights reserved.

A Sabin 2-related poliovirus recombinant contains a homologous sequence of human enterovirus species C in the viral polymerase coding region.

PubMed

Zhang, Yong; Zhang, Fan; Zhu, Shuangli; Chen, Li; Yan, Dongmei; Wang, Dongyan; Tang, Ruiyan; Zhu, Hui; Hou, Xiaohui; An, Hongqiu; Zhang, Hong; Xu, Wenbo

2010-02-01

A type 2 vaccine-related poliovirus (strain CHN3024), differing from the Sabin 2 strain by 0.44% in the VP1 coding region was isolated from a patient with vaccine-associated paralytic poliomyelitis. Sequences downstream of nucleotide position 6735 (3D(pol) coding region) were derived from an unidentified sequence; no close match for a potential parent was found, but it could be classified into a non-polio human enteroviruses species C (HEV-C) phylogeny. The virus differed antigenically from the parental Sabin strain, having an amino acid substitution in the neutralizing antigenic site 1. The similarity between CHN3024 and Sabin 2 sequences suggests that the recombination was recent; this is supported by the estimation that the initiating OPV dose was given only 36-75 days before sampling. The patient's clinical manifestations, intratypic differentiation examination, and whole-genome sequencing showed that this recombinant exhibited characteristics of neurovirulent vaccine-derived polioviruses (VDPV), which may, thus, pose a potential threat to a polio-free world.

Quantitative bioluminescence imaging of transgene expression in intact porcine antral follicles in vitro.

PubMed

Jung, Song-yi; Willard, Scott T

2014-01-30

The porcine oocyte maturation in vivo occurs within the ovarian follicle and is regulated by the interactions between oocytes and surrounding follicular components, including theca, granulosa, and cumulus cells, and follicular fluid. Therefore, the antral follicle is an essential microenvironment for efficient oocyte maturation and its developmental competence. Quantitative bioluminescence imaging of firefly luciferase reporter genes in an intact antral follicle would allow investigation of changes in cellular and molecular events and in the context of the whole follicles. In this study, we investigate factors influencing bioluminescence measurements as a first step towards developing a new bioluminescence imaging system for intact antral follicles. We analyzed the time course of bioluminescence emitted from transfected living intact follicles using a cationic lipid mediated gene transfer method with increasing doses (1-3 μg) of firefly luciferase reporter gene (pGL4). In addition, a standard luciferase assay was used to confirm the luciferase expression in granulosa cells in the transfected intact antral follicles. Finally, the dose effects of substrate, D-luciferin, were determined for optimal quantitative bioluminescence imaging of intact porcine antral follicles in vitro. The level of luciferase activity of follicles with 3 μg pGL4 was significantly (P < 0.05) greater than the 1 μg and 2 μg groups at 1 min after D-luciferin injection. The bioluminescence intensity of transfected follicles reached a peak at 1 min, and then it was significantly (P < 0.05) reduced within 2 min after injection of D-luciferin; with the level of bioluminescence emission remained constant from 2.5 to 10 min. The bioluminescence emission was maximal with 300 μg of D-luciferin. The results of this study suggested that the investigation of factors influencing bioluminescence measurements is a critical step toward developing a new bioluminescence imaging model. This

Quantitative bioluminescence imaging of transgene expression in intact porcine antral follicles in vitro

PubMed Central

2014-01-01

Background The porcine oocyte maturation in vivo occurs within the ovarian follicle and is regulated by the interactions between oocytes and surrounding follicular components, including theca, granulosa, and cumulus cells, and follicular fluid. Therefore, the antral follicle is an essential microenvironment for efficient oocyte maturation and its developmental competence. Quantitative bioluminescence imaging of firefly luciferase reporter genes in an intact antral follicle would allow investigation of changes in cellular and molecular events and in the context of the whole follicles. In this study, we investigate factors influencing bioluminescence measurements as a first step towards developing a new bioluminescence imaging system for intact antral follicles. Methods We analyzed the time course of bioluminescence emitted from transfected living intact follicles using a cationic lipid mediated gene transfer method with increasing doses (1-3 μg) of firefly luciferase reporter gene (pGL4). In addition, a standard luciferase assay was used to confirm the luciferase expression in granulosa cells in the transfected intact antral follicles. Finally, the dose effects of substrate, D-luciferin, were determined for optimal quantitative bioluminescence imaging of intact porcine antral follicles in vitro. Results The level of luciferase activity of follicles with 3 μg pGL4 was significantly (P < 0.05) greater than the 1 μg and 2 μg groups at 1 min after D-luciferin injection. The bioluminescence intensity of transfected follicles reached a peak at 1 min, and then it was significantly (P < 0.05) reduced within 2 min after injection of D-luciferin; with the level of bioluminescence emission remained constant from 2.5 to 10 min. The bioluminescence emission was maximal with 300 μg of D-luciferin. Conclusions The results of this study suggested that the investigation of factors influencing bioluminescence measurements is a critical step toward developing a

Dissipation of the Proton Electrochemical Potential in Intact and Lysed Chloroplasts 1

PubMed Central

Nishio, John N.; Whitmarsh, John

1991-01-01

Effective ionophore:chlorophyll ratios were determined for various ionophores that decrease the electrical potential across thylakoid membranes in intact and hypo-osmotically lysed chloroplasts isolated from spinach (Spinacia oleracea). The efficacy of gramicidin D, valinomycin, carbonylcyanide m-chlorophenylhydrazone, and dicyclohexano-18-crown-6 in collapsing the electrical potential was determined spectrophotometrically by the decay half-time of the absorbance change at 518 nanometers induced by a saturating, single turnover flash. The results show that the effectiveness of the ionophores in collapsing the electrical potential in intact and lysed chloroplasts depends on the amount of ionophore-accessible membrane in the assay medium. Only gramicidin exhibited a significant difference in efficacy between intact and lysed chloroplasts. The ratio of gramicidin to chlorophyll required to collapse the electrical potential was more than 50 times higher in intact chloroplasts than in lysed chloroplasts. The efficacy of carbonylcyanide m-chlorophenylhydrazone was significantly reduced in the presence of bovine serum albumin. The other ionophores tested maintained their potency in the presence of bovine serum albumin. Valinomycin was the most effective ionophore tested for collapsing the electrical potential in intact chloroplasts, whereas gramicidin was the most potent ionophore in lysed chloroplasts. The significance of the ionophore:chlorophyll ratios required to collapse the electrical potential is discussed with regard to bioenergetic studies, especially those that examine the contribution of the transmembrane electrochemical potential to protein transport into chloroplasts. PMID:16668015

Childrearing Fathers in Intact Families With Preschoolers.

ERIC Educational Resources Information Center

Radin, Norma

Few empirical studies have specifically examined antecedents and consequences of reversing childrearing roles. A sample of 59 white, intact, middle-class families with a preschool-aged child, 32 with boys and 27 with girls, was studied. Also explored were the father's sex-role orientation and selected paternal behaviors and attitudes. It was found…

Less Daily Computer Use is Related to Smaller Hippocampal Volumes in Cognitively Intact Elderly.

PubMed

Silbert, Lisa C; Dodge, Hiroko H; Lahna, David; Promjunyakul, Nutta-On; Austin, Daniel; Mattek, Nora; Erten-Lyons, Deniz; Kaye, Jeffrey A

2016-01-01

Computer use is becoming a common activity in the daily life of older individuals and declines over time in those with mild cognitive impairment (MCI). The relationship between daily computer use (DCU) and imaging markers of neurodegeneration is unknown. The objective of this study was to examine the relationship between average DCU and volumetric markers of neurodegeneration on brain MRI. Cognitively intact volunteers enrolled in the Intelligent Systems for Assessing Aging Change study underwent MRI. Total in-home computer use per day was calculated using mouse movement detection and averaged over a one-month period surrounding the MRI. Spearman's rank order correlation (univariate analysis) and linear regression models (multivariate analysis) examined hippocampal, gray matter (GM), white matter hyperintensity (WMH), and ventricular cerebral spinal fluid (vCSF) volumes in relation to DCU. A voxel-based morphometry analysis identified relationships between regional GM density and DCU. Twenty-seven cognitively intact participants used their computer for 51.3 minutes per day on average. Less DCU was associated with smaller hippocampal volumes (r = 0.48, p = 0.01), but not total GM, WMH, or vCSF volumes. After adjusting for age, education, and gender, less DCU remained associated with smaller hippocampal volume (p = 0.01). Voxel-wise analysis demonstrated that less daily computer use was associated with decreased GM density in the bilateral hippocampi and temporal lobes. Less daily computer use is associated with smaller brain volume in regions that are integral to memory function and known to be involved early with Alzheimer's pathology and conversion to dementia. Continuous monitoring of daily computer use may detect signs of preclinical neurodegeneration in older individuals at risk for dementia.

Ensemble coding of face identity is present but weaker in congenital prosopagnosia.

PubMed

Robson, Matthew K; Palermo, Romina; Jeffery, Linda; Neumann, Markus F

2018-03-01

Individuals with congenital prosopagnosia (CP) are impaired at identifying individual faces but do not appear to show impairments in extracting the average identity from a group of faces (known as ensemble coding). However, possible deficits in ensemble coding in a previous study (CPs n = 4) may have been masked because CPs relied on pictorial (image) cues rather than identity cues. Here we asked whether a larger sample of CPs (n = 11) would show intact ensemble coding of identity when availability of image cues was minimised. Participants viewed a "set" of four faces and then judged whether a subsequent individual test face, either an exemplar or a "set average", was in the preceding set. Ensemble coding occurred when matching (vs. mismatching) averages were mistakenly endorsed as set members. We assessed both image- and identity-based ensemble coding, by varying whether test faces were either the same or different images of the identities in the set. CPs showed significant ensemble coding in both tasks, indicating that their performance was independent of image cues. As a group, CPs' ensemble coding was weaker than controls in both tasks, consistent with evidence that perceptual processing of face identity is disrupted in CP. This effect was driven by CPs (n= 3) who, in addition to having impaired face memory, also performed particularly poorly on a measure of face perception (CFPT). Future research, using larger samples, should examine whether deficits in ensemble coding may be restricted to CPs who also have substantial face perception deficits. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multi-Axis Prosthetic Knee Resembles Alpine Skiing Movements of an Intact Leg

PubMed Central

Demšar, Ivan; Duhovnik, Jože; Lešnik, Blaž; Supej, Matej

2015-01-01

The purpose of the study was to analyse the flexion angles of the ski boot, ankle and knee joints of an above-knee prosthesis and to compare them with an intact leg and a control group of skiers. One subject with an above-knee amputation of the right leg and eight healthy subjects simulated the movement of a skiing turn by performing two-leg squats in laboratory conditions. By adding additional loads in proportion to body weight (BW; +1/3 BW, +2/3 BW, +3/3 BW), various skiing regimes were simulated. Change of Flexion Angle (CoFA) and Range of Motion (RoM) in the ski boot, ankle and knee joints were calculated and compared. An average RoM in the skiing boot on the side of prosthesis (4.4 ± 1.1°) was significantly lower compared to an intact leg (5.9 ± 1.8°) and the control group (6.5 ± 2.3°). In the ankle joint, the average RoM was determined to be 13.2±2.9° in the prosthesis, 12.7 ± 2.8° in an intact leg and 14.8±3.6 in the control group. However, the RoM of the knee joint in the prosthesis (42.2 ± 4.2°) was significantly larger than that of the intact leg (34.7 ± 4.4°). The average RoM of the knee joint in the control group was 47.8 ± 5.4°. The influences of additional loads on the kinematics of the lower extremities were different on the side of the prosthesis and on the intact leg. In contrast, additional loads did not produce any significant differences in the control group. Although different CoFAs in the ski boot, ankle and knee joints were used, an above-knee prosthesis with a built-in multi-axis prosthetic knee enables comparable leg kinematics in simulated alpine skiing. Key points The RoM in the ski boot on the side of the prosthetic leg was smaller than the RoM of the intact leg and the control group of healthy subjects. The RoM in the ankle joint of prosthetic leg was comparable to that of the intact leg and the control group of healthy subjects. The RoM in the prosthetic knee joint was greater than the RoM in the knee joint of the

Accelerate Implementation of the WHO Global Code of Practice on International Recruitment of Health Personnel: Experiences From the South East Asia Region

PubMed Central

Tangcharoensathien, Viroj; Travis, Phyllida

2016-01-01

Strengthening the health workforce and universal health coverage (UHC) are among key targets in the heath-related Sustainable Development Goals (SDGs) to be committed by the United Nations (UN) Member States in September 2015. The health workforce, the backbone of health systems, contributes to functioning delivery systems. Equitable distribution of functioning services is indispensable to achieve one of the UHC goals of equitable access. This commentary argues the World Health Organization (WHO) Global Code of Practice on International Recruitment of Health Personnel is relevant to the countries in the South East Asia Region (SEAR) as there is a significant outflow of health workers from several countries and a significant inflow in a few, increased demand for health workforce in high- and middle-income countries, and slow progress in addressing the "push factors." Awareness and implementation of the Code in the first report in 2012 was low but significantly improved in the second report in 2015. An inter-country workshop in 2015 convened by WHO SEAR to review progress in implementation of the Code was an opportunity for countries to share lessons on policy implementation, on retention of health workers, scaling up health professional education and managing in and out migration. The meeting noted that capturing outmigration of health personnel, which is notoriously difficult for source countries, is possible where there is an active recruitment management through government to government (G to G) contracts or licensing the recruiters and mandatory reporting requirement by them. According to the 2015 second report on the Code, the size and profile of outflow health workers from SEAR source countries is being captured and now also increasingly being shared by destination country professional councils. This is critical information to foster policy action and implementation of the Code in the Region. PMID:26673648

Vehicle influence on permeation through intact and compromised skin.

PubMed

Gujjar, Meera; Banga, Ajay K

2014-09-10

The purpose of this study was to compare the transdermal permeation of a model compound, diclofenac diethylamine, from a hydrophilic and lipophilic vehicle across in vitro models simulating compromised skin. Mineral oil served as a lipophilic vehicle while 10mM phosphate buffered saline served as a hydrophilic vehicle. Compromised skin was simulated by tape stripping, delipidization, or microneedle application and compared with intact skin as a control. Transepidermal water loss was measured to assess barrier function. Skin compromised with tape stripping and delipidization significantly (p<0.05) increased permeation of diclofenac diethylamine compared to intact and microneedle treated skin with phosphate buffered saline vehicle. A similar trend in permeation was observed with mineral oil as the vehicle. For both vehicles, permeation across skin increased in the same order and correlated with degree of barrier impairment as indicated by transepidermal water loss values: intact

Antimicrobial activity of a new intact skin antisepsis formulation.

PubMed

Russo, Antonello; Viotti, Pier Luigi; Vitali, Matteo; Clementi, Massimo

2003-04-01

Different antiseptic formulations have shown limitations when applied to disinfecting intact skin, notably short-term tolerability and/or efficacy. The purpose of this study was optimizing a new antiseptic formulation specifically targeted at intact skin disinfection and evaluating its in vitro microbicidal activity and in vivo efficacy. The biocidal properties of the antiseptic solution containing 0.5% chloramine-T diluted in 50% isopropyl alcohol (Cloral; Eurospital SpA Trieste, Italy) were measured in vitro versus gram-positive-, gram-negative-, and acid-alcohol-resistant germs and fungi with standard suspension tests in the presence of fetal bovine serum. Virus-inhibiting activity was evaluated in vitro against human cytomegalovirus, herpes simplex virus, poliovirus, hepatitis B virus, and hepatitis C virus. Tests used different methods for the different biologic and in vitro replication capacity of these human viruses. Lastly, Cloral tolerability and skin colonization retardation efficacy after disinfection were studied in vivo. The antiseptic under review showed fast and sustained antimicrobial activity. The efficacy of Cloral against clinically important bacterial and viral pathogens and fungi was highlighted under the experimental conditions described in this article. Finally, microbial regrowth lag and no side effects were documented in vivo after disinfection of 11 volunteers. A stable chloramine-T solution in isopropyl alcohol may be suggested for intact skin antisepsis.

The PPAR{gamma} coding region and its role in visceral obesity

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

Boon Yin, Khoo; Institute for Research in Molecular Medicine; Najimudin, Nazalan

Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) is a ligand activated transcription factor, plays many essential roles of biological function in higher organisms. The PPAR{gamma} is mainly expressed in adipose tissue. It regulates the transcriptional activity of genes by binding with other transcription factor. The PPAR{gamma} coding region has been found to be closest to that of monkey in ours and other research groups. Thus, monkey is a more suitable animal model for future PPAR{gamma} studying, although mice and rat are frequently being used. The PPAR{gamma} is involved in regulating alterations of adipose tissue masses result from changes in mature adipocyte sizemore » and/or number through a complex interplay process called adipogenesis. However, the role of PPAR{gamma} in negatively regulating the process of adipogenesis remains unclear. This review may help we investigate the differential expression of key transcription factor in adipose tissue in response to visceral obesity-induced diet in vivo. The study may also provide valuable information to define a more appropriate physiological condition in adipogenesis which may help to prevent diseases cause by negative regulation of the transcription factors in adipose tissue.« less

Investigation of Mitochondrial Dysfunction by Sequential Microplate-Based Respiration Measurements from Intact and Permeabilized Neurons

PubMed Central

Clerc, Pascaline; Polster, Brian M.

2012-01-01

Mitochondrial dysfunction is a component of many neurodegenerative conditions. Measurement of oxygen consumption from intact neurons enables evaluation of mitochondrial bioenergetics under conditions that are more physiologically realistic compared to isolated mitochondria. However, mechanistic analysis of mitochondrial function in cells is complicated by changing energy demands and lack of substrate control. Here we describe a technique for sequentially measuring respiration from intact and saponin-permeabilized cortical neurons on single microplates. This technique allows control of substrates to individual electron transport chain complexes following permeabilization, as well as side-by-side comparisons to intact cells. To illustrate the utility of the technique, we demonstrate that inhibition of respiration by the drug KB-R7943 in intact neurons is relieved by delivery of the complex II substrate succinate, but not by complex I substrates, via acute saponin permeabilization. In contrast, methyl succinate, a putative cell permeable complex II substrate, failed to rescue respiration in intact neurons and was a poor complex II substrate in permeabilized cells. Sequential measurements of intact and permeabilized cell respiration should be particularly useful for evaluating indirect mitochondrial toxicity due to drugs or cellular signaling events which cannot be readily studied using isolated mitochondria. PMID:22496810

Intact long-type dupA as a marker for gastroduodenal diseases in Okinawan subpopulation, Japan.

PubMed

Takahashi, Ayaka; Shiota, Seiji; Matsunari, Osamu; Watada, Masahide; Suzuki, Rumiko; Nakachi, Saori; Kinjo, Nagisa; Kinjo, Fukunori; Yamaoka, Yoshio

2013-02-01

Helicobacter pylori dupA can be divided into two types according to the presence or absence of the mutation. In addition, full-sequenced data revealed that dupA has two types with different lengths depend on the presence of approximately 600 bp in the putative 5' region (presence; long-type and absence; short-type), which has not been taken into account in previous studies. A total of 319 strains isolated from Okinawa, the south islands of Japan, were included. The status of dupA and cagA was determined by polymerase chain reaction. The presence of mutations in long-type dupA was determined by DNA sequencing. The prevalence of long-type dupA was 26.3% (84/319). Sequence analysis showed that there were only six cases (7.1%) with point mutations lead to stop codon among 84 long-type dupA strains studied. Interestingly, intact long-type dupA without frameshift mutation, but not short-type dupA, was significantly associated with gastric ulcer and gastric cancer than gastritis (p = .001 and p = .019, respectively). After adjustment by age, gender, and cagA, the presence of intact long-type dupA was significantly associated with gastric ulcer and gastric cancer compared with gastritis (odds ratio [OR] = 3.35, 95% confidence interval [CI] = 1.55-7.24 and OR = 4.14, 95% CI = 1.23-13.94, respectively). Intact long-type dupA is a real virulence marker for severe outcomes in Okinawa, Japan. The previous information gained from PCR-based methods without taking long-type dupA into account must be interpreted with caution. © 2012 Blackwell Publishing Ltd.

Intact long-type dupA as a marker for gastroduodenal diseases in Okinawan subpopulation, Japan

PubMed Central

Takahashi, Ayaka; Shiota, Seiji; Matsunari, Osamu; Watada, Masahide; Suzuki, Rumiko; Nakachi, Saori; Kinjo, Nagisa; Kinjo, Fukunori; Yamaoka, Yoshio

2012-01-01

Background Helicobacter pylori dupA can be divided into two types according to the presence or absence of the mutation. In addition, full-sequenced data revealed that dupA has two types with different lengths depend on the presence of approximately 600 bp in the putative 5' region (presence; long-type and absence; short-type), which has not been taken into account in previous studies. Methods A total of 319 strains isolated from Okinawa, the south islands of Japan, were included. The status of dupA and cagA was determined by polymerase chain reaction. The presence of mutations in long-type dupA was determined by DNA sequencing. Results The prevalence of long-type dupA was 26.3% (84/319). Sequence analysis showed that there were only 6 cases (7.1%) with point mutations lead to stop codon among 84 long-type dupA strains studied. Interestingly, intact long-type dupA without frameshift mutation, but not short-type dupA was significantly associated with gastric ulcer and gastric cancer than gastritis (P = 0.001 and P = 0.019, respectively). After adjustment by age, gender and cagA, the presence of intact long-type dupA was significantly associated with gastric ulcer and gastric cancer compared with gastritis (odds ratio [OR] = 3.35, 95% confidence interval [CI] = 1.55–7.24 and OR = 4.14, 95% CI = 1.23–13.94, respectively). Conclusions Intact long-type dupA is a real virulence marker for severe outcomes in Okinawa, Japan. The previous information gained from PCR-based methods without taking long-type dupA into account must be interpreted with caution. PMID:23067336

Error-Rate Bounds for Coded PPM on a Poisson Channel

NASA Technical Reports Server (NTRS)

Moision, Bruce; Hamkins, Jon

2009-01-01

Equations for computing tight bounds on error rates for coded pulse-position modulation (PPM) on a Poisson channel at high signal-to-noise ratio have been derived. These equations and elements of the underlying theory are expected to be especially useful in designing codes for PPM optical communication systems. The equations and the underlying theory apply, more specifically, to a case in which a) At the transmitter, a linear outer code is concatenated with an inner code that includes an accumulator and a bit-to-PPM-symbol mapping (see figure) [this concatenation is known in the art as "accumulate-PPM" (abbreviated "APPM")]; b) The transmitted signal propagates on a memoryless binary-input Poisson channel; and c) At the receiver, near-maximum-likelihood (ML) decoding is effected through an iterative process. Such a coding/modulation/decoding scheme is a variation on the concept of turbo codes, which have complex structures, such that an exact analytical expression for the performance of a particular code is intractable. However, techniques for accurately estimating the performances of turbo codes have been developed. The performance of a typical turbo code includes (1) a "waterfall" region consisting of a steep decrease of error rate with increasing signal-to-noise ratio (SNR) at low to moderate SNR, and (2) an "error floor" region with a less steep decrease of error rate with increasing SNR at moderate to high SNR. The techniques used heretofore for estimating performance in the waterfall region have differed from those used for estimating performance in the error-floor region. For coded PPM, prior to the present derivations, equations for accurate prediction of the performance of coded PPM at high SNR did not exist, so that it was necessary to resort to time-consuming simulations in order to make such predictions. The present derivation makes it unnecessary to perform such time-consuming simulations.

Comparison of Ripening Processes in Intact Tomato Fruit and Excised Pericarp Discs 1

PubMed Central

Campbell, Alan D.; Huysamer, Marius; Stotz, Henrik U.; Greve, L. Carl; Labavitch, John M.

1990-01-01

Physiological processes characteristic of ripening in tissues of intact tomato fruit (Lycopersicon esculentum Mill.) were examined in excised pericarp discs. Pericarp discs were prepared from mature-green tomato fruit and stored in 24-well culture plates, in which individual discs could be monitored for color change, ethylene biosynthesis, and respiration, and selected for cell wall analysis. Within the context of these preparation and handling procedures, most whole fruit ripening processes were maintained in pericarp discs. Pericarp discs and matched intact fruit passed through the same skin color stages at similar rates, as expressed in the L*a*b* color space, changing from green (a* < −5) to red (a* > 15) in about 6 days. Individual tissues of the pericarp discs changed color in the same sequence seen in intact fruit (exocarp, endocarp, then vascular parenchyma). Discs from different areas changed in the same spatial sequence seen in intact fruit (bottom, middle, top). Pericarp discs exhibited climacteric increases in ethylene biosynthesis and CO2 production comparable with those seen in intact fruit, but these were more tightly linked to rate of color change, reaching a peak around a* = 5. Tomato pericarp discs decreased in firmness as color changed. Cell wall carbohydrate composition changed with color as in intact fruit: the quantity of water-soluble pectin eluted from the starch-free alcohol insoluble substances steadily increased and more tightly bound, water-insoluble, pectin decreased in inverse relationship. The cell wall content of the neutral sugars arabinose, rhamnose, and galactose steadily decreased as color changed. The extractable activity of specific cell wall hydrolases changed as in intact fruit: polygalacturonase activity, not detectable in green discs (a* = −5), appeared as discs turned yellow-red (a* = 5), and increased another eight-fold as discs became full red (a* value +20). Carboxymethyl-cellulase activity, low in extracts from

Novel exon 1 protein-coding regions N-terminally extend human KCNE3 and KCNE4.

PubMed

Abbott, Geoffrey W

2016-08-01

The 5 human (h)KCNE β subunits each regulate various cation channels and are linked to inherited cardiac arrhythmias. Reported here are previously undiscovered protein-coding regions in exon 1 of hKCNE3 and hKCNE4 that extend their encoded extracellular domains by 44 and 51 residues, which yields full-length proteins of 147 and 221 residues, respectively. Full-length hKCNE3 and hKCNE4 transcript and protein are expressed in multiple human tissues; for hKCNE4, only the longer protein isoform is detectable. Two-electrode voltage-clamp electrophysiology revealed that, when coexpressed in Xenopus laevis oocytes with various potassium channels, the newly discovered segment preserved conversion of KCNQ1 by hKCNE3 to a constitutively open channel, but prevented its inhibition of Kv4.2 and KCNQ4. hKCNE4 slowing of Kv4.2 inactivation and positive-shifted steady-state inactivation were also preserved in the longer form. In contrast, full-length hKCNE4 inhibition of KCNQ1 was limited to 40% at +40 mV vs. 80% inhibition by the shorter form, and augmentation of KCNQ4 activity by hKCNE4 was entirely abolished by the additional segment. Among the genome databases analyzed, the longer KCNE3 is confined to primates; full-length KCNE4 is widespread in vertebrates but is notably absent from Mus musculus Findings highlight unexpected KCNE gene diversity, raise the possibility of dynamic regulation of KCNE partner modulation via splice variation, and suggest that the longer hKCNE3 and hKCNE4 proteins should be adopted in future mechanistic and genetic screening studies.-Abbott, G. W. Novel exon 1 protein-coding regions N-terminally extend human KCNE3 and KCNE4. © FASEB.

Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice

PubMed Central

Rozhdestvensky, Timofey S.; Robeck, Thomas; Galiveti, Chenna R.; Raabe, Carsten A.; Seeger, Birte; Wolters, Anna; Gubar, Leonid V.; Brosius, Jürgen; Skryabin, Boris V.

2016-01-01

Prader-Willi syndrome (PWS) is a neurogenetic disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. The PWS-critical region (PWScr) contains an array of non-protein coding IPW-A exons hosting intronic SNORD116 snoRNA genes. Deletion of PWScr is associated with PWS in humans and growth retardation in mice exhibiting ~15% postnatal lethality in C57BL/6 background. Here we analysed a knock-in mouse containing a 5′HPRT-LoxP-NeoR cassette (5′LoxP) inserted upstream of the PWScr. When the insertion was inherited maternally in a paternal PWScr-deletion mouse model (PWScrp−/m5′LoxP), we observed compensation of growth retardation and postnatal lethality. Genomic methylation pattern and expression of protein-coding genes remained unaltered at the PWS-locus of PWScrp−/m5′LoxP mice. Interestingly, ubiquitous Snord116 and IPW-A exon transcription from the originally silent maternal chromosome was detected. In situ hybridization indicated that PWScrp−/m5′LoxP mice expressed Snord116 in brain areas similar to wild type animals. Our results suggest that the lack of PWScr RNA expression in certain brain areas could be a primary cause of the growth retardation phenotype in mice. We propose that activation of disease-associated genes on imprinted regions could lead to general therapeutic strategies in associated diseases. PMID:26848093

Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice.

PubMed

Ma, Jianxin; Bennetzen, Jeffrey L

2006-01-10

Centromeres have many unusual biological properties, including kinetochore attachment and severe repression of local meiotic recombination. These properties are partly an outcome, partly a cause, of unusual DNA structure in the centromeric region. Although several plant and animal genomes have been sequenced, most centromere sequences have not been completed or analyzed in depth. To shed light on the unique organization, variability, and evolution of centromeric DNA, detailed analysis of a 1.97-Mb sequence that includes centromere 8 (CEN8) of japonica rice was undertaken. Thirty-three long-terminal repeat (LTR)-retrotransposon families (including 11 previously unknown) were identified in the CEN8 region, totaling 245 elements and fragments that account for 67% of the region. The ratio of solo LTRs to intact elements in the CEN8 region is approximately 0.9:1, compared with approximately 2.2:1 in noncentromeric regions of rice. However, the ratio of solo LTRs to intact elements in the core of the CEN8 region ( approximately 2.5:1) is higher than in any other region investigated in rice, suggesting a hotspot for unequal recombination. Comparison of the CEN8 region of japonica and its orthologous segments from indica rice indicated that approximately 15% of the intact retrotransposons and solo LTRs were inserted into CEN8 after the divergence of japonica and indica from a common ancestor, compared with approximately 50% for previously studied euchromatic regions. Frequent DNA rearrangements were observed in the CEN8 region, including a 212-kb subregion that was found to be composed of three rearranged tandem repeats. Phylogenetic analysis also revealed recent segmental duplication and extensive rearrangement and reshuffling of the CentO satellite repeats.

Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

PubMed Central

Fayaz, Shima; Fard-Esfahani, Pezhman; Fard-Esfahani, Armaghan; Mostafavi, Ehsan; Meshkani, Reza; Mirmiranpour, Hossein; Khaghani, Shahnaz

2012-01-01

Homologous recombination (HR) is the major pathway for repairing double strand breaks (DSBs) in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC) we used high resolution melting (HRM) analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536) was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432–4.969; p = 0.38) compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion. PMID:22481871

Coded Cooperation for Multiway Relaying in Wireless Sensor Networks †

PubMed Central

Si, Zhongwei; Ma, Junyang; Thobaben, Ragnar

2015-01-01

Wireless sensor networks have been considered as an enabling technology for constructing smart cities. One important feature of wireless sensor networks is that the sensor nodes collaborate in some manner for communications. In this manuscript, we focus on the model of multiway relaying with full data exchange where each user wants to transmit and receive data to and from all other users in the network. We derive the capacity region for this specific model and propose a coding strategy through coset encoding. To obtain good performance with practical codes, we choose spatially-coupled LDPC (SC-LDPC) codes for the coded cooperation. In particular, for the message broadcasting from the relay, we construct multi-edge-type (MET) SC-LDPC codes by repeatedly applying coset encoding. Due to the capacity-achieving property of the SC-LDPC codes, we prove that the capacity region can theoretically be achieved by the proposed MET SC-LDPC codes. Numerical results with finite node degrees are provided, which show that the achievable rates approach the boundary of the capacity region in both binary erasure channels and additive white Gaussian channels. PMID:26131675

(Photosynthesis in intact plants)

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

Not Available

Progress in the two years since the last renewal application has been excellent. We have made substantial contributions on both main fronts of the projects, and are particularly happy with the progress of our research on intact plants. The approach of basing our field work on a sound foundation of laboratory studies has enabled is to use methods which provide unambiguous assays of well characterized reactions. We have also made excellent progress in several laboratory studies which will have direct applications in future field work, and have introduced to the laboratory a range of molecular genetics techniques which will allowmore » us to explore new options in the attempt to understand function at the level of molecular structure.« less

A progressive data compression scheme based upon adaptive transform coding: Mixture block coding of natural images

NASA Technical Reports Server (NTRS)

Rost, Martin C.; Sayood, Khalid

1991-01-01

A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.

Building a Better Campus: An Update on Building Codes.

ERIC Educational Resources Information Center

Madden, Michael J.

2002-01-01

Discusses the implications for higher education institutions in terms of facility planning, design, construction, and renovation of the move from regionally-developed model-building codes to two international sets of codes. Also addresses the new performance-based design option within the codes. (EV)

Conservation of an Intact vif Gene of Human Immunodeficiency Virus Type 1 during Maternal-Fetal Transmission

PubMed Central

Yedavalli, Venkat R. K.; Chappey, Colombe; Matala, Erik; Ahmad, Nafees

1998-01-01

The human immunodeficiency virus type 1 (HIV-1) vif gene is conserved among most lentiviruses, suggesting that vif is important for natural infection. To determine whether an intact vif gene is positively selected during mother-to-infant transmission, we analyzed vif sequences from five infected mother-infant pairs following perinatal transmission. The coding potential of the vif open reading frame directly derived from uncultured peripheral blood mononuclear cell DNA was maintained in most of the 78,912 bp sequenced. We found that 123 of the 137 clones analyzed showed an 89.8% frequency of intact vif open reading frames. There was a low degree of heterogeneity of vif genes within mothers, within infants, and between epidemiologically linked mother-infant pairs. The distances between vif sequences were greater in epidemiologically unlinked individuals than in epidemiologically linked mother-infant pairs. Furthermore, the epidemiologically linked mother-infant pair vif sequences displayed similar patterns that were not seen in vif sequences from epidemiologically unlinked individuals. The functional domains, including the two cysteines at positions 114 and 133, a serine phosphorylation site at position 144, and the C-terminal basic amino acids essential for vif protein function, were highly conserved in most of the sequences. Phylogenetic analyses of 137 mother-infant pair vif sequences and 187 other available vif sequences from HIV-1 databases revealed distinct clusters for vif sequences from each mother-infant pair and for other vif sequences. Taken together, these findings suggest that vif plays an important role in HIV-1 infection and replication in mothers and their perinatally infected infants. PMID:9445004

Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

NASA Astrophysics Data System (ADS)

Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

2008-03-01

Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

Regional vertical total electron content (VTEC) modeling together with satellite and receiver differential code biases (DCBs) using semi-parametric multivariate adaptive regression B-splines (SP-BMARS)

NASA Astrophysics Data System (ADS)

Durmaz, Murat; Karslioglu, Mahmut Onur

2015-04-01

There are various global and regional methods that have been proposed for the modeling of ionospheric vertical total electron content (VTEC). Global distribution of VTEC is usually modeled by spherical harmonic expansions, while tensor products of compactly supported univariate B-splines can be used for regional modeling. In these empirical parametric models, the coefficients of the basis functions as well as differential code biases (DCBs) of satellites and receivers can be treated as unknown parameters which can be estimated from geometry-free linear combinations of global positioning system observables. In this work we propose a new semi-parametric multivariate adaptive regression B-splines (SP-BMARS) method for the regional modeling of VTEC together with satellite and receiver DCBs, where the parametric part of the model is related to the DCBs as fixed parameters and the non-parametric part adaptively models the spatio-temporal distribution of VTEC. The latter is based on multivariate adaptive regression B-splines which is a non-parametric modeling technique making use of compactly supported B-spline basis functions that are generated from the observations automatically. This algorithm takes advantage of an adaptive scale-by-scale model building strategy that searches for best-fitting B-splines to the data at each scale. The VTEC maps generated from the proposed method are compared numerically and visually with the global ionosphere maps (GIMs) which are provided by the Center for Orbit Determination in Europe (CODE). The VTEC values from SP-BMARS and CODE GIMs are also compared with VTEC values obtained through calibration using local ionospheric model. The estimated satellite and receiver DCBs from the SP-BMARS model are compared with the CODE distributed DCBs. The results show that the SP-BMARS algorithm can be used to estimate satellite and receiver DCBs while adaptively and flexibly modeling the daily regional VTEC.

Reflectance Spectra Comparison of Orbital Debris, Intact Spacecraft, and Intact Rocket Bodies in the GEO Regime

NASA Technical Reports Server (NTRS)

Barker, Ed; Abercromby, Kira J.; Abell, Paul

2009-01-01

A key objective of NASA s Orbital Debris program office at Johnson Space Center (JSC) is to characterize the debris environment by way of assessing the physical properties (type, mass, density, and size) of objects in orbit. Knowledge of the geosynchronous orbit (GEO) debris environment in particular can be used to determine the hazard probability at specific GEO altitudes and aid predictions of the future environment. To calculate an optical size from an intensity measurement of an object in the GEO regime, a 0.175 albedo is assumed currently. However, identification of specific material type or types could improve albedo accuracy and yield a more accurate size estimate for the debris piece. Using spectroscopy, it is possible to determine the surface materials of space objects. The study described herein used the NASA Infrared Telescope Facility (IRTF) to record spectral data in the 0.6 to 2.5 micron regime on eight catalogued space objects. For comparison, all of the objects observed were in GEO or near-GEO. The eight objects consisted of two intact spacecraft, three rocket bodies, and three catalogued debris pieces. Two of the debris pieces stemmed from Titan 3C transtage breakup and the third is from COSMOS 2054. The reflectance spectra of the Titan 3C pieces share similar slopes (increasing with wavelength) and lack any strong absorption features. The COSMOS debris spectra is flat and has no absorption features. In contrast, the intact spacecraft show classic absorption features due to solar panels with a strong band gap feature near 1 micron. The two spacecraft are spin-stabilized objects and therefore have solar panels surrounding the outer surface. Two of the three rocket bodies are inertial upper stage (IUS) rocket bodies and have similar looking spectra. The slopes flatten out near 1.5 microns with absorption features in the near-infrared that are similar to that of white paint. The third rocket body has a similar flattening of slope but with fewer

Reflectance Spectra Comparison of Orbital Debris, Intact Spacecraft, and Intact Rocket Bodies in the GEO Regime

NASA Astrophysics Data System (ADS)

Albercromby, Kira J.; Abell, Paul; Barker, Ed

2009-03-01

A key objective of NASA's Orbital Debris program office at Johnson Space Center (JSC) is to characterize the debris environment by way of assessing the physical properties (type, mass, density, and size) of objects in orbit. Knowledge of the geosynchronous orbit (GEO) debris environment in particular can be used to determine the hazard probability at specific GEO altitudes and aid predictions of the future environment. To calculate an optical size from an intensity measurement of an object in the GEO regime, a 0.175 albedo is assumed currently. However, identification of specific material type or types could improve albedo accuracy and yield a more accurate size estimate for the debris piece. Using spectroscopy, it is possible to determine the surface materials of space objects. The study described herein used the NASA Infrared Telescope Facility (IRTF) to record spectral data in the ~ 0.65 to 2.5 micron regime on eight catalogued space objects. For comparison, all of the objects observed were in GEO or near-GEO. The eight objects consisted of two intact spacecraft, three rocket bodies, and three catalogued debris pieces. Two of the debris pieces stemmed from Titan 3C transtage breakup and the third is from COSMOS 2054. The reflectance spectra of the Titan 3C pieces share similar slopes (increasing with wavelength) and lack any strong absorption features. The COSMOS debris spectrum has a slight slope and has no absorption features. In contrast, the intact spacecraft show classic absorption features due to solar cells with a strong band gap feature near 1 micron. The two spacecraft were spin-stabilized objects and therefore have solar panels surrounding the outer surface. Two of the three rocket bodies are inertial upper stage (IUS) rocket bodies and have similar looking spectra. The slopes flatten out near 1.5 microns with absorption features in the near-infrared that are similar to that of white paint. The third rocket body has a similar flattening of slope but

The mitochondrial COB region in yeast codes for apocytochrome b and is mosaic.

PubMed

Haid, A; Schweyen, R J; Bechmann, H; Kaudewitz, F; Solioz, M; Schatz, G

1979-03-01

Mitochondrial mutants of Saccharomyces cerevisiae defective in cytochrome b were analyzed genetically and biochemically in order to elucidate the role of the mitochondrial genetic system in the biosynthesis of this cytochrome. The mutants mapped between OLI1 and OLI2 on mitochondrial DNA in a region called COB. A fine structure map of the COB region was constructed by rho- deletion mapping and recombination analysis. The combined genetic and biochemical data indicate that the COB region is mosaic and contains at least five distinct clusters of mutants, A-E, with A being closest to OLI2 and E being closest to OLI1. Clusters A, C and E are probably coding regions for apocytochrome b, whereas clusters B and D seem to be involved in as yet unknown functions. These conclusions rest on the following evidence. 1. Most mutants in clusters A, C and E have specifically lost cytochrome b. Many of them accumulate smaller mitochondrial translation products; some of these were identified as fragments of apocytochrome b by proteolytic fingerprinting. The molecular weight of these fragments depends on the map position of the mutant, increasing in the direction OLI2 leads to OLI1. The mutant closest to OLI1 accumulates an apocytochrome b which is slightly larger than that of wild type. 2. A mutant in cluster C exhibits a spectral absorption band of cytochrome b that is shifted 1.5 nm to the red. 3. Mutants in clusters B and D are pleiotropic. A majority of them are conditional and lack the absorption bands of both cytochrome b and cytochrome aa3; these mutants also fail to accumulate apocytochrome b and subunit I of cytochrome c oxidase and instead form a large number of abnormal translation products whose nature is unknown. 4. Zygotic complementation tests reveal at least two complementation groups: The first group includes all mutants in cluster B and the second group includes mutants in clusters (A + C + D + E).

Silica Aerogel Captures Cosmic Dust Intact

NASA Technical Reports Server (NTRS)

Tsou, P.

1994-01-01

The mesostructure of silica aerogel resembles stings of grapes, ranging in size from 10 to 100 angstrom. This fine mesostructure transmits nearly 90 percent of incident light in the visible, while providing sufficiently gentle dissipation of the kinetric energy of hypervelocity cosmic dust particles to permit their intact capture. We introduced silica aerogel in 1987 as capture medium to take advantage of its low density, fine mesostruicture and most importantly, its transparency, allowing optical location of captured micron sized particles.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity.

PubMed

Hrdlickova, Barbara; Kumar, Vinod; Kanduri, Kartiek; Zhernakova, Daria V; Tripathi, Subhash; Karjalainen, Juha; Lund, Riikka J; Li, Yang; Ullah, Ubaid; Modderman, Rutger; Abdulahad, Wayel; Lähdesmäki, Harri; Franke, Lude; Lahesmaa, Riitta; Wijmenga, Cisca; Withoff, Sebo

2014-01-01

Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID), our understanding of the disease mechanisms is still limited. In particular, more than 90% of the risk variants lie in non-coding regions, and almost 10% of these map to long non-coding RNA transcripts (lncRNAs). lncRNAs are known to show more cell-type specificity than protein-coding genes. We aimed to characterize lncRNAs and protein-coding genes located in loci associated with nine AIDs which have been well-defined by Immunochip analysis and by transcriptome analysis across seven populations of peripheral blood leukocytes (granulocytes, monocytes, natural killer (NK) cells, B cells, memory T cells, naive CD4(+) and naive CD8(+) T cells) and four populations of cord blood-derived T-helper cells (precursor, primary, and polarized (Th1, Th2) T-helper cells). We show that lncRNAs mapping to loci shared between AID are significantly enriched in immune cell types compared to lncRNAs from the whole genome (α <0.005). We were not able to prioritize single cell types relevant for specific diseases, but we observed five different cell types enriched (α <0.005) in five AID (NK cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, and psoriasis; memory T and CD8(+) T cells in juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis; Th0 and Th2 cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, and rheumatoid arthritis). Furthermore, we show that co-expression analyses of lncRNAs and protein-coding genes can predict the signaling pathways in which these AID-associated lncRNAs are involved. The observed enrichment of lncRNA transcripts in AID loci implies lncRNAs play an important role in AID etiology and suggests that lncRNA genes should be studied in more detail to interpret GWAS

Extracellular production of an intact and biologically active human growth hormone by the Bacillus brevis system.

PubMed

Kajino, T; Saito, Y; Asami, O; Yamada, Y; Hirai, M; Udata, S

1997-10-01

The characteristic features of the Bacillus brevis system are very high productivity of heterologous proteins and very low extracellular protease activity. However, degradation of some heterologous proteins, especially mammalian proteins, can be observed and resulted in a lowering of protein productivity. By using a mutant expressing low levels of proteases and the addition of EDTA to the medium, intact human growth hormone (hGH) was successfully produced with the B. brevis system. Signal peptide modification with higher basicity in the amino terminal region and higher hydrophobicity in the middle region brought about a twelve-fold increase in hGH production. The hGH yield was further elevated to 240 mg L-1 by optimization of culture conditions. Thus, biologically active and mature hGH can be efficiently produced directly in the medium with the B. brevis system.

Developmental amnesia: a new pattern of dissociation with intact episodic memory.

PubMed

Temple, Christine M; Richardson, Paul

2004-01-01

A case of developmental amnesia is reported for a child, CL, of normal intelligence, who has intact episodic memory but impaired semantic memory for both semantic knowledge of facts and semantic knowledge of words, including general world knowledge, knowledge of word meanings and superordinate knowledge of words. In contrast to the deficits in semantic memory, there are no impairments in episodic memory for verbal or visual material, assessed by recall or recognition. Lexical decision was also intact, indicating impairment in semantic knowledge of vocabulary rather than absence of lexical representations. The case forms a double dissociation to the cases of Vargha-Khadem et al. [Science 277 (1997) 376; Episodic memory: new directions in research (2002) 153]; Gadian et al. [Brain 123 (2000) 499] for whom semantic memory was intact but episodic memory was impaired. This double dissociation suggests that semantic memory and episodic memory have the capacity to develop separately and supports models of modularity within memory development and a functional architecture for the developmental disorders within which there is residual normality rather than pervasive abnormality. Knowledge of arithmetical facts is also spared for CL, consistent with adult studies arguing for numeracy knowledge distinct from other semantics. Reading was characterised by difficulty with irregular words and homophones but intact reading of nonwords. CL has surface dyslexia with poor lexico-semantic reading skills but good phonological reading skills. The case was identified following screening from a population of normal schoolchildren suggesting that developmental amnesias may be more pervasive than has been recognised previously.

Improving the sensitivity and specificity of the abbreviated injury scale coding system.

PubMed Central

Kramer, C F; Barancik, J I; Thode, H C

1990-01-01

The Abbreviated Injury Scale with Epidemiologic Modifications (AIS 85-EM) was developed to make it possible to code information about anatomic injury types and locations that, although generally available from medical records, is not codable under the standard Abbreviated Injury Scale, published by the American Association for Automotive Medicine in 1985 (AIS 85). In a population-based sample of 3,223 motor vehicle trauma cases, 68 percent of the patients had one or more injuries that were coded to the AIS 85 body region nonspecific category external. When the same patients' injuries were coded using the AIS 85-EM coding procedure, only 15 percent of the patients had injuries that could not be coded to a specific body region. With AIS 85-EM, the proportion of codable head injury cases increased from 16 percent to 37 percent, thereby improving the potential for identifying cases with head and threshold brain injury. The data suggest that body region coding of all injuries is necessary to draw valid and reliable conclusions about changes in injury patterns and their sequelae. The increased specificity of body region coding improves assessments of the efficacy of injury intervention strategies and countermeasure programs using epidemiologic methodology. PMID:2116633

Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes

PubMed Central

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U.; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N.; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O.

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

PubMed

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

Disruption of hierarchical predictive coding during sleep

PubMed Central

Strauss, Melanie; Sitt, Jacobo D.; King, Jean-Remi; Elbaz, Maxime; Azizi, Leila; Buiatti, Marco; Naccache, Lionel; van Wassenhove, Virginie; Dehaene, Stanislas

2015-01-01

When presented with an auditory sequence, the brain acts as a predictive-coding device that extracts regularities in the transition probabilities between sounds and detects unexpected deviations from these regularities. Does such prediction require conscious vigilance, or does it continue to unfold automatically in the sleeping brain? The mismatch negativity and P300 components of the auditory event-related potential, reflecting two steps of auditory novelty detection, have been inconsistently observed in the various sleep stages. To clarify whether these steps remain during sleep, we recorded simultaneous electroencephalographic and magnetoencephalographic signals during wakefulness and during sleep in normal subjects listening to a hierarchical auditory paradigm including short-term (local) and long-term (global) regularities. The global response, reflected in the P300, vanished during sleep, in line with the hypothesis that it is a correlate of high-level conscious error detection. The local mismatch response remained across all sleep stages (N1, N2, and REM sleep), but with an incomplete structure; compared with wakefulness, a specific peak reflecting prediction error vanished during sleep. Those results indicate that sleep leaves initial auditory processing and passive sensory response adaptation intact, but specifically disrupts both short-term and long-term auditory predictive coding. PMID:25737555

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.

PubMed

Suyama, Mikita; Lathe, Warren C; Bork, Peer

2005-10-10

We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.

Sympathetic Nervous Regulation of Calcium and Action Potential Alternans in the Intact Heart.

PubMed

Winter, James; Bishop, Martin J; Wilder, Catherine D E; O'Shea, Christopher; Pavlovic, Davor; Shattock, Michael J

2018-01-01

Rationale: Arrhythmogenic cardiac alternans are thought to be an important determinant for the initiation of ventricular fibrillation. There is limited information on the effects of sympathetic nerve stimulation (SNS) on alternans in the intact heart and the conclusions of existing studies, focused on investigating electrical alternans, are conflicted. Meanwhile, several lines of evidence implicate instabilities in Ca handling, not electrical restitution, as the primary mechanism underpinning alternans. Despite this, there have been no studies on Ca alternans and SNS in the intact heart. The present study sought to address this, by application of voltage and Ca optical mapping for the simultaneous study of APD and Ca alternans in the intact guinea pig heart during direct SNS. Objective : To determine the effects of SNS on APD and Ca alternans in the intact guinea pig heart and to examine the mechanism(s) by which the effects of SNS are mediated. Methods and Results : Studies utilized simultaneous voltage and Ca optical mapping in isolated guinea pig hearts with intact innervation. Alternans were induced using a rapid dynamic pacing protocol. SNS was associated with rate-independent shortening of action potential duration (APD) and the suppression of APD and Ca alternans, as indicated by a shift in the alternans threshold to faster pacing rates. Qualitatively similar results were observed with exogenous noradrenaline perfusion. In contrast with previous reports, both SNS and noradrenaline acted to flatten the slope of the electrical restitution curve. Pharmacological block of the slow delayed rectifying potassium current (I Ks ), sufficient to abolish I Ks -mediated APD-adaptation, partially reversed the effects of SNS on pacing-induced alternans. Treatment with cyclopiazonic acid, an inhibitor of the sarco(endo)plasmic reticulum ATPase, had opposite effects to that of SNS, acting to increase susceptibility to alternans, and suggesting that accelerated Ca reuptake

A Unified Mathematical Framework for Coding Time, Space, and Sequences in the Hippocampal Region

PubMed Central

MacDonald, Christopher J.; Tiganj, Zoran; Shankar, Karthik H.; Du, Qian; Hasselmo, Michael E.; Eichenbaum, Howard

2014-01-01

The medial temporal lobe (MTL) is believed to support episodic memory, vivid recollection of a specific event situated in a particular place at a particular time. There is ample neurophysiological evidence that the MTL computes location in allocentric space and more recent evidence that the MTL also codes for time. Space and time represent a similar computational challenge; both are variables that cannot be simply calculated from the immediately available sensory information. We introduce a simple mathematical framework that computes functions of both spatial location and time as special cases of a more general computation. In this framework, experience unfolding in time is encoded via a set of leaky integrators. These leaky integrators encode the Laplace transform of their input. The information contained in the transform can be recovered using an approximation to the inverse Laplace transform. In the temporal domain, the resulting representation reconstructs the temporal history. By integrating movements, the equations give rise to a representation of the path taken to arrive at the present location. By modulating the transform with information about allocentric velocity, the equations code for position of a landmark. Simulated cells show a close correspondence to neurons observed in various regions for all three cases. In the temporal domain, novel secondary analyses of hippocampal time cells verified several qualitative predictions of the model. An integrated representation of spatiotemporal context can be computed by taking conjunctions of these elemental inputs, leading to a correspondence with conjunctive neural representations observed in dorsal CA1. PMID:24672015

Karyopherin-mediated nuclear import of the homing endonuclease VMA1-derived endonuclease is required for self-propagation of the coding region.

PubMed

Nagai, Yuri; Nogami, Satoru; Kumagai-Sano, Fumi; Ohya, Yoshikazu

2003-03-01

VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae, enters the nucleus to generate a double-strand break in the VDE-negative allelic locus, mediating the self-propagating gene conversion called homing. Although VDE is excluded from the nucleus in mitotic cells, it relocalizes at premeiosis, becoming localized in both the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE is induced by inactivation of TOR kinases, which constitute central regulators of cell differentiation in S. cerevisiae, and by nutrient depletion. A functional genomic approach revealed that at least two karyopherins, Srp1p and Kap142p, are required for the nuclear localization pattern. Genetic and physical interactions between Srp1p and VDE imply direct involvement of karyopherin-mediated nuclear transport in this process. Inactivation of TOR signaling or acquisition of an extra nuclear localization signal in the VDE coding region leads to artificial nuclear localization of VDE and thereby induces homing even during mitosis. These results serve as evidence that VDE utilizes the host systems of nutrient signal transduction and nucleocytoplasmic transport to ensure the propagation of its coding region.

Karyopherin-Mediated Nuclear Import of the Homing Endonuclease VMA1-Derived Endonuclease Is Required for Self-Propagation of the Coding Region

PubMed Central

Nagai, Yuri; Nogami, Satoru; Kumagai-Sano, Fumi; Ohya, Yoshikazu

2003-01-01

VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae, enters the nucleus to generate a double-strand break in the VDE-negative allelic locus, mediating the self-propagating gene conversion called homing. Although VDE is excluded from the nucleus in mitotic cells, it relocalizes at premeiosis, becoming localized in both the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE is induced by inactivation of TOR kinases, which constitute central regulators of cell differentiation in S. cerevisiae, and by nutrient depletion. A functional genomic approach revealed that at least two karyopherins, Srp1p and Kap142p, are required for the nuclear localization pattern. Genetic and physical interactions between Srp1p and VDE imply direct involvement of karyopherin-mediated nuclear transport in this process. Inactivation of TOR signaling or acquisition of an extra nuclear localization signal in the VDE coding region leads to artificial nuclear localization of VDE and thereby induces homing even during mitosis. These results serve as evidence that VDE utilizes the host systems of nutrient signal transduction and nucleocytoplasmic transport to ensure the propagation of its coding region. PMID:12588991

Predictors of attachment security in preschool children from intact and divorced families.

PubMed

Nair, Hira; Murray, Ann D

2005-09-01

The authors selected 58 mother-child dyads from divorced and intact families to participate in a study on the impact of divorce on preschoolers' attachment security. The authors explored pathways that lead to security of attachment. They found that mothers from divorced families were younger, had lower income levels, and had lower levels of education compared with their intact counterparts. Divorced mothers also reported significantly higher levels of stress, depression, need for social support, and conflict with their spouses. Mothers from intact families were more likely to use positive (authoritative) parenting styles compared with divorced mothers. Children in the divorced group had lower security scores on the Attachment Q-Set instrument (E. Waters, 1995). Regression analyses indicated that parenting style made a direct (independent) contribution to attachment security. In addition, temperament was related to attachment security, but temperament did not diminish the association of parenting style with attachment security. Furthermore, regression analyses indicated that the relationship of divorce to attachment security was mediated by parenting style.

Toward best practices in data processing and analysis for intact biotherapeutics by MS in quantitative bioanalysis.

PubMed

Kellie, John F; Kehler, Jonathan R; Karlinsey, Molly Z; Summerfield, Scott G

2017-12-01

Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented. Linearity, bias and other metrics are presented along with recommendations made on the viability of existing quantitation approaches. This communication is intended to start a discussion around intact protein data analysis and processing, recognizing that other published contributions will be required.

DROP: Detecting Return-Oriented Programming Malicious Code

NASA Astrophysics Data System (ADS)

Chen, Ping; Xiao, Hai; Shen, Xiaobin; Yin, Xinchun; Mao, Bing; Xie, Li

Return-Oriented Programming (ROP) is a new technique that helps the attacker construct malicious code mounted on x86/SPARC executables without any function call at all. Such technique makes the ROP malicious code contain no instruction, which is different from existing attacks. Moreover, it hides the malicious code in benign code. Thus, it circumvents the approaches that prevent control flow diversion outside legitimate regions (such as W ⊕ X ) and most malicious code scanning techniques (such as anti-virus scanners). However, ROP has its own intrinsic feature which is different from normal program design: (1) uses short instruction sequence ending in "ret", which is called gadget, and (2) executes the gadgets contiguously in specific memory space, such as standard GNU libc. Based on the features of the ROP malicious code, in this paper, we present a tool DROP, which is focused on dynamically detecting ROP malicious code. Preliminary experimental results show that DROP can efficiently detect ROP malicious code, and have no false positives and negatives.

SOLITARY CHEMORECEPTOR CELL SURVIVAL IS INDEPENDENT OF INTACT TRIGEMINAL INNERVATION

PubMed Central

Gulbransen, Brian; Silver, Wayne; Finger, Tom

2008-01-01

Nasal solitary chemoreceptor cells (SCCs) are a population of specialized chemosensory epithelial cells presumed to broaden trigeminal chemoreceptivity in mammals (Finger et al., 2003). SCCs are innervated by peptidergic trigeminal nerve fibers (Finger et al., 2003) but it is currently unknown if intact innervation is necessary for SCC development or survival. We tested the dependence of SCCs on innervation by eliminating trigeminal nerve fibers during development with neurogenin-1 knockout mice, during early postnatal development with capsaicin desensitization, and during adulthood with trigeminal lesioning. Our results demonstrate that elimination of innervation at any of these times does not result in decreased SCC numbers. In conclusion, neither SCC development nor mature cell maintenance is dependent on intact trigeminal innervation. PMID:18300260

Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry.

PubMed

Kellie, John F; Higgs, Richard E; Ryder, John W; Major, Anthony; Beach, Thomas G; Adler, Charles H; Merchant, Kalpana; Knierman, Michael D

2014-07-23

A robust top down proteomics method is presented for profiling alpha-synuclein species from autopsied human frontal cortex brain tissue from Parkinson's cases and controls. The method was used to test the hypothesis that pathology associated brain tissue will have a different profile of post-translationally modified alpha-synuclein than the control samples. Validation of the sample processing steps, mass spectrometry based measurements, and data processing steps were performed. The intact protein quantitation method features extraction and integration of m/z data from each charge state of a detected alpha-synuclein species and fitting of the data to a simple linear model which accounts for concentration and charge state variability. The quantitation method was validated with serial dilutions of intact protein standards. Using the method on the human brain samples, several previously unreported modifications in alpha-synuclein were identified. Low levels of phosphorylated alpha synuclein were detected in brain tissue fractions enriched for Lewy body pathology and were marginally significant between PD cases and controls (p = 0.03).

Ambient ionisation mass spectrometry for in situ analysis of intact proteins

PubMed Central

Kocurek, Klaudia I.; Griffiths, Rian L.

2018-01-01

Abstract Ambient surface mass spectrometry is an emerging field which shows great promise for the analysis of biomolecules directly from their biological substrate. In this article, we describe ambient ionisation mass spectrometry techniques for the in situ analysis of intact proteins. As a broad approach, the analysis of intact proteins offers unique advantages for the determination of primary sequence variations and posttranslational modifications, as well as interrogation of tertiary and quaternary structure and protein‐protein/ligand interactions. In situ analysis of intact proteins offers the potential to couple these advantages with information relating to their biological environment, for example, their spatial distributions within healthy and diseased tissues. Here, we describe the techniques most commonly applied to in situ protein analysis (liquid extraction surface analysis, continuous flow liquid microjunction surface sampling, nano desorption electrospray ionisation, and desorption electrospray ionisation), their advantages, and limitations and describe their applications to date. We also discuss the incorporation of ion mobility spectrometry techniques (high field asymmetric waveform ion mobility spectrometry and travelling wave ion mobility spectrometry) into ambient workflows. Finally, future directions for the field are discussed. PMID:29607564

Effect of exercise and exogenous glucocorticoid on serum level of intact parathyroid hormone.

PubMed

Tsai, K S; Lin, J C; Chen, C K; Cheng, W C; Yang, C H

1997-11-01

Most previous studies suggest that physical exercise, or physiological response to exercise such as cortisol and adrenaline secretion regulate parathyroid hormone (PTH) secretion in humans. To investigate the effects and possible interaction of exercise and excessive glucocorticoid on PTH secretion, we examined the serum of levels of intact-PTH, cortisol, adrenocorticotrophic hormone (ACTH), calcium, magnesium and phosphorus before and during one-hour of bicycle-ergometric exercise at 60% of maximal oxygen uptake. These exercise tests were performed on eight Chinese male volunteers aged between 20 and 25 years, once with and once without pretreatment with 0.5 mg of dexamethasone taken orally 9.5 hours in advance. The results showed that dexamethasone pretreatment significantly lowered basal levels of cortisol and ACTH, but intact PTH did not change. After 60 minutes of bicycling, intact PTH level increases by 50% of baseline both with and without dexamethasone pretreatment. Serum levels of calcium, corrected for changes in serum albumin concentration, phosphorus and magnesium also increased in both cases. This study demonstrated an increase of intact-PTH with exercise which was not associated with hypocalcemia or hypomagnesemia, and was not altered in the presence of mild exogenous glucocorticoid excess and suppressed endogenous cortisol secretion.

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Roux, Nicolas; Anbergen, Hauke; Collier, Nathaniel; Costard, Francois; Ferrry, Michel; Frampton, Andrew; Frederick, Jennifer; Holmen, Johan; Jost, Anne; Kokh, Samuel; Kurylyk, Barret; McKenzie, Jeffrey; Molson, John; Orgogozo, Laurent; Rivière, Agnès; Rühaak, Wolfram; Selroos, Jan-Olof; Therrien, René; Vidstrand, Patrik

2015-04-01

The impacts of climate change in boreal regions has received considerable attention recently due to the warming trends that have been experienced in recent decades and are expected to intensify in the future. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) that interact with the surrounding permafrost. For example, the thermal state of the surrounding soil influences the energy and water budget of the surface water bodies. Also, these water bodies generate taliks (unfrozen zones below) that disturb the thermal regimes of permafrost and may play a key role in the context of climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model the past and future evolution of landscapes, rivers, lakes and associated groundwater systems in a changing climate. However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, and the lack of study can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. Numerical approaches can only be validated against analytical solutions for a purely thermic 1D equation with phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare the results from different codes to provided test cases and/or to have controlled experiments for validation. Such inter-code comparisons can propel discussions to try to improve code performances. A benchmark exercise was initialized in 2014 with a kick-off meeting in Paris in November. Participants from USA, Canada, Germany, Sweden and France convened, representing altogether 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones. They

Intact parathyroid hormone and whole parathyroid hormone assay results disagree in hemodialysis patients under cinacalcet hydrochloride therapy.

PubMed

Koda, Ryo; Kazama, Junichiro James; Matsuo, Koji; Kawamura, Kazuko; Yamamoto, Suguru; Wakasugi, Minako; Takeda, Tetsuro; Narita, Ichiei

2015-08-01

The parathyroid gland secretes 1-84 and 7-84 parathyroid hormone (PTH) fragments, and its regulation is dependent on stimulation of the extracellular calcium-sensing receptor. While the intact PTH system detects both PTH fragments, the whole PTH system detects the 1-84PTH but not the 7-84PTH. Cinacalcet hydrochloride (CH) binds to calcium-sensing receptor as a calcimimetic. Here we investigated the role of CH treatment in the assessment of parathyroid gland function. Stable adult dialysis patients for whom CH therapy was planned were included. Patients for whom CH therapy was not planned were simultaneously included as the control group. The CH group (n = 44) showed significantly higher circulating levels of Ca, intact PTH, and whole PTH, before the CH treatment than the control group (n = 112). The Ca, intact PTH, and whole PTH levels decreased along with the CH therapy, and the Ca levels became comparable in the 8th week of treatment and thereafter. The CH group in the 8th week and thereafter showed significantly lower whole/intact PTH ratios than the control group, while the whole/intact PTH ratio was not significantly different between before and during the CH therapy. A multiple regression analysis revealed that the whole/intact PTH ratio was almost constant, but both the serum Ca level and a CH therapy could potentially modify the fixed number. When the whole PTH levels were estimated by intact PTH levels using the relationship between them in the control group, the levels were clearly overestimated in the CH group. Although the direct effect of CH on the whole/intact PTH ratio is masked by its hypocalcemic action, we could successfully demonstrate that the ratio in CH users is lower than that in the non-users with comparable levels of serum Ca. Evaluating parathyroid function with intact PTH according to the clinical practice guidelines in patients being treated with CH may lead to significant overestimation and subsequent overtreatment.

Low temperature and defoliation affect fructan-metabolizing enzymes in different regions of the rhizophores of Vernonia herbacea.

PubMed

Portes, Maria Teresa; Figueiredo-Ribeiro, Rita de Cássia L; de Carvalho, Maria Angela M

2008-10-09

In addition to the storage function, fructans in Asteraceae from floras with seasonal growth have been associated with drought and freezing tolerance. Vernonia herbacea, native of the Brazilian Cerrado, bears underground reserve organs, rhizophores, accumulating inulin-type fructans. The rhizophore is a cauline branched system with positive geotropic growth, with the apex (distal region) presenting younger tissues; sprouting of new shoots occurs by development of buds located on the opposite end (proximal region). Plants induced to sprouting by excision of the aerial organs present increased 1-fructan exohydrolase (1-FEH) activity in the proximal region, while plants at the vegetative stage present high 1-sucrose:sucrose fructosyltransferase (1-SST) in the distal region. The aim of the present study was to analyze how low temperature (5 degrees C) could affect fructan-metabolizing enzymes and fructan composition in the different regions of the rhizophores of intact and excised plants. 1-SST and 1-fructan:fructan fructosyltransferase (1-FFT) were higher in the distal region decreasing towards the proximal region in intact plants at the vegetative phase, and were drastically diminished when cold and/or excision were imposed. In contrast, 1-FEH increased in the proximal region of treated plants, mainly in excised plants subjected to cold. The ratio fructo-oligo to fructo-polysaccharides was significantly higher in plants exposed to low temperature (1.17 in intact plants and 1.64 in excised plants) than in plants exposed to natural temperature conditions (0.84 in intact vegetative plants and 0.58 in excised plants), suggesting that oligosaccharides are involved in the tolerance of plants to low temperature via 1-FEH, in addition to 1-FFT. Principal component analysis indicated different response mechanisms in fructan metabolism under defoliation and low temperature, which could be interpreted as part of the strategies to undergo unfavorable environmental conditions

Dor procedure for pulmonary atresia with intact ventricular septum in an infant.

PubMed

Kang, Yoonjin; Kwak, Jae Gun; Kim, Eung Rae; Kim, Woong-Han

2018-02-01

Pulmonary atresia with intact ventricular septum and right ventricle-dependent coronary circulation confers a high risk for myocardial infarction and complications of ischaemia, including left ventricle aneurysms. We describe an infant with pulmonary atresia with intact ventricular septum and right ventricle-dependent coronary circulation and a left ventricle apical aneurysm who successfully underwent the Dor procedure and a subsequent Fontan operation. Surgery for postinfarction left ventricle aneurysm can be considered in infants. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Patient Dashboard: the use of a colour-coded computerised clinical reminder in Whanganui regional general practices.

PubMed

McMenamin, John; Nicholson, Rick; Leech, Ken

2011-12-01

Clinical reminders have been shown to help general practice achieve an increase in some preventive care items, especially if they identify a patient's eligibility for the target item, prompt clinicians at the right time, provide a fast link to management tools and facilitate clinical recording. WRPHO has introduced the Patient Dashboard clinical reminder and monitored its impact on health targets. This paper reports the impact of a computerised colour-coded clinical reminder on achieving agreed health targets in Whanganui regional practices. Patient Dashboard was developed from previous versions in Auckland and Northland and provided to Whanganui regional practices with Primary Health Organisation (PHO) support. The Dashboard was linked with existing and new clinical management tools which automatically updated clinical records. Data from practices was pooled by Whanganui Regional Primary Health Organisation and target achievement rates reported over 15 months. Over the initial 15 months of Patient Dashboard use, recording of smoking status increased from 74% to 82% and of alcohol use from 15% to 47%. Screening for diabetes increased from 62% to 74%, cardiovascular risk assessment from 20% to 43%, cervical screening from 71% to 79%, and breast screening from 60% to 80%. Patient Dashboard was associated with increased performance indicators both for those targets which were part of a PHO programme and for targets without additional support.

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.

PubMed

Gerresheim, Gesche K; Dünnes, Nadia; Nieder-Röhrmann, Anika; Shalamova, Lyudmila A; Fricke, Markus; Hofacker, Ivo; Höner Zu Siederdissen, Christian; Marz, Manja; Niepmann, Michael

2017-02-01

We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3' untranslated region (3'UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites. This suggests that the dynamics of miRNA/Ago2 binding not only depends on the target site itself but also on flanking sequence context to a considerable extent, in particular in a small viral genome in which strong selection constraints act on coding sequence and overlapping cis-signals and model the accessibility of cis-signals. In full-length genomes, single and combination mutations in the miR-122 target sites reveal that site 5B.2 is positively involved in regulating overall genome replication efficiency, whereas mutation of site 5B.3 showed a weaker effect. Mutation of the 3'UTR site and double or triple mutants showed no significant overall effect on genome replication, whereas in a translation reporter RNA, the 3'UTR target site inhibits translation directed by the HCV 5'UTR. Thus, the miR-122 target sites in the 3'-region of the HCV genome are involved in a complex interplay in regulating different steps of the HCV replication cycle.

Solitary chemoreceptor cell survival is independent of intact trigeminal innervation.

PubMed

Gulbransen, Brian; Silver, Wayne; Finger, Thomas E

2008-05-01

Nasal solitary chemoreceptor cells (SCCs) are a population of specialized chemosensory epithelial cells presumed to broaden trigeminal chemoreceptivity in mammals (Finger et al. [2003] Proc Natl Acad Sci USA 100:8981-8986). SCCs are innervated by peptidergic trigeminal nerve fibers (Finger et al. [2003]) but it is currently unknown if intact innervation is necessary for SCC development or survival. We tested the dependence of SCCs on innervation by eliminating trigeminal nerve fibers during development with neurogenin-1 knockout mice, during early postnatal development with capsaicin desensitization, and during adulthood with trigeminal lesioning. Our results demonstrate that elimination of innervation at any of these times does not result in decreased SCC numbers. In conclusion, neither SCC development nor mature cell maintenance is dependent on intact trigeminal innervation. (c) 2008 Wiley-Liss, Inc.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

PubMed

Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

2012-01-01

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

Visual Speech Fills in Both Discrimination and Identification of Non-Intact Auditory Speech in Children

ERIC Educational Resources Information Center

Jerger, Susan; Damian, Markus F.; McAlpine, Rachel P.; Abdi, Herve

2018-01-01

To communicate, children must discriminate and identify speech sounds. Because visual speech plays an important role in this process, we explored how visual speech influences phoneme discrimination and identification by children. Critical items had intact visual speech (e.g. baez) coupled to non-intact (excised onsets) auditory speech (signified…

Perforated Patch-clamp Recording of Mouse Olfactory Sensory Neurons in Intact Neuroepithelium: Functional Analysis of Neurons Expressing an Identified Odorant Receptor

PubMed Central

Jarriault, David; Grosmaitre, Xavier

2015-01-01

Analyzing the physiological responses of olfactory sensory neurons (OSN) when stimulated with specific ligands is critical to understand the basis of olfactory-driven behaviors and their modulation. These coding properties depend heavily on the initial interaction between odor molecules and the olfactory receptor (OR) expressed in the OSNs. The identity, specificity and ligand spectrum of the expressed OR are critical. The probability to find the ligand of the OR expressed in an OSN chosen randomly within the epithelium is very low. To address this challenge, this protocol uses genetically tagged mice expressing the fluorescent protein GFP under the control of the promoter of defined ORs. OSNs are located in a tight and organized epithelium lining the nasal cavity, with neighboring cells influencing their maturation and function. Here we describe a method to isolate an intact olfactory epithelium and record through patch-clamp recordings the properties of OSNs expressing defined odorant receptors. The protocol allows one to characterize OSN membrane properties while keeping the influence of the neighboring tissue. Analysis of patch-clamp results yields a precise quantification of ligand/OR interactions, transduction pathways and pharmacology, OSNs' coding properties and their modulation at the membrane level.  PMID:26275097

Comparative Evaluation of Impact Strength of Fragment Bonded Teeth and Intact Teeth: An In Vitro Study

PubMed Central

Venugopal, L; Lakshmi, M Narasimha; Babu, Devatha Ashok; Kiran, V Ravi

2014-01-01

Background: To test and compare the impact strength of fragment bonded teeth with that of intact teeth by using impact testing machine (pendulum type) as a mode of load. Materials and Methods: Forty extracted, maxillary, central incisors selected for this study (20 control group and 20 experimental group). In experimental group, teeth crowns were fractured with a microtome at 2.5 mm from mesioincisal angle cervically, fractured portion is attached to original crown portion with 3 M single bond dentin bonding agent and 3 M Z ‘100’, composite resin. Impact strength of fragment bonded teeth and intact teeth tested with impact testing machine and compared. Results: Mean impact strength of fragment bonded teeth (30.76 KJ/M2 ) is not statistically significant deferent from mean impact strength of intact teeth (31.11 KJ/M2 ). Conclusion: Mean impact strength of fragment bonded teeth is not statistically different with that of intact teeth. Hence, after fracture of teeth if it is restored with fragment reattachment by using 3 M single bond dentin bonding agent and 3 M Z ‘100’ composite resin is having impact strength like that of intact teeth. How to cite the article: Venugopal L, Lakshmi MN, Babu DA, Kiran VR. Comparative evaluation of impact strength of fragment bonded teeth and intact teeth: An in vitro study. J Int Oral Health 2014;6(3):73-6. PMID:25083037

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

Oligodeoxynucleotide Probes for Detecting Intact Cells

NASA Technical Reports Server (NTRS)

Rosson, Reinhardt A.; Maurina-Brunker, Julie; Langley, Kim; Pynnonen, Christine M.

2004-01-01

A rapid, sensitive test using chemiluminescent oligodeoxynucleotide probes has been developed for detecting, identifying, and enumerating intact cells. The test is intended especially for use in detecting and enumerating bacteria and yeasts in potable water. As in related tests that have been developed recently for similar purposes, the oligodeoxynucleotide probes used in this test are typically targeted at either singlecopy deoxyribonucleic acid (DNA) genes (such as virulence genes) or the multiple copies (10,000 to 50,000 copies per cell) of 16S ribosomal ribonucleic acids (rRNAs). Some of those tests involve radioisotope or fluorescent labeling of the probes for reporting hybridization of probes to target nucleic acids. Others of those tests involve labeling with enzymes plus the use of chemiluminescent or chromogenic substrates to report hybridization via color or the emission of light, respectively. The present test is of the last-mentioned type. The chemiluminescence in the present test can be detected easily with relatively simple instrumentation. In developing the present test, the hybridization approach was chosen because hybridization techniques are very specific. Hybridization detects stable, inheritable genetic targets within microorganisms. These targets are not dependent on products of gene expression that can vary with growth conditions or physiological states of organisms in test samples. Therefore, unique probes can be designed to detect and identify specific genera or species of bacteria or yeast (in terms of rRNA target sequences) or can be designed to detect and identify virulence genes (genomic target sequences). Because of the inherent specificity of this system, there are few problems of cross-reactivity. Hybridization tests are rapid, but hybridization tests now available commercially lack sensitivity; typically, between 10(exp 6) and 10(exp 7) cells of the target organism are needed to ensure a reliable test. Consequently, the numbers of

Introduction of the ASGARD Code

NASA Technical Reports Server (NTRS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv; Fayock, Brian

2017-01-01

ASGARD stands for 'Automated Selection and Grouping of events in AIA Regional Data'. The code is a refinement of the event detection method in Ugarte-Urra & Warren (2014). It is intended to automatically detect and group brightenings ('events') in the AIA EUV channels, to record event parameters, and to find related events over multiple channels. Ultimately, the goal is to automatically determine heating and cooling timescales in the corona and to significantly increase statistics in this respect. The code is written in IDL and requires the SolarSoft library. It is parallelized and can run with multiple CPUs. Input files are regions of interest (ROIs) in time series of AIA images from the JSOC cutout service (http://jsoc.stanford.edu/ajax/exportdata.html). The ROIs need to be tracked, co-registered, and limited in time (typically 12 hours).

Penetration of Ufenamate into Intact, Stripped, or Delipidized Skin Using Different Vehicles.

PubMed

Iino, Hayato; Fujii, Makiko; Fujino, Manami; Koizumi, Naoya; Watanabe, Yoshiteru

2015-01-01

The purpose of this study was to clarify the effect of skin condition on skin penetration of the very high lipophilic drug, ufenamate (UF). UF was applied to stripped or delipidized skin using liquid paraffin (LP) or purified water containing polysorbate 80 at a dose of 2 µL/cm(2). We found that UF penetration into intact and stripped skin using a water vehicle was respectively 5 and 10 times higher than that using LP. UF is freely soluble in oil and insoluble in water; thus, activity in water is higher than that in LP. Therefore, it is useful to use a water-based vehicle for both intact sites and those with defective stratum corneum (SC). Conversely, we found that delipidization of SC decreased the penetration of UF significantly with both LP and water, and the amount measured in the epidermis was 1 µg/cm(2) with both vehicles. This indicates that UF is not suitable for so-called "dry skin." This study revealed clinically relevant differences in the penetration of UF into intact, stripped, or delipidized skin conditions.

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

PubMed

Hezroni, Hadas; Ben-Tov Perry, Rotem; Meir, Zohar; Housman, Gali; Lubelsky, Yoav; Ulitsky, Igor

2017-08-30

Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.

Differences in School Behavior and Achievement between Children from Intact, Reconstituted, and Single-Parent Families.

ERIC Educational Resources Information Center

Featherstone, Darin R.; And Others

1992-01-01

Analyzed differences in school behavior and achievement among students (n=530) in grades six through nine from intact, reconstituted, and single-parent families. Students from intact, two-parent families had fewer absences and tardies, higher grade point averages, and fewer negative and more positive teacher behavioral ratings than did those from…

Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.

PubMed

Auer, Paul L; Nalls, Mike; Meschia, James F; Worrall, Bradford B; Longstreth, W T; Seshadri, Sudha; Kooperberg, Charles; Burger, Kathleen M; Carlson, Christopher S; Carty, Cara L; Chen, Wei-Min; Cupples, L Adrienne; DeStefano, Anita L; Fornage, Myriam; Hardy, John; Hsu, Li; Jackson, Rebecca D; Jarvik, Gail P; Kim, Daniel S; Lakshminarayan, Kamakshi; Lange, Leslie A; Manichaikul, Ani; Quinlan, Aaron R; Singleton, Andrew B; Thornton, Timothy A; Nickerson, Deborah A; Peters, Ulrike; Rich, Stephen S

2015-07-01

Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk. To investigate the contribution of rare and common genetic variants to ischemic stroke risk by targeting the protein-coding regions of the human genome. The National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) analyzed approximately 6000 participants from numerous cohorts of European and African ancestry. For discovery, 365 cases of ischemic stroke (small-vessel and large-vessel subtypes) and 809 European ancestry controls were sequenced; for replication, 47 affected sibpairs concordant for stroke subtype and an African American case-control series were sequenced, with 1672 cases and 4509 European ancestry controls genotyped. The ESP's exome sequencing and genotyping started on January 1, 2010, and continued through June 30, 2012. Analyses were conducted on the full data set between July 12, 2012, and July 13, 2013. Discovery of new variants or genes contributing to ischemic stroke risk and subtype (primary analysis) and determination of support for protein-coding variants contributing to risk in previously published candidate genes (secondary analysis). We identified 2 novel genes associated with an increased risk of ischemic stroke: a protein-coding variant in PDE4DIP (rs1778155; odds ratio, 2.15; P = 2.63 × 10(-8)) with an intracellular signal transduction mechanism and in ACOT4 (rs35724886; odds ratio, 2.04; P = 1.24 × 10(-7)) with a fatty acid metabolism; confirmation of PDE4DIP was observed in affected sibpair families with large-vessel stroke

Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry

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

Wu, Si; Brown, Joseph N.; Tolic, Nikola

There are several notable challenges inherent to fully characterizing the entirety of the human saliva proteome using bottom-up approaches, including polymorphic isoforms, post-translational modifications, unique splice variants, deletions, and truncations. To address these challenges, we have developed a top-down based liquid chromatography-mass spectrometry (LC-MS) approach, which cataloged 20 major human salivary proteins with a total of 83 proteoforms, containing a broad range of post-translational modifications. Among these proteins, several previously reported disease biomarker proteins were identified at the intact protein level, such as beta-2 microglobulin (B2M). In addition, intact glycosylated proteoforms of several saliva proteins were also characterized, including intactmore » N-glycosylated protein prolactin inducible protein (PIP) and O-glycosylated acidic protein rich protein (aPRP). These characterized proteoforms constitute an intact saliva proteoform database, which was used for quantitative comparison of intact salivary proteoforms among six healthy individuals. Human parotid (PS) and submandibular/sublingual gland (SMSL) secretion samples (2 μg of protein each) from six healthy individuals were compared using RPLC coupled with the 12T FTICR mass spectrometer. Significantly different protein and PTM patterns were resolved with high reproducibility between PS and SMSL glands. The results from this study provide further insight into the potential mechanisms of PTM pathways in oral glandular secretion, expanding our knowledge of this complex yet easily accessible fluid. Intact protein LC-MS approach presented herein can potentially be applied for rapid and accurate identification of biomarkers from only a few microliters of human glandular saliva.« less

Meta-analysis of peak wall stress in ruptured, symptomatic and intact abdominal aortic aneurysms.

PubMed

Khosla, S; Morris, D R; Moxon, J V; Walker, P J; Gasser, T C; Golledge, J

2014-10-01

Abdominal aortic aneurysm (AAA) is an important cause of sudden death; however, there are currently incomplete means to predict the risk of AAA rupture. AAA peak wall stress (PWS) can be estimated using finite element analysis (FEA) methods from computed tomography (CT) scans. The question is whether AAA PWS can predict AAA rupture. The aim of this systematic review was to compare PWS in patients with ruptured and intact AAA. The MEDLINE database was searched on 25 May 2013. Case-control studies assessing PWS in asymptomatic intact, and acutely symptomatic or ruptured AAA from CT scans using FEA were included. Data were extracted independently. A random-effects model was used to calculate standard mean differences (SMDs) for PWS measurements. Nine studies assessing 348 individuals were identified and used in the meta-analysis. Results from 204 asymptomatic intact and 144 symptomatic or ruptured AAAs showed that PWS was significantly greater in the symptomatic/ ruptured AAAs compared with the asymptomatic intact AAAs (SMD 0·95, 95 per cent confidence interval 0·71 to 1·18; P < 0·001). The findings remained significant after adjustment for mean systolic blood pressure, standardized at 120 mmHg (SMD 0·68, 0·39 to 0·96; P < 0·001). Minimal heterogeneity between studies was noted (I(2)  = 0 per cent). This study suggests that PWS is greater in symptomatic or ruptured AAA than in asymptomatic intact AAA. © 2014 BJS Society Ltd. Published by John Wiley & Sons Ltd.

Hundreds of conserved non-coding genomic regions are independently lost in mammals

PubMed Central

Hiller, Michael; Schaar, Bruce T.; Bejerano, Gill

2012-01-01

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals. PMID:23042682

Demonstration of pelvic anatomy by modified midline transection that maintains intact internal pelvic organs.

PubMed

Steinke, Hanno; Saito, Toshiyuki; Herrmann, Gudrun; Miyaki, Takayoshi; Hammer, Niels; Sandrock, Mara; Itoh, Masahiro; Spanel-Borowski, Katharina

2010-01-01

Gross dissection for demonstrating anatomy of the human pelvis has traditionally involved one of two approaches, each with advantages and disadvantages. Classic hemisection in the median plane through the pelvic ring transects the visceral organs but maintains two symmetric pelvic halves. An alternative paramedial transection compromises one side of the bony pelvis but leaves the internal organs intact. The authors propose a modified technique that combines advantages of both classical dissections. This novel approach involves dividing the pubic symphysis and sacrum in the median plane after shifting all internal organs to one side. The hemipelvis without internal organs is immediately available for further dissection of the lower limb. The hemipelvis with intact internal organs is ideal for showing the complex spatial relationships of the pelvic organs and vessels relative to the intact pelvic floor.

10. VIEW SHOWING FRAGMENTED AND INTACT ORIGINAL SIDEWALK ALONG SOUTH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. VIEW SHOWING FRAGMENTED AND INTACT ORIGINAL SIDEWALK ALONG SOUTH SIDE OF SHERMAN CANAL, BETWEEN DELL AVENUE VEHICULAR BRIDGE AND GRAND CANAL COURT PEDESTRIAN BRIDGE, LOOKING EAST - Venice Canals, Community of Venice, Los Angeles, Los Angeles County, CA

Functional interrogation of non-coding DNA through CRISPR genome editing.

PubMed

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Functional interrogation of non-coding DNA through CRISPR genome editing

PubMed Central

Canver, Matthew C.; Bauer, Daniel E.; Orkin, Stuart H.

2017-01-01

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. PMID:28288828

Integrating Mass Spectrometry of Intact Protein Complexes into Structural Proteomics

PubMed Central

Hyung, Suk-Joon; Ruotolo, Brandon T.

2013-01-01

Summary Mass spectrometry analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other mass spectrometry approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative mass spectrometry approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly-advancing area. PMID:22611037

A motion compensation technique using sliced blocks and its application to hybrid video coding

NASA Astrophysics Data System (ADS)

Kondo, Satoshi; Sasai, Hisao

2005-07-01

This paper proposes a new motion compensation method using "sliced blocks" in DCT-based hybrid video coding. In H.264 ? MPEG-4 Advance Video Coding, a brand-new international video coding standard, motion compensation can be performed by splitting macroblocks into multiple square or rectangular regions. In the proposed method, on the other hand, macroblocks or sub-macroblocks are divided into two regions (sliced blocks) by an arbitrary line segment. The result is that the shapes of the segmented regions are not limited to squares or rectangles, allowing the shapes of the segmented regions to better match the boundaries between moving objects. Thus, the proposed method can improve the performance of the motion compensation. In addition, adaptive prediction of the shape according to the region shape of the surrounding macroblocks can reduce overheads to describe shape information in the bitstream. The proposed method also has the advantage that conventional coding techniques such as mode decision using rate-distortion optimization can be utilized, since coding processes such as frequency transform and quantization are performed on a macroblock basis, similar to the conventional coding methods. The proposed method is implemented in an H.264-based P-picture codec and an improvement in bit rate of 5% is confirmed in comparison with H.264.

Load-unloading response of intact and artificially degraded articular cartilage correlated with near infrared (NIR) absorption spectra.

PubMed

Afara, I O; Singh, S; Oloyede, A

2013-04-01

The conventional mechanical properties of articular cartilage, such as compressive stiffness, have been demonstrated to be limited in their capacity to distinguish intact (visually normal) from degraded cartilage samples. In this paper, we explore the correlation between a new mechanical parameter, namely the reswelling of articular cartilage following unloading from a given compressive load, and the near infrared (NIR) spectrum. The capacity to distinguish mechanically intact from proteoglycan-depleted tissue relative to the "reswelling" characteristic was first established, and the result was subsequently correlated with the NIR spectral data of the respective tissue samples. To achieve this, normal intact and enzymatically degraded samples were subjected to both NIR probing and mechanical compression based on a load-unload-reswelling protocol. The parameter δr, characteristic of the osmotic "reswelling" of the matrix after unloading to a constant small load in the order of the osmotic pressure of cartilage, was obtained for the different sample types. Multivariate statistics was employed to determine the degree of correlation between δr and the NIR absorption spectrum of relevant specimens using Partial Least Squared (PLS) regression. The results show a strong relationship (R(2)=95.89%, p<0.0001) between the spectral data and δr. This correlation of δr with NIR spectral data suggests the potential for determining the reswelling characteristics non-destructively. It was also observed that δr values bear a significant relationship with the cartilage matrix integrity, indicated by its proteoglycan content, and can therefore differentiate between normal and artificially degraded proteoglycan-depleted cartilage samples. It is therefore argued that the reswelling of cartilage, which is both biochemical (osmotic) and mechanical (hydrostatic pressure) in origin, could be a strong candidate for characterizing the tissue, especially in regions surrounding focal

XGC developments for a more efficient XGC-GENE code coupling

NASA Astrophysics Data System (ADS)

Dominski, Julien; Hager, Robert; Ku, Seung-Hoe; Chang, Cs

2017-10-01

In the Exascale Computing Program, the High-Fidelity Whole Device Modeling project initially aims at delivering a tightly-coupled simulation of plasma neoclassical and turbulence dynamics from the core to the edge of the tokamak. To permit such simulations, the gyrokinetic codes GENE and XGC will be coupled together. Numerical efforts are made to improve the numerical schemes agreement in the coupling region. One of the difficulties of coupling those codes together is the incompatibility of their grids. GENE is a continuum grid-based code and XGC is a Particle-In-Cell code using unstructured triangular mesh. A field-aligned filter is thus implemented in XGC. Even if XGC originally had an approximately field-following mesh, this field-aligned filter permits to have a perturbation discretization closer to the one solved in the field-aligned code GENE. Additionally, new XGC gyro-averaging matrices are implemented on a velocity grid adapted to the plasma properties, thus ensuring same accuracy from the core to the edge regions.

Interleukin-1 homologues IL-1F7b and IL-18 contain functional mRNA instability elements within the coding region responsive to lipopolysaccharide

PubMed Central

2004-01-01

IL-1F7b, a novel homologue of the IL-1 (interleukin 1) family, was discovered by computational cloning. We demonstrated that IL-1F7b shares critical amino acid residues with IL-18 and binds to the IL-18-binding protein enhancing its ability to inhibit IL-18-induced interferon-γ. We also showed that low levels of IL-1F7b are constitutively present intracellularly in human blood monocytes. In this study, we demonstrate that similar to IL-18, both mRNA and intracellular protein expression of IL-1F7b are up-regulated by LPS (lipopolysaccharide) in human monocytes. In stable transfectants of murine RAW264.7 macrophage cells, there was no IL-1F7b protein expression despite a highly active CMV promoter. We found that IL-1F7b-specific mRNA was rapidly degraded in transfected cells, via a 3′-UTR (untranslated region)-independent control of IL-1F7b transcript stability. After LPS stimulation, there was a rapid transient increase in IL-1F7b-specific mRNA and concomitant protein levels. Using sequence alignment, we found a conserved ten-nucleotide homology box within the open reading frame of IL-F7b, which is flanking the coding region instability elements of some selective genes. In-frame deletion of downstream exon 5 from the full-length IL-1F7b cDNA markedly increased the levels of IL-1F7b mRNA. A similar coding region element is located in IL-18. When transfected into RAW264.7 macrophages, IL-18 mRNA was also unstable unless treated with LPS. These results indicate that both IL-1F7b and IL-18 mRNA contain functional instability determinants within their coding region, which influence mRNA decay as a novel mechanism to regulate the expression of IL-1 family members. PMID:15046617

Risks for Conduct Disorder Symptoms Associated with Parental Alcoholism in Stepfather Families versus Intact Families from a Community Sample

ERIC Educational Resources Information Center

Foley, Debra L.; Pickles, Andrew; Rutter, Michael; Gardner, Charles O.; Maes, Hermine H.; Silberg, Judy L.; Eaves, Lindon J.

2004-01-01

Background: It is not known if the prevalence of parental psychiatric disorders is higher in stepfather than intact families, or if parental alcoholism is differentially associated with risk for conduct disorder (CD) symptoms in stepfather families versus intact families. Method: The sample comprised 839 girls and 741 boys from 792 intact families…

Behavior Management Style of Single Parents and Intact Families.

ERIC Educational Resources Information Center

Smith, Douglas K.; And Others

Studies examining the behavior management styles of parents as a function of family intactness and parent employment status are lacking. To assess parental style of behavior management, the Parental Management Questionnaire (PMQ) was completed by 1,957 parents of elementary school children (50% response rate). The PMQ is based on Aronfreed's…

Factors mediating cheatgrass invasion of intact salt desert shrubland

Treesearch

Susan E. Meyer; Susan C. Garvin; Julie Beckstead

2001-01-01

Cheatgrass (Bromus tectorum) has recently displaced salt desert shrubland in many areas of the Great Basin. We studied the dynamics of cheatgrass invasion into an intact shadscale-gray molly community in Dugway Valley, Utah, by adding seeds and manipulating disturbance regime and resource availability. Shrub clipping or cryptobiotic crust trampling on large plots...

Complete coding regions of the prototypes enterovirus B93 and C95: phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains.

PubMed

Junttila, N; Lévêque, N; Magnius, L O; Kabue, J P; Muyembe-Tamfum, J J; Maslin, J; Lina, B; Norder, H

2015-03-01

Complete coding regions were sequenced for two new enterovirus genomes: EV-B93 previously identified by VP1 sequencing, derived from a child with acute flaccid paralysis in the Democratic Republic of Congo; and EV-C95 from a French soldier with acute gastroenteritis in Djibouti. The EV-B93 P1 had more than 30% nucleotide divergence from other EV-B types, with highest similarity to E-15 and EV-B80. The P1 nucleotide sequence of EV-C95 was most similar, 71%, to CV-A21. Complete coding regions for the new enteroviruses were compared with those of 135 EV-B and 176 EV-C strains representing all types available in GenBank. When strains from the same outbreak or strains isolated during the same year in the same geographical region were excluded, 27 of the 58 EV-B, and 16 of the 23 EV-C types were represented by more than one sequence. However, for EV-B the P3 sequences formed three clades mainly according to origin or time of isolation, irrespective of type, while for EV-C the P3 sequences segregated mainly according to disease manifestation, with most strains causing paralysis, including polioviruses, forming one clade, and strains causing respiratory illness forming another. There was no intermixing of types between these two clades, apart from two EV-C96 strains. The EV-B P3 sequences had lower inter-clade and higher intra-clade variability as compared to the EV-C sequences, which may explain why inter-clade recombinations are more frequent in EV-B. Further analysis of more isolates may shed light on the role of recombinations in the evolution of EV-B in geographical context. © 2014 Wiley Periodicals, Inc.

Intact capture of hypervelocity projectiles

NASA Technical Reports Server (NTRS)

Tsou, P.

1990-01-01

The ability to capture projectiles intact at hypervelocities opens new applications in science and technology that would either not be possible or would be very costly by other means. This capability has been demonstrated in the laboratory for aluminum projectiles of 1.6 mm diameter, captured at 6 km/s, in one unmelted piece, and retaining up to 95% of the original mass. Furthermore, capture was accomplished passively using microcellular underdense polymer foam. Another advantage of capturing projectiles in an underdense medium is the ability of such a medium to preserve a record of the projectile's original velocity components of speed and direction. A survey of these experimental results is described in terms of a dozen parameters which characterize the amount of capture and the effect on the projectile due to different capture media.

Intact capture of hypervelocity projectiles.

PubMed

Tsou, P

1990-01-01

The ability to capture projectiles intact at hypervelocities opens new applications in science and technology that would either not be possible or would be very costly by other means. This capability has been demonstrated in the laboratory for aluminum projectiles of 1.6 mm diameter, captured at 6 km/s, in one unmelted piece, and retaining up to 95% of the original mass. Furthermore, capture was accomplished passively using microcellular underdense polymer foam. Another advantage of capturing projectiles in an underdense medium is the ability of such a medium to preserve a record of the projectile's original velocity components of speed and direction. A survey of these experimental results is described in terms of a dozen parameters which characterize the amount of capture and the effect on the projectile due to different capture media.

3D perfusion mapping in the intact mouse heart after myocardial infarction using myocardial contrast echocardiography

NASA Astrophysics Data System (ADS)

Li, Yinbo; Yang, Zequan; French, Brent A.; Hossack, John A.

2005-04-01

An intact mouse model of surgically-induced myocardial infarction (MI) caused by permanent occlusion of the Left Anterior Descending (LAD) coronary artery was studied. Normal mice with no occlusion were also studied as controls. For each mouse, contrast enhanced ultrasound images of the heart were acquired in parallel cross-sections perpendicular to the sternum at millimeter increments. For accurate 3D reconstruction, ECG gating and a tri-axial adjustable micromanipulator were used for temporal and spatial registration. Ultrasound images at steady-state of blood refilling were color-coded in each slice to show relative perfusion. Myocardial perfusion defects and necrosis were also examined postmortem by staining with Phthalo blue and TTC red dyes. Good correlation (R>0.93) in perfused area size was observed between in vivo measurements and histological staining. A 3D multi-slice model and a 3D rendering of perfusion distribution were created and showed a promising match with postmortem results, lending further credence to its use as a more comprehensive and more reliable tool for in vivo assessment of myocardial perfusion than 2D tomographic analysis.

Quantitative proteomic analysis of intact plastids.

PubMed

Shiraya, Takeshi; Kaneko, Kentaro; Mitsui, Toshiaki

2014-01-01

Plastids are specialized cell organelles in plant cells that are differentiated into various forms including chloroplasts, chromoplasts, and amyloplasts, and fulfill important functions in maintaining the overall cell metabolism and sensing environmental factors such as sunlight. It is therefore important to grasp the mechanisms of differentiation and functional changes of plastids in order to enhance the understanding of vegetality. In this chapter, details of a method for the extraction of intact plastids that makes analysis possible while maintaining the plastid functions are provided; in addition, a quantitative shotgun method for analyzing the composition and changes in the content of proteins in plastids as a result of environmental impacts is described.

Comparison of allergenicity and immunogenicity of an intact allergen vaccine and commercially available allergoid products for birch pollen immunotherapy.

PubMed

Lund, L; Henmar, H; Würtzen, P A; Lund, G; Hjortskov, N; Larsen, J N

2007-04-01

Specific immunotherapy with intact allergen vaccine is a well-documented treatment for allergic diseases. Different vaccine formulations are currently commercially available, the active ingredient either being intact allergens or chemically modified allergoids. The rationale behind allergoids is to decrease allergenicity while maintaining immunogenicity. However, data from the German health authorities based on reporting of adverse events over a 10-year period did not indicate increased safety of allergoids over intact allergens. The objective of this study was to investigate the effect of chemical modification on allergenicity and immunogenicity comparing four commercial allergoid products for birch pollen immunotherapy with an intact allergen vaccine. Solid-phase IgE inhibition and histamine release assays were selected as model systems for allergenicity, and a combination of human T cell proliferation and IgG titres following mouse immunizations were used to address the immunogenicity of the intact allergen vaccine and the four allergoids. In all assays, the products were normalized with respect to the manufacturer's recommended maintenance dose. IgE inhibition experiments showed a change in epitope composition comparing intact allergen vaccine with allergoid. One allergoid product induced enhanced histamine release compared to the intact allergens, while the other three allergoids showed reduced release. Standard T cell stimulation assays using lines from allergic patients showed a reduced response for all allergoids compared with the intact allergen vaccine regardless of the cell type used for antigen presentation. All allergoids showed reduced capacity to induce allergen-specific IgG responses in mice. While some allergoids were associated with reduced allergenicity, a clear reduction in immunogenicity was observed for all allergoid products compared with the intact allergen vaccine, and the commercial allergoids tested therefore do not fulfil the allergoid

Raman spectroscopy of normal oral buccal mucosa tissues: study on intact and incised biopsies

NASA Astrophysics Data System (ADS)

Deshmukh, Atul; Singh, S. P.; Chaturvedi, Pankaj; Krishna, C. Murali

2011-12-01

Oral squamous cell carcinoma is one of among the top 10 malignancies. Optical spectroscopy, including Raman, is being actively pursued as alternative/adjunct for cancer diagnosis. Earlier studies have demonstrated the feasibility of classifying normal, premalignant, and malignant oral ex vivo tissues. Spectral features showed predominance of lipids and proteins in normal and cancer conditions, respectively, which were attributed to membrane lipids and surface proteins. In view of recent developments in deep tissue Raman spectroscopy, we have recorded Raman spectra from superior and inferior surfaces of 10 normal oral tissues on intact, as well as incised, biopsies after separation of epithelium from connective tissue. Spectral variations and similarities among different groups were explored by unsupervised (principal component analysis) and supervised (linear discriminant analysis, factorial discriminant analysis) methodologies. Clusters of spectra from superior and inferior surfaces of intact tissues show a high overlap; whereas spectra from separated epithelium and connective tissue sections yielded clear clusters, though they also overlap on clusters of intact tissues. Spectra of all four groups of normal tissues gave exclusive clusters when tested against malignant spectra. Thus, this study demonstrates that spectra recorded from the superior surface of an intact tissue may have contributions from deeper layers but has no bearing from the classification of a malignant tissues point of view.

Transport of Indole-3-Acetic Acid during Gravitropism in Intact Maize Coleoptiles 1

PubMed Central

Parker, Karen E.; Briggs, Winslow R.

1990-01-01

We have investigated the transport of tritiated indole-3-acetic acid (IAA) in intact, red light-grown maize (Zea mays) coleoptiles during gravitropic induction and the subsequent development of curvature. This auxin is transported down the length of gravistimulated coleoptiles at a rate comparable to that in normal, upright plants. Transport is initially symmetrical across the coleoptile, but between 30 and 40 minutes after plants are turned horizontal a lateral redistribution of the IAA already present in the transport stream occurs. By 60 minutes after the beginning of the gravitropic stimulus, the ratio of tritiated tracer auxin in the lower half with respect to the upper half is approximately 2:1. The redistribution of growth that causes gravitropic curvature follows the IAA redistribution by 5 or 10 minutes at the minimum in most regions of the coleoptile. Immobilization of tracer auxin from the transport stream during gravitropism was not detectable in the most apical 10 millimeters. Previous reports have shown that in intact, red light-grown maize coleoptiles, endogenous auxin is limiting for growth, the tissue is linearly responsive to linearly increasing concentrations of small amounts of added auxin, and the lag time for the stimulation of straight growth by added IAA is approximately 8 or 9 minutes (TI Baskin, M Iino, PB Green, WR Briggs [1985] Plant Cell Environ 8: 595-603; TI Baskin, WR Briggs, M Iino [1986] Plant Physiol 81: 306-309). We conclude that redistribution of IAA in the transport stream occurs in maize coleoptiles during gravitropism, and is sufficient in degree and timing to be the immediate cause of gravitropic curvature. PMID:16667914

40 CFR 261.41 - Notification and Recordkeeping for Used, Intact Cathode Ray Tubes (CRTs) Exported for Reuse.

Code of Federal Regulations, 2011 CFR

2011-07-01

... to export used, intact CRTs for reuse, the notifier's name, address, and EPA ID number (if applicable) and the name and phone number of a contact person. (b) Persons who export used, intact CRTs for reuse...

40 CFR 261.41 - Notification and Recordkeeping for Used, Intact Cathode Ray Tubes (CRTs) Exported for Reuse.

Code of Federal Regulations, 2012 CFR

2012-07-01

... to export used, intact CRTs for reuse, the notifier's name, address, and EPA ID number (if applicable) and the name and phone number of a contact person. (b) Persons who export used, intact CRTs for reuse...

40 CFR 261.41 - Notification and Recordkeeping for Used, Intact Cathode Ray Tubes (CRTs) Exported for Reuse.

Code of Federal Regulations, 2010 CFR

2010-07-01

... to export used, intact CRTs for reuse, the notifier's name, address, and EPA ID number (if applicable) and the name and phone number of a contact person. (b) Persons who export used, intact CRTs for reuse...

40 CFR 261.41 - Notification and Recordkeeping for Used, Intact Cathode Ray Tubes (CRTs) Exported for Reuse.

Code of Federal Regulations, 2013 CFR

2013-07-01

... to export used, intact CRTs for reuse, the notifier's name, address, and EPA ID number (if applicable) and the name and phone number of a contact person. (b) Persons who export used, intact CRTs for reuse...

The Structure Of Intact Side Tissue Loss Based On FTIR Spectroscopic Measurements

NASA Astrophysics Data System (ADS)

Hussain, N.; Al-Hadithi, K. O.; Jaafar, M. S.

2009-09-01

Laser applications in dentistry were strongly evolved during the last three decades. Among those applications are laser ablation of dental hard tissue, caries inhibition treatments by localized surface heating, and surface conditioning for bonding. In addition, infra-red lasers are ideally suited for the selective and precise removal of carious dental hard tissue while minimizing the healthy tissue loss. In the present study we applied laser spectroscopy technique FTIR for the study of the structure of intact side tissue of teeth. The aim of the recent work is to study the effect of race and sex (genealogy) on the structure of intact side tissue loss. Our sample consists of twenty Malay females' teeth where the FTIR has been applied. The data show a decrease in the amounts of main substances (like Hydroxyapatite crystals ([Ca5(PO4)3(OH)4], CaF2) than those in healthy teeth. The measured spectra represent the enamel with the characteristic peaks due to the phosphate group in carbonated, hydroxyapatite at 1000 cm-1 and two small peaks near 1500 cm-1 due to the carbonate group. The data explains the effect of the several factors on the intact side tissue loss.

Reliability of cause of death coding: an international comparison.

PubMed

Antini, Carmen; Rajs, Danuta; Muñoz-Quezada, María Teresa; Mondaca, Boris Andrés Lucero; Heiss, Gerardo

2015-07-01

This study evaluates the agreement of nosologic coding of cardiovascular causes of death between a Chilean coder and one in the United States, in a stratified random sample of death certificates of persons aged ≥ 60, issued in 2008 in the Valparaíso and Metropolitan regions, Chile. All causes of death were converted to ICD-10 codes in parallel by both coders. Concordance was analyzed with inter-coder agreement and Cohen's kappa coefficient by level of specification ICD-10 code for the underlying cause and the total causes of death coding. Inter-coder agreement was 76.4% for all causes of death and 80.6% for the underlying cause (agreement at the four-digit level), with differences by the level of specification of the ICD-10 code, by line of the death certificate, and by number of causes of death per certificate. Cohen's kappa coefficient was 0.76 (95%CI: 0.68-0.84) for the underlying cause and 0.75 (95%CI: 0.74-0.77) for the total causes of death. In conclusion, causes of death coding and inter-coder agreement for cardiovascular diseases in two regions of Chile are comparable to an external benchmark and with reports from other countries.

Brief surgical procedure code lists for outcomes measurement and quality improvement in resource-limited settings.

PubMed

Liu, Charles; Kayima, Peter; Riesel, Johanna; Situma, Martin; Chang, David; Firth, Paul

2017-11-01

The lack of a classification system for surgical procedures in resource-limited settings hinders outcomes measurement and reporting. Existing procedure coding systems are prohibitively large and expensive to implement. We describe the creation and prospective validation of 3 brief procedure code lists applicable in low-resource settings, based on analysis of surgical procedures performed at Mbarara Regional Referral Hospital, Uganda's second largest public hospital. We reviewed operating room logbooks to identify all surgical operations performed at Mbarara Regional Referral Hospital during 2014. Based on the documented indication for surgery and procedure(s) performed, we assigned each operation up to 4 procedure codes from the International Classification of Diseases, 9th Revision, Clinical Modification. Coding of procedures was performed by 2 investigators, and a random 20% of procedures were coded by both investigators. These codes were aggregated to generate procedure code lists. During 2014, 6,464 surgical procedures were performed at Mbarara Regional Referral Hospital, to which we assigned 435 unique procedure codes. Substantial inter-rater reliability was achieved (κ = 0.7037). The 111 most common procedure codes accounted for 90% of all codes assigned, 180 accounted for 95%, and 278 accounted for 98%. We considered these sets of codes as 3 procedure code lists. In a prospective validation, we found that these lists described 83.2%, 89.2%, and 92.6% of surgical procedures performed at Mbarara Regional Referral Hospital during August to September of 2015, respectively. Empirically generated brief procedure code lists based on International Classification of Diseases, 9th Revision, Clinical Modification can be used to classify almost all surgical procedures performed at a Ugandan referral hospital. Such a standardized procedure coding system may enable better surgical data collection for administration, research, and quality improvement in resource

Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein.

PubMed

Anderson, Caitlin E; Holstein, Carly A; Strauch, Eva-Maria; Bennett, Steven; Chevalier, Aaron; Nelson, Jorgen; Fu, Elain; Baker, David; Yager, Paul

2017-06-20

Influenza is a ubiquitous and recurring infection that results in approximately 500 000 deaths globally each year. Commercially available rapid diagnostic tests are based upon detection of the influenza nucleoprotein, which are limited in that they are unable to differentiate by species and require an additional viral lysis step. Sample preprocessing can be minimized or eliminated by targeting the intact influenza virus, thereby reducing assay complexity and leveraging the large number of hemagglutinin proteins on the surface of each virus. Here, we report the development of a paper-based influenza assay that targets the hemagglutinin protein; the assay employs a combination of antibodies and novel computationally designed, recombinant affinity proteins as the capture and detection agents. This system leverages the customizability of recombinant protein design to target the conserved receptor-binding pocket of the hemagglutinin protein and to match the trimeric nature of hemagglutinin for improved avidity. Using this assay, we demonstrate the first instance of intact influenza virus detection using a combination of antibody and affinity proteins within a porous network. The recombinant head region binder based assays yield superior analytical sensitivity as compared to the antibody based assay, with lower limits of detection of 3.54 × 10 7 and 1.34 × 10 7 CEID 50 /mL for the mixed and all binder stacks, respectively. Not only does this work describe the development of a novel influenza assay, it also demonstrates the power of recombinant affinity proteins for use in rapid diagnostic assays.

40 CFR 261.40 - Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 26 2014-07-01 2014-07-01 false Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling. 261.40 Section 261.40 Protection of Environment...) Exported for Recycling. Used, intact CRTs exported for recycling are not solid wastes if they meet the...

40 CFR 261.40 - Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling. 261.40 Section 261.40 Protection of Environment...) Exported for Recycling. Used, intact CRTs exported for recycling are not solid wastes if they meet the...

40 CFR 261.40 - Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 27 2012-07-01 2012-07-01 false Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling. 261.40 Section 261.40 Protection of Environment...) Exported for Recycling. Used, intact CRTs exported for recycling are not solid wastes if they meet the...

40 CFR 261.40 - Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling. 261.40 Section 261.40 Protection of Environment...) Exported for Recycling. Used, intact CRTs exported for recycling are not solid wastes if they meet the...

40 CFR 261.40 - Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Conditional Exclusion for Used, Intact Cathode Ray Tubes (CRTs) Exported for Recycling. 261.40 Section 261.40 Protection of Environment...) Exported for Recycling. Used, intact CRTs exported for recycling are not solid wastes if they meet the...

Express diagnostics of intact and pathological dental hard tissues by optical PNC method

NASA Astrophysics Data System (ADS)

Masychev, Victor I.; Alexandrov, Michail T.

2000-03-01

The results of hard tooth tissues research by the optical PNC- method in experimental and clinical conditions are presented. In the experiment under 90 test-sample of tooth slices with thickness about 1 mm (enamel, dentine and cement) were researched. The results of the experiment were processed by the method of correlation analyze. Clinical researches were executed on teeth of 210 patients. The regions of tooth tissue diseases with initial, moderate and deep caries were investigated. Spectral characteristics of intact and pathologically changed tooth tissues are presented and their peculiar features are discussed. The results the optical PNC- method application while processing tooth carious cavities are presented in order to estimate efficiency of the mechanical and antiseptic processing of teeth. It is revealed that the PNC-method can be used as for differential diagnostics of a degree dental carious stage, as for estimating of carefulness of tooth cavity processing before filling.

CHORUS code for solar and planetary convection

NASA Astrophysics Data System (ADS)

Wang, Junfeng

Turbulent, density stratified convection is ubiquitous in stars and planets. Numerical simulation has become an indispensable tool for understanding it. A primary contribution of this dissertation work is the creation of the Compressible High-ORder Unstructured Spectral-difference (CHORUS) code for simulating the convection and related fluid dynamics in the interiors of stars and planets. In this work, the CHORUS code is verified by using two newly defined benchmark cases and demonstrates excellent parallel performance. It has unique potential to simulate challenging physical phenomena such as multi-scale solar convection, core convection, and convection in oblate, rapidly-rotating stars. In order to exploit its unique capabilities, the CHORUS code has been extended to perform the first 3D simulations of convection in oblate, rapidly rotating solar-type stars. New insights are obtained with respect to the influence of oblateness on the convective structure and heat flux transport. With the presence of oblateness resulting from the centrifugal force effect, the convective structure in the polar regions decouples from the main convective modes in the equatorial regions. Our convection simulations predict that heat flux peaks in both the polar and equatorial regions, contrary to previous theoretical results that predict darker equators. High latitudinal zonal jets are also observed in the simulations.

HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample.

PubMed

Ramalho, Jaqueline; Veiga-Castelli, Luciana C; Donadi, Eduardo A; Mendes-Junior, Celso T; Castelli, Erick C

2017-11-01

The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by

From Primary to Secondary Science: Keeping the Threads Intact

ERIC Educational Resources Information Center

Mould, Kirsten

2015-01-01

There are many transition points in the school life of a child, but the move from primary to secondary school is a particularly significant one. How can both the social and academic threads remain intact? In this article, Kristen Mould discusses the main issues relating to transition from primary to secondary science. She cites the primary factors…

A hybrid LBG/lattice vector quantizer for high quality image coding

NASA Technical Reports Server (NTRS)

Ramamoorthy, V.; Sayood, K.; Arikan, E. (Editor)

1991-01-01

It is well known that a vector quantizer is an efficient coder offering a good trade-off between quantization distortion and bit rate. The performance of a vector quantizer asymptotically approaches the optimum bound with increasing dimensionality. A vector quantized image suffers from the following types of degradations: (1) edge regions in the coded image contain staircase effects, (2) quasi-constant or slowly varying regions suffer from contouring effects, and (3) textured regions lose details and suffer from granular noise. All three of these degradations are due to the finite size of the code book, the distortion measures used in the design, and due to the finite training procedure involved in the construction of the code book. In this paper, we present an adaptive technique which attempts to ameliorate the edge distortion and contouring effects.

Decomposition of intact chicken feathers by a thermophile in combination with an acidulocomposting garbage-treatment process.

PubMed

Shigeri, Yasushi; Matsui, Tatsunobu; Watanabe, Kunihiko

2009-11-01

In order to develop a practical method for the decomposition of intact chicken feathers, a moderate thermophile strain, Meiothermus ruber H328, having strong keratinolytic activity, was used in a bio-type garbage-treatment machine working with an acidulocomposting process. The addition of strain H328 cells (15 g) combined with acidulocomposting in the garbage machine resulted in 70% degradation of intact chicken feathers (30 g) within 14 d. This degradation efficiency is comparable to a previous result employing the strain as a single bacterium in flask culture, and it indicates that strain H328 can promote intact feather degradation activity in a garbage machine currently on the market.

14. Aerial view showing bldg grouping with bldg #2 intact ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. Aerial view showing bldg grouping with bldg #2 intact previous to fire (long pitched roof with 7 distinct dormers near image center) - photo by Eastern Topographics, Wolfeboro, N.H., Sept. 1985 - Lawrence Machine Shop, Building No. 2, Union & Canal Streets, Lawrence, Essex County, MA

Lossy to lossless object-based coding of 3-D MRI data.

PubMed

Menegaz, Gloria; Thiran, Jean-Philippe

2002-01-01

We propose a fully three-dimensional (3-D) object-based coding system exploiting the diagnostic relevance of the different regions of the volumetric data for rate allocation. The data are first decorrelated via a 3-D discrete wavelet transform. The implementation via the lifting steps scheme allows to map integer-to-integer values, enabling lossless coding, and facilitates the definition of the object-based inverse transform. The coding process assigns disjoint segments of the bitstream to the different objects, which can be independently accessed and reconstructed at any up-to-lossless quality. Two fully 3-D coding strategies are considered: embedded zerotree coding (EZW-3D) and multidimensional layered zero coding (MLZC), both generalized for region of interest (ROI)-based processing. In order to avoid artifacts along region boundaries, some extra coefficients must be encoded for each object. This gives rise to an overheading of the bitstream with respect to the case where the volume is encoded as a whole. The amount of such extra information depends on both the filter length and the decomposition depth. The system is characterized on a set of head magnetic resonance images. Results show that MLZC and EZW-3D have competitive performances. In particular, the best MLZC mode outperforms the others state-of-the-art techniques on one of the datasets for which results are available in the literature.

Prevalence of depressive symptoms in older nursing home residents with intact cognitive function in Taiwan.

PubMed

Hu, Sophia H; Chuang, Yeu-Hui; Ting, Yeh-Feng; Lin, Kuan-Yu; Hsieh, Chia-Jung

2018-03-25

The investigators aimed to explore the prevalence of depressive symptoms and associated factors among older residents with intact cognitive function in nursing homes in Taiwan. A cross-sectional descriptive and correlational research design was used. A convenience sample of 178 older residents without cognitive impairment was recruited from 36 nursing homes in Southern Taiwan. The questionnaires included demographic data; the Barthel Index, which assesses the ability to perform activities of daily living; and the Geriatric Depression Scale Short Form. Among older residents in nursing homes with intact cognitive function, 39.3% had depressive symptoms. Age, religion, previous living status, previous working status, being totally dependent in physical function, and being severely dependent in physical function were significant predictors of depressive symptoms among cognitively intact older residents. The findings highlight the critical mental healthcare issues among older residents with intact cognitive function in nursing homes. Practical strategies for preventing the occurrence of depressive symptoms and caring for those who have depressive symptoms should be developed, especially for younger or dependent older residents or residents who have never been employed, have no religious beliefs, or have lived alone before they moved into an institution. © 2018 Wiley Periodicals, Inc.

Differentiation and Cell-Cell Interactions of Neural Progenitor Cells Transplanted into Intact Adult Brain.

PubMed

Sukhinich, K K; Kosykh, A V; Aleksandrova, M A

2015-11-01

We studied the behavior and cell-cell interactions of embryonic brain cell from GFP-reporter mice after their transplantation into the intact adult brain. Fragments or cell suspensions of fetal neocortical cells at different stages of development were transplanted into the neocortex and striatum of adult recipients. Even in intact brain, the processes of transplanted neurons formed extensive networks in the striatum and neocortical layers I and V-VI. Processes of transplanted cells at different stages of development attained the rostral areas of the frontal cortex and some of them reached the internal capsule. However, the cells transplanted in suspension had lower process growth potency than cells from tissue fragments. Tyrosine hydroxylase fibers penetrated from the recipient brain into grafts at both early and late stages of development. Our experiments demonstrated the formation of extensive reciprocal networks between the transplanted fetal neural cells and recipient brain neurons even in intact brain.

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

NASA Technical Reports Server (NTRS)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Space research with intact organisms: The role of Space Station Freedom

NASA Technical Reports Server (NTRS)

Phillips, Robert W.; Haddy, Francis J.

1993-01-01

The study of intact organisms has provided biologists with a good working knowledge of most of the common organisms that have evolved in the 1 g environment of Earth. Reasonably accurate predictions can be made about organismal responses to most stimuli on Earth. To extend this knowledge to life without gravity, we must have access to the space environment for prolonged periods. Space Station Freedom will provide a facility with which to begin this type of research. Spaceflight research to date has been limited to relatively short-term exposures that have been informative but incomplete. This paper provides a brief background of known changes that have occurred in intact organisms in the space environment and proposes the kinds of experiments that are needed to expand our knowledge of life on Earth and in space.

Code Properties from Holographic Geometries

NASA Astrophysics Data System (ADS)

Pastawski, Fernando; Preskill, John

2017-04-01

Almheiri, Dong, and Harlow [J. High Energy Phys. 04 (2015) 163., 10.1007/JHEP04(2015)163] proposed a highly illuminating connection between the AdS /CFT holographic correspondence and operator algebra quantum error correction (OAQEC). Here, we explore this connection further. We derive some general results about OAQEC, as well as results that apply specifically to quantum codes that admit a holographic interpretation. We introduce a new quantity called price, which characterizes the support of a protected logical system, and find constraints on the price and the distance for logical subalgebras of quantum codes. We show that holographic codes defined on bulk manifolds with asymptotically negative curvature exhibit uberholography, meaning that a bulk logical algebra can be supported on a boundary region with a fractal structure. We argue that, for holographic codes defined on bulk manifolds with asymptotically flat or positive curvature, the boundary physics must be highly nonlocal, an observation with potential implications for black holes and for quantum gravity in AdS space at distance scales that are small compared to the AdS curvature radius.

In vitro permeation of palladium powders through intact and damaged human skin.

PubMed

Crosera, Matteo; Mauro, Marcella; Bovenzi, Massimo; Adami, Gianpiero; Baracchini, Elena; Maina, Giovanni; Larese Filon, Francesca

2018-05-01

The use of palladium (Pd) has grown in the last decades, commonly used in automotive catalytic converters, jewellery and dental restorations sectors. Both general and working population can be exposed to this metal, which may act as skin sensitizer. This study investigated in vitro palladium powders permeation through excised intact and damaged human skin using the Franz diffusion cell method and the effect of rapid skin decontamination using sodium laureth-sulphate. 1 mL of a 10 min sonicated suspension made of 2.5 g of Pd powder in 50 mL synthetic sweat at pH 4.5 and room temperature was applied to the outer surface of the skin membranes for 24 h. Pd permeation, assessed by ICP-MS, was higher when damaged skin was used (p = 0.03). Final flux permeation values and lag times were 0.02 ± 0.01 μg cm -2  h -1 and 6.00 ± 3.95 h for intact, and 0.10 ± 0.02 μg cm -2  h -1 and 2.05 ± 1.49 h for damaged skin samples, respectively. Damaged skin protocol enhances Pd skin penetration inside dermal layer (p = 0.04), thus making the metal available for systemic uptake. Pd penetration (p = 0.02) and permeation (p = 0.012) through intact skin decreased significantly when a cleaning procedure was applied. This study demonstrates that after skin exposure to Pd powders a small permeation of the metal happen both through intact and damaged skin and that an early decontamination with a common cleanser can significantly decrease the final amount of metal available forsystemic uptake. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of ignoring baseline on modeling transitions from intact cognition to dementia.

PubMed

Yu, Lei; Tyas, Suzanne L; Snowdon, David A; Kryscio, Richard J

2009-07-01

This paper evaluates the effect of ignoring baseline when modeling transitions from intact cognition to dementia with mild cognitive impairment (MCI) and global impairment (GI) as intervening cognitive states. Transitions among states are modeled by a discrete-time Markov chain having three transient (intact cognition, MCI, and GI) and two competing absorbing states (death and dementia). Transition probabilities depend on two covariates, age and the presence/absence of an apolipoprotein E-epsilon4 allele, through a multinomial logistic model with shared random effects. Results are illustrated with an application to the Nun Study, a cohort of 678 participants 75+ years of age at baseline and followed longitudinally with up to ten cognitive assessments per nun.

Effects of ignoring baseline on modeling transitions from intact cognition to dementia

PubMed Central

Yu, Lei; Tyas, Suzanne L.; Snowdon, David A.; Kryscio, Richard J.

2009-01-01

This paper evaluates the effect of ignoring baseline when modeling transitions from intact cognition to dementia with mild cognitive impairment (MCI) and global impairment (GI) as intervening cognitive states. Transitions among states are modeled by a discrete-time Markov chain having three transient (intact cognition, MCI, and GI) and two competing absorbing states (death and dementia). Transition probabilities depend on two covariates, age and the presence/absence of an apolipoprotein E-ε4 allele, through a multinomial logistic model with shared random effects. Results are illustrated with an application to the Nun Study, a cohort of 678 participants 75+ years of age at baseline and followed longitudinally with up to ten cognitive assessments per nun. PMID:20161282

Influence of the estrus cycle on the evaluation of a vaginal irritation study in intact and ovariectomized rats

PubMed Central

Ishii, Aiko; Ogawa, Bunichiro; Koyama, Tomoko; Nakanishi, Yutaka; Sasaki, Minoru

2017-01-01

When conducting vaginal irritation studies, ovariectomized rats or rabbits are typically used according to practical reports. In the present study, we evaluated the influence of the estrus cycle in a vaginal irritation study using intact rats and ovariectomized rats, which exhibit a late diestrus-like condition, to determine whether intact rats can be useful for evaluating vaginal irritancy. Rats were divided into 4 groups: proestrus, estrus, and metestrus or diestrus in intact rats and ovariectomized rats. All the rats in each group were treated with a vehicle or sodium dodecyl sulfate, as the irritant, in single-dose and 4-day repeat-dose vaginal irritation studies. Each rat’s vagina was examined histopathologically, and the irritation score was calculated using a semiquantitative scoring system. In the single-dose study, the irritation scores for the proestrus or ovariectomized groups treated with sodium dodecyl sulfate were higher than those of the estrus group or metestrus or diestrus group. In the 4-day repeat-dose study, a significant histopathological difference was not found among the intact rats (proestrus, estrus, and metestrus or diestrus groups), and the irritation score range of the intact rats was similar to that of the ovariectomized rats, though the mean score of the intact rats was slightly lower than that of the ovariectomized rats. These results suggest that intact rats might be well suited for 4-day vaginal irritation studies and useful for evaluating vaginal irritancy using not only the mean score, but also individual irritation score ranges, whereas the estrus cycle would need to be identified in single-dose vaginal irritation studies. PMID:28458454

A combinatorial model for dentate gyrus sparse coding

DOE PAGES

Severa, William; Parekh, Ojas; James, Conrad D.; ...

2016-12-29

The dentate gyrus forms a critical link between the entorhinal cortex and CA3 by providing a sparse version of the signal. Concurrent with this increase in sparsity, a widely accepted theory suggests the dentate gyrus performs pattern separation—similar inputs yield decorrelated outputs. Although an active region of study and theory, few logically rigorous arguments detail the dentate gyrus’s (DG) coding. We suggest a theoretically tractable, combinatorial model for this action. The model provides formal methods for a highly redundant, arbitrarily sparse, and decorrelated output signal.To explore the value of this model framework, we assess how suitable it is for twomore » notable aspects of DG coding: how it can handle the highly structured grid cell representation in the input entorhinal cortex region and the presence of adult neurogenesis, which has been proposed to produce a heterogeneous code in the DG. We find tailoring the model to grid cell input yields expansion parameters consistent with the literature. In addition, the heterogeneous coding reflects activity gradation observed experimentally. Lastly, we connect this approach with more conventional binary threshold neural circuit models via a formal embedding.« less

Design of ACM system based on non-greedy punctured LDPC codes

NASA Astrophysics Data System (ADS)

Lu, Zijun; Jiang, Zihong; Zhou, Lin; He, Yucheng

2017-08-01

In this paper, an adaptive coded modulation (ACM) scheme based on rate-compatible LDPC (RC-LDPC) codes was designed. The RC-LDPC codes were constructed by a non-greedy puncturing method which showed good performance in high code rate region. Moreover, the incremental redundancy scheme of LDPC-based ACM system over AWGN channel was proposed. By this scheme, code rates vary from 2/3 to 5/6 and the complication of the ACM system is lowered. Simulations show that more and more obvious coding gain can be obtained by the proposed ACM system with higher throughput.

A single base substitution in the coding region for neurophysin II associated with familial central diabetes insipidus.

PubMed Central

Ito, M; Mori, Y; Oiso, Y; Saito, H

1991-01-01

To elucidate the molecular mechanism of familial central diabetes insipidus (FDI), we sequenced the arginine vasopressin-neurophysin II (AVP-NPII) gene in 2 patients belonging to a pedigree that is consistent with an autosomal dominant mode of inheritance. 10 patients with idiopathic central diabetes insipidus (IDI) and 5 normals were also studied. The AVP-NPII gene, locating on chromosome 20, consists of three exons that encode putative signal peptide, AVP, NPII, and glycoprotein. Using polymerase chain reaction, fragments including the promoter region and all coding regions were amplified from genomic DNA and subjected to direct sequencing. Sequences of 10 patients with IDI were identical with those of normals, while in 2 patients with FDI, a single base substitution was detected in one of two alleles of the AVP-NPII gene, indicating they were heterozygotes for this mutation. It was a G----A transition at nucleotide position 1859 in the second exon, resulting in a substitution of Gly for Ser at amino acid position 57 in the NPII moiety. It was speculated that the mutated AVP-NPII precursor or the mutated NPII molecule, through their conformational changes, might be responsible for AVP deficiency. Images PMID:1840604

Evidence does not support absorption of intact solid lipid nanoparticles via oral delivery

NASA Astrophysics Data System (ADS)

Hu, Xiongwei; Fan, Wufa; Yu, Zhou; Lu, Yi; Qi, Jianping; Zhang, Jian; Dong, Xiaochun; Zhao, Weili; Wu, Wei

2016-03-01

Whether and to what extent solid lipid nanoparticles (SLNs) can be absorbed integrally via oral delivery should be clarified because it is the basis for elucidation of absorption mechanisms. To address this topic, the in vivo fate of SLNs as well as their interaction with biomembranes is investigated using water-quenching fluorescent probes that can signal structural variations of lipid-based nanocarriers. Live imaging indicates prolonged retention of SLNs in the stomach, whereas in the intestine, SLNs can be digested quickly. No translocation of intact SLNs to other organs or tissues can be observed. The in situ perfusion study shows bioadhesion of both SLNs and simulated mixed micelles (SMMs) to intestinal mucus, but no evidence of penetration of integral nanocarriers. Both SLNs and SMMs exhibit significant cellular uptake, but fail to penetrate cell monolayers. Confocal laser scanning microscopy reveals that nanocarriers mainly concentrate on the surface of the monolayers, and no evidence of penetration of intact vehicles can be obtained. The mucous layer acts as a barrier to the penetration of both SLNs and SMMs. Both bile salt-decoration and SMM formulation help to strengthen the interaction with biomembranes. It is concluded that evidence does not support absorption of intact SLNs via oral delivery.Whether and to what extent solid lipid nanoparticles (SLNs) can be absorbed integrally via oral delivery should be clarified because it is the basis for elucidation of absorption mechanisms. To address this topic, the in vivo fate of SLNs as well as their interaction with biomembranes is investigated using water-quenching fluorescent probes that can signal structural variations of lipid-based nanocarriers. Live imaging indicates prolonged retention of SLNs in the stomach, whereas in the intestine, SLNs can be digested quickly. No translocation of intact SLNs to other organs or tissues can be observed. The in situ perfusion study shows bioadhesion of both SLNs and

Gene end-like sequences within the 3' non-coding region of the Nipah virus genome attenuate viral gene transcription.

PubMed

Sugai, Akihiro; Sato, Hiroki; Yoneda, Misako; Kai, Chieko

2017-08-01

The regulation of transcription during Nipah virus (NiV) replication is poorly understood. Using a bicistronic minigenome system, we investigated the involvement of non-coding regions (NCRs) in the transcriptional re-initiation efficiency of NiV RNA polymerase. Reporter assays revealed that attenuation of NiV gene expression was not constant at each gene junction, and that the attenuating property was controlled by the 3' NCR. However, this regulation was independent of the gene-end, gene-start and intergenic regions. Northern blot analysis indicated that regulation of viral gene expression by the phosphoprotein (P) and large protein (L) 3' NCRs occurred at the transcription level. We identified uridine-rich tracts within the L 3' NCR that are similar to gene-end signals. These gene-end-like sequences were recognized as weak transcription termination signals by the viral RNA polymerase, thereby reducing downstream gene transcription. Thus, we suggest that NiV has a unique mechanism of transcriptional regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

Simultaneous perception of a spoken and a signed language: The brain basis of ASL-English code-blends

PubMed Central

Weisberg, Jill; McCullough, Stephen; Emmorey, Karen

2018-01-01

Code-blends (simultaneous words and signs) are a unique characteristic of bimodal bilingual communication. Using fMRI, we investigated code-blend comprehension in hearing native ASL-English bilinguals who made a semantic decision (edible?) about signs, audiovisual words, and semantically equivalent code-blends. English and ASL recruited a similar fronto-temporal network with expected modality differences: stronger activation for English in auditory regions of bilateral superior temporal cortex, and stronger activation for ASL in bilateral occipitotemporal visual regions and left parietal cortex. Code-blend comprehension elicited activity in a combination of these regions, and no cognitive control regions were additionally recruited. Furthermore, code-blends elicited reduced activation relative to ASL presented alone in bilateral prefrontal and visual extrastriate cortices, and relative to English alone in auditory association cortex. Consistent with behavioral facilitation observed during semantic decisions, the findings suggest that redundant semantic content induces more efficient neural processing in language and sensory regions during bimodal language integration. PMID:26177161

Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India.

PubMed

Subramaniam, Saravanan; Mohapatra, Jajati K; Das, Biswajit; Sharma, Gaurav K; Biswal, Jitendra K; Mahajan, Sonalika; Misri, Jyoti; Dash, Bana B; Pattnaik, Bramhadev

2015-07-01

Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.

Designing medical foods for inherited metabolic disorders: why intact protein is superior to amino acids.

PubMed

Ney, Denise Marie; Etzel, Mark Raymond

2017-04-01

Phenylketonuria and tyrosinemia are inherited metabolic disorders characterized by high blood levels of phenylalanine (Phe) or tyrosine (Tyr), due to mutations in genes affecting Phe and Tyr metabolism, respectively. The primary management is a lifelong diet restricted in protein from natural foods in combination with medical foods comprised mixtures of synthetic amino acids. Compliance is often poor after childhood leading to neuropsychological sequela. Glycomacropeptide, an intact 64 amino acid glycophosphopeptide isolated from cheese whey, provides a new paradigm for the management of phenylketonuria and tyrosinemia because glycomacropeptide contains no Phe and Tyr in its pure form, and is also a prebiotic. Medical foods made from glycomacropeptide have been used successfully for the management of phenylketonuria and tyrosinemia. Preclinical and clinical studies demonstrate that intact protein from glycomacropeptide provides a more acceptable and physiologic source of defined protein compared to amino acids in medical foods. For example, harmful gut bacteria were reduced, beneficial short chain fatty acids increased, renal workload decreased, protein utilization increased, and bone fragility decreased using intact protein versus amino acids. Advances in biotechnology will propel the transition from synthetic amino acids to intact proteins for the management of inherited metabolic disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Code stroke in Asturias.

PubMed

Benavente, L; Villanueva, M J; Vega, P; Casado, I; Vidal, J A; Castaño, B; Amorín, M; de la Vega, V; Santos, H; Trigo, A; Gómez, M B; Larrosa, D; Temprano, T; González, M; Murias, E; Calleja, S

2016-04-01

Intravenous thrombolysis with alteplase is an effective treatment for ischaemic stroke when applied during the first 4.5 hours, but less than 15% of patients have access to this technique. Mechanical thrombectomy is more frequently able to recanalise proximal occlusions in large vessels, but the infrastructure it requires makes it even less available. We describe the implementation of code stroke in Asturias, as well as the process of adapting various existing resources for urgent stroke care in the region. By considering these resources, and the demographic and geographic circumstances of our region, we examine ways of reorganising the code stroke protocol that would optimise treatment times and provide the most appropriate treatment for each patient. We distributed the 8 health districts in Asturias so as to permit referral of candidates for reperfusion therapies to either of the 2 hospitals with 24-hour stroke units and on-call neurologists and providing IV fibrinolysis. Hospitals were assigned according to proximity and stroke severity; the most severe cases were immediately referred to the hospital with on-call interventional neurology care. Patient triage was provided by pre-hospital emergency services according to the NIHSS score. Modifications to code stroke in Asturias have allowed us to apply reperfusion therapies with good results, while emphasising equitable care and managing the severity-time ratio to offer the best and safest treatment for each patient as soon as possible. Copyright © 2015 Sociedad Española de Neurología. Published by Elsevier España, S.L.U. All rights reserved.

The next-generation ESL continuum gyrokinetic edge code

NASA Astrophysics Data System (ADS)

Cohen, R.; Dorr, M.; Hittinger, J.; Rognlien, T.; Collela, P.; Martin, D.

2009-05-01

The Edge Simulation Laboratory (ESL) project is developing continuum-based approaches to kinetic simulation of edge plasmas. A new code is being developed, based on a conservative formulation and fourth-order discretization of full-f gyrokinetic equations in parallel-velocity, magnetic-moment coordinates. The code exploits mapped multiblock grids to deal with the geometric complexities of the edge region, and utilizes a new flux limiter [P. Colella and M.D. Sekora, JCP 227, 7069 (2008)] to suppress unphysical oscillations about discontinuities while maintaining high-order accuracy elsewhere. The code is just becoming operational; we will report initial tests for neoclassical orbit calculations in closed-flux surface and limiter (closed plus open flux surfaces) geometry. It is anticipated that the algorithmic refinements in the new code will address the slow numerical instability that was observed in some long simulations with the existing TEMPEST code. We will also discuss the status and plans for physics enhancements to the new code.

Comparisons of time explicit hybrid kinetic-fluid code Architect for Plasma Wakefield Acceleration with a full PIC code

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

Massimo, F., E-mail: francesco.massimo@ensta-paristech.fr; Dipartimento SBAI, Università di Roma “La Sapienza“, Via A. Scarpa 14, 00161 Roma; Atzeni, S.

Architect, a time explicit hybrid code designed to perform quick simulations for electron driven plasma wakefield acceleration, is described. In order to obtain beam quality acceptable for applications, control of the beam-plasma-dynamics is necessary. Particle in Cell (PIC) codes represent the state-of-the-art technique to investigate the underlying physics and possible experimental scenarios; however PIC codes demand the necessity of heavy computational resources. Architect code substantially reduces the need for computational resources by using a hybrid approach: relativistic electron bunches are treated kinetically as in a PIC code and the background plasma as a fluid. Cylindrical symmetry is assumed for themore » solution of the electromagnetic fields and fluid equations. In this paper both the underlying algorithms as well as a comparison with a fully three dimensional particle in cell code are reported. The comparison highlights the good agreement between the two models up to the weakly non-linear regimes. In highly non-linear regimes the two models only disagree in a localized region, where the plasma electrons expelled by the bunch close up at the end of the first plasma oscillation.« less

Influence of fluoride varnish on shear bond strength of a universal adhesive on intact and demineralized enamel.

PubMed

Ortiz-Ruiz, Antonio José; Muñoz-Gómez, Iban Jesús; Pérez-Pardo, Ana; Germán-Cecilia, Concepción; Martínez-Beneyto, Yolanda; Vicente, Ascensión

2018-04-27

The aim was to evaluate the effect of fluoride varnish on the shear bond strength (SBS) on polished and non-polished intact and demineralized enamel. Bovine incisors (half demineralized) were used. Bifluorid 12™ was applied. Bonding was made with Futurabond ® M + and GrandioSO, 24 h and 7 days after varnishing. In some groups, varnish was removed by polishing before bonding. SBS was measured. Fracture type was determined by stereomicroscopy and scanning electron microscope (SEM) observations of the enamel surface were made. Between-group differences were determined by one-way ANOVA and the Tukey test. Associations between study factors and fracture modes were analysed using contingency tables and Pearson's chi-squared test. For intact enamel, SBS on varnished enamel at 24 h was significantly less than in the other groups. SBS recovered 7 days after varnishing. Varnish elimination after 24 h significantly increased the SBS. However, removal at 7 days did not modify SBS. SBS on demineralized enamel groups was significantly less than in intact enamel, except for demineralized enamel varnished and removed at 7 days. Demineralized enamel was associated with cohesive enamel fractures and intact enamel with cohesive fractures of the composite and adhesive fractures. SEM of varnish surfaces showed a homogenous layer scattered with amorphous precipitate. In conclusion, on intact enamel fluoride varnish had a negative effect on SBS at 24 h, which disappeared after 7 days. On demineralized enamel, varnish did not reduce SBS at either time. Polishing the varnished enamel surface showed a similar SBS to intact enamel after 7 days.

Ca2+ release triggered by nicotinate adenine dinucleotide phosphate in intact sea urchin eggs.

PubMed Central

Perez-Terzic, C M; Chini, E N; Shen, S S; Dousa, T P; Clapham, D E

1995-01-01

Nicotinate adenine dinucleotide phosphate (NAADP) was recently identified [Lee and Aarhus (1995) J. Biol. Chem. 270, 2152-2157; Chini, Beers and Dousa (1995) J. Biol. Chem. 270, 3116-3223] as a potent Ca(2+)-releasing agent in sea urchin egg homogenates. NAADP triggered Ca2+ release by a mechanism that was distinct from inositol 1,4,5-trisphosphate (InsP3)- and cyclic ADP-ribose (cADPR)-induced Ca2+ release. When NAADP was microinjected into intact sea urchin eggs it induced a dose-dependent increase in cytoplasmic free Ca2+ which was independent of the extracellular [Ca2+]. The Ca2+ waves elicited by microinjections of NAADP originated at the site of injection and swept across the cytosol. As previously found in sea urchin egg homogenates, NAADP-induced Ca2+ release in intact eggs was not blocked by heparin or by prior desensitization to InsP3 or cADPR. Thio-NADP, a specific inhibitor of the NAADP-induced Ca2+ release in sea urchin homogenates [Chini, Beers and Dousa (1995) J. Biol. Chem. 270, 3116-3223] blocked NAADP (but not InsP3 or cADPR) injection-induced Ca2+ release in intact sea urchin eggs. Finally, fertilization of sea urchin eggs abrogated subsequent NAADP-induced Ca2+ release, suggesting that the NAADP-sensitive Ca2+ pool may participate in the fertilization response. This study demonstrates that NAADP acts as a selective Ca(2+)-releasing agonist in intact cells. Images Figure 2 PMID:8554544

Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

PubMed Central

Gulyaeva, Anastasia; Hoogendoorn, Erik; Giles, Julia; Samborskiy, Dmitry

2017-01-01

ABSTRACT In five experimentally characterized arterivirus species, the 5′-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5′ rapid amplification of cDNA ends (RACE) protocol. By combining profile-profile comparisons and phylogeny reconstruction, we identified an association of the four distinct domain layouts of nsp1-nsp2 with major phylogenetic lineages, implicating domain gain, including duplication, and loss in the early nsp1 evolution. Specifically, WPDV encodes highly divergent homologs of PLP1a, PLP1b, PLP1c, and PLP2, with PLP1a lacking the catalytic Cys residue, but does not encode nsp1 Zn finger (ZnF) and “nuclease” domains, which are conserved in other arteriviruses. Unexpectedly, our analysis revealed that the only catalytically active nsp1 PLP of equine arteritis virus (EAV), known as PLP1b, is most similar to PLP1c and thus is likely to be a PLP1b paralog. In all non-WPDV arteriviruses, PLP1b/c and PLP1a show contrasting patterns of conservation, with the N- and C-terminal subdomains, respectively, being enriched with conserved residues, which is indicative of different functional specializations. The least conserved domain of nsp2, the hypervariable region (HVR), has its size varied 5-fold and includes up to four copies of a novel PxPxPR motif that is potentially recognized by SH3 domain-containing proteins. Apparently, only EAV lacks the signal that directs −2 ribosomal frameshifting in the nsp2 coding region. IMPORTANCE Arteriviruses comprise a family of mammalian enveloped positive-strand RNA viruses

The effect of self-transcendence on depression in cognitively intact nursing home patients.

PubMed

Haugan, Gørill; Innstrand, Siw Tone

2012-01-01

Aims. This study's aim was to test the effects of self-transcendence on depression among cognitively intact nursing home patients. Background. Depression is considered the most frequent mental disorder among the elderly population. Specifically, the depression rate among nursing home patients is three to four times higher than that among community-dwelling elderly. Therefore, finding new and alternative ways to prevent and decrease depression is of great importance for nursing home patients' well-being. Self-transcendence is related to spiritual as well as nonspiritual factors, and it is described as a correlate and resource for well-being among vulnerable populations and at the end of life. Methods. A two-factor construct of the self-transcendence scale (interpersonal and intrapersonal) and the hospital anxiety and depression scale (HADS) was applied. A sample of 202 cognitively intact nursing home patients in central Norway was selected to respond to the questionnaires in 2008/2009. Results. A hypothesized SEM model demonstrated significant direct relationships and total effects of self-transcendence on depression. Conclusion and Implication for Practice. Facilitating patients' self-transcendence, both interpersonally and intrapersonally, might decrease depression among cognitively intact nursing home patients.

The Effect of Self-Transcendence on Depression in Cognitively Intact Nursing Home Patients

PubMed Central

Haugan, Gørill; Innstrand, Siw Tone

2012-01-01

Aims. This study's aim was to test the effects of self-transcendence on depression among cognitively intact nursing home patients. Background. Depression is considered the most frequent mental disorder among the elderly population. Specifically, the depression rate among nursing home patients is three to four times higher than that among community-dwelling elderly. Therefore, finding new and alternative ways to prevent and decrease depression is of great importance for nursing home patients' well-being. Self-transcendence is related to spiritual as well as nonspiritual factors, and it is described as a correlate and resource for well-being among vulnerable populations and at the end of life. Methods. A two-factor construct of the self-transcendence scale (interpersonal and intrapersonal) and the hospital anxiety and depression scale (HADS) was applied. A sample of 202 cognitively intact nursing home patients in central Norway was selected to respond to the questionnaires in 2008/2009. Results. A hypothesized SEM model demonstrated significant direct relationships and total effects of self-transcendence on depression. Conclusion and Implication for Practice. Facilitating patients' self-transcendence, both interpersonally and intrapersonally, might decrease depression among cognitively intact nursing home patients. PMID:23738199

51. Projection room, looking SW. Original Movietone projection equipment intact. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

51. Projection room, looking SW. Original Movietone projection equipment intact. Old photo label identifying directional view is inaccurate. This image proves the projection room was expanded southward from its original design prior to the theatre's opening (see also photo WA-197-36). - Fox Theater, Seventh Avenue & Olive Way, Seattle, King County, WA

Ethanol vapor and saprophytic yeast treatments reduce decay and maintain quality of intact and fresh-cut cherries

USDA-ARS?s Scientific Manuscript database

The objective of this study was to evaluate the use of an ethanol vapor release pad and a saprophytic yeast (Cryptococcus infirmo-miniatum) to reduce decay and maintain postharvest quality of intact or fresh-cut sweet cherries (Prunus avium L.) cv. Lapins and Bing. Intact or fresh-cut fruit were pac...

Feasible pickup from intact ossicular chain with floating piezoelectric microphone.

PubMed

Kang, Hou-Yong; Na, Gao; Chi, Fang-Lu; Jin, Kai; Pan, Tie-Zheng; Gao, Zhen

2012-02-22

Many microphones have been developed to meet with the implantable requirement of totally implantable cochlear implant (TICI). However, a biocompatible one without destroying the intactness of the ossicular chain still remains under investigation. Such an implantable floating piezoelectric microphone (FPM) has been manufactured and shows an efficient electroacoustic performance in vitro test at our lab. We examined whether it pick up sensitively from the intact ossicular chain and postulated whether it be an optimal implantable one. Animal controlled experiment: five adult cats (eight ears) were sacrificed as the model to test the electroacoustic performance of the FPM. Three groups were studied: (1) the experiment group (on malleus): the FPM glued onto the handle of the malleus of the intact ossicular chains; (2) negative control group (in vivo): the FPM only hung into the tympanic cavity; (3) positive control group (Hy-M30): a HiFi commercial microphone placed close to the site of the experiment ear. The testing speaker played pure tones orderly ranged from 0.25 to 8.0 kHz. The FPM inside the ear and the HiFi microphone simultaneously picked up acoustic vibration which recorded as .wav files to analyze. The FPM transformed acoustic vibration sensitively and flatly as did the in vitro test across the frequencies above 2.0 kHz, whereas inefficiently below 1.0 kHz for its overloading mass. Although the HiFi microphone presented more efficiently than the FPM did, there was no significant difference at 3.0 kHz and 8.0 kHz. It is feasible to develop such an implantable FPM for future TICIs and TIHAs system on condition that the improvement of Micro Electromechanical System and piezoelectric ceramic material technology would be applied to reduce its weight and minimize its size.

Identification and characterization of long non-coding RNAs in subcutaneous adipose tissue from castrated and intact full-sib pair Huainan male pigs

USDA-ARS?s Scientific Manuscript database

Testosterone deficiency is associated with obesity in humans. It has been proven that long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism; therefore, we first study the role of lncRNAs on testosterone deficiency-induced fat deposition using castrated male pigs as the model animal. The ...

Three-Dimensional Optical Mapping of Nanoparticle Distribution in Intact Tissues.

PubMed

Sindhwani, Shrey; Syed, Abdullah Muhammad; Wilhelm, Stefan; Glancy, Dylan R; Chen, Yih Yang; Dobosz, Michael; Chan, Warren C W

2016-05-24

The role of tissue architecture in mediating nanoparticle transport, targeting, and biological effects is unknown due to the lack of tools for imaging nanomaterials in whole organs. Here, we developed a rapid optical mapping technique to image nanomaterials in intact organs ex vivo and in three-dimensions (3D). We engineered a high-throughput electrophoretic flow device to simultaneously transform up to 48 tissues into optically transparent structures, allowing subcellular imaging of nanomaterials more than 1 mm deep into tissues which is 25-fold greater than current techniques. A key finding is that nanomaterials can be retained in the processed tissue by chemical cross-linking of surface adsorbed serum proteins to the tissue matrix, which enables nanomaterials to be imaged with respect to cells, blood vessels, and other structures. We developed a computational algorithm to analyze and quantitatively map nanomaterial distribution. This method can be universally applied to visualize the distribution and interactions of materials in whole tissues and animals including such applications as the imaging of nanomaterials, tissue engineered constructs, and biosensors within their intact biological environment.

Human blindsight is mediated by an intact geniculo-extrastriate pathway

PubMed Central

Ajina, Sara; Pestilli, Franco; Rokem, Ariel; Kennard, Christopher; Bridge, Holly

2015-01-01

Although damage to the primary visual cortex (V1) causes hemianopia, many patients retain some residual vision; known as blindsight. We show that blindsight may be facilitated by an intact white-matter pathway between the lateral geniculate nucleus and motion area hMT+. Visual psychophysics, diffusion-weighted magnetic resonance imaging and fibre tractography were applied in 17 patients with V1 damage acquired during adulthood and 9 age-matched controls. Individuals with V1 damage were subdivided into blindsight positive (preserved residual vision) and negative (no residual vision) according to psychophysical performance. All blindsight positive individuals showed intact geniculo-hMT+ pathways, while this pathway was significantly impaired or not measurable in blindsight negative individuals. Two white matter pathways previously implicated in blindsight: (i) superior colliculus to hMT+ and (ii) between hMT+ in each hemisphere were not consistently present in blindsight positive cases. Understanding the visual pathways crucial for residual vision may direct future rehabilitation strategies for hemianopia patients. DOI: http://dx.doi.org/10.7554/eLife.08935.001 PMID:26485034

The intact Kunitz domain protects the amyloid precursor protein from being processed by matriptase-2.

PubMed

Beckmann, Anna-Madeleine; Glebov, Konstantin; Walter, Jochen; Merkel, Olaf; Mangold, Martin; Schmidt, Frederike; Becker-Pauly, Christoph; Gütschow, Michael; Stirnberg, Marit

2016-08-01

Proteolytic processing of the amyloid precursor protein (APP) leads to amyloid-β (Aβ) peptides. So far, the mechanism of APP processing is insufficiently characterized at the molecular level. Whereas the knowledge of Aβ generation by several proteases has been expanded, the contribution of the Kunitz-type protease inhibitor domain (KPI) present in two major APP isoforms to the complex proteolytic processing of APP is poorly understood. In this study, we have identified KPI-containing APP as a very potent, slow-binding inhibitor for the membrane-bound proteolytic regulator of iron homeostasis matriptase-2 by forming stable complexes with its target protease in HEK cells. Inhibition and complex formation depend on the intact KPI domain. By inhibiting matriptase-2, KPI-containing APP is protected from matriptase-2-mediated proteolysis within the Aβ region, thus preventing the generation of N-terminally truncated Aβ.

Volumetric in vivo imaging of microvascular perfusion within the intact cochlea in mice using ultra-high sensitive optical microangiography.

PubMed

Subhash, Hrebesh M; Davila, Viviana; Sun, Hai; Nguyen-Huynh, Anh T; Shi, Xiaorui; Nuttall, Alfred L; Wang, Ruikang K

2011-02-01

Studying the inner ear microvascular dynamics is extremely important to understand the cochlear function and to further advance the diagnosis, prevention, and treatment of many otologic disorders. However, there is currently no effective imaging tool available that is able to access the blood flow within the intact cochlea. In this paper, we report the use of an ultrahigh sensitive optical micro-angiography (UHS-OMAG) imaging system to image 3-D microvascular perfusion within the intact cochlea in living mice. The UHS-OMAG image system used in this study is based on spectral domain optical coherence tomography, which uses a broadband light source centered at 1300 nm with an imaging rate of 47[Formula: see text] 000 A-scans/s, capable of acquiring high-resolution B scans at 300 frames/s. The technique is sensitive enough to image very slow blood flow velocities, such as those found in capillary networks. The 3-D imaging acquisition time for a whole cochlea is  ∼ 4.1 s. We demonstrate that volumetric reconstruction of microvascular flow obtained by UHS-OMAG provides a comprehensive perfusion map of several regions of the cochlea, including the otic capsule, the stria vascularis of the apical and middle turns and the radiating arterioles that emanate from the modiolus.

Concatenated Coding Using Trellis-Coded Modulation

NASA Technical Reports Server (NTRS)

Thompson, Michael W.

1997-01-01

In the late seventies and early eighties a technique known as Trellis Coded Modulation (TCM) was developed for providing spectrally efficient error correction coding. Instead of adding redundant information in the form of parity bits, redundancy is added at the modulation stage thereby increasing bandwidth efficiency. A digital communications system can be designed to use bandwidth-efficient multilevel/phase modulation such as Amplitude Shift Keying (ASK), Phase Shift Keying (PSK), Differential Phase Shift Keying (DPSK) or Quadrature Amplitude Modulation (QAM). Performance gain can be achieved by increasing the number of signals over the corresponding uncoded system to compensate for the redundancy introduced by the code. A considerable amount of research and development has been devoted toward developing good TCM codes for severely bandlimited applications. More recently, the use of TCM for satellite and deep space communications applications has received increased attention. This report describes the general approach of using a concatenated coding scheme that features TCM and RS coding. Results have indicated that substantial (6-10 dB) performance gains can be achieved with this approach with comparatively little bandwidth expansion. Since all of the bandwidth expansion is due to the RS code we see that TCM based concatenated coding results in roughly 10-50% bandwidth expansion compared to 70-150% expansion for similar concatenated scheme which use convolution code. We stress that combined coding and modulation optimization is important for achieving performance gains while maintaining spectral efficiency.

Individual tree detection in intact forest and degraded forest areas in the north region of Mato Grosso State, Brazilian Amazon

NASA Astrophysics Data System (ADS)

Santos, E. G.; Jorge, A.; Shimabukuro, Y. E.; Gasparini, K.

2017-12-01

The State of Mato Grosso - MT has the second largest area with degraded forest among the states of the Brazilian Legal Amazon. Land use and land cover change processes that occur in this region cause the loss of forest biomass, releasing greenhouse gases that contribute to the increase of temperature on earth. These degraded forest areas lose biomass according to the intensity and magnitude of the degradation type. The estimate of forest biomass, commonly performed by forest inventory through sample plots, shows high variance in degraded forest areas. Due to this variance and complexity of tropical forests, the aim of this work was to estimate forest biomass using LiDAR point clouds in three distinct forest areas: one degraded by fire, another by selective logging and one area of intact forest. The approach applied in these areas was the Individual Tree Detection (ITD). To isolate the trees, we generated Canopy Height Models (CHM) images, which are obtained by subtracting the Digital Elevation Model (MDE) and the Digital Terrain Model (MDT), created by the cloud of LiDAR points. The trees in the CHM images are isolated by an algorithm provided by the Quantitative Ecology research group at the School of Forestry at Northern Arizona University (SILVA, 2015). With these points, metrics were calculated for some areas, which were used in the model of biomass estimation. The methodology used in this work was expected to reduce the error in biomass estimate in the study area. The cloud points of the most representative trees were analyzed, and thus field data was correlated with the individual trees found by the proposed algorithm. In a pilot study, the proposed methodology was applied generating the individual tree metrics: total height and area of the crown. When correlating 339 isolated trees, an unsatisfactory R² was obtained, as heights found by the algorithm were lower than those obtained in the field, with an average difference of 2.43 m. This shows that the

QR Codes: Taking Collections Further

ERIC Educational Resources Information Center

Ahearn, Caitlin

2014-01-01

With some thought and direction, QR (quick response) codes are a great tool to use in school libraries to enhance access to information. From March through April 2013, Caitlin Ahearn interned at Sanborn Regional High School (SRHS) under the supervision of Pam Harland. As a result of Harland's un-Deweying of the nonfiction collection at SRHS,…

Microseismic Analysis of Fracture of an Intact Rock Asperity Traversing a Sawcut Fault

NASA Astrophysics Data System (ADS)

Mclaskey, G.; Lockner, D. A.

2017-12-01

Microseismic events carry information related to stress state, fault geometry, and other subsurface properties, but their relationship to large and potentially damaging earthquakes is not well defined. We conducted laboratory rock mechanics experiments that highlight the interaction between a sawcut fault and an asperity composed of an intact rock "pin". The sample is a 76 mm diameter cylinder of Westerly granite with a 21 mm diameter cylinder (the pin) of intact Westerly granite that crosses the sawcut fault. Upon loading to 80 MPa in a triaxial machine, we first observed a slip event that ruptured the sawcut fault, slipped about 35 mm, but was halted by the rock pin. With continued loading, the rock pin failed in a swarm of thousands of M -7 seismic events similar to the localized microcracking that occurs during the final fracture nucleation phase in an intact rock sample. Once the pin was fractured to a critical point, it permitted complete rupture events on the sawcut fault (stick-slip instabilities). No seismicity was detected on the sawcut fault plane until the pin was sheared. Subsequent slip events were preceded by 10s of foreshocks, all located on the fault plane. We also identified an aseismic zone on the fault plane surrounding the fractured rock pin. A post-mortem analysis of the sample showed a thick gouge layer where the pin intersected the fault, suggesting that this gouge propped open the fault and prevented microseismic events in its vicinity. This experiment is an excellent case study in microseismicity since the events separate neatly into three categories: slip on the sawcut fault, fracture of the intact rock pin, and off-fault seismicity associated with pin-related rock joints. The distinct locations, timing, and focal mechanisms of the different categories of microseismic events allow us to study how their occurrence is related to the mechanics of the deforming rock.

Non-coding genomic regions possessing enhancer and silencer potential are associated with healthy aging and exceptional survival.

PubMed

Kim, Sangkyu; Welsh, David A; Myers, Leann; Cherry, Katie E; Wyckoff, Jennifer; Jazwinski, S Michal

2015-02-28

We have completed a genome-wide linkage scan for healthy aging using data collected from a family study, followed by fine-mapping by association in a separate population, the first such attempt reported. The family cohort consisted of parents of age 90 or above and their children ranging in age from 50 to 80. As a quantitative measure of healthy aging, we used a frailty index, called FI34, based on 34 health and function variables. The linkage scan found a single significant linkage peak on chromosome 12. Using an independent cohort of unrelated nonagenarians, we carried out a fine-scale association mapping of the region suggestive of linkage and identified three sites associated with healthy aging. These healthy-aging sites (HASs) are located in intergenic regions at 12q13-14. HAS-1 has been previously associated with multiple diseases, and an enhancer was recently mapped and experimentally validated within the site. HAS-2 is a previously uncharacterized site possessing genomic features suggestive of enhancer activity. HAS-3 contains features associated with Polycomb repression. The HASs also contain variants associated with exceptional longevity, based on a separate analysis. Our results provide insight into functional genomic networks involving non-coding regulatory elements that are involved in healthy aging and longevity.

Non-coding genomic regions possessing enhancer and silencer potential are associated with healthy aging and exceptional survival

PubMed Central

Kim, Sangkyu; Welsh, David A.; Myers, Leann; Cherry, Katie E.; Wyckoff, Jennifer; Jazwinski, S. Michal

2015-01-01

We have completed a genome-wide linkage scan for healthy aging using data collected from a family study, followed by fine-mapping by association in a separate population, the first such attempt reported. The family cohort consisted of parents of age 90 or above and their children ranging in age from 50 to 80. As a quantitative measure of healthy aging, we used a frailty index, called FI34, based on 34 health and function variables. The linkage scan found a single significant linkage peak on chromosome 12. Using an independent cohort of unrelated nonagenarians, we carried out a fine-scale association mapping of the region suggestive of linkage and identified three sites associated with healthy aging. These healthy-aging sites (HASs) are located in intergenic regions at 12q13–14. HAS-1 has been previously associated with multiple diseases, and an enhancer was recently mapped and experimentally validated within the site. HAS-2 is a previously uncharacterized site possessing genomic features suggestive of enhancer activity. HAS-3 contains features associated with Polycomb repression. The HASs also contain variants associated with exceptional longevity, based on a separate analysis. Our results provide insight into functional genomic networks involving non-coding regulatory elements that are involved in healthy aging and longevity. PMID:25682868

Intact figure-ground segmentation in schizophrenia.

PubMed

Herzog, Michael H; Kopmann, Sabine; Brand, Andreas

2004-11-30

As revealed by backward masking studies, schizophrenic patients show strong impairments of early visual processing. However, the underlying temporal mechanisms are not yet well understood. To shed light on the exact timing of these deficits, we employed a paradigm in which two masks follow each other. We investigated 16 medicated schizophrenic patients and a matched group of 14 controls with a new backward masking technique, shine-through. In accordance with other masking studies, schizophrenic patients require a dramatically longer processing time to reach a predefined performance level compared with healthy subjects. However, patients are surprisingly sensitive to subtle differences in the timing of the two masks, revealing good temporal resolution. This good temporal resolution indicates intact and fast perceptual grouping and figure-ground segmentation in spite of high susceptibility to masking procedures in schizophrenia.

Video coding for 3D-HEVC based on saliency information

NASA Astrophysics Data System (ADS)

Yu, Fang; An, Ping; Yang, Chao; You, Zhixiang; Shen, Liquan

2016-11-01

As an extension of High Efficiency Video Coding ( HEVC), 3D-HEVC has been widely researched under the impetus of the new generation coding standard in recent years. Compared with H.264/AVC, its compression efficiency is doubled while keeping the same video quality. However, its higher encoding complexity and longer encoding time are not negligible. To reduce the computational complexity and guarantee the subjective quality of virtual views, this paper presents a novel video coding method for 3D-HEVC based on the saliency informat ion which is an important part of Human Visual System (HVS). First of all, the relationship between the current coding unit and its adjacent units is used to adjust the maximum depth of each largest coding unit (LCU) and determine the SKIP mode reasonably. Then, according to the saliency informat ion of each frame image, the texture and its corresponding depth map will be divided into three regions, that is, salient area, middle area and non-salient area. Afterwards, d ifferent quantization parameters will be assigned to different regions to conduct low complexity coding. Finally, the compressed video will generate new view point videos through the renderer tool. As shown in our experiments, the proposed method saves more bit rate than other approaches and achieves up to highest 38% encoding time reduction without subjective quality loss in compression or rendering.

Length of time domestic dogs (Canis familiaris) spend smelling urine of gonadectomised and intact conspecifics.

PubMed

Riach, Anna C; Asquith, Rachel; Fallon, Melissa L D

2017-09-01

Domestic dogs (Canis familiaris) use urine to communicate among themselves, however, it is unknown whether the gonadectomy (neutering or spaying) of a dog affects this communication in anyway. Urine samples from 10 intact and 10 gonadectomised, unfamiliar dogs were presented to 12 tester dogs to sniff under controlled conditions in a pilot study. The amount of time the tester dogs spent sniffing each sample was recorded. Overall, tester dogs were recorded smelling the urine of gonadectomised individuals for a longer time. In addition to the type of urine sample, the result is likely to have been influenced by the sex and status (gonadectomised or intact) of the tester dogs. The observed increase in the length of time spent sniffing urine from gonadectomised individuals could be explained by the tester dogs experiencing more difficulty in gaining information from the urine or facing more confusion while analysing the urine compared to the intact urine they have evolved to smell. Copyright © 2017 Elsevier B.V. All rights reserved.

Population Studies of Intact Vitamin D Binding Protein by Affinity Capture ESI-TOF-MS

PubMed Central

Borges, Chad R.; Jarvis, Jason W.; Oran, Paul E.; Rogers, Stephen P.; Nelson, Randall W.

2008-01-01

Blood plasma proteins with molecular weights greater than approximately 30 kDa are refractory to comprehensive, high-throughput qualitative characterization of microheterogeneity across human populations. Analytical techniques for obtaining high mass resolution for targeted, intact protein characterization and, separately, high sample throughput exist, but efficient means of coupling these assay characteristics remain rather limited. This article discusses the impetus for analyzing intact proteins in a targeted manner across populations and describes the methodology required to couple mass spectrometric immunoassay with electrospray ionization mass spectrometry for the purpose of qualitatively characterizing a prototypical large plasma protein, vitamin D binding protein, across populations. PMID:19137103

Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins.

PubMed

Kishida, Takushi; Suzuki, Miwa; Takayama, Asuka

2018-01-01

Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans. Copyright © 2017 Elsevier Inc. All rights reserved.

Purification and Thermal Stability of Intact Bacillus subtilis Flagella

PubMed Central

Dimmitt, K.; Simon, M.

1971-01-01

Flagella were prepared and purified in a relatively intact form from bacterial lysates. Immunochemical tests showed that over 95% of the protein in the final preparation consisted of flagellar antigen. These flagella are more stable to thermal denaturation than flagella filaments obtained by shearing. Their thermal properties more closely resemble those of flagella in the native state on bacteria. The presence of the hook structure is responsible for this extra stability. Images PMID:4993323

Risks for conduct disorder symptoms associated with parental alcoholism in stepfather families versus intact families from a community sample.

PubMed

Foley, Debra L; Pickles, Andrew; Rutter, Michael; Gardner, Charles O; Maes, Hermine H; Silberg, Judy L; Eaves, Lindon J

2004-05-01

It is not known if the prevalence of parental psychiatric disorders is higher in stepfather than intact families, or if parental alcoholism is differentially associated with risk for conduct disorder (CD) symptoms in stepfather families versus intact families. The sample comprised 839 girls and 741 boys from 792 intact families and 99 girls and 67 boys from 83 stepfather families from a population-based registry of twins aged between 8 and 17 years. Children's current psychiatric symptoms were assessed at personal interview with the child, mother and father. Parental histories of psychiatric disorder were assessed at personal interview with each residential parent. Associations between CD symptoms and parental alcoholism were characterized using both linear and Poisson regression, and results are presented with and without adjustment for maternal drug use during pregnancy, parental conflict, and estimated socioeconomic status (SES) based on census tract data. Mothers from stepfather families had a higher lifetime prevalence of alcoholism, antisocial personality disorder, depression and social phobia than mothers from intact families. Stepfathers had a higher lifetime prevalence of alcoholism and depression than biological fathers from intact families. Children from stepfather families had more externalizing (CD/ODD) symptoms than children from intact families. Girls who lived with an alcoholic stepfather had significantly more CD symptoms than girls who lived with an alcoholic biological father. Boys who lived with an alcoholic stepfather had significantly fewer CD symptoms than boys who lived with an alcoholic biological father. This sex difference was statistically significant. Adjustment for maternal drug use during pregnancy, parental conflict, and estimated SES based on census tract data did not change these findings. Children living in stepfather families are exposed to more parental psychiatric risk factors than children from intact families. The increased

NESSY: NLTE spectral synthesis code for solar and stellar atmospheres

NASA Astrophysics Data System (ADS)

Tagirov, R. V.; Shapiro, A. I.; Schmutz, W.

2017-07-01

Context. Physics-based models of solar and stellar magnetically-driven variability are based on the calculation of synthetic spectra for various surface magnetic features as well as quiet regions, which are a function of their position on the solar or stellar disc. Such calculations are performed with radiative transfer codes tailored for modeling broad spectral intervals. Aims: We aim to present the NLTE Spectral SYnthesis code (NESSY), which can be used for modeling of the entire (UV-visible-IR and radio) spectra of solar and stellar magnetic features and quiet regions. Methods: NESSY is a further development of the COde for Solar Irradiance (COSI), in which we have implemented an accelerated Λ-iteration (ALI) scheme for co-moving frame (CMF) line radiation transfer based on a new estimate of the local approximate Λ-operator. Results: We show that the new version of the code performs substantially faster than the previous one and yields a reliable calculation of the entire solar spectrum. This calculation is in a good agreement with the available observations.

Nurse-patient interaction: a resource for hope in cognitively intact nursing home patients.

PubMed

Haugan, Gørill; Moksnes, Unni Karin; Espnes, Geir Arild

2013-09-01

Nursing home care increasingly targets those elderly with the greatest needs in terms of personal daily activities, whereas services supporting spiritual needs such as hope tend to be ignored. Hope is seen to be a dynamic life force vital to well-being. Nursing home patients are frail, vulnerable, and dependent, which may lead to their hope being intimately related to the nurse-patient interaction. The purpose of this study was to investigate the relationship between nurse-patient interaction and hope among cognitively intact nursing home patients. Cross-sectional data were obtained by means of one-on-one interviews; 202 cognitively intact nursinghome patients representing 44 Norwegian nursing homes responded to the Herth Hope Index and the Nurse-Patient Interaction Scale. The hypothesized relationships between a two-factor construct of hope and nurse-patient interaction were assessed by means of structural equation modelling. The structural equation model revealed a good fit to the data, showing significant influence of nurse-patient interaction on nursing home patients' level of hope. Nurse-patient interaction significantly influences hope in cognitively intact nursing home patients. Offering connectedness should be a central and integral aspect of holistic nursing home care. Providing continuing educational programs for caregivers focusing on how to interact with patients in a health-promoting and hopeful manner seems essential.

A proposed new generation of intact stability criteria for assessment of ship stability in longitudinal waves

NASA Astrophysics Data System (ADS)

Andrei, C.

2017-08-01

Intact ship stability assessment to prevent stability failure in heavy weather conditions is of paramount importance on board vessel. The possibility of assessment the causes that can lead to loss of ship’s stability as well as the assessment of intact stability in heavy seas is a important problem and has attracted a huge interest of the national and international regulatory authorities. Despite the regulations in force, referring to intact ship stability, many ships continued to lose the stability and or capsize due to failure modes that presently are not covered by such regulations. Based on this aspect has been identified the necessity of modelling an updated criteria for assessment of ship’s stability taking into consideration actual possible situations for loss of stability in heavy seas as a measure of increasing she safety of ships. In this respect, the goal of this paper is to illustrate a possible criteria for assessment ship’s stability in heavy seas through a method of determination the possible problems in a form of dynamic stability criteria. A new intact stability criteria is proposed and developed based on separate levels for assessment of vulnerability and susceptibility of ships in situations of parametric rolling and pure loss of stability encountered in extreme sea conditions. Mathematical models correlated with ship’s construction particulars and weather conditions were developed for every separate level in order to assess the ship’s stability. The objective of the proposed criteria is to bring to officers on board ships the possibility of assessment the ship’s intact stability, as a measure of prevention and improvement of safety during the voyage.

Examples of Linking Codes Within GeoFramework

NASA Astrophysics Data System (ADS)

Tan, E.; Choi, E.; Thoutireddy, P.; Aivazis, M.; Lavier, L.; Quenette, S.; Gurnis, M.

2003-12-01

Geological processes usually encompass a broad spectrum of length and time scales. Traditionally, a modeling code (solver) is written to solve a problem with specific length and time scales in mind. The utility of the solver beyond the designated purpose is usually limited. Furthermore, two distinct solvers, even if each can solve complementary parts of a new problem, are difficult to link together to solve the problem as a whole. For example, Lagrangian deformation model with visco-elastoplastic crust is used to study deformation near plate boundary. Ideally, the driving force of the deformation should be derived from underlying mantle convection, and it requires linking the Lagrangian deformation model with a Eulerian mantle convection model. As our understanding of geological processes evolves, the need of integrated modeling codes, which should reuse existing codes as much as possible, begins to surface. GeoFramework project addresses this need by developing a suite of reusable and re-combinable tools for the Earth science community. GeoFramework is based on and extends Pyre, a Python-based modeling framework, recently developed to link solid (Lagrangian) and fluid (Eulerian) models, as well as mesh generators, visualization packages, and databases, with one another for engineering applications. Under the framework, a solver is aware of the existence of other solvers and can interact with each other via exchanging information across adjacent boundary. A solver needs to conform a standard interface and provide its own implementation for exchanging boundary information. The framework also provides facilities to control the coordination between interacting solvers. We will show an example of linking two solvers within GeoFramework. CitcomS is a finite element code which solves for thermal convection within a 3D spherical shell. CitcomS can solve for problems either within a full spherical (global) domain or a restricted (regional) domain of a full sphere by using

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy.

PubMed

Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

2015-12-07

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica-associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random-coil and β-strand conformations. Furthermore, biosilica-associated long-chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

46 CFR 178.325 - Intact stability requirements for a sailing vessel.

Code of Federal Regulations, 2010 CFR

2010-10-01

... in subchapter S of this chapter while under sail as well as the intact stability requirements of...) and with storm sails set and trimmed flat (if a sailing vessel). (d) A sailing vessel that is not... whether the vessel has adequate stability and satisfactory handling characteristics under sail for...

Compound-specific stable isotope analysis of nitrogen-containing intact polar lipids.

PubMed

Svensson, Elisabeth; Schouten, Stefan; Stam, Axel; Middelburg, Jack J; Sinninghe Damsté, Jaap S

2015-12-15

Compound-specific isotope analysis (CSIA) of nitrogen in amino acids has proven a valuable tool in many fields (e.g. ecology). Several intact polar lipids (IPLs) also contain nitrogen, and their nitrogen isotope ratios have the potential to elucidate food-web interactions or metabolic pathways. Here we have developed novel methodology for the determination of δ(15)N values of nitrogen-containing headgroups of IPLs using gas chromatography coupled with isotope-ratio mass spectrometry. Intact polar lipids with nitrogen-containing headgroups were hydrolyzed and the resulting compounds were derivatized by (1) acetylation with pivaloyl chloride for compounds with amine and hydroxyl groups or (2) esterification using acidified 2-propanol followed by acetylation with pivaloyl chloride for compounds with both carboxyl and amine groups. The δ(15)N values of the derivatives were subsequently determined using gas chromatography/combustion/isotope-ratio mass spectrometry. Intact polar lipids with ethanolamine and amino acid headgroups, such as phosphatidylethanolamine and phosphatidylserine, were successfully released from the IPLs and derivatized. Using commercially available pure compounds it was established that δ(15)N values of ethanolamine and glycine were not statistically different from the offline-determined values. Application of the technique to microbial cultures and a microbial mat showed that the method works well for the release and derivatization of the headgroup of phosphatidylethanolamine, a common IPL in bacteria. A method to enable CSIA of nitrogen of selected IPLs has been developed. The method is suitable for measuring natural stable nitrogen isotope ratios in microbial lipids, in particular phosphatidylethanolamine, and will be especially useful for tracing the fate of nitrogen in deliberate tracer experiments. Copyright © 2015 John Wiley & Sons, Ltd.

Prototypic and Arkypallidal Neurons in the Dopamine-Intact External Globus Pallidus

PubMed Central

Abdi, Azzedine; Mallet, Nicolas; Mohamed, Foad Y.; Sharott, Andrew; Dodson, Paul D.; Nakamura, Kouichi C.; Suri, Sana; Avery, Sophie V.; Larvin, Joseph T.; Garas, Farid N.; Garas, Shady N.; Vinciati, Federica; Morin, Stéphanie; Bezard, Erwan

2015-01-01

Studies in dopamine-depleted rats indicate that the external globus pallidus (GPe) contains two main types of GABAergic projection cell; so-called “prototypic” and “arkypallidal” neurons. Here, we used correlative anatomical and electrophysiological approaches in rats to determine whether and how this dichotomous organization applies to the dopamine-intact GPe. Prototypic neurons coexpressed the transcription factors Nkx2-1 and Lhx6, comprised approximately two-thirds of all GPe neurons, and were the major GPe cell type innervating the subthalamic nucleus (STN). In contrast, arkypallidal neurons expressed the transcription factor FoxP2, constituted just over one-fourth of GPe neurons, and innervated the striatum but not STN. In anesthetized dopamine-intact rats, molecularly identified prototypic neurons fired at relatively high rates and with high regularity, regardless of brain state (slow-wave activity or spontaneous activation). On average, arkypallidal neurons fired at lower rates and regularities than prototypic neurons, and the two cell types could be further distinguished by the temporal coupling of their firing to ongoing cortical oscillations. Complementing the activity differences observed in vivo, the autonomous firing of identified arkypallidal neurons in vitro was slower and more variable than that of prototypic neurons, which tallied with arkypallidal neurons displaying lower amplitudes of a “persistent” sodium current important for such pacemaking. Arkypallidal neurons also exhibited weaker driven and rebound firing compared with prototypic neurons. In conclusion, our data support the concept that a dichotomous functional organization, as actioned by arkypallidal and prototypic neurons with specialized molecular, structural, and physiological properties, is fundamental to the operations of the dopamine-intact GPe. PMID:25926446

Ingested soluble CD14 from milk is transferred intact into the blood of newborn rats.

PubMed

Ward, Tonya L; Spencer, William J; Davis, Laura D R; Harrold, Joann; Mack, David R; Altosaar, Illimar

2014-02-01

Milk acts as an edible immune system that is transferred from mother to newborn. Soluble Cluster of Differentiation 14 (sCD14) is a protein found in significant quantities in human milk (~8-29 µg/ml). At a 10-fold lower concentration in the blood (~3 µg/ml), the most notable role of sCD14 is to sequester lipopolysaccharides of Gram-negative bacteria from immune cells. To explore the pharmacodynamics of this milk protein and its biological fate, the biodistribution of radiolabeled sCD14 ((14)C, (125)I) was monitored in 10-d-old rat pups. Up to 3.4 ± 2.2% of the radiolabeled sCD14 administered was observed, intact, in the pup blood for up to 8 h post-ingestion. Additionally, 30.3 ± 13.0% of the radiolabeled sCD14 administered was observed degraded in the stomach at 8 h post-ingestion. A reservoir of intact, administered sCD14 (3.2 ± 0.3%), however, remained in the stomach at 8 h post-ingestion. Intact sCD14 was observed in the small intestine at 5.5 ± 1.6% of the dose fed at 8 h post-ingestion. The presence of intact sCD14 in the blood and the gastrointestinal tract of newborns post-ingestion has implications in the development of allergies, obesity, and other inflammation-related pathogeneses later in life.

Extension of the XGC code for global gyrokinetic simulations in stellarator geometry

NASA Astrophysics Data System (ADS)

Cole, Michael; Moritaka, Toseo; White, Roscoe; Hager, Robert; Ku, Seung-Hoe; Chang, Choong-Seock

2017-10-01

In this work, the total-f, gyrokinetic particle-in-cell code XGC is extended to treat stellarator geometries. Improvements to meshing tools and the code itself have enabled the first physics studies, including single particle tracing and flux surface mapping in the magnetic geometry of the heliotron LHD and quasi-isodynamic stellarator Wendelstein 7-X. These have provided the first successful test cases for our approach. XGC is uniquely placed to model the complex edge physics of stellarators. A roadmap to such a global confinement modeling capability will be presented. Single particle studies will include the physics of energetic particles' global stochastic motions and their effect on confinement. Good confinement of energetic particles is vital for a successful stellarator reactor design. These results can be compared in the core region with those of other codes, such as ORBIT3d. In subsequent work, neoclassical transport and turbulence can then be considered and compared to results from codes such as EUTERPE and GENE. After sufficient verification in the core region, XGC will move into the stellarator edge region including the material wall and neutral particle recycling.

Allergenicity, immunogenicity and dose-relationship of three intact allergen vaccines and four allergoid vaccines for subcutaneous grass pollen immunotherapy

PubMed Central

Henmar, H; Lund, G; Lund, L; Petersen, A; Würtzen, P A

2008-01-01

Different vaccines containing intact allergens or chemically modified allergoids as active ingredients are commercially available for specific immunotherapy. Allergoids are claimed to have decreased allergenicity without loss of immunogenicity and this is stated to allow administration of high allergoid doses. We compared the allergenicity and immunogenicity of four commercially available chemically modified grass pollen allergoid products with three commercially available intact grass pollen allergen vaccines. The allergenicity was investigated with immunoglobulin (Ig)E-inhibition and basophil activation assays. Human T cell proliferation and specific IgG-titres following mouse immunizations were used to address immunogenicity. Furthermore, intact allergen vaccines with different contents of active ingredients were selected to study the influence of the allergen dose. In general, a lower allergenicity for allergen vaccines was clearly linked to a reduced immunogenicity. Compared with the vaccine with the highest amount of intact allergen, the allergoids caused reduced basophil activation as well as diminished immunogenicity demonstrated by reduced T cell activation and/or reduced induction of murine grass-specific IgG antibodies. Interestingly, intact allergen vaccines with lower content of active ingredient exhibited similarly reduced allergenicity, while immunogenicity was still higher or equal to that of allergoids. The low allergenicity observed for some allergoids was inherently linked to a significantly lower immunogenic response questioning the rationale behind the chemical modification into allergoids. In addition, the linkage between allergenicity, immunogenicity and dose found for intact allergen vaccines and the immunogen as well as allergenic immune responses observed for allergoids suggest that the modified allergen vaccines do not contain high doses of immunologically active ingredients. PMID:18647321

Allergenicity, immunogenicity and dose-relationship of three intact allergen vaccines and four allergoid vaccines for subcutaneous grass pollen immunotherapy.

PubMed

Henmar, H; Lund, G; Lund, L; Petersen, A; Würtzen, P A

2008-09-01

Different vaccines containing intact allergens or chemically modified allergoids as active ingredients are commercially available for specific immunotherapy. Allergoids are claimed to have decreased allergenicity without loss of immunogenicity and this is stated to allow administration of high allergoid doses. We compared the allergenicity and immunogenicity of four commercially available chemically modified grass pollen allergoid products with three commercially available intact grass pollen allergen vaccines. The allergenicity was investigated with immunoglobulin (Ig)E-inhibition and basophil activation assays. Human T cell proliferation and specific IgG-titres following mouse immunizations were used to address immunogenicity. Furthermore, intact allergen vaccines with different contents of active ingredients were selected to study the influence of the allergen dose. In general, a lower allergenicity for allergen vaccines was clearly linked to a reduced immunogenicity. Compared with the vaccine with the highest amount of intact allergen, the allergoids caused reduced basophil activation as well as diminished immunogenicity demonstrated by reduced T cell activation and/or reduced induction of murine grass-specific IgG antibodies. Interestingly, intact allergen vaccines with lower content of active ingredient exhibited similarly reduced allergenicity, while immunogenicity was still higher or equal to that of allergoids. The low allergenicity observed for some allergoids was inherently linked to a significantly lower immunogenic response questioning the rationale behind the chemical modification into allergoids. In addition, the linkage between allergenicity, immunogenicity and dose found for intact allergen vaccines and the immunogen as well as allergenic immune responses observed for allergoids suggest that the modified allergen vaccines do not contain high doses of immunologically active ingredients.

Infectious mutants of cassava latent virus generated in vivo from intact recombinant DNA clones containing single copies of the genome.

PubMed Central

Stanley, J; Townsend, R

1986-01-01

Intact recombinant DNAs containing single copies of either component of the cassava latent virus genome can elicit infection when mechanically inoculated to host plants in the presence of the appropriate second component. Characterisation of infectious mutant progeny viruses, by analysis of virus-specific supercoiled DNA intermediates, indicates that most if not all of the cloning vector has been deleted, achieved at least in some cases by intermolecular recombination in vivo between DNAs 1 and 2. Significant rearrangements within the intergenic region of DNA 2, predominantly external to the common region, can be tolerated without loss of infectivity suggesting a somewhat passive role in virus multiplication for the sequences in question. Although packaging constraints might impose limits on the amount of DNA within geminate particles, isolation of an infectious coat protein mutant defective in virion production suggests that packaging is not essential for systemic spread of the viral DNA. Images PMID:2875435

Rapid differentiation of Listeria monocytogenes epidemic clones III and IV and their intact compared with heat-killed populations using Fourier transform infrared spectroscopy and chemometrics.

PubMed

Nyarko, Esmond B; Puzey, Kenneth A; Donnelly, Catherine W

2014-06-01

The objectives of this study were to determine if Fourier transform infrared (FT-IR) spectroscopy and multivariate statistical analysis (chemometrics) could be used to rapidly differentiate epidemic clones (ECs) of Listeria monocytogenes, as well as their intact compared with heat-killed populations. FT-IR spectra were collected from dried thin smears on infrared slides prepared from aliquots of 10 μL of each L. monocytogenes ECs (ECIII: J1-101 and R2-499; ECIV: J1-129 and J1-220), and also from intact and heat-killed cell populations of each EC strain using 250 scans at a resolution of 4 cm(-1) in the mid-infrared region in a reflectance mode. Chemometric analysis of spectra involved the application of the multivariate discriminant method for canonical variate analysis (CVA) and linear discriminant analysis (LDA). CVA of the spectra in the wavelength region 4000 to 600 cm(-1) separated the EC strains while LDA resulted in a 100% accurate classification of all spectra in the data set. Further, CVA separated intact and heat-killed cells of each EC strain and there was 100% accuracy in the classification of all spectra when LDA was applied. FT-IR spectral wavenumbers 1650 to 1390 cm(-1) were used to separate heat-killed and intact populations of L. monocytogenes. The FT-IR spectroscopy method allowed discrimination between strains that belong to the same EC. FT-IR is a highly discriminatory and reproducible method that can be used for the rapid subtyping of L. monocytogenes, as well as for the detection of live compared with dead populations of the organism. Fourier transform infrared (FT-IR) spectroscopy and multivariate statistical analysis can be used for L. monocytogenes source tracking and for clinical case isolate comparison during epidemiological investigations since the method is capable of differentiating epidemic clones and it uses a library of well-characterized strains. The FT-IR method is potentially less expensive and more rapid compared to genetic

Self-complementary circular codes in coding theory.

PubMed

Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

2018-04-01

Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

A benchmark study of scoring methods for non-coding mutations.

PubMed

Drubay, Damien; Gautheret, Daniel; Michiels, Stefan

2018-05-15

Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance. We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases). Using the ClinVar benchmark, CADD was the best tool for detecting the pathogenic variants that are mainly located in protein coding gene regions. Using the COSMIC benchmark, FATHMM-MKL, GWAVA and SOMliver outperformed the other tools for pathogenic variants that are typically located in lincRNAs, pseudogenes and other parts of the non-coding genome. However, all tools had low precision, which could potentially be improved by future non-coding genome feature discoveries. These results may have been influenced by the presence of potential benign variants in the COSMIC database. The development of a gold standard as consistent as ClinVar for these regions will be necessary to confirm our tool ranking. The Snakemake, C++ and R codes are freely available from https://github.com/Oncostat/BenchmarkNCVTools and supported on Linux. damien.drubay@gustaveroussy.fr or stefan.michiels@gustaveroussy.fr. Supplementary data are available at Bioinformatics online.

The best bits in an iris code.

PubMed

Hollingsworth, Karen P; Bowyer, Kevin W; Flynn, Patrick J

2009-06-01

Iris biometric systems apply filters to iris images to extract information about iris texture. Daugman's approach maps the filter output to a binary iris code. The fractional Hamming distance between two iris codes is computed and decisions about the identity of a person are based on the computed distance. The fractional Hamming distance weights all bits in an iris code equally. However, not all the bits in an iris code are equally useful. Our research is the first to present experiments documenting that some bits are more consistent than others. Different regions of the iris are compared to evaluate their relative consistency, and contrary to some previous research, we find that the middle bands of the iris are more consistent than the inner bands. The inconsistent-bit phenomenon is evident across genders and different filter types. Possible causes of inconsistencies, such as segmentation, alignment issues, and different filters are investigated. The inconsistencies are largely due to the coarse quantization of the phase response. Masking iris code bits corresponding to complex filter responses near the axes of the complex plane improves the separation between the match and nonmatch Hamming distance distributions.

Coset Codes Viewed as Terminated Convolutional Codes

NASA Technical Reports Server (NTRS)

Fossorier, Marc P. C.; Lin, Shu

1996-01-01

In this paper, coset codes are considered as terminated convolutional codes. Based on this approach, three new general results are presented. First, it is shown that the iterative squaring construction can equivalently be defined from a convolutional code whose trellis terminates. This convolutional code determines a simple encoder for the coset code considered, and the state and branch labelings of the associated trellis diagram become straightforward. Also, from the generator matrix of the code in its convolutional code form, much information about the trade-off between the state connectivity and complexity at each section, and the parallel structure of the trellis, is directly available. Based on this generator matrix, it is shown that the parallel branches in the trellis diagram of the convolutional code represent the same coset code C(sub 1), of smaller dimension and shorter length. Utilizing this fact, a two-stage optimum trellis decoding method is devised. The first stage decodes C(sub 1), while the second stage decodes the associated convolutional code, using the branch metrics delivered by stage 1. Finally, a bidirectional decoding of each received block starting at both ends is presented. If about the same number of computations is required, this approach remains very attractive from a practical point of view as it roughly doubles the decoding speed. This fact is particularly interesting whenever the second half of the trellis is the mirror image of the first half, since the same decoder can be implemented for both parts.

DNA methylation of miRNA coding sequences putatively associated with childhood obesity.

PubMed

Mansego, M L; Garcia-Lacarte, M; Milagro, F I; Marti, A; Martinez, J A

2017-02-01

Epigenetic mechanisms may be involved in obesity onset and its consequences. The aim of the present study was to evaluate whether DNA methylation status in microRNA (miRNA) coding regions is associated with childhood obesity. DNA isolated from white blood cells of 24 children (identification sample: 12 obese and 12 non-obese) from the Grupo Navarro de Obesidad Infantil study was hybridized in a 450 K methylation microarray. Several CpGs whose DNA methylation levels were statistically different between obese and non-obese were validated by MassArray® in 95 children (validation sample) from the same study. Microarray analysis identified 16 differentially methylated CpGs between both groups (6 hypermethylated and 10 hypomethylated). DNA methylation levels in miR-1203, miR-412 and miR-216A coding regions significantly correlated with body mass index standard deviation score (BMI-SDS) and explained up to 40% of the variation of BMI-SDS. The network analysis identified 19 well-defined obesity-relevant biological pathways from the KEGG database. MassArray® validation identified three regions located in or near miR-1203, miR-412 and miR-216A coding regions differentially methylated between obese and non-obese children. The current work identified three CpG sites located in coding regions of three miRNAs (miR-1203, miR-412 and miR-216A) that were differentially methylated between obese and non-obese children, suggesting a role of miRNA epigenetic regulation in childhood obesity. © 2016 World Obesity Federation.

Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

PubMed Central

Durbin, Kenneth R.; Tran, John C.; Zamdborg, Leonid; Sweet, Steve M. M.; Catherman, Adam D.; Lee, Ji Eun; Li, Mingxi; Kellie, John F.; Kelleher, Neil L.

2011-01-01

Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale. PMID:20848673

Elements in the murine c-mos messenger RNA 5'-untranslated region repress translation of downstream coding sequences.

PubMed

Steel, L F; Telly, D L; Leonard, J; Rice, B A; Monks, B; Sawicki, J A

1996-10-01

Murine c-mos transcripts isolated from testes have 5'-untranslated regions (5'UTRs) of approximately 300 nucleotides with a series of four overlapping open reading frames (ORFs) upstream of the AUG codon that initiates the Mos ORF. Ovarian c-mos transcripts have shorter 5'UTRs (70-80 nucleotides) and contain only 1-2 of the upstream ORFs (uORFs). To test whether these 5'UTRs affect translational efficiency, we have constructed plasmids for the expression of chimeric transcripts with a mos-derived 5'UTR fused to the Escherichia coli beta-galactosidase coding region. Translational efficiency has been evaluated by measuring beta-galactosidase activity NIH3T3 cells transiently transfected with these plasmids and with plasmids where various mutations have been introduced into the 5'UTR. We show that the 5'UTR characteristic of testis-specific c-mos mRNA strongly represses translation relative to the translation of transcripts that contain a 5'UTR derived from beta-globin mRNA, and this is mainly due to the four uORFs. Each of the four upstream AUG triplets can be recognized as a start site for translation, and no single uAUG dominates the repressive effect. The uORFs repress translation by a mechanism that is not affected by the amino acid sequence in the COOH-terminal region of the uORF-encoded peptides. The very short uORF (AUGUGA) present in ovary-specific transcripts does not repress translation. Staining of testis sections from transgenic mice carrying chimeric beta-galactosidase transgene constructs, which contain a mos 5'UTR with or without the uATGs, suggests that the uORFs can dramatically change the pattern of expression in spermatogenic cells.

Combinatorial neural codes from a mathematical coding theory perspective.

PubMed

Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L

2013-07-01

Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli.

Comparison between air pollution concentrations measured at the nearest monitoring station to the delivery hospital and those measured at stations nearest the residential postal code regions of pregnant women in Fukuoka.

PubMed

Michikawa, Takehiro; Morokuma, Seiichi; Nitta, Hiroshi; Kato, Kiyoko; Yamazaki, Shin

2017-06-13

Numerous earlier studies examining the association of air pollution with maternal and foetal health estimated maternal exposure to air pollutants based on the women's residential addresses. However, residential addresses, which are personally identifiable information, are not always obtainable. Since a majority of pregnant women reside near their delivery hospitals, the concentrations of air pollutants at the respective delivery hospitals may be surrogate markers of pollutant exposure at home. We compared air pollutant concentrations measured at the nearest monitoring station to Kyushu University Hospital with those measured at the closest monitoring stations to the respective residential postal code regions of pregnant women in Fukuoka. Aggregated postal code data for the home addresses of pregnant women who delivered at Kyushu University Hospital in 2014 was obtained from Kyushu University Hospital. For each of the study's 695 women who resided in Fukuoka Prefecture, we assigned pollutant concentrations measured at the nearest monitoring station to Kyushu University Hospital and pollutant concentrations measured at the nearest monitoring station to their respective residential postal code regions. Among the 695 women, 584 (84.0%) resided in the proximity of the nearest monitoring station to hospital or one of the four other stations (as the nearest stations to their respective residential postal code region) in Fukuoka city. Pearson's correlation for daily mean concentrations among the monitoring stations in Fukuoka city was strong for fine particulate matter (PM 2.5 ), suspended particulate matter (SPM), and photochemical oxidants (Ox) (coefficients ≥0.9), but moderate for coarse particulate matter (the result of subtracting the PM 2.5 from the SPM concentrations), nitrogen dioxide, and sulphur dioxide. Hospital-based and residence-based concentrations of PM 2.5 , SPM, and Ox were comparable. For PM 2.5 , SPM, and Ox, exposure estimation based on the delivery

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison phase results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Rühaak, Wolfram

2016-04-01

Climate change impacts in permafrost regions have received considerable attention recently due to the pronounced warming trends experienced in recent decades and which have been projected into the future. Large portions of these permafrost regions are characterized by surface water bodies (lakes, rivers) that interact with the surrounding permafrost often generating taliks (unfrozen zones) within the permafrost that allow for hydrologic interactions between the surface water bodies and underlying aquifers and thus influence the hydrologic response of a landscape to climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model past and future evolution such units (Kurylyk et al. 2014). However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, which can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. A benchmark exercise was initialized at the end of 2014. Participants convened from USA, Canada, Europe, representing 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones (Kurylyk et al. 2014; Grenier et al. in prep.; Rühaak et al. 2015). They range from simpler, purely thermal 1D cases to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in a cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test case databases at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases TH2 & TH3. Both cases

The relationships between self-transcendence and spiritual well-being in cognitively intact nursing home patients.

PubMed

Haugan, Gørill; Rannestad, Toril; Hammervold, Randi; Garåsen, Helge; Espnes, Geir A

2014-03-01

Self-transcendence is considered a developmental process of personal maturity and a vital resource of well-being in later adulthood. Measurement of the associations between self-transcendence and spiritual well-being in cognitively intact nursing home patients has not been previously published. The aim of this study was to identify the relationships between self-transcendence and spiritual well-being in cognitively intact nursing home patients. A cross-sectional design using the self-transcendence scale and the FACIT-Sp spiritual well-being questionnaire was adopted. A sample of 202 cognitively intact nursing home patients in mid-Norway was selected to respond to the questionnaires in 2008 and 2009. Statistical analyses were conducted using lisrel 8.8 (Scientific Software International, Chicago, IL, USA) and structural equation modelling. A hypothesised structural equation model comprising a two-factor construct of self-transcendence and a three-factor construct of spiritual well-being demonstrated significant direct relationships between self-transcendence and spiritual well-being and total effects of self-transcendence on spiritual well-being. Facilitating patients' self-transcendence, both interpersonally and intrapersonally, might increase spiritual well-being among cognitively intact nursing home patients, which is seen to be of great importance to nursing home patients' overall satisfaction and satisfaction with staff. The two-factor construct of self-transcendence and the three-factor construct of FACIT-Sp allow a more complex examination of the associations between the constructs and prove more specific guidelines for nursing interventions promoting well-being in nursing home patients. © 2013 Blackwell Publishing Ltd.

Spectrophotometric Evaluation of the Pulpal Peroxide Levels in Intact and Restored Teeth - An Invitro Study.

PubMed

Patri, Gaurav; Acharya, Gourismita; Agrawal, Pratik; Panda, Vijeta

2016-08-01

Hydrogen peroxide (30%) is a commonly used "in office" bleaching agent. Deleterious effects of hydrogen peroxide on the pulp have been observed. The present study was conducted with the aim to evaluate the penetration of 30% hydrogen peroxide into the pulp chamber through intact teeth and through the surface of teeth, restored with either hybrid composite or Resin Modified Glass Ionomer Cement (RMGIC). Sixty extracted human maxillary central incisors were selected and divided into six groups. Two groups were restored with hybrid composite resin and two with RMGIC, while two groups were left intact. The teeth with acetate buffer solution in their pulp cavity were then immersed in either 30% hydrogen peroxide or distilled water depending upon the group, for 60 minutes at 37°C. Then horseradish peroxidase and leucocrystal violet were added to the acetate buffer solution present in the pulp chamber after it was transferred to a test tube and the optical density of the resultant blue solution obtained was measured spectrophotometrically. The data obtained were analyzed using one way ANOVA and Student's t-test. The data obtained established that hydrogen peroxide penetrated into the pulp from the bleaching agent used. Hydrogen peroxide (30%) showed the highest pulpal peroxide level in teeth restored with RMGIC followed by teeth restored with hybrid composite resin and the least amount of penetration was observed in intact teeth. The amount of peroxide penetration into the tooth is more through restored tooth than intact tooth and is also dependant on the type of restorative materials used.

Isolation of Intact Chloroplasts from Euglena gracilis by Zonal Centrifugation 1

PubMed Central

Vasconcelos, Aurea; Pollack, Marilyn; Mendiola, Leticia R.; Hoffmann, H.-P.; Brown, D. H.; Price, C. A.

1971-01-01

Chloroplasts were separated from Euglena gracilis by zonal centrifugation at low speed in density gradients of Ficoll or dextran. The chloroplasts were intact by the criteria of ultrastructure and their content of ribulose diphosphate carboxylase and soluble protein. The chloroplasts also contained ribosomes and ribosomal RNA uncontaminated by the corresponding cytoplasmic particles. Images PMID:16657599

Design and characterisation of a phased antenna array for intact breast hyperthermia.

PubMed

Curto, Sergio; Garcia-Miquel, Aleix; Suh, Minyoung; Vidal, Neus; Lopez-Villegas, Jose M; Prakash, Punit

2018-05-01

Currently available hyperthermia technology is not well suited to treating cancer malignancies in the intact breast. This study investigates a microwave applicator incorporating multiple patch antennas, with the goal of facilitating controllable power deposition profiles for treating lesions at diverse locations within the intact breast. A 3D-computational model was implemented to assess power deposition profiles with 915 MHz applicators incorporating a hemispheric groundplane and configurations of 2, 4, 8, 12, 16 and 20 antennas. Hemispheric breast models of 90 mm and 150 mm diameter were considered, where cuboid target volumes of 10 mm edge length (1 cm 3 ) and 30 mm edge length (27 cm 3 ) were positioned at the centre of the breast, and also located 15 mm from the chest wall. The average power absorption (αPA) ratio expressed as the ratio of the PA in the target volume and in the full breast was evaluated. A 4-antenna proof-of-concept array was fabricated and experimentally evaluated. Computational models identified an optimal inter-antenna spacing of 22.5° along the applicator circumference. Applicators with 8 and 12 antennas excited with constant phase presented the highest αPA at centrally located and deep-seated targets, respectively. Experimental measurements with a 4-antenna proof-of-concept array illustrated the potential for electrically steering power deposition profiles by adjusting the relative phase of the signal at antenna inputs. Computational models and experimental results suggest that the proposed applicator may have potential for delivering conformal thermal therapy in the intact breast.

Software Certification - Coding, Code, and Coders

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Holzmann, Gerard J.

2011-01-01

We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

Dopant-specific unzipping of carbon nanotubes for intact crystalline graphene nanostructures

PubMed Central

Lim, Joonwon; Narayan Maiti, Uday; Kim, Na-Young; Narayan, Rekha; Jun Lee, Won; Sung Choi, Dong; Oh, Youngtak; Min Lee, Ju; Yong Lee, Gil; Hun Kang, Seok; Kim, Hyunwoo; Kim, Yong-Hyun; Ouk Kim, Sang

2016-01-01

Atomic level engineering of graphene-based materials is in high demand to enable customize structures and properties for different applications. Unzipping of the graphene plane is a potential means to this end, but uncontrollable damage of the two-dimensional crystalline framework during harsh unzipping reaction has remained a key challenge. Here we present heteroatom dopant-specific unzipping of carbon nanotubes as a reliable and controllable route to customized intact crystalline graphene-based nanostructures. Substitutional pyridinic nitrogen dopant sites at carbon nanotubes can selectively initiate the unzipping of graphene side walls at a relatively low electrochemical potential (0.6 V). The resultant nanostructures consisting of unzipped graphene nanoribbons wrapping around carbon nanotube cores maintain the intact two-dimensional crystallinity with well-defined atomic configuration at the unzipped edges. Large surface area and robust electrical connectivity of the synergistic nanostructure demonstrate ultrahigh-power supercapacitor performance, which can serve for AC filtering with the record high rate capability of −85° of phase angle at 120 Hz. PMID:26796993

cAMP Response Element-Binding Protein Is Required for Dopamine-Dependent Gene Expression in the Intact But Not the Dopamine-Denervated Striatum

PubMed Central

Andersson, Malin; Konradi, Christine; Cenci, M. Angela

2014-01-01

The cAMP response element-binding protein (CREB) is believed to play a pivotal role in dopamine (DA) receptor-mediated nuclear signaling and neuroplasticity. Here we demonstrate that the significance of CREB for gene expression depends on the experimental paradigm. We compared the role of CREB in two different but related models: L-DOPA administration to unilaterally 6-hydroxydopamine lesioned rats, and cocaine administration to neurologically intact animals. Antisense technology was used to produce a local knockdown of CREB in the lateral caudate–putamen, a region that mediates the dyskinetic or stereotypic manifestations associated with L-DOPA or cocaine treatment, respectively. In intact rats, CREB antisense reduced both basal and cocaine-induced expression of c-Fos, FosB/ΔFosB, and prodynorphin mRNA. In the DA-denervated striatum, CREB was not required for L-DOPA to induce these gene products, nor did CREB contribute considerably to DNA binding activity at cAMP responsive elements (CREs) and CRE-like enhancers. ΔFosB-related proteins and JunD were the main contributors to both CRE and AP-1 DNA–protein complexes in L-DOPA-treated animals. In behavioral studies, intrastriatal CREB knockdown caused enhanced activity scores in intact control animals and exacerbated the dyskinetic effects of acute L-DOPA treatment in 6-OHDA-lesioned animals. These data demonstrate that CREB is not required for the development of L-DOPA-induced dyskinesia in hemiparkinsonian rats. Moreover, our results reveal an unexpected alteration of nuclear signaling mechanisms in the parkinsonian striatum treated with L-DOPA, where AP-1 transcription factors appear to supersede CREB in the activation of CRE-containing genes. PMID:11739600

Discussion on LDPC Codes and Uplink Coding

NASA Technical Reports Server (NTRS)

Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

2007-01-01

This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

A double-blind, placebo-controlled, randomized trial of Ginkgo biloba extract EGb 761 in a sample of cognitively intact older adults: neuropsychological findings.

PubMed

Mix, Joseph A; Crews, W David

2002-08-01

There appears to be an absence of large-scaled clinical trials that have examined the efficacy of Ginkgo biloba extract on the neuropsychological functioning of cognitively intact older adults. The importance of such clinical research appears paramount in light of the plethora of products containing Ginkgo biloba that are currently being widely marketed to predominantly cognitively intact adults with claims of enhanced cognitive performances. The purpose of this research was to conduct the first known, large-scaled clinical trial of the efficacy of Ginkgo biloba extract (EGb 761) on the neuropsychological functioning of cognitively intact older adults. Two hundred and sixty-two community-dwelling volunteers (both male and female) 60 years of age and older, who reported no history of dementia or significant neurocognitive impairments and obtained Mini-Mental State Examination total scores of at least 26, were examined via a 6-week, randomized, double-blind, fixed-dose, placebo-controlled, parallel-group, clinical trial. Participants were randomly assigned to receive either Ginkgo biloba extract EGb 761(n = 131; 180 mg/day) or placebo (n = 131) for 6 weeks. Efficacy measures consisted of participants' raw change in performance scores from pretreatment baseline to those obtained just prior to termination of treatment on the following standardized neuropsychological measures: Selective Reminding Test (SRT), Wechsler Adult Intelligence Scale-III Block Design (WAIS-III BD) and Digit Symbol-Coding (WAIS-III DS) subtests, and the Wechsler Memory Scale-III Faces I (WMS-III FI) and Faces II (WMS-III FII) subtests. A subjective Follow-up Self-report Questionnaire was also administered to participants just prior to termination of the treatment phase. Analyses of covariance indicated that cognitively intact participants who received 180 mg of EGb 761 daily for 6 weeks exhibited significantly more improvement on SRT tasks involving delayed (30 min) free recall (p < 0.04) and

Electromotile hearing: Acoustic tones mask psychophysical response to high-frequency electrical stimulation of intact guinea pig cochleaea)

PubMed Central

Le Prell, Colleen G.; Kawamoto, Kohei; Raphael, Yehoash; Dolan, David F.

2011-01-01

When sinusoidal electric stimulation is applied to the intact cochlea, a frequency-specific acoustic emission can be recorded in the ear canal. Acoustic emissions are produced by basilar membrane motion, and have been used to suggest a corresponding acoustic sensation termed “electromotile hearing.” Electromotile hearing has been specifically attributed to electric stimulation of outer hair cells in the intact organ of Corti. To determine the nature of the auditory perception produced by electric stimulation of a cochlea with intact outer hair cells, we tested guinea pigs in a psychophysical task. First, subjects were trained to report detection of sinusoidal acoustic stimuli and dynamic range was assessed using response latency. Subjects were then implanted with a ball electrode placed into scala tympani. Following the surgical implant procedure, subjects were transferred to a task in which acoustic signals were replaced by sinusoidal electric stimulation, and dynamic range was assessed again. Finally, the ability of acoustic pure-tone stimuli to mask the detection of the electric signals was assessed. Based on the masking effects, we conclude that sinusoidal electric stimulation of the intact cochlea results in perception of a tonal (rather than a broad-band or noisy) sound at a frequency of 8 kHz or above. PMID:17225416

A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells.

PubMed

Saathoff, Hinnerk; Brofelth, Mattias; Trinh, Anne; Parker, Benjamin L; Ryan, Daniel P; Low, Jason K K; Webb, Sarah R; Silva, Ana P G; Mackay, Joel P; Shepherd, Nicholas E

2015-03-01

We have developed an approach for directly isolating an intact multi-protein chromatin remodeling complex from mammalian cell extracts using synthetic peptide affinity reagent 4. FOG1(1-15), a short peptide sequence known to target subunits of the nucleosome remodeling and deacetylase (NuRD) complex, was joined via a 35-atom hydrophilic linker to the StreptagII peptide. Loading this peptide onto Streptactin beads enabled capture of the intact NuRD complex from MEL cell nuclear extract. Gentle biotin elution yielded the desired intact complex free of significant contaminants and in a form that was catalytically competent in a nucleosome remodeling assay. The efficiency of 4 in isolating the NuRD complex was comparable to other reported methods utilising recombinantly produced GST-FOG1(1-45). Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Code for Calculating Regional Seismic Travel Time

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

BALLARD, SANFORD; HIPP, JAMES; & BARKER, GLENN

The RSTT software computes predictions of the travel time of seismic energy traveling from a source to a receiver through 2.5D models of the seismic velocity distribution within the Earth. The two primary applications for the RSTT library are tomographic inversion studies and seismic event location calculations. In tomographic inversions studies, a seismologist begins with number of source-receiver travel time observations and an initial starting model of the velocity distribution within the Earth. A forward travel time calculator, such as the RSTT library, is used to compute predictions of each observed travel time and all of the residuals (observed minusmore » predicted travel time) are calculated. The Earth model is then modified in some systematic way with the goal of minimizing the residuals. The Earth model obtained in this way is assumed to be a better model than the starting model if it has lower residuals. The other major application for the RSTT library is seismic event location. Given an Earth model, an initial estimate of the location of a seismic event, and some number of observations of seismic travel time thought to have originated from that event, location codes systematically modify the estimate of the location of the event with the goal of minimizing the difference between the observed and predicted travel times. The second application, seismic event location, is routinely implemented by the military as part of its effort to monitor the Earth for nuclear tests conducted by foreign countries.« less

Practices in Code Discoverability: Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, A.; Teuben, P.; Nemiroff, R. J.; Shamir, L.

2012-09-01

Here we describe the Astrophysics Source Code Library (ASCL), which takes an active approach to sharing astrophysics source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL now has over 340 codes in it and continues to grow. In 2011, the ASCL has on average added 19 codes per month. An advisory committee has been established to provide input and guide the development and expansion of the new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This paper provides the history and description of the ASCL. It lists the requirements for including codes, examines the advantages of the ASCL, and outlines some of its future plans.

Introduction of the ASGARD code (Automated Selection and Grouping of events in AIA Regional Data)

NASA Astrophysics Data System (ADS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv K.; Fayock, Brian

2017-08-01

We have developed the ASGARD code to automatically detect and group brightenings ("events") in AIA data. The event selection and grouping can be optimized to the respective dataset with a multitude of control parameters. The code was initially written for IRIS data, but has since been optimized for AIA. However, the underlying algorithm is not limited to either and could be used for other data as well.Results from datasets in various AIA channels show that brightenings are reliably detected and that coherent coronal structures can be isolated by using the obtained information about the start, peak, and end times of events. We are presently working on a follow-up algorithm to automatically determine the heating and cooling timescales of coronal structures. This will be done by correlating the information from different AIA channels with different temperature responses. We will present the code and preliminary results.

Light and transmission electron microscopy of the intact interfaces between non-submerged titanium-coated epoxy resin implants and bone or gingiva.

PubMed

Listgarten, M A; Buser, D; Steinemann, S G; Donath, K; Lang, N P; Weber, H P

1992-02-01

This experiment was aimed at studying the intact tissue/implant interface of non-submerged dental implants with a titanium surface. Epoxy-resin replicas were fabricated from 3.05 x 8 mm cylindrical titanium implants with a plasma-sprayed apical portion and a smooth coronal collar. The replicas were coated with a 90-120-nm-thick layer of pure titanium and autoclaved. The coated replicas were inserted as non-submerged endosseous implants in the edentulous premolar region of dog mandibles and allowed to heal for three months. Jaw sections containing the implants were processed for light and electron microscopic study of the intact tissue/implant interface with and without prior demineralization. Gingival connective tissue fibers were closely adapted to the titanium layer, in an orientation more or less parallel to the implant surface. There was no evidence of any fiber insertions into the surface irregularities of the smooth or rough titanium surface. Undemineralized bone was intimately adapted to the titanium surface without any intervening space. In demineralized sections, the collagen fibers of the bone matrix tended to be somewhat thinner and occasionally less densely packed in the vicinity of the implant surface. However, they extended all the way to the titanium surface, without any intervening fibril-free layer.

Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate

PubMed Central

Mangold, Elisabeth; Böhmer, Anne C.; Ishorst, Nina; Hoebel, Ann-Kathrin; Gültepe, Pinar; Schuenke, Hannah; Klamt, Johanna; Hofmann, Andrea; Gölz, Lina; Raff, Ruth; Tessmann, Peter; Nowak, Stefanie; Reutter, Heiko; Hemprich, Alexander; Kreusch, Thomas; Kramer, Franz-Josef; Braumann, Bert; Reich, Rudolf; Schmidt, Gül; Jäger, Andreas; Reiter, Rudolf; Brosch, Sibylle; Stavusis, Janis; Ishida, Miho; Seselgyte, Rimante; Moore, Gudrun E.; Nöthen, Markus M.; Borck, Guntram; Aldhorae, Khalid A.; Lace, Baiba; Stanier, Philip; Knapp, Michael; Ludwig, Kerstin U.

2016-01-01

Nonsyndromic cleft lip with/without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO) are the most frequent subphenotypes of orofacial clefts. A common syndromic form of orofacial clefting is Van der Woude syndrome (VWS) where individuals have CL/P or CPO, often but not always associated with lower lip pits. Recently, ∼5% of VWS-affected individuals were identified with mutations in the grainy head-like 3 gene (GRHL3). To investigate GRHL3 in nonsyndromic clefting, we sequenced its coding region in 576 Europeans with nsCL/P and 96 with nsCPO. Most strikingly, nsCPO-affected individuals had a higher minor allele frequency for rs41268753 (0.099) than control subjects (0.049; p = 1.24 × 10−2). This association was replicated in nsCPO/control cohorts from Latvia, Yemen, and the UK (pcombined = 2.63 × 10−5; ORallelic = 2.46 [95% CI 1.6–3.7]) and reached genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 × 10−9). Notably, rs41268753 is not associated with nsCL/P (p = 0.45). rs41268753 encodes the highly conserved p.Thr454Met (c.1361C>T) (GERP = 5.3), which prediction programs denote as deleterious, has a CADD score of 29.6, and increases protein binding capacity in silico. Sequencing also revealed four novel truncating GRHL3 mutations including two that were de novo in four families, where all nine individuals harboring mutations had nsCPO. This is important for genetic counseling: given that VWS is rare compared to nsCPO, our data suggest that dominant GRHL3 mutations are more likely to cause nonsyndromic than syndromic CPO. Thus, with rare dominant mutations and a common risk variant in the coding region, we have identified an important contribution for GRHL3 in nsCPO. PMID:27018475

Interocular transfer of depth discrimination in intact and in DSO-sectioned pigeons.

PubMed

Musumeci, D; Lemeignan, M; Bloch, S

1991-07-22

Interocular transfer (IOT) of a depth discrimination task was studied in intact pigeons and with a section of the supraoptic decussation (DSO). Animals were trained to respond to the nearer of two small light emitting diodes placed at different depths in the left and right compartments of a black tunnel. The near stimulus (at 10.5 cm from the eyes) and the far one (at 21 cm) could only be seen one at a time. Though the task was difficult to learn monocularly, intact as well as lesioned animals had good transfer scores with the untrained eye. Success in transfer may be related to the presentation of the discriminanda which assured that their images impinged upon the retinal 'red field'. DSO-transection did not affect IOT possibly because differential oculomotor adjustments needed for focusing near or far targets provide central bilateral and/or binocular information which is not conveyed by the DSO.

New quantum codes constructed from quaternary BCH codes

NASA Astrophysics Data System (ADS)

Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

2016-10-01

In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells

PubMed Central

Orlova-Fink, Nina; Einkauf, Kevin; Chowdhury, Fatema Z.; Sun, Xiaoming; Harrington, Sean; Kuo, Hsiao-Hsuan; Hua, Stephane; Chen, Hsiao-Rong; Ouyang, Zhengyu; Reddy, Kavidha; Dong, Krista; Ndung’u, Thumbi; Walker, Bruce D.; Rosenberg, Eric S.; Yu, Xu G.

2017-01-01

HIV-1 causes a chronic, incurable disease due to its persistence in CD4+ T cells that contain replication-competent provirus, but exhibit little or no active viral gene expression and effectively resist combination antiretroviral therapy (cART). These latently infected T cells represent an extremely small proportion of all circulating CD4+ T cells but possess a remarkable long-term stability and typically persist throughout life, for reasons that are not fully understood. Here we performed massive single-genome, near-full-length next-generation sequencing of HIV-1 DNA derived from unfractionated peripheral blood mononuclear cells, ex vivo-isolated CD4+ T cells, and subsets of functionally polarized memory CD4+ T cells. This approach identified multiple sets of independent, near-full-length proviral sequences from cART-treated individuals that were completely identical, consistent with clonal expansion of CD4+ T cells harboring intact HIV-1. Intact, near-full-genome HIV-1 DNA sequences that were derived from such clonally expanded CD4+ T cells constituted 62% of all analyzed genome-intact sequences in memory CD4 T cells, were preferentially observed in Th1-polarized cells, were longitudinally detected over a duration of up to 5 years, and were fully replication- and infection-competent. Together, these data suggest that clonal proliferation of Th1-polarized CD4+ T cells encoding for intact HIV-1 represents a driving force for stabilizing the pool of latently infected CD4+ T cells. PMID:28628034

Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells.

PubMed

Lee, Guinevere Q; Orlova-Fink, Nina; Einkauf, Kevin; Chowdhury, Fatema Z; Sun, Xiaoming; Harrington, Sean; Kuo, Hsiao-Hsuan; Hua, Stephane; Chen, Hsiao-Rong; Ouyang, Zhengyu; Reddy, Kavidha; Dong, Krista; Ndung'u, Thumbi; Walker, Bruce D; Rosenberg, Eric S; Yu, Xu G; Lichterfeld, Mathias

2017-06-30

HIV-1 causes a chronic, incurable disease due to its persistence in CD4+ T cells that contain replication-competent provirus, but exhibit little or no active viral gene expression and effectively resist combination antiretroviral therapy (cART). These latently infected T cells represent an extremely small proportion of all circulating CD4+ T cells but possess a remarkable long-term stability and typically persist throughout life, for reasons that are not fully understood. Here we performed massive single-genome, near-full-length next-generation sequencing of HIV-1 DNA derived from unfractionated peripheral blood mononuclear cells, ex vivo-isolated CD4+ T cells, and subsets of functionally polarized memory CD4+ T cells. This approach identified multiple sets of independent, near-full-length proviral sequences from cART-treated individuals that were completely identical, consistent with clonal expansion of CD4+ T cells harboring intact HIV-1. Intact, near-full-genome HIV-1 DNA sequences that were derived from such clonally expanded CD4+ T cells constituted 62% of all analyzed genome-intact sequences in memory CD4 T cells, were preferentially observed in Th1-polarized cells, were longitudinally detected over a duration of up to 5 years, and were fully replication- and infection-competent. Together, these data suggest that clonal proliferation of Th1-polarized CD4+ T cells encoding for intact HIV-1 represents a driving force for stabilizing the pool of latently infected CD4+ T cells.

Tolerance of a standard intact protein formula versus a partially hydrolyzed formula in healthy, term infants

PubMed Central

Berseth, Carol Lynn; Mitmesser, Susan Hazels; Ziegler, Ekhard E; Marunycz, John D; Vanderhoof, Jon

2009-01-01

Background Parents who perceive common infant behaviors as formula intolerance-related often switch formulas without consulting a health professional. Up to one-half of formula-fed infants experience a formula change during the first six months of life. Methods The objective of this study was to assess discontinuance due to study physician-assessed formula intolerance in healthy, term infants. Infants (335) were randomized to receive either a standard intact cow milk protein formula (INTACT) or a partially hydrolyzed cow milk protein formula (PH) in a 60 day non-inferiority trial. Discontinuance due to study physician-assessed formula intolerance was the primary outcome. Secondary outcomes included number of infants who discontinued for any reason, including parent-assessed. Results Formula intolerance between groups (INTACT, 12.3% vs. PH, 13.7%) was similar for infants who completed the study or discontinued due to study physician-assessed formula intolerance. Overall study discontinuance based on parent- vs. study physician-assessed intolerance for all infants (14.4 vs.11.1%) was significantly different (P = 0.001). Conclusion This study demonstrated no difference in infant tolerance of intact vs. partially hydrolyzed cow milk protein formulas for healthy, term infants over a 60-day feeding trial, suggesting nonstandard partially hydrolyzed formulas are not necessary as a first-choice for healthy infants. Parents frequently perceived infant behavior as formula intolerance, paralleling previous reports of unnecessary formula changes. Trial Registration clinicaltrials.gov: NCT00666120 PMID:19545360

On the resilience of nitrogen assimilation by intact roots under starvation, as revealed by isotopic and metabolomic techniques.

PubMed

Bathellier, Camille; Tcherkez, Guillaume; Mauve, Caroline; Bligny, Richard; Gout, Elizabeth; Ghashghaie, Jaleh

2009-09-01

The response of root metabolism to variations in carbon source availability is critical for whole-plant nitrogen (N) assimilation and growth. However, the effect of changes in the carbohydrate input to intact roots is currently not well understood and, for example, both smaller and larger values of root:shoot ratios or root N uptake have been observed so far under elevated CO(2). In addition, previous studies on sugar starvation mainly focused on senescent or excised organs while an increasing body of data suggests that intact roots may behave differently with, for example, little protein remobilization. Here, we investigated the carbon and nitrogen primary metabolism in intact roots of French bean (Phaseolus vulgaris L.) plants maintained under continuous darkness for 4 days. We combined natural isotopic (15)N/(14)N measurements, metabolomic and (13)C-labeling data and show that intact roots continued nitrate assimilation to glutamate for at least 3 days while the respiration rate decreased. The activity of the tricarboxylic acid cycle diminished so that glutamate synthesis was sustained by the anaplerotic phosphoenolpyruvate carboxylase fixation. Presumably, the pentose phosphate pathway contributed to provide reducing power for nitrate reduction. All the biosynthetic metabolic fluxes were nevertheless down-regulated and, consequently, the concentration of all amino acids decreased. This is the case of asparagine, strongly suggesting that, as opposed to excised root tips, protein remobilization in intact roots remained very low for 3 days in spite of the restriction of respiratory substrates. Copyright (c) 2009 John Wiley & Sons, Ltd.

Regional Hearing Clerk

EPA Pesticide Factsheets

The Regional Hearing Clerk receives filings for proceedings under the Consolidated Rules of Practice Governing the Administrative Assessment of Civil Penalties and the Revocation/Termination or Suspension of Permits, 40 Code of Federal Regulations Part 22

Investigation of Ion Transmission Effects on Intact Protein Quantification in a Triple Quadrupole Mass Spectrometer

NASA Astrophysics Data System (ADS)

Wang, Evelyn H.; Appulage, Dananjaya Kalu; McAllister, Erin A.; Schug, Kevin A.

2017-09-01

Recently, direct intact protein quantitation using triple quadrupole mass spectrometry (QqQ-MS) and multiple reaction monitoring (MRM) was demonstrated (J. Am. Soc. Mass Spectrom. 27, 886-896 (2016)). Even though QqQ-MS is known to provide extraordinary detection sensitivity for quantitative analysis, we found that intact proteins exhibited a less than 5% ion transmission from the first quadrupole to the third quadrupole mass analyzer in the presence of zero collision energy (ZCE). With the goal to enhance intact protein quantitation sensitivity, ion scattering effects, proton transfer effects, and mass filter resolution widths were examined for their contributions to the lost signal. Protein standards myoglobin and ubiquitin along with small molecules reserpine and vancomycin were analyzed together with various collision induced dissociation (CID) gases (N2, He, and Ar) at different gas pressures. Mass resolution settings played a significant role in reducing ion transmission signal. By narrowing the mass resolution window by 0.35 m/z on each side, roughly 75%-90% of the ion signal was lost. The multiply charged proteins experienced additional proton transfer effects, corresponding to 10-fold signal reduction. A study of increased sensitivity of the method was also conducted with various MRM summation techniques. Although the degree of enhancement was analyte-dependent, an up to 17-fold increase in sensitivity was observed for ubiquitin using a summation of multiple MRM transitions. Biological matrix, human urine, and equine plasma were spiked with proteins to demonstrate the specificity of the method. This study provides additional insight into optimizing the use and sensitivity of QqQ-MS for intact protein quantification. [Figure not available: see fulltext.

Sediment carbon and nutrient fluxes from cleared and intact temperate mangrove ecosystems and adjacent sandflats.

PubMed

Bulmer, Richard H; Schwendenmann, Luitgard; Lohrer, Andrew M; Lundquist, Carolyn J

2017-12-01

The loss of mangrove ecosystems is associated with numerous impacts on coastal and estuarine function, including sediment carbon and nutrient cycling. In this study we compared in situ fluxes of carbon dioxide (CO 2 ) from the sediment to the atmosphere, and fluxes of dissolved inorganic nutrients and oxygen across the sediment-water interface, in intact and cleared mangrove and sandflat ecosystems in a temperate estuary. Measurements were made 20 and 25months after mangrove clearance, in summer and winter, respectively. Sediment CO 2 efflux was over two-fold higher from cleared than intact mangrove ecosystems at 20 and 25months after mangrove clearance. The higher CO 2 efflux from the cleared site was explained by an increase in respiration of dead root material along with sediment disturbance following mangrove clearance. In contrast, sediment CO 2 efflux from the sandflat site was negligible (≤9.13±1.18mmolm -2 d -1 ), associated with lower sediment organic matter content. The fluxes of inorganic nutrients (NH 4 + , NO x and PO 4 3- ) from intact and cleared mangrove sediments were low (≤20.37±18.66μmolm -2 h - 1 ). The highest NH 4 + fluxes were measured at the sandflat site (69.21±13.49μmolm -2 h - 1 ). Lower inorganic nutrient fluxes within the cleared and intact mangrove sites compared to the sandflat site were associated with lower abundance of larger burrowing macrofauna. Further, a higher fraction of organic matter, silt and clay content in mangrove sediments may have limited nutrient exchange. Copyright © 2017 Elsevier B.V. All rights reserved.

Spherical hashing: binary code embedding with hyperspheres.

PubMed

Heo, Jae-Pil; Lee, Youngwoon; He, Junfeng; Chang, Shih-Fu; Yoon, Sung-Eui

2015-11-01

Many binary code embedding schemes have been actively studied recently, since they can provide efficient similarity search, and compact data representations suitable for handling large scale image databases. Existing binary code embedding techniques encode high-dimensional data by using hyperplane-based hashing functions. In this paper we propose a novel hypersphere-based hashing function, spherical hashing, to map more spatially coherent data points into a binary code compared to hyperplane-based hashing functions. We also propose a new binary code distance function, spherical Hamming distance, tailored for our hypersphere-based binary coding scheme, and design an efficient iterative optimization process to achieve both balanced partitioning for each hash function and independence between hashing functions. Furthermore, we generalize spherical hashing to support various similarity measures defined by kernel functions. Our extensive experiments show that our spherical hashing technique significantly outperforms state-of-the-art techniques based on hyperplanes across various benchmarks with sizes ranging from one to 75 million of GIST, BoW and VLAD descriptors. The performance gains are consistent and large, up to 100 percent improvements over the second best method among tested methods. These results confirm the unique merits of using hyperspheres to encode proximity regions in high-dimensional spaces. Finally, our method is intuitive and easy to implement.

Validation of Living Donor Nephrectomy Codes

PubMed Central

Lam, Ngan N.; Lentine, Krista L.; Klarenbach, Scott; Sood, Manish M.; Kuwornu, Paul J.; Naylor, Kyla L.; Knoll, Gregory A.; Kim, S. Joseph; Young, Ann; Garg, Amit X.

2018-01-01

Background: Use of administrative data for outcomes assessment in living kidney donors is increasing given the rarity of complications and challenges with loss to follow-up. Objective: To assess the validity of living donor nephrectomy in health care administrative databases compared with the reference standard of manual chart review. Design: Retrospective cohort study. Setting: 5 major transplant centers in Ontario, Canada. Patients: Living kidney donors between 2003 and 2010. Measurements: Sensitivity and positive predictive value (PPV). Methods: Using administrative databases, we conducted a retrospective study to determine the validity of diagnostic and procedural codes for living donor nephrectomies. The reference standard was living donor nephrectomies identified through the province’s tissue and organ procurement agency, with verification by manual chart review. Operating characteristics (sensitivity and PPV) of various algorithms using diagnostic, procedural, and physician billing codes were calculated. Results: During the study period, there were a total of 1199 living donor nephrectomies. Overall, the best algorithm for identifying living kidney donors was the presence of 1 diagnostic code for kidney donor (ICD-10 Z52.4) and 1 procedural code for kidney procurement/excision (1PC58, 1PC89, 1PC91). Compared with the reference standard, this algorithm had a sensitivity of 97% and a PPV of 90%. The diagnostic and procedural codes performed better than the physician billing codes (sensitivity 60%, PPV 78%). Limitations: The donor chart review and validation study was performed in Ontario and may not be generalizable to other regions. Conclusions: An algorithm consisting of 1 diagnostic and 1 procedural code can be reliably used to conduct health services research that requires the accurate determination of living kidney donors at the population level. PMID:29662679

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Biological and bionic hands: natural neural coding and artificial perception.

PubMed

Bensmaia, Sliman J

2015-09-19

The first decade and a half of the twenty-first century brought about two major innovations in neuroprosthetics: the development of anthropomorphic robotic limbs that replicate much of the function of a native human arm and the refinement of algorithms that decode intended movements from brain activity. However, skilled manipulation of objects requires somatosensory feedback, for which vision is a poor substitute. For upper-limb neuroprostheses to be clinically viable, they must therefore provide for the restoration of touch and proprioception. In this review, I discuss efforts to elicit meaningful tactile sensations through stimulation of neurons in somatosensory cortex. I focus on biomimetic approaches to sensory restoration, which leverage our current understanding about how information about grasped objects is encoded in the brain of intact individuals. I argue that not only can sensory neuroscience inform the development of sensory neuroprostheses, but also that the converse is true: stimulating the brain offers an exceptional opportunity to causally interrogate neural circuits and test hypotheses about natural neural coding.

Palladium nanoparticles exposure: Evaluation of permeation through damaged and intact human skin.

PubMed

Larese Filon, Francesca; Crosera, Matteo; Mauro, Marcella; Baracchini, Elena; Bovenzi, Massimo; Montini, Tiziano; Fornasiero, Paolo; Adami, Gianpiero

2016-07-01

The intensified use of palladium nanoparticles (PdNPs) in many chemical reactions, jewellery, electronic devices, in car catalytic converters and in biomedical applications lead to a significant increase in palladium exposure. Pd can cause allergic contact dermatitis when in contact with the skin. However, there is still a lack of toxicological data related to nano-structured palladium and information on human cutaneous absorption. In fact, PdNPs, can be absorbed through the skin in higher amounts than bulk Pd because NPs can release more ions. In our study, we evaluated the absorption of PdNPs, with a size of 10.7 ± 2.8 nm, using intact and damaged human skin in Franz cells. 0.60 mg cm(-2) of PdNPs were applied on skin surface for 24 h. Pd concentrations in the receiving solutions at the end of experiments were 0.098 ± 0.067 μg cm(-2) and 1.06 ± 0.44 μg cm(-2) in intact skin and damaged skin, respectively. Pd flux permeation after 24 h was 0.005 ± 0.003 μg cm(-2) h(-1) and 0.057 ± 0.030 μg cm(-2) h(-1) and lag time 4.8 ± 1.7 and 4.2 ± 3.6 h, for intact and damaged skin respectively. This study indicates that Pd can penetrate human skin. Copyright © 2016 Elsevier Ltd. All rights reserved.

Need for lung resection in patients with intact or ruptured hydatid cysts.

PubMed

Vasquez, J C; Montesinos, E; Peralta, J; Rojas, L; DeLaRosa, J; Leon, J J

2009-08-01

Lung hydatid cyst caused by Echinococcus granulosus is endemic in many areas of the world. We aimed to compare the outcome of surgical treatment in intact and ruptured (infected or noninfected) cysts. We reviewed the medical records of 115 patients with lung hydatid disease who were surgically treated between 2001 and 2005 in a tertiary hospital in Lima, Peru. Patients were divided into 3 groups based on cyst characteristics: intact cysts (n = 41), ruptured noninfected cysts (n = 47) and ruptured infected cysts (n = 27). If a patient had more than one type of cyst, the most severe form of disease was recorded. Data related to symptoms, morbidity and mortality were recorded and compared. We also calculated direct patient costs. Mean age of patients was 23.6 +/- 15.1 years old. Ruptured cysts were present in 64 % of patients and giant cysts (> 10 cm diameter) were present in 26 % of patients. Hemoptysis was present in 47.0 % of patients and was more frequent in patients with ruptured infected cysts. Lung resection was performed in 58 % of patients. The most common postoperative complication was infection of the operative wound (6.08 %). Perioperative mortality was zero. Patients with ruptured cysts had a longer hospitalization time and higher total cost (12.28 +/- 0.92 days, US$ 890.34 +/- 303.35) than patients with intact cysts (10.17 +/- 0.79 days, US$ 724.81 +/- 14.38). Surgical treatment of lung hydatid disease is safe, with a good outcome and a low mortality rate. The lung resection rate was higher than most published series and reflects the relatively high proportion of patients with giant and ruptured infected cysts.

Study of SOL in DIII-D tokamak with SOLPS suite of codes.

NASA Astrophysics Data System (ADS)

Pankin, Alexei; Bateman, Glenn; Brennan, Dylan; Coster, David; Hogan, John; Kritz, Arnold; Kukushkin, Andrey; Schnack, Dalton; Snyder, Phil

2005-10-01

The scrape-of-layer (SOL) region in DIII-D tokamak is studied with the SOLPS integrated suite of codes. The SOLPS package includes the 3D multi-species Monte-Carlo neutral code EIRINE and 2D multi-fluid code B2. The EIRINE and B2 codes are cross-coupled through B2-EIRINE interface. The results of SOLPS simulations are used in the integrated modeling of the plasma edge in DIII-D tokamak with the ASTRA transport code. Parameterized dependences for neutral particle fluxes that are computed with the SOLPS code are implemented in a model for the H-mode pedestal and ELMs [1] in the ASTRA code. The effects of neutrals on the H-mode pedestal and ELMs are studied in this report. [1] A. Y. Pankin, I. Voitsekhovitch, G. Bateman, et al., Plasma Phys. Control. Fusion 47, 483 (2005).

A systems neurophysiology approach to voluntary event coding.

PubMed

Petruo, Vanessa A; Stock, Ann-Kathrin; Münchau, Alexander; Beste, Christian

2016-07-15

Mechanisms responsible for the integration of perceptual events and appropriate actions (sensorimotor processes) have been subject to intense research. Different theoretical frameworks have been put forward with the "Theory of Event Coding (TEC)" being one of the most influential. In the current study, we focus on the concept of 'event files' within TEC and examine what sub-processes being dissociable by means of cognitive-neurophysiological methods are involved in voluntary event coding. This was combined with EEG source localization. We also introduce reward manipulations to delineate the neurophysiological sub-processes most relevant for performance variations during event coding. The results show that processes involved in voluntary event coding included predominantly stimulus categorization, feature unbinding and response selection, which were reflected by distinct neurophysiological processes (the P1, N2 and P3 ERPs). On a system's neurophysiological level, voluntary event-file coding is thus related to widely distributed parietal-medial frontal networks. Attentional selection processes (N1 ERP) turned out to be less important. Reward modulated stimulus categorization in parietal regions likely reflecting aspects of perceptual decision making but not in other processes. The perceptual categorization stage appears central for voluntary event-file coding. Copyright © 2016 Elsevier Inc. All rights reserved.

Combination of SDS-PAGE and intact mass analysis for rapid determination of heterogeneities in monoclonal antibody therapeutics.

PubMed

Yamada, Hideaki; Matsumura, Chiemi; Yamada, Keita; Teshima, Koichiro; Hiroshima, Takashi; Kinoshita, Mitsuhiro; Suzuki, Shigeo; Kakehi, Kazuaki

2017-05-01

mAbs are currently mainstream in biopharmaceuticals, and their market has been growing due to their high target specificity. Characterization of heterogeneities in mAbs is performed to secure their quality and safety by physicochemical analyses. However, they require time-consuming task, which often strain the resources of drug development in pharmaceuticals. Rapid and direct method to determine the heterogeneities should be a powerful tool for pharmaceutical analysis. Considering the advantages of electrophoresis and MS, this study addresses the combination of SDS-PAGE and intact mass analysis, which provides direct, rapid, and orthogonal determination of heterogeneities in mAb therapeutics. mAb therapeutics that migrated in SDS-PAGE were recovered from gel by treatment with SDC-containing buffer. Usage of SDC-containing buffer as extraction solvent and ethanol-based staining solution enhanced the recovery of intact IgG from SDS-PAGE gels. Recovery of mAbs reached more than 86% with 0.2% SD. The heterogeneities, especially N-glycan variants in the recovered mAb therapeutics, were clearly determined by intact mass analysis. We believe that the study is important in pharmaceuticals‧ perspective since orthogonal combination of gel electrophoresis and intact mass analysis should be pivotal role for rapid and precise characterization of mAbs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of the coding region and mRNA variants of the apyrase gene from pea (Pisum sativum)

NASA Technical Reports Server (NTRS)

Shibata, K.; Abe, S.; Davies, E.

2001-01-01

Partial amino acid sequences of a 49 kDa apyrase (ATP diphosphohydrolase, EC 3.6.1.5) from the cytoskeletal fraction of etiolated pea stems were used to derive oligonucleotide DNA primers to generate a cDNA fragment of pea apyrase mRNA by RT-PCR and these primers were used to screen a pea stem cDNA library. Two almost identical cDNAs differing in just 6 nucleotides within the coding regions were found, and these cDNA sequences were used to clone genomic fragments by PCR. Two nearly identical gene fragments containing 8 exons and 7 introns were obtained. One of them (H-type) encoded the mRNA sequence described by Hsieh et al. (1996) (DDBJ/EMBL/GenBank Z32743), while the other (S-type) differed by the same 6 nucleotides as the mRNAs, suggesting that these genes may be alleles. The six nucleotide differences between these two alleles were found solely in the first exon, and these mutation sites had two types of consensus sequences. These mRNAs were found with varying lengths of 3' untranslated regions (3'-UTR). There are some similarities between the 3'-UTR of these mRNAs and those of actin and actin binding proteins in plants. The putative roles of the 3'-UTR and alternative polyadenylation sites are discussed in relation to their possible role in targeting the mRNAs to different subcellular compartments.

41 CFR 105-72.502 - Codes of conduct.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false Codes of conduct. 105-72.502 Section 105-72.502 Public Contracts and Property Management Federal Property Management Regulations System (Continued) GENERAL SERVICES ADMINISTRATION Regional Offices-General Services...

Correlation of intact sensibility and neuropathic pain-related behaviors in eight inbred and outbred rat strains and selection lines.

PubMed

Shir, Y; Zeltser, R; Vatine, J J; Carmi, G; Belfer, I; Zangen, A; Overstreet, D; Raber, P; Seltzer, Z

2001-02-01

In some rat strains, total hindpaw denervation triggers autotomy, a behavior of self mutilation presumably related to neuropathic pain. Partial sciatic ligation (PSL) in rats produces tactile allodynia and heat hyperalgesia but not autotomy. Our aims in this study were to examine: (1) whether sensibility of intact rats to noxious and non-noxious stimuli is strain-dependent; (2) whether sensibility of intact rats could predict levels of autotomy, or of allodynia and hyperalgesia in the PSL model; and (3) whether autotomy levels are correlated with levels of allodynia or hyperalgesia. Here we report that in two inbred rat strains (Lewis and Fisher 344), two outbred rat strains (Sabra and Sprague-Dawley) and four selection lines of rats (Genetically Epilepsy-Prone Rats, High Autotomy, Low Autotomy and Flinders Sensitive Line), tactile sensitivity and response duration to noxious heat of intact animals were strain-dependent. Levels of autotomy following hindpaw denervation and of allodynia and hyperalgesia in the PSL model were also strain-dependent. Thus, these traits are determined in part by genetic factors. Sensory sensibility of intact rats was not correlated with levels of autotomy following total denervation, or allodynia and hyperalgesia following partial denervation. We suggest that preoperative sensibility of intact rats is not a predictor of levels of neuropathic disorders following nerve injury. Likewise, no correlation was found between autotomy, allodynia and hyperalgesia, suggesting that neuropathic pain behaviors triggered by nerve injury of different etiologies are mediated by differing mechanisms.

The effect of intact talin and talin tail fragment on actin filament dynamics and structure depends on pH and ionic strength.

PubMed

Goldmann, W H; Hess, D; Isenberg, G

1999-03-01

We employed quasi-elastic light scattering and electron microscopy to investigate the influence of intact talin and talin tail fragment on actin filament dynamics and network structure. Using these methods, we confirm previous reports that intact talin induces cross-linking as well as filament shortening on actin networks. We now show that the effect of intact talin as well as talin tail fragment on actin networks is controlled by pH and ionic strength. At pH 7.5, actin filament dynamics in the presence of intact talin and talin tail fragment are characterized by a rapid decay of the dynamic structure factor and by a square root power law for the stretched exponential decay which is in contrast with the theory for pure actin solutions. At pH 6 and low ionic strength, intact talin cross-links actin filaments more tightly than talin tail fragment. Talin head fragment showed no effect on actin networks, indicating that the actin binding sites reside probably exclusively within the tail domain.

GBS: Global 3D simulation of tokamak edge region

NASA Astrophysics Data System (ADS)

Zhu, Ben; Fisher, Dustin; Rogers, Barrett; Ricci, Paolo

2012-10-01

A 3D two-fluid global code, namely Global Braginskii Solver (GBS), is being developed to explore the physics of turbulent transport, confinement, self-consistent profile formation, pedestal scaling and related phenomena in the edge region of tokamaks. Aimed at solving drift-reduced Braginskii equations [1] in complex magnetic geometry, the GBS is used for turbulence simulation in SOL region. In the recent upgrade, the simulation domain is expanded into close flux region with twist-shift boundary conditions. Hence, the new GBS code is able to explore global transport physics in an annular full-torus domain from the top of the pedestal into the far SOL. We are in the process of identifying and analyzing the linear and nonlinear instabilities in the system using the new GBS code. Preliminary results will be presented and compared with other codes if possible.[4pt] [1] A. Zeiler, J. F. Drake and B. Rogers, Phys. Plasmas 4, 2134 (1997)

Isolation and characterization of a cDNA clone for the complete protein coding region of the delta subunit of the mouse acetylcholine receptor.

PubMed Central

LaPolla, R J; Mayne, K M; Davidson, N

1984-01-01

A mouse cDNA clone has been isolated that contains the complete coding region of a protein highly homologous to the delta subunit of the Torpedo acetylcholine receptor (AcChoR). The cDNA library was constructed in the vector lambda 10 from membrane-associated poly(A)+ RNA from BC3H-1 mouse cells. Surprisingly, the delta clone was selected by hybridization with cDNA encoding the gamma subunit of the Torpedo AcChoR. The nucleotide sequence of the mouse cDNA clone contains an open reading frame of 520 amino acids. This amino acid sequence exhibits 59% and 50% sequence homology to the Torpedo AcChoR delta and gamma subunits, respectively. However, the mouse nucleotide sequence has several stretches of high homology with the Torpedo gamma subunit cDNA, but not with delta. The mouse protein has the same general structural features as do the Torpedo subunits. It is encoded by a 3.3-kilobase mRNA. There is probably only one, but at most two, chromosomal genes coding for this or closely related sequences. Images PMID:6096870

Context-aware and locality-constrained coding for image categorization.

PubMed

Xiao, Wenhua; Wang, Bin; Liu, Yu; Bao, Weidong; Zhang, Maojun

2014-01-01

Improving the coding strategy for BOF (Bag-of-Features) based feature design has drawn increasing attention in recent image categorization works. However, the ambiguity in coding procedure still impedes its further development. In this paper, we introduce a context-aware and locality-constrained Coding (CALC) approach with context information for describing objects in a discriminative way. It is generally achieved by learning a word-to-word cooccurrence prior to imposing context information over locality-constrained coding. Firstly, the local context of each category is evaluated by learning a word-to-word cooccurrence matrix representing the spatial distribution of local features in neighbor region. Then, the learned cooccurrence matrix is used for measuring the context distance between local features and code words. Finally, a coding strategy simultaneously considers locality in feature space and context space, while introducing the weight of feature is proposed. This novel coding strategy not only semantically preserves the information in coding, but also has the ability to alleviate the noise distortion of each class. Extensive experiments on several available datasets (Scene-15, Caltech101, and Caltech256) are conducted to validate the superiority of our algorithm by comparing it with baselines and recent published methods. Experimental results show that our method significantly improves the performance of baselines and achieves comparable and even better performance with the state of the arts.

Ground-state coding in partially connected neural networks

NASA Technical Reports Server (NTRS)

Baram, Yoram

1989-01-01

Patterns over (-1,0,1) define, by their outer products, partially connected neural networks, consisting of internally strongly connected, externally weakly connected subnetworks. The connectivity patterns may have highly organized structures, such as lattices and fractal trees or nests. Subpatterns over (-1,1) define the subcodes stored in the subnetwork, that agree in their common bits. It is first shown that the code words are locally stable stares of the network, provided that each of the subcodes consists of mutually orthogonal words or of, at most, two words. Then it is shown that if each of the subcodes consists of two orthogonal words, the code words are the unique ground states (absolute minima) of the Hamiltonian associated with the network. The regions of attraction associated with the code words are shown to grow with the number of subnetworks sharing each of the neurons. Depending on the particular network architecture, the code sizes of partially connected networks can be vastly greater than those of fully connected ones and their error correction capabilities can be significantly greater than those of the disconnected subnetworks. The codes associated with lattice-structured and hierarchical networks are discussed in some detail.

A long-term, integrated impact assessment of alternative building energy code scenarios in China

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

Yu, Sha; Eom, Jiyong; Evans, Meredydd

2014-04-01

China is the second largest building energy user in the world, ranking first and third in residential and commercial energy consumption. Beginning in the early 1980s, the Chinese government has developed a variety of building energy codes to improve building energy efficiency and reduce total energy demand. This paper studies the impact of building energy codes on energy use and CO2 emissions by using a detailed building energy model that represents four distinct climate zones each with three building types, nested in a long-term integrated assessment framework GCAM. An advanced building stock module, coupled with the building energy model, ismore » developed to reflect the characteristics of future building stock and its interaction with the development of building energy codes in China. This paper also evaluates the impacts of building codes on building energy demand in the presence of economy-wide carbon policy. We find that building energy codes would reduce Chinese building energy use by 13% - 22% depending on building code scenarios, with a similar effect preserved even under the carbon policy. The impact of building energy codes shows regional and sectoral variation due to regionally differentiated responses of heating and cooling services to shell efficiency improvement.« less

[Variation of CAG repeats in coding region of ATXN2 gene in different ethnic groups].

PubMed

Chen, Xiao-Chen; Sun, Hao; Mi, Dong-Qing; Huang, Xiao-Qin; Lin, Ke-Qin; Yi, Wen; Yu, Liang; Shi, Lei; Shi, Li; Yang, Zhao-Qing; Chu, Jia-You

2011-04-01

Toinvestigate CAG repeats variation of ATXN2 gene coding region in six ethnic groups that live in comparatively different environments, to evaluate whether these variations are under positive selection, and to find factors driving selection effects, 291 unrelated healthy individuals were collected from six ethnic groups and their STR geneotyping was performed. The frequencies of alleles and genotypes were counted and thereby Slatkin's linearized Fst values were calculated. The UPGMA tree against this gene was constructed. The MDS analysis among these groups was carried out as well. The results from the linearized Fst values indicated that there were significant evolutionary differences of the STR in ATXN2 gene between Hui and Yi groups, but not among the other 4 groups. Further analysis was performed by combining our data with published data obtained from other groups. These results indicated that there were significant differences between Japanese and other groups including Hui, Hani, Yunnan Mongolian, and Inner Mongolian. Both Hui and Mongolian from Inner Mongolia were significantly different from Han. In conclusion, the six ethnic groups had their own distribution characterizations of allelic frequencies of ATXN2 STR, and the potential cause of frequency changes in rare alleles could be the consequence of positive selection.

Exotic plant species associations with horse trails, old roads, and intact native communities in the Missouri Ozarks

USGS Publications Warehouse

Stroh, E.D.; Struckhoff, M.A.

2009-01-01

We compared the extent to which exotic species are associated with horse trails, old roads, and intact communities within three native vegetation types in Ozark National Scenic Riverways, Missouri. We used a general linear model procedure and a Bonferroni multiple comparison test to compare exotic species richness, exotic to native species ratios, and exotic species percent cover across three usage types (horse trails, old roads, and intact communities) and three community types (river bottoms, upland waterways, and glades). We found that both exotic species richness and the ratio of exotic species to native species were greater in plots located along horse trails than in plots located either in intact native communities or along old roads. Native community types did not differ in the number of exotic species present, but river bottoms had a significantly higher exotic to native species ratio than glades. Continued introduction of exotic plant propagules may explain why horse trails contain more exotic species than other areas in a highly disturbed landscape.

Intact vinculin protein is required for control of cell shape, cell mechanics, and rac-dependent lamellipodia formation

NASA Technical Reports Server (NTRS)

Goldmann, Wolfgang H.; Ingber, Donald E.

2002-01-01

Studies were carried out using vinculin-deficient F9 embryonic carcinoma (gamma229) cells to analyze the relationship between structure and function within the focal adhesion protein vinculin, in the context of control of cell shape, cell mechanics, and movement. Atomic force microscopy studies revealed that transfection of the head (aa 1-821) or tail (aa 811-1066) domain of vinculin, alone or together, was unable to fully reverse the decrease in cell stiffness, spreading, and lamellipodia formation caused by vinculin deficiency. In contrast, replacement with intact vinculin completely restored normal cell mechanics and spreading regardless of whether its tyrosine phosphorylation site was deleted. Constitutively active rac also only induced extension of lamellipodia when microinjected into cells that expressed intact vinculin protein. These data indicate that vinculin's ability to physically couple integrins to the cytoskeleton, to mechanically stabilize cell shape, and to support rac-dependent lamellipodia formation all appear to depend on its intact three-dimensional structure.

Elemental and isotopic imaging to study biogeochemical functioning of intact soil micro-environments

NASA Astrophysics Data System (ADS)

Mueller, Carsten W.

2017-04-01

The complexity of soils extends from the ecosystem-scale to individual micro-aggregates, where nano-scale interactions between biota, organic matter (OM) and mineral particles are thought to control the long-term fate of soil carbon and nitrogen. It is known that such biogeochemical processes show disproportionally high reaction rates within nano- to micro-meter sized isolated zones ('hot spots') in comparison to surrounding areas. However, the majority of soil research is conducted on large bulk (> 1 g) samples, which are often significantly altered prior to analysis and analysed destructively. Thus it has previously been impossible to study elemental flows (e.g. C and N) between plants, microbes and soil in complex environments at the necessary spatial resolution within an intact soil system. By using nano-scale secondary ion mass spectrometry (NanoSIMS) in concert with other imaging techniques (e.g. scanning electron microscopy (SEM) and micro computed tomography (µCT)), classic analyses (isotopic and elemental analysis) and biochemical methods (e.g. GC-MS) it is possible to exhibit a more complete picture of soil processes at the micro-scale. I will present exemplarily results about the fate and distribution of organic C and N in complex micro-scale soil structures for a range of intact soil systems. Elemental imaging was used to study initial soil formation as an increase in the structural connectivity of micro-aggregates. Element distribution will be presented as a key to detect functional spatial patterns and biogeochemical hot spots in macro-aggregate functioning and development. In addition isotopic imaging will be demonstrated as a key to trace the fate of plant derived OM in the intact rhizosphere from the root to microbiota and mineral soil particles. Especially the use of stable isotope enrichment (e.g. 13CO2, 15NH4+) in conjunction with NanoSIMS allows to directly trace the fate of OM or nutrients in soils at the relevant scale (e.g. assimilate C

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

PubMed

Gel, Bernat; Díez-Villanueva, Anna; Serra, Eduard; Buschbeck, Marcus; Peinado, Miguel A; Malinverni, Roberto

2016-01-15

Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). rmalinverni@carrerasresearch.org. © The Author 2015. Published by Oxford University Press.

Fabrication of enzyme-based coatings on intact multi-walled carbon nanotubes as highly effective electrodes in biofuel cells

NASA Astrophysics Data System (ADS)

Kim, Byoung Chan; Lee, Inseon; Kwon, Seok-Joon; Wee, Youngho; Kwon, Ki Young; Jeon, Chulmin; An, Hyo Jin; Jung, Hee-Tae; Ha, Su; Dordick, Jonathan S.; Kim, Jungbae

2017-01-01

CNTs need to be dispersed in aqueous solution for their successful use, and most methods to disperse CNTs rely on tedious and time-consuming acid-based oxidation. Here, we report the simple dispersion of intact multi-walled carbon nanotubes (CNTs) by adding them directly into an aqueous solution of glucose oxidase (GOx), resulting in simultaneous CNT dispersion and facile enzyme immobilization through sequential enzyme adsorption, precipitation, and crosslinking (EAPC). The EAPC achieved high enzyme loading and stability because of crosslinked enzyme coatings on intact CNTs, while obviating the chemical pretreatment that can seriously damage the electron conductivity of CNTs. EAPC-driven GOx activity was 4.5- and 11-times higher than those of covalently-attached GOx (CA) on acid-treated CNTs and simply-adsorbed GOx (ADS) on intact CNTs, respectively. EAPC showed no decrease of GOx activity for 270 days. EAPC was employed to prepare the enzyme anodes for biofuel cells, and the EAPC anode produced 7.5-times higher power output than the CA anode. Even with a higher amount of bound non-conductive enzymes, the EAPC anode showed 1.7-fold higher electron transfer rate than the CA anode. The EAPC on intact CNTs can improve enzyme loading and stability with key routes of improved electron transfer in various biosensing and bioelectronics devices.

The fourfold way of the genetic code.

PubMed

Jiménez-Montaño, Miguel Angel

2009-11-01

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.

Numerical and analytical bounds on threshold error rates for hypergraph-product codes

NASA Astrophysics Data System (ADS)

Kovalev, Alexey A.; Prabhakar, Sanjay; Dumer, Ilya; Pryadko, Leonid P.

2018-06-01

We study analytically and numerically decoding properties of finite-rate hypergraph-product quantum low density parity-check codes obtained from random (3,4)-regular Gallager codes, with a simple model of independent X and Z errors. Several nontrivial lower and upper bounds for the decodable region are constructed analytically by analyzing the properties of the homological difference, equal minus the logarithm of the maximum-likelihood decoding probability for a given syndrome. Numerical results include an upper bound for the decodable region from specific heat calculations in associated Ising models and a minimum-weight decoding threshold of approximately 7 % .

Bioequivalence of cyclobenzaprine hydrochloride extended-release capsule taken intact or sprinkled over applesauce
.

PubMed

Adar, Liat; Zarycranski, William; Conner, Jill B; Dragone, Jeffrey; Janka, Lindsay; Rabinovich-Guilatt, Laura

2017-12-01

Difficulty swallowing pills can compromise pain control in painful musculoskeletal disorders. This open-label, 2-period crossover study assessed pharmacokinetics and safety of cyclobenzaprine extended-release (CER) 30-mg capsule contents sprinkled over applesauce compared with intact capsules in healthy subjects. 32 subjects were randomized to treatment sequences AB or BA (A = single CER intact capsule; B = single CER capsule contents sprinkled over applesauce (15 mL)). Treatments were separated by a ≥ 14-day washout. Pharmacokinetic assessments included maximum observed plasma drug concentration (C_max), time to C_max (t_max), time to first quantifiable plasma drug concentration (t_lag), and area under the plasma drug concentration-vs.-time curve from time 0 to the last measurable drug concentration (AUC_0-t) and extrapolated to infinity (AUC_0-∞). Bioequivalence was established if the 90% confidence intervals (CIs) of the geometric least squares (LS) means ratios of B:A of C_max, AUC_0-t, and AUC_0-∞ were 80 - 125%. Safety was also assessed. Mean plasma drug concentration-vs.-time profiles were similar for CER intact and sprinkled over applesauce. The 90% CIs of LS means ratios indicated bioequivalence: C_max 91.96 - 100.76%, AUC_0-t 96.18 - 103.50%, and AUC_0-∞ 95.70 - 103.07%. Median t_max was not significantly different (p > 0.05), and median t_lag was the same (1 hour). All adverse effects were mild and resolved during the study. No clinically meaningful changes were noted for clinical laboratory values. CER capsules intact and sprinkled over applesauce are bioequivalent. Sprinkling CER capsule contents is not expected to affect efficacy or safety and can, therefore, be an option for patients with musculoskeletal pain and difficulty swallowing capsules.
.

Low Density Parity Check Codes: Bandwidth Efficient Channel Coding

NASA Technical Reports Server (NTRS)

Fong, Wai; Lin, Shu; Maki, Gary; Yeh, Pen-Shu

2003-01-01

Low Density Parity Check (LDPC) Codes provide near-Shannon Capacity performance for NASA Missions. These codes have high coding rates R=0.82 and 0.875 with moderate code lengths, n=4096 and 8176. Their decoders have inherently parallel structures which allows for high-speed implementation. Two codes based on Euclidean Geometry (EG) were selected for flight ASIC implementation. These codes are cyclic and quasi-cyclic in nature and therefore have a simple encoder structure. This results in power and size benefits. These codes also have a large minimum distance as much as d,,, = 65 giving them powerful error correcting capabilities and error floors less than lo- BER. This paper will present development of the LDPC flight encoder and decoder, its applications and status.

Effect of lipoteichoic acid and lipids on lysis of intact cells of Streptococcus faecalis.

PubMed Central

Cleveland, R F; Daneo-Moore, L; Wicken, A J; Shockman, G D

1976-01-01

Autolysis of intact cells of Streptococcus faecalis was inhibited to a greater extent by phospholipids than by lipoteichoic acid, suggesting a possible difference in the accessibility of native autolysin to these substances. PMID:821938

Color-Coded Organelles.

ERIC Educational Resources Information Center

McLaughlin, Esther; And Others

1994-01-01

Describes how red beets can be used to demonstrate a variety of membrane phenomena. Some of the activities include observation of vacuoles; vacuoles in intact cells; isolation of vacuoles in physiological studies; demonstration of membrane integrity; and demonstration of ion diffusion and active transport with purified vacuoles. (ZWH)

Porcine intact and wounded skin responses to atmospheric nonthermal plasma.

PubMed

Wu, Andrew S; Kalghatgi, Sameer; Dobrynin, Danil; Sensenig, Rachel; Cerchar, Ekaternia; Podolsky, Erica; Dulaimi, Essel; Paff, Michelle; Wasko, Kimberly; Arjunan, Krishna Priya; Garcia, Kristin; Fridman, Gregory; Balasubramanian, Manjula; Ownbey, Robert; Barbee, Kenneth A; Fridman, Alexander; Friedman, Gary; Joshi, Suresh G; Brooks, Ari D

2013-01-01

Thermal plasma is a valued tool in surgery for its coagulative and ablative properties. We suggested through in vitro studies that nonthermal plasma can sterilize tissues, inactive pathogens, promote coagulation, and potentiate wound healing. The present research was undertaken to study acute toxicity in porcine skin tissues. We demonstrate that floating electrode-discharge barrier discharge (FE-DBD) nonthermal plasma is electrically safe to apply to living organisms for short periods. We investigated the effects of FE-DBD plasma on Yorkshire pigs on intact and wounded skin immediately after treatment or 24h posttreatment. Macroscopic or microscopic histological changes were identified using histological and immunohistochemical techniques. The changes were classified into four groups for intact skin: normal features, minimal changes or congestive changes, epidermal layer damage, and full burn and into three groups for wounded skin: normal, clot or scab, and full burn-like features. Immunohistochemical staining for laminin layer integrity showed compromise over time. A marker for double-stranded DNA breaks, γ-H2AX, increased over plasma-exposure time. These findings identified a threshold for plasma exposure of up to 900s at low power and <120s at high power. Nonthermal FE-DBD plasma can be considered safe for future studies of external use under these threshold conditions for evaluation of sterilization, coagulation, and wound healing. Copyright © 2013 Elsevier Inc. All rights reserved.

Benchmark studies of the gyro-Landau-fluid code and gyro-kinetic codes on kinetic ballooning modes

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

Tang, T. F.; Lawrence Livermore National Laboratory, Livermore, California 94550; Xu, X. Q.

2016-03-15

A Gyro-Landau-Fluid (GLF) 3 + 1 model has been recently implemented in BOUT++ framework, which contains full Finite-Larmor-Radius effects, Landau damping, and toroidal resonance [Ma et al., Phys. Plasmas 22, 055903 (2015)]. A linear global beta scan has been conducted using the JET-like circular equilibria (cbm18 series), showing that the unstable modes are kinetic ballooning modes (KBMs). In this work, we use the GYRO code, which is a gyrokinetic continuum code widely used for simulation of the plasma microturbulence, to benchmark with GLF 3 + 1 code on KBMs. To verify our code on the KBM case, we first perform the beta scan basedmore » on “Cyclone base case parameter set.” We find that the growth rate is almost the same for two codes, and the KBM mode is further destabilized as beta increases. For JET-like global circular equilibria, as the modes localize in peak pressure gradient region, a linear local beta scan using the same set of equilibria has been performed at this position for comparison. With the drift kinetic electron module in the GYRO code by including small electron-electron collision to damp electron modes, GYRO generated mode structures and parity suggest that they are kinetic ballooning modes, and the growth rate is comparable to the GLF results. However, a radial scan of the pedestal for a particular set of cbm18 equilibria, using GYRO code, shows different trends for the low-n and high-n modes. The low-n modes show that the linear growth rate peaks at peak pressure gradient position as GLF results. However, for high-n modes, the growth rate of the most unstable mode shifts outward to the bottom of pedestal and the real frequency of what was originally the KBMs in ion diamagnetic drift direction steadily approaches and crosses over to the electron diamagnetic drift direction.« less

High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins

PubMed Central

Berridge, Georgina; Chalk, Rod; D’Avanzo, Nazzareno; Dong, Liang; Doyle, Declan; Kim, Jung-In; Xia, Xiaobing; Burgess-Brown, Nicola; deRiso, Antonio; Carpenter, Elisabeth Paula; Gileadi, Opher

2011-01-01

We have developed a method for intact mass analysis of detergent-solubilized and purified integral membrane proteins using liquid chromatography–mass spectrometry (LC–MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2–5 μg of protein. The method is also compatible with our standard LC–MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment. PMID:21093405

Error-correction coding

NASA Technical Reports Server (NTRS)

Hinds, Erold W. (Principal Investigator)

1996-01-01

This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

Predictors of Attachment Security in Preschool Children from Intact and Divorced Families

ERIC Educational Resources Information Center

Nair, Hira; Murray, Ann D.

2005-01-01

The authors selected 58 mother-child dyads from divorced and intact families to participate in a study on the impact of divorce on preschoolers' attachment security. The authors explored pathways that lead to security of attachment. They found that mothers from divorced families were younger, had lower income levels, and had lower levels of…

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification.

PubMed

Liu, Ming-Qi; Zeng, Wen-Feng; Fang, Pan; Cao, Wei-Qian; Liu, Chao; Yan, Guo-Quan; Zhang, Yang; Peng, Chao; Wu, Jian-Qiang; Zhang, Xiao-Jin; Tu, Hui-Jun; Chi, Hao; Sun, Rui-Xiang; Cao, Yong; Dong, Meng-Qiu; Jiang, Bi-Yun; Huang, Jiang-Ming; Shen, Hua-Li; Wong, Catherine C L; He, Si-Min; Yang, Peng-Yuan

2017-09-05

The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with 15 N/ 13 C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.

A new infusion pathway intactness monitoring system.

PubMed

Ogawa, Hidekuni; Yonezawa, Yoshiharu; Maki, Hiromichi; Ninomiya, Ishio; Sata, Koji; Hamada, Shingo; Caldwell, W Morton

2006-01-01

A new infusion pathway monitoring system has been developed for hospital and home use. The system consists of linear integrated circuits and a low-power 8-bit single chip microcomputer which constantly monitors the infusion pathway intactness. An AC (alternating current) voltage is induced on the patient's body by electrostatic coupling from the normal 100 volt, 60 Hz AC power line wiring field in the patient's room. The induced AC voltage can be recorded by a main electrode wrapped around the infusion polyvinyl chloride tube. A reference electrode is wrapped on the electrode to monitor the AC voltage around the main electrode. If the injection needle or infusion tube becomes detached, then the system detects changes in the induced AC voltages and alerts the nursing station, via the nurse call system or PHS (personal handy phone system).

Identification Code of Interstellar Cloud within IRAF

NASA Astrophysics Data System (ADS)

Lee, Youngung; Jung, Jae Hoon; Kim, Hyun-Goo

1997-12-01

We present a code which identifies individual clouds in crowded region using IMFORT interface within Image Reduction and Analysis Facility(IRAF). We define a cloud as an object composed of all pixels in longitude, latitude, and velocity that are simply connected and that lie above some threshold temperature. The code searches the whole pixels of the data cube in efficient way to isolate individual clouds. Along with identification of clouds it is designed to estimate their mean values of longitudes, latitudes, and velocities. In addition, a function of generating individual images(or cube data) of identified clouds is added up. We also present identified individual clouds using a 12CO survey data cube of Galactic Anticenter Region(Lee et al. 1997) as a test example. We used a threshold temperature of 5 sigma rms noise level of the data. With a higher threshold temperature, we isolated subclouds of a huge cloud identified originally. As the most important parameter to identify clouds is the threshold value, its effect to the size and velocity dispersion is discussed rigorously.

The design of wavefront coded imaging system

NASA Astrophysics Data System (ADS)

Lan, Shun; Cen, Zhaofeng; Li, Xiaotong

2016-10-01

Wavefront Coding is a new method to extend the depth of field, which combines optical design and signal processing together. By using optical design software ZEMAX ,we designed a practical wavefront coded imaging system based on a conventional Cooke triplet system .Unlike conventional optical system, the wavefront of this new system is modulated by a specially designed phase mask, which makes the point spread function (PSF)of optical system not sensitive to defocus. Therefore, a series of same blurred images obtained at the image plane. In addition, the optical transfer function (OTF) of the wavefront coded imaging system is independent of focus, which is nearly constant with misfocus and has no regions of zeros. All object information can be completely recovered through digital filtering at different defocus positions. The focus invariance of MTF is selected as merit function in this design. And the coefficients of phase mask are set as optimization goals. Compared to conventional optical system, wavefront coded imaging system obtains better quality images under different object distances. Some deficiencies appear in the restored images due to the influence of digital filtering algorithm, which are also analyzed in this paper. The depth of field of the designed wavefront coded imaging system is about 28 times larger than initial optical system, while keeping higher optical power and resolution at the image plane.

A Data Parallel Multizone Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Jespersen, Dennis C.; Levit, Creon; Kwak, Dochan (Technical Monitor)

1995-01-01

We have developed a data parallel multizone compressible Navier-Stokes code on the Connection Machine CM-5. The code is set up for implicit time-stepping on single or multiple structured grids. For multiple grids and geometrically complex problems, we follow the "chimera" approach, where flow data on one zone is interpolated onto another in the region of overlap. We will describe our design philosophy and give some timing results for the current code. The design choices can be summarized as: 1. finite differences on structured grids; 2. implicit time-stepping with either distributed solves or data motion and local solves; 3. sequential stepping through multiple zones with interzone data transfer via a distributed data structure. We have implemented these ideas on the CM-5 using CMF (Connection Machine Fortran), a data parallel language which combines elements of Fortran 90 and certain extensions, and which bears a strong similarity to High Performance Fortran (HPF). One interesting feature is the issue of turbulence modeling, where the architecture of a parallel machine makes the use of an algebraic turbulence model awkward, whereas models based on transport equations are more natural. We will present some performance figures for the code on the CM-5, and consider the issues involved in transitioning the code to HPF for portability to other parallel platforms.

Plasma concentrations of lidocaine in dogs following lidocaine patch application over an incision compared to intact skin.

PubMed

Joudrey, S D; Robinson, D A; Kearney, M T; Papich, M G; da Cunha, A F

2015-12-01

The objective was to compare plasma lidocaine concentrations when a commercially available 5% lidocaine patch was placed on intact skin vs. an incision. Our hypothesis was that greater absorption of lidocaine would occur from the incision site compared to intact skin. Ten dogs were used in a crossover design. A patch was placed over an incision, and then after a washout period, a patch was placed over intact skin. Plasma lidocaine concentrations were measured at patch placement; 20, 40 and 60 min; and 2, 4, 6, 12, 24, 36, 48, 72 and 96 h after patch placement. After patch removal, the skin was graded using a subjective skin reaction system. No dogs required rescue analgesia, and no toxicity or skin reaction was noted. Mean ± SD AUC and CMAX were 3054.29 ± 1095.93 ng·h/mL and 54.1 ± 15.84 ng/mL in the Incision Group, and 2269.9 ± 1037.08 ng·h/mL and 44.5 ± 16.34 ng/mL in the No-Incision Group, respectively. The AUC was significantly higher in the Incision Group. The results of the study demonstrate that the actual body exposure to lidocaine was significantly higher when an incision was present compared to intact skin. No adverse effects were observed from either treatment. Efficacy was not evaluated. © 2015 John Wiley & Sons Ltd.

A Pharmacokinetic Study Comparing Eslicarbazepine Acetate Administered Orally as a Crushed or Intact Tablet in Healthy Volunteers.

PubMed

Sunkaraneni, Soujanya; Kharidia, Jahnavi; Schutz, Ralph; Blum, David; Cheng, Hailong

2016-07-01

The relative bioequivalence of crushed versus intact eslicarbazepine acetate (ESL) tablets (800 mg) administered orally in healthy adults was evaluated in an open-label, randomized, 2-period crossover study with a 5-day washout between treatments. Sample blood levels of eslicarbazepine and (R)-licarbazepine were determined; pharmacokinetic parameters were derived for eslicarbazepine. Bioequivalence was established if the 90% confidence intervals (CIs) for the geometric mean treatment ratios of eslicarbazepine AUC(0-∞) and Cmax were within the prespecified 80%-125% range. Twenty-seven subjects in the intent-to-treat population (n = 28) completed both treatment periods. Eslicarbazepine exposure measures were similar for crushed versus intact ESL tablets: average Cmax , 11 700 versus 11 500 ng/mL; AUC(0-∞) , 225 000 versus 234 000 ng·h/mL; AUC(0-last) , 222 000 versus 231 000 ng·h/mL, respectively. Geometric least squares mean ratios (90%CIs) comparing eslicarbazepine exposure measures were within the 80%-125% range (Cmax , 102.63% [97.07%-108.51%]; AUC(0-∞) , 96.72% [94.36%-99.13%]; AUC0-last , 96.69% [94.24%-99.21%]). In conclusion, ESL administered orally as a crushed tablet sprinkled on applesauce, or intact were bioequivalent in healthy subjects. Eslicarbazepine bioavailability was not significantly altered by crushing, indicating that ESL tablets can be administered intact or crushed. © 2016, The American College of Clinical Pharmacology.

Sensitivity Analysis and Uncertainty Quantification for the LAMMPS Molecular Dynamics Simulation Code

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

Picard, Richard Roy; Bhat, Kabekode Ghanasham

2017-07-18

We examine sensitivity analysis and uncertainty quantification for molecular dynamics simulation. Extreme (large or small) output values for the LAMMPS code often occur at the boundaries of input regions, and uncertainties in those boundary values are overlooked by common SA methods. Similarly, input values for which code outputs are consistent with calibration data can also occur near boundaries. Upon applying approaches in the literature for imprecise probabilities (IPs), much more realistic results are obtained than for the complacent application of standard SA and code calibration.

Quality of head injury coding from autopsy reports with AIS © 2005 update 2008.

PubMed

Schick, Sylvia; Humrich, Anton; Graw, Matthias

2018-02-28

ABSTACT Objective: Coding injuries from autopsy reports of traffic accident victims according to Abbreviated Injury Scale AIS © 2005 update 2008 [1] is quite time consuming. The suspicion arose, that many issues leading to discussion between coder and control reader were based on information required by the AIS that was not documented in the autopsy reports. To quantify this suspicion, we introduced an AIS-detail-indicator (AIS-DI). To each injury in the AIS Codebook one letter from A to N was assigned indicating the level of detail. Rules were formulated to receive repeatable assignments. This scheme was applied to a selection of 149 multiply injured traffic fatalities. The frequencies of "not A" codes were calculated for each body region and it was analysed, why the most detailed level A had not been coded. As a first finding, the results of the head region are presented. 747 AIS head injury codes were found in 137 traffic fatalities, and 60% of these injuries were coded with an AIS-DI of level A. There are three different explanations for codes of AIS-DI "not A": Group 1 "Missing information in autopsy report" (5%), Group 2 "Clinical data required by AIS" (20%), and Group 3 "AIS system determined" (15%). Groups 1 and 2 show consequences for the ISS in 25 cases. Other body regions might perform differently. The AIS-DI can indicate the quality of the underlying data basis and, depending on the aims of different AIS users it can be a helpful tool for quality checks.

Rate-compatible punctured convolutional codes (RCPC codes) and their applications

NASA Astrophysics Data System (ADS)

Hagenauer, Joachim

1988-04-01

The concept of punctured convolutional codes is extended by punctuating a low-rate 1/N code periodically with period P to obtain a family of codes with rate P/(P + l), where l can be varied between 1 and (N - 1)P. A rate-compatibility restriction on the puncturing tables ensures that all code bits of high rate codes are used by the lower-rate codes. This allows transmission of incremental redundancy in ARQ/FEC (automatic repeat request/forward error correction) schemes and continuous rate variation to change from low to high error protection within a data frame. Families of RCPC codes with rates between 8/9 and 1/4 are given for memories M from 3 to 6 (8 to 64 trellis states) together with the relevant distance spectra. These codes are almost as good as the best known general convolutional codes of the respective rates. It is shown that the same Viterbi decoder can be used for all RCPC codes of the same M. The application of RCPC codes to hybrid ARQ/FEC schemes is discussed for Gaussian and Rayleigh fading channels using channel-state information to optimize throughput.

Aboveground biomass variability across intact and degraded forests in the Brazilian Amazon

Treesearch

Marcos Longo; Michael Keller; Maiza N. dos-Santos; Veronika Leitold; Ekena R. Pinagé; Alessandro Baccini; Sassan Saatchi; Euler M. Nogueira; Mateus Batistella; Douglas C. Morton

2016-01-01

Deforestation rates have declined in the Brazilian Amazon since 2005, yet degradation from logging, fire, and fragmentation has continued in frontier forests. In this study we quantified the aboveground carbon density (ACD) in intact and degraded forests using the largest data set of integrated forest inventory plots (n = 359) and airborne lidar data (18,000 ha)...

Intact Pneumococci Trigger Transcription of Interferon-Related Genes in Human Monocytes, while Fragmented, Autolyzed Bacteria Subvert This Response

PubMed Central

Nordén, Rickard; Martner, Anna; Samuelsson, Ebba; Hynsjö, Lars; Wold, Agnes E.

2017-01-01

ABSTRACT A peculiar trait of pneumococci (Streptococcus pneumoniae) is their propensity to undergo spontaneous lysis during stationary growth due to activation of the enzyme autolysin (LytA), which fragments the peptidoglycan cell wall. The fragments that are generated upon autolysis impair phagocytosis and reduce production of interleukin-12 (IL-12) and gamma interferon (IFN-γ) by human leukocytes in response to intact pneumococci, thereby impeding crucial host defenses. The objective was to identify additional monocyte genes whose transcription is induced by intact pneumococci and subverted by autolyzed bacteria. Monocytes were isolated from healthy blood donors and stimulated for 3 h with UV-inactivated S. pneumoniae (Rx1PLY− LytA+ strain), which is capable of autolyzing, its LytA− isogenic autolysin-deficient mutant, or a mixture of the two (containing twice the initial bacterial concentration). Gene expression was assessed by Illumina microarray, and selected findings were confirmed by reverse transcription-quantitative real-time PCR (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and flow cytometry. In all, we identified 121 genes that were upregulated to a significantly higher degree by intact than autolyzed pneumococci. These included IFNB1 and a large set of interferon-induced genes, such as IFIT3, RSAD2, CFCL1, and CXCL10 genes, as well as IL12B and CD40 genes. RT-qPCR revealed that transcription of these genes in response to intact pneumococci diminished when autolyzed pneumococci were admixed and that this pattern was independent of pneumolysin. Thus, transcription of interferon-related genes is triggered by intact pneumococci and subverted by fragments generated by spontaneous bacterial autolysis. We suggest that interferon-related pathways are important for elimination of pneumococci and that autolysis contributes to virulence by extinguishing these pathways. PMID:28223347

Amino acid codes in mitochondria as possible clues to primitive codes

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1981-01-01

Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a 'frozen accident.' The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.

2-Methoxyestradiol Reduces Angiotensin II-Induced Hypertension and Renal Dysfunction in Ovariectomized Female and Intact Male Mice.

PubMed

Pingili, Ajeeth K; Davidge, Karen N; Thirunavukkarasu, Shyamala; Khan, Nayaab S; Katsurada, Akemi; Majid, Dewan S A; Gonzalez, Frank J; Navar, L Gabriel; Malik, Kafait U

2017-06-01

Cytochrome P450 1B1 protects against angiotensin II (Ang II)-induced hypertension and associated cardiovascular changes in female mice, most likely via production of 2-methoxyestradiol. This study was conducted to determine whether 2-methoxyestradiol ameliorates Ang II-induced hypertension, renal dysfunction, and end-organ damage in intact Cyp1b1 -/- , ovariectomized female, and Cyp1b1 +/+ male mice. Ang II or vehicle was infused for 2 weeks and administered concurrently with 2-methoxyestradiol. Mice were placed in metabolic cages on day 12 of Ang II infusion for urine collection for 24 hours. 2-Methoxyestradiol reduced Ang II-induced increases in systolic blood pressure, water consumption, urine output, and proteinuria in intact female Cyp1b1 -/- and ovariectomized mice. 2-Methoxyestradiol also reduced Ang II-induced increase in blood pressure, water intake, urine output, and proteinuria in Cyp1b1 +/+ male mice. Treatment with 2-methoxyestradiol attenuated Ang II-induced end-organ damage in intact Cyp1b1 -/- and ovariectomized Cyp1b1 +/+ and Cyp1b1 -/- female mice and Cyp1b1 +/+ male mice. 2-Methoxyestradiol mitigated Ang II-induced increase in urinary excretion of angiotensinogen in intact Cyp1b1 -/- and ovariectomized Cyp1b1 +/+ and Cyp1b1 -/- female mice but not in Cyp1b1 +/+ male mice. The G protein-coupled estrogen receptor 1 antagonist G-15 failed to alter Ang II-induced increases in blood pressure and renal function in Cyp1b1 +/+ female mice. These data suggest that 2-methoxyestradiol reduces Ang II-induced hypertension and associated end-organ damage in intact Cyp1b1 -/- , ovariectomized Cyp1b1 +/+ and Cyp1b1 -/- female mice, and Cyp1b1 +/+ male mice independent of G protein-coupled estrogen receptor 1. Therefore, 2-methoxyestradiol could serve as a therapeutic agent for treating hypertension and associated pathogenesis in postmenopausal females, and in males. © 2017 American Heart Association, Inc.

2-METHOXYESTRADIOL REDUCES ANGIOTENSIN II-INDUCED HYPERTENSION AND RENAL DYSFUNCTION IN OVARIECTOMIZED FEMALE AND INTACT MALE MICE

PubMed Central

Pingili, Ajeeth K.; Davidge, Karen N.; Thirunavukkarasu, Shyamala; Khan, Nayaab S.; Katsurada, Akemi; Majid, Dewan S. A.; Gonzalez, Frank J.; Navar, L. Gabriel; Malik, Kafait U.

2017-01-01

cytochrome P45 1B1 protects against angiotensin II-induced hypertension and associated cardiovascular changes in female mice, most likely via production of 2-methoxyestradiol. This study was conducted to determine if 2-methoxyestradiol ameliorates angiotensin II-induced hypertension, renal dysfunction, and end-organ damage in intact Cyp1b1−/−, ovariectomized female, and in Cyp1b1+/+ male mice. Ang II or vehicle was infused for 2 weeks and administered concurrently with 2-methoxyestradiol. Mice were placed in metabolic cages on day 12 of Ang II infusion for urine collection for 24 h. 2-Methoxyestradiol reduced angiotensin II-induced increases in systolic blood pressure, water consumption, urine output, and proteinuria in intact female Cyp1b1−/− and ovariectomized mice. 2-Methoxyestradiol also reduced Ang II-induced increase in blood pressure, water intake, urine output, and proteinuria in Cyp1b1+/+ male mice. Treatment with 2-methoxyestradiol attenuated Ang II-induced end-organ damage in intact Cyp1b1−/− and ovariectomized Cyp1b1+/+ and Cyp1b1−/− female mice, and Cyp1b1+/+ male mice. 2-Methoxyestradiol mitigated Ang II-induced increase in urinary excretion of angiotensinogen in intact Cyp1b1−/− and ovariectomized Cyp1b1+/+ and Cyp1b1−/− female mice but not in Cyp1b1+/+ male mice. The G-protein-coupled estrogen receptor 1 antagonist G-15 failed to alter Ang II-induced increases in blood pressure and renal function in Cyp1b1+/+ female mice. These data suggest that 2-methoxyestradiol reduces angiotensin II-induced hypertension and associated end-organ damage in intact Cyp1b1−/−, ovariectomized Cyp1b1+/+ and Cyp1b1−/− female mice, and Cyp1b1+/+ male mice independent of G protein-coupled estrogen receptor 1. Therefore, 2-methoxyestradiol could serve as a therapeutic agent for treating hypertension and associated pathogenesis in postmenopausal females, and in males. PMID:28416584

Analysis of quantum error-correcting codes: Symplectic lattice codes and toric codes

NASA Astrophysics Data System (ADS)

Harrington, James William

Quantum information theory is concerned with identifying how quantum mechanical resources (such as entangled quantum states) can be utilized for a number of information processing tasks, including data storage, computation, communication, and cryptography. Efficient quantum algorithms and protocols have been developed for performing some tasks (e.g. , factoring large numbers, securely communicating over a public channel, and simulating quantum mechanical systems) that appear to be very difficult with just classical resources. In addition to identifying the separation between classical and quantum computational power, much of the theoretical focus in this field over the last decade has been concerned with finding novel ways of encoding quantum information that are robust against errors, which is an important step toward building practical quantum information processing devices. In this thesis I present some results on the quantum error-correcting properties of oscillator codes (also described as symplectic lattice codes) and toric codes. Any harmonic oscillator system (such as a mode of light) can be encoded with quantum information via symplectic lattice codes that are robust against shifts in the system's continuous quantum variables. I show the existence of lattice codes whose achievable rates match the one-shot coherent information over the Gaussian quantum channel. Also, I construct a family of symplectic self-dual lattices and search for optimal encodings of quantum information distributed between several oscillators. Toric codes provide encodings of quantum information into two-dimensional spin lattices that are robust against local clusters of errors and which require only local quantum operations for error correction. Numerical simulations of this system under various error models provide a calculation of the accuracy threshold for quantum memory using toric codes, which can be related to phase transitions in certain condensed matter models. I also present

Local transmural action potential gradients are absent in the isolated, intact dog heart but present in the corresponding coronary-perfused wedge.

PubMed

Boukens, Bastiaan J; Meijborg, Veronique M F; Belterman, Charly N; Opthof, Tobias; Janse, Michiel J; Schuessler, Richard B; Coronel, Ruben; Efimov, Igor R

2017-05-01

The left ventricular (LV) coronary-perfused canine wedge preparation is a model commonly used for studying cardiac repolarization. In wedge studies, transmembrane potentials typically are recorded; whereas, extracellular electrical recordings are commonly used in intact hearts. We compared electrically measured activation recovery interval (ARI) patterns in the intact heart with those recorded at the same location in the LV wedge preparation. We also compared electrically recorded and optically obtained ARIs in the LV wedge preparation. Five Langendorff-perfused canine hearts were paced from the right atrium. Local activation and repolarization times were measured with eight transmural needle electrodes. Subsequently, left ventricular coronary-perfused wedge preparations were prepared from these hearts while the electrodes remained in place. Three electrodes remained at identical positions as in the intact heart. Both electrograms and optical action potentials were recorded (pacing cycle length 400-4000 msec) and activation and repolarization patterns were analyzed. ARIs found in the subepicardium were shorter than in the subendocardium in the LV wedge preparation but not in the intact heart. The transmural ARI gradient recorded at the cut surface of the wedge was not different from that recorded internally. ARIs recorded internally and at the cut surface in the LV wedge preparation, both correlated with optically recorded action potentials. ARI and RT gradients in the LV wedge preparation differed from those in the intact canine heart, implying that those observations in human LV wedge preparations also should be extrapolated to the intact human heart with caution. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Provisional Coding Practices: Are They Really a Waste of Time?

PubMed

Krypuy, Matthew; McCormack, Lena

2006-11-01

In order to facilitate effective clinical coding and hence the precise financial reimbursement of acute services, in 2005 Western District Health Service (WDHS) (located in regional Victoria, Australia) undertook a provisional coding trial for inpatient medical episodes to determine the magnitude and accuracy of clinical documentation. Utilising clinical coding software installed on a laptop computer, provisional coding was undertaken for all current overnight inpatient episodes under each physician one day prior to attending their daily ward round. The provisionally coded episodes were re-coded upon the completion of the discharge summary and the final Diagnostic Related Group (DRG) allocation and weight were compared to the provisional DRG assignment. A total of 54 out of 220 inpatient medical episodes were provisionally coded. This represented approximately a 25% cross section of the population selected for observation. Approximately 67.6% of the provisionally allocated DRGs were accurate in contrast to 32.4% which were subject to change once the discharge summary was completed. The DRG changes were primarily due to: disease progression of a patient during their care episode which could not be identified by clinical coding staff due to discharge prior to the following scheduled ward round; the discharge destination of particular patients; and the accuracy of clinical documentation on the discharge summary. The information gathered from the provisional coding trial supported the hypothesis that clinical documentation standards were sufficient and adequate to support precise clinical coding and DRG assignment at WDHS. The trial further highlighted the importance of a complete and accurate discharge summary available during the coding process of acute inpatient episodes.

Number of minimum-weight code words in a product code

NASA Technical Reports Server (NTRS)

Miller, R. L.

1978-01-01

Consideration is given to the number of minimum-weight code words in a product code. The code is considered as a tensor product of linear codes over a finite field. Complete theorems and proofs are presented.

Intact error monitoring in combat Veterans with post-traumatic stress disorder.

PubMed

Swick, Diane; Honzel, Nikki; Turken, U

2015-11-30

The error-related negativity (ERN) is a neuroelectric signature of performance monitoring during speeded response time tasks. Previous studies indicate that individuals with anxiety disorders show ERN enhancements that correlate with the degree of clinical symptomology. Less is known about the error monitoring system in post-traumatic stress disorder (PTSD). PTSD is characterized by impairments in the regulation of fear and other emotional responses, as well as deficits in maintaining cognitive control. Here, combat Veterans with PTSD were compared to control Veterans in two different versions of the flanker task (n=13 or 14 per group). Replicating and extending previous findings, PTSD patients showed an intact ERN in both experiments. In addition, task performance and error compensation behavior were intact. Finally, ERN amplitude showed no relationship with self-reported PTSD, depression, or post-concussive symptoms. These results suggest that error monitoring represents a relative strength in PTSD that can dissociate from cognitive control functions that are impaired, such as response inhibition and sustained attention. A healthy awareness of errors in external actions could be leveraged to improve interoceptive awareness of emotional state. The results could have positive implications for PTSD treatments that rely on self-monitoring abilities, such as neurofeedback and mindfulness training. Published by Elsevier Ireland Ltd.

Double Outlet Right Ventricle With Intact Ventricular Septum: Avulsion or Exclusion.

PubMed

Menon, Sabarinath; Kumar, C J Ashok; Mathew, Thomas; Venkateshwarn, S; Jayakumar, K; Dharan, Baiju S

2016-03-01

Double outlet right ventricle (DORV) is almost always associated with a ventricular septal defect. The variant of DORV with intact ventricular septum is very uncommon and may be associated with fetal demise or death immediately after birth. Reports of successful palliation of these patients to the stage of superior cavopulmonary anastomosis (bidirectional Glenn shunt) are rare. We describe the case of a child with DORV with intact ventricular septum who underwent successful palliation. This condition often provides a diagnostic, interventional, and surgical challenge. Patients generally require either balloon atrial septostomy or surgical atrial septectomy for survival, with the addition of a Blalock-Tausig shunt or pulmonary artery band depending on the pulmonary blood flow. Very few patients survive to a Glenn procedure. For those who do survive, a decision must be made regarding the management of the hypertensive and hypoplastic left ventricle (LV) and associated mitral regurgitation. The LV can be excluded by either mitral valve avulsion or closure (exclusion) of the mitral valve with a patch. The choice of the technique should be carefully made and depends in part on the size of the LV. In our patient, who was successfully palliated by bidirectional Glenn shunt, the LV was managed by means of mitral valve avulsion. © The Author(s) 2015.

Performance of Low-Density Parity-Check Coded Modulation

NASA Astrophysics Data System (ADS)

Hamkins, J.

2011-02-01

This article presents the simulated performance of a family of nine AR4JA low-density parity-check (LDPC) codes when used with each of five modulations. In each case, the decoder inputs are codebit log-likelihood ratios computed from the received (noisy) modulation symbols using a general formula which applies to arbitrary modulations. Suboptimal soft-decision and hard-decision demodulators are also explored. Bit-interleaving and various mappings of bits to modulation symbols are considered. A number of subtle decoder algorithm details are shown to affect performance, especially in the error floor region. Among these are quantization dynamic range and step size, clipping degree-one variable nodes, "Jones clipping" of variable nodes, approximations of the min* function, and partial hard-limiting messages from check nodes. Using these decoder optimizations, all coded modulations simulated here are free of error floors down to codeword error rates below 10^{-6}. The purpose of generating this performance data is to aid system engineers in determining an appropriate code and modulation to use under specific power and bandwidth constraints, and to provide information needed to design a variable/adaptive coded modulation (VCM/ACM) system using the AR4JA codes. IPNPR Volume 42-185 Tagged File.txt

Biotransformation of the citrus flavone tangeretin in rats. Identification of metabolites with intact flavane nucleus.

PubMed

Nielsen, S E; Breinholt, V; Cornett, C; Dragsted, L O

2000-09-01

The present study was carried out in order to investigate the in vivo biotransformation and excretion of the flavone, tangeretin, found in citrus fruits, by analysing urine and faeces samples from rats after repeated administration of 100 mg/kg body weight/day tangeretin. The formed metabolites were separated and identified by HPLC and the structures elucidated by LC/MS and 1H NMR. Ten new, major metabolites with intact flavonoid structure were identified. The metabolites identified were either demethylated or hydroxylated derivatives of the parent compound and metabolic changes were found primarily to occur in the 4' position of the B-ring. The total urinary excretion of tangeretin metabolites with intact flavan nucleus was about 11% of the administered daily dose.

Coarse coding and discourse comprehension in adults with right hemisphere brain damage

PubMed Central

Tompkins, Connie A.; Scharp, Victoria L.; Meigh, Kimberly M.; Fassbinder, Wiltrud

2009-01-01

Background Various investigators suggest that some discourse-level comprehension difficulties in adults with right hemisphere brain damage (RHD) have a lexical-semantic basis. As words are processed, the intact right hemisphere arouses and sustains activation of a wide-ranging network of secondary or peripheral meanings and features—a phenomenon dubbed “coarse coding”. Coarse coding impairment has been postulated to underpin some prototypical RHD comprehension deficits, such as difficulties with nonliteral language interpretation, discourse integration, some kinds of inference generation, and recovery when a reinterpretation is needed. To date, however, no studies have addressed the hypothesised link between coarse coding deficit and discourse comprehension in RHD. Aims The current investigation examined whether coarse coding was related to performance on two measures of narrative comprehension in adults with RHD. Methods & Procedures Participants were 32 adults with unilateral RHD from cerebrovascular accident, and 38 adults without brain damage. Coarse coding was operationalised as poor activation of peripheral/weakly related semantic features of words. For the coarse coding assessment, participants listened to spoken sentences that ended in a concrete noun. Each sentence was followed by a spoken target phoneme string. Targets were subordinate semantic features of the sentence-final nouns that were incompatible with their dominant mental representations (e.g., “rotten” for apple). Targets were presented at two post-noun intervals. A lexical decision task was used to gauge both early activation and maintenance of activation of these weakly related semantic features. One of the narrative tasks assessed comprehension of implied main ideas and details, while the other indexed high-level inferencing and integration. Both comprehension tasks were presented auditorily. For all tasks, accuracy of performance was the dependent measure. Correlations were computed

Intact Rapid Facial Mimicry as well as Generally Reduced Mimic Responses in Stable Schizophrenia Patients

PubMed Central

Chechko, Natalya; Pagel, Alena; Otte, Ellen; Koch, Iring; Habel, Ute

2016-01-01

Spontaneous emotional expressions (rapid facial mimicry) perform both emotional and social functions. In the current study, we sought to test whether there were deficits in automatic mimic responses to emotional facial expressions in patients (15 of them) with stable schizophrenia compared to 15 controls. In a perception-action interference paradigm (the Simon task; first experiment), and in the context of a dual-task paradigm (second experiment), the task-relevant stimulus feature was the gender of a face, which, however, displayed a smiling or frowning expression (task-irrelevant stimulus feature). We measured the electromyographical activity in the corrugator supercilii and zygomaticus major muscle regions in response to either compatible or incompatible stimuli (i.e., when the required response did or did not correspond to the depicted facial expression). The compatibility effect based on interactions between the implicit processing of a task-irrelevant emotional facial expression and the conscious production of an emotional facial expression did not differ between the groups. In stable patients (in spite of a reduced mimic reaction), we observed an intact capacity to respond spontaneously to facial emotional stimuli. PMID:27303335

Importance of an intact dura in management of compound elevated fractures; a short series and literature review.

PubMed

Mohindra, Sandeep; Singh, Harnarayan; Savardekar, Amey

2012-01-01

To describe compound elevated fractures (CEFs) of the skull vault, with radiological pictures, management problems and prognosticative factors. The authors describe three cases of CEFs of the cranium, their mode of injury, clinical findings, radiological images and management problems. The authors have reviewed the existing literature regarding epidemiological data, neurological status, dural breech, methods of management and final outcome, in respect of CEFs. The first case had no dural breech, the second case had completely shattered dura, with extruding brain matter from the wound, while the third case had an elevated bone flap in consequence to large extradural haematoma. The patients with intact dura had relatively favourable outcome, when compared to patients with shattered dura. Three cases are added to the existing 10 such cases described in English literature. The major cause of unfavourable outcome remains sepsis and the presence of intact dura places these cases in the relatively safe category, regarding infective complications. The authors attempt at highlighting the importance of intact dura with such an injury. The review of literature supports favourable outcomes in patients having no dural breech.

Mu-Like Prophage in Serogroup B Neisseria meningitidis Coding for Surface-Exposed Antigens

PubMed Central

Masignani, Vega; Giuliani, Marzia Monica; Tettelin, Hervé; Comanducci, Maurizio; Rappuoli, Rino; Scarlato, Vincenzo

2001-01-01

Sequence analysis of the genome of Neisseria meningititdis serogroup B revealed the presence of an ∼35-kb region inserted within a putative gene coding for an ABC-type transporter. The region contains 46 open reading frames, 29 of which are colinear and homologous to the genes of Escherichia coli Mu phage. Two prophages with similar organizations were also found in serogroup A meningococcus, and one was found in Haemophilus influenzae. Early and late phage functions are well preserved in this family of Mu-like prophages. Several regions of atypical nucleotide content were identified. These likely represent genes acquired by horizontal transfer. Three of the acquired genes are shown to code for surface-associated antigens, and the encoded proteins are able to induce bactericidal antibodies. PMID:11254622

Can breathing-like pressure oscillations reverse or prevent narrowing of small intact airways?

PubMed

Harvey, Brian C; Parameswaran, Harikrishnan; Lutchen, Kenneth R

2015-07-01

Periodic length fluctuations of airway smooth muscle during breathing are thought to modulate airway responsiveness in vivo. Recent animal and human intact airway studies have shown that pressure fluctuations simulating breathing can only marginally reverse airway narrowing and are ineffective at protecting against future narrowing. However, these previous studies were performed on relatively large (>5 mm diameter) airways, which are inherently stiffer than smaller airways for which a preponderance of airway constriction in asthma likely occurs. The goal of this study was to determine the effectiveness of breathing-like transmural pressure oscillations to reverse induced narrowing and/or protect against future narrowing of smaller, more compliant intact airways. We constricted smaller (luminal diameter = 2.92 ± 0.29 mm) intact airway segments twice with ACh (10(-6) M), once while applying tidal-like pressure oscillations (5-15 cmH2O) before, during, and after inducing constriction (Pre + Post) and again while only imposing the tidal-like pressure oscillation after induced constriction (Post Only). Smaller airways were 128% more compliant than previously studied larger airways. This increased compliance translated into 196% more strain and 76% greater recovery (41 vs. 23%) because of tidal-like pressure oscillations. Larger pressure oscillations (5-25 cmH2O) caused more recovery (77.5 ± 16.5%). However, pressure oscillations applied before and during constriction resulted in the same steady-state diameter as when pressure oscillations were only applied after constriction. These data show that reduced straining of the airways before a challenge likely does not contribute to the emergence of airway hyperreactivity observed in asthma but may serve to sustain a given level of constriction. Copyright © 2015 the American Physiological Society.

Effects of reactive Mn(III)-oxalate complexes on structurally intact plant cell walls

NASA Astrophysics Data System (ADS)

Summering, J. A.; Keiluweit, M.; Goni, M. A.; Nico, P. S.; Kleber, M.

2011-12-01

Lignin components in the in plant litter are commonly assumed to have longer residence times in soil than many other compounds, which are supposedly, more easily degradable. The supposed resistance of lignin compounds to decomposition is generally attributed to the complex chain of biochemical steps required to create footholds in the non-porous structure of ligno-cellulose in cell walls. Interestingly, Mn(III) complexes have shown the ability to degrade ligno-cellulose. Mn(III) chelated by ligands such as oxalate are soluble oxidizers with a high affinity for lignin structures. Here we determined (i) the formation and decay kinetics of the Mn(III)-oxalate complexes in aqueous solution and (ii) the effects that these complexes have on intact ligno-cellulose. UV/vis spectroscopy and iodometric titrations confirmed the transient nature of Mn(III)-oxalate complexes with decay rates being in the order of hours. Zinnia elegans tracheary elements - a model ligno-cellulose substrate - were treated with Mn(III)-oxalate complexes in a newly developed flow-through reactor. Soluble decomposition products released during the treatment were analyzed by GC/MS and the degree of cell integrity was measured by cell counts, pre- and post-treatment counts indicate a decrease in intact Zinnia elegans as a result of Mn(III)-treatment. GC/MS results showed the release of a multitude of solubilized lignin breakdown products from plant cell walls. We conclude that Mn(III)-oxalate complexes have the ability to lyse intact plant cells and solubilize lignin. Lignin decomposition may thus be seen as resource dependent, with Mn(III) a powerful resource that should be abundant in terrestrial characterized by frequent redox fluctuations.

The intact capture of hypervelocity dust particles using underdense foams

NASA Technical Reports Server (NTRS)

Maag, Carl R.; Borg, J.; Tanner, William G.; Stevenson, T. J.; Bibring, J.-P.

1994-01-01

The impact of a hypervelocity projectile (greater than 3 km/s) is a process that subjects both the impactor and the impacted material to a large transient pressure distribution. The resultant stresses cause a large degree of fragmentation, melting, vaporization, and ionization (for normal densities). The pressure regime magnitude, however, is directly related to the density relationship between the projectile and target materials. As a consequence, a high-density impactor on a low-density target will experience the lowest level of damage. Historically, there have been three different approaches toward achieving the lowest possible target density. The first employs a projectile impinging on a foil or film of moderate density, but whose thickness is much less than the particle diameter. This results in the particle experiencing a pressure transient with both a short duration and a greatly reduced destructive effect. A succession of these films, spaced to allow nondestructive energy dissipation between impacts, will reduce the impactor's kinetic energy without allowing its internal energy to rise to the point where destruction of the projectile mass will occur. An added advantage to this method is that it yields the possibility of regions within the captured particle where a minimum of thermal modification has taken place. Polymer foams have been employed as the primary method of capturing particles with minimum degradation. The manufacture of extremely low bulk density materials is usually achieved by the introduction of voids into the material base. It must be noted, however, that a foam structure only has a true bulk density of the mixture at sizes much larger than the cell size, since for impact processes this is of paramount importance. The scale at which the bulk density must still be close to that of the mixture is approximately equal to the impactor. When this density criterion is met, shock pressures during impact are minimized, which in turn maximizes the

Data compression using adaptive transform coding. Appendix 1: Item 1. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Rost, Martin Christopher

1988-01-01

Adaptive low-rate source coders are described in this dissertation. These coders adapt by adjusting the complexity of the coder to match the local coding difficulty of the image. This is accomplished by using a threshold driven maximum distortion criterion to select the specific coder used. The different coders are built using variable blocksized transform techniques, and the threshold criterion selects small transform blocks to code the more difficult regions and larger blocks to code the less complex regions. A theoretical framework is constructed from which the study of these coders can be explored. An algorithm for selecting the optimal bit allocation for the quantization of transform coefficients is developed. The bit allocation algorithm is more fully developed, and can be used to achieve more accurate bit assignments than the algorithms currently used in the literature. Some upper and lower bounds for the bit-allocation distortion-rate function are developed. An obtainable distortion-rate function is developed for a particular scalar quantizer mixing method that can be used to code transform coefficients at any rate.

Reconciling certification and intact forest landscape conservation.

PubMed

Kleinschroth, Fritz; Garcia, Claude; Ghazoul, Jaboury

2018-05-29

In 2014, the Forest Stewardship Council (FSC) added a new criterion to its principles that requires protection of intact forest landscapes (IFLs). An IFL is an extensive area of forest that lacks roads and other signs of human activity as detected through remote sensing. In the Congo basin, our analysis of road networks in formally approved concessionary logging areas revealed greater loss of IFL in certified than in noncertified concessions. In areas of informal (i.e., nonregulated) extraction, road networks are known to be less detectable by remote sensing. Under the current definition of IFL, companies certified under FSC standards are likely to be penalized relative to the noncertified as well as the informal logging sector on account of their planned road networks, despite an otherwise better standard of forest management. This could ultimately undermine certification and its wider adoption, with implications for the future of sustainable forest management.

Isolation of intact sub-dermal secretory cavities from Eucalyptus

PubMed Central

2010-01-01

Background The biosynthesis of plant natural products in sub-dermal secretory cavities is poorly understood at the molecular level, largely due to the difficulty of physically isolating these structures for study. Our aim was to develop a protocol for isolating live and intact sub-dermal secretory cavities, and to do this, we used leaves from three species of Eucalyptus with cavities that are relatively large and rich in essential oils. Results Leaves were digested using a variety of commercially available enzymes. A pectinase from Aspergillus niger was found to allow isolation of intact cavities after a relatively short incubation (12 h), with no visible artifacts from digestion and no loss of cellular integrity or cavity contents. Several measurements indicated the potential of the isolated cavities for further functional studies. First, the cavities were found to consume oxygen at a rate that is comparable to that estimated from leaf respiratory rates. Second, mRNA was extracted from cavities, and it was used to amplify a cDNA fragment with high similarity to that of a monoterpene synthase. Third, the contents of the cavity lumen were extracted, showing an unexpectedly low abundance of volatile essential oils and a sizeable amount of non-volatile material, which is contrary to the widely accepted role of secretory cavities as predominantly essential oil repositories. Conclusions The protocol described herein is likely to be adaptable to a range of Eucalyptus species with sub-dermal secretory cavities, and should find wide application in studies of the developmental and functional biology of these structures, and the biosynthesis of the plant natural products they contain. PMID:20807444

Peptide code-on-a-microplate for protease activity analysis via MALDI-TOF mass spectrometric quantitation.

PubMed

Hu, Junjie; Liu, Fei; Ju, Huangxian

2015-04-21

A peptide-encoded microplate was proposed for MALDI-TOF mass spectrometric (MS) analysis of protease activity. The peptide codes were designed to contain a coding region and the substrate of protease for enzymatic cleavage, respectively, and an internal standard method was proposed for the MS quantitation of the cleavage products of these peptide codes. Upon the cleavage reaction in the presence of target proteases, the coding regions were released from the microplate, which were directly quantitated by using corresponding peptides with one-amino acid difference as the internal standards. The coding region could be used as the unique "Protease ID" for the identification of corresponding protease, and the amount of the cleavage product was used for protease activity analysis. Using trypsin and chymotrypsin as the model proteases to verify the multiplex protease assay, the designed "Trypsin ID" and "Chymotrypsin ID" occurred at m/z 761.6 and 711.6. The logarithm value of the intensity ratio of "Protease ID" to internal standard was proportional to trypsin and chymotrypsin concentration in a range from 5.0 to 500 and 10 to 500 nM, respectively. The detection limits for trypsin and chymotrypsin were 2.3 and 5.2 nM, respectively. The peptide-encoded microplate showed good selectivity. This proposed method provided a powerful tool for convenient identification and activity analysis of multiplex proteases.

Uplink Coding

NASA Technical Reports Server (NTRS)

Pollara, Fabrizio; Hamkins, Jon; Dolinar, Sam; Andrews, Ken; Divsalar, Dariush

2006-01-01

This viewgraph presentation reviews uplink coding. The purpose and goals of the briefing are (1) Show a plan for using uplink coding and describe benefits (2) Define possible solutions and their applicability to different types of uplink, including emergency uplink (3) Concur with our conclusions so we can embark on a plan to use proposed uplink system (4) Identify the need for the development of appropriate technology and infusion in the DSN (5) Gain advocacy to implement uplink coding in flight projects Action Item EMB04-1-14 -- Show a plan for using uplink coding, including showing where it is useful or not (include discussion of emergency uplink coding).

Surface plasmon resonance sensing: from purified biomolecules to intact cells.

PubMed

Su, Yu-Wen; Wang, Wei

2018-04-12

Surface plasmon resonance (SPR) has become a well-recognized label-free technique for measuring the binding kinetics between biomolecules since the invention of the first SPR-based immunosensor in 1980s. The most popular and traditional format for SPR analysis is to monitor the real-time optical signals when a solution containing ligand molecules is flowing over a sensor substrate functionalized with purified receptor molecules. In recent years, rapid development of several kinds of SPR imaging techniques have allowed for mapping the dynamic distribution of local mass density within single living cells with high spatial and temporal resolutions and reliable sensitivity. Such capability immediately enabled one to investigate the interaction between important biomolecules and intact cells in a label-free, quantitative, and single cell manner, leading to an exciting new trend of cell-based SPR bioanalysis. In this Trend Article, we first describe the principle and technical features of two types of SPR imaging techniques based on prism and objective, respectively. Then we survey the intact cell-based applications in both fundamental cell biology and drug discovery. We conclude the article with comments and perspectives on the future developments. Graphical abstract Recent developments in surface plasmon resonance (SPR) imaging techniques allow for label-free mapping the mass-distribution within single living cells, leading to great expansions in biomolecular interactions studies from homogeneous substrates functionalized with purified biomolecules to heterogeneous substrates containing individual living cells.

Multiple component codes based generalized LDPC codes for high-speed optical transport.

PubMed

Djordjevic, Ivan B; Wang, Ting

2014-07-14

A class of generalized low-density parity-check (GLDPC) codes suitable for optical communications is proposed, which consists of multiple local codes. It is shown that Hamming, BCH, and Reed-Muller codes can be used as local codes, and that the maximum a posteriori probability (MAP) decoding of these local codes by Ashikhmin-Lytsin algorithm is feasible in terms of complexity and performance. We demonstrate that record coding gains can be obtained from properly designed GLDPC codes, derived from multiple component codes. We then show that several recently proposed classes of LDPC codes such as convolutional and spatially-coupled codes can be described using the concept of GLDPC coding, which indicates that the GLDPC coding can be used as a unified platform for advanced FEC enabling ultra-high speed optical transport. The proposed class of GLDPC codes is also suitable for code-rate adaption, to adjust the error correction strength depending on the optical channel conditions.

Family Relationships and the Psychosocial Adjustment of School-Aged Children in Intact Families

ERIC Educational Resources Information Center

Hakvoort, Esther M.; Bos, Henny M. W.; Van Balen, Frank; Hermanns, Jo M. A.

2010-01-01

The authors investigated whether the quality of three family relationships (i.e., marital, parent-child, sibling) in intact families are associated with each other and with children's psychosocial adjustment. Data were collected by means of maternal and child reports (N = 88) using standardized instruments (i.e., Marital Satisfaction Scale,…

Cavitation Modeling in Euler and Navier-Stokes Codes

NASA Technical Reports Server (NTRS)

Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.

1993-01-01

Many previous researchers have modeled sheet cavitation by means of a constant pressure solution in the cavity region coupled with a velocity potential formulation for the outer flow. The present paper discusses the issues involved in extending these cavitation models to Euler or Navier-Stokes codes. The approach taken is to start from a velocity potential model to ensure our results are compatible with those of previous researchers and available experimental data, and then to implement this model in both Euler and Navier-Stokes codes. The model is then augmented in the Navier-Stokes code by the inclusion of the energy equation which allows the effect of subcooling in the vicinity of the cavity interface to be modeled to take into account the experimentally observed reduction in cavity pressures that occurs in cryogenic fluids such as liquid hydrogen. Although our goal is to assess the practicality of implementing these cavitation models in existing three-dimensional, turbomachinery codes, the emphasis in the present paper will center on two-dimensional computations, most specifically isolated airfoils and cascades. Comparisons between velocity potential, Euler and Navier-Stokes implementations indicate they all produce consistent predictions. Comparisons with experimental results also indicate that the predictions are qualitatively correct and give a reasonable first estimate of sheet cavitation effects in both cryogenic and non-cryogenic fluids. The impact on CPU time and the code modifications required suggests that these models are appropriate for incorporation in current generation turbomachinery codes.

Model Children's Code.

ERIC Educational Resources Information Center

New Mexico Univ., Albuquerque. American Indian Law Center.

The Model Children's Code was developed to provide a legally correct model code that American Indian tribes can use to enact children's codes that fulfill their legal, cultural and economic needs. Code sections cover the court system, jurisdiction, juvenile offender procedures, minor-in-need-of-care, and termination. Almost every Code section is…

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region.

PubMed

Chureau, Corinne; Chantalat, Sophie; Romito, Antonio; Galvani, Angélique; Duret, Laurent; Avner, Philip; Rougeulle, Claire

2011-02-15

X chromosome inactivation (XCI) is an essential epigenetic process which involves several non-coding RNAs (ncRNAs), including Xist, the master regulator of X-inactivation initiation. Xist is flanked in its 5' region by a large heterochromatic hotspot, which contains several transcription units including a gene of unknown function, Ftx (five prime to Xist). In this article, we describe the characterization and functional analysis of murine Ftx. We present evidence that Ftx produces a conserved functional long ncRNA, and additionally hosts microRNAs (miR) in its introns. Strikingly, Ftx partially escapes X-inactivation and is upregulated specifically in female ES cells at the onset of X-inactivation, an expression profile which closely follows that of Xist. We generated Ftx null ES cells to address the function of this gene. In these cells, only local changes in chromatin marks are detected within the hotspot, indicating that Ftx is not involved in the global maintenance of the heterochromatic structure of this region. The Ftx mutation, however, results in widespread alteration of transcript levels within the X-inactivation center (Xic) and particularly important decreases in Xist RNA levels, which were correlated with increased DNA methylation at the Xist CpG island. Altogether our results indicate that Ftx is a positive regulator of Xist and lead us to propose that Ftx is a novel ncRNA involved in XCI.

New quantum codes derived from a family of antiprimitive BCH codes

NASA Astrophysics Data System (ADS)

Liu, Yang; Li, Ruihu; Lü, Liangdong; Guo, Luobin

The Bose-Chaudhuri-Hocquenghem (BCH) codes have been studied for more than 57 years and have found wide application in classical communication system and quantum information theory. In this paper, we study the construction of quantum codes from a family of q2-ary BCH codes with length n=q2m+1 (also called antiprimitive BCH codes in the literature), where q≥4 is a power of 2 and m≥2. By a detailed analysis of some useful properties about q2-ary cyclotomic cosets modulo n, Hermitian dual-containing conditions for a family of non-narrow-sense antiprimitive BCH codes are presented, which are similar to those of q2-ary primitive BCH codes. Consequently, via Hermitian Construction, a family of new quantum codes can be derived from these dual-containing BCH codes. Some of these new antiprimitive quantum BCH codes are comparable with those derived from primitive BCH codes.

Surface acoustic wave coding for orthogonal frequency coded devices

NASA Technical Reports Server (NTRS)

Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

2011-01-01

Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

Intact skull chronic windows for mesoscopic wide-field imaging in awake mice

PubMed Central

Silasi, Gergely; Xiao, Dongsheng; Vanni, Matthieu P.; Chen, Andrew C. N.; Murphy, Timothy H.

2016-01-01

Background Craniotomy-based window implants are commonly used for microscopic imaging, in head-fixed rodents, however their field of view is typically small and incompatible with mesoscopic functional mapping of cortex. New Method We describe a reproducible and simple procedure for chronic through-bone wide-field imaging in awake head-fixed mice providing stable optical access for chronic imaging over large areas of the cortex for months. Results The preparation is produced by applying clear-drying dental cement to the intact mouse skull, followed by a glass coverslip to create a partially transparent imaging surface. Surgery time takes about 30 minutes. A single set-screw provides a stable means of attachment for mesoscale assessment without obscuring the cortical field of view. Comparison with Existing Methods We demonstrate the utility of this method by showing seed-pixel functional connectivity maps generated from spontaneous cortical activity of GCAMP6 signals in both awake and anesthetized mice. Conclusions We propose that the intact skull preparation described here may be used for most longitudinal studies that do not require micron scale resolution and where cortical neural or vascular signals are recorded with intrinsic sensors. PMID:27102043

Fluorescent-Protein Stabilization and High-Resolution Imaging of Cleared, Intact Mouse Brains

PubMed Central

Schwarz, Martin K.; Scherbarth, Annemarie; Sprengel, Rolf; Engelhardt, Johann; Theer, Patrick; Giese, Guenter

2015-01-01

In order to observe and quantify long-range neuronal connections in intact mouse brain by light microscopy, it is first necessary to clear the brain, thus suppressing refractive-index variations. Here we describe a method that clears the brain and preserves the signal from proteinaceous fluorophores using a pH-adjusted non-aqueous index-matching medium. Successful clearing is enabled through the use of either 1-propanol or tert-butanol during dehydration whilst maintaining a basic pH. We show that high-resolution fluorescence imaging of entire, structurally intact juvenile and adult mouse brains is possible at subcellular resolution, even following many months in clearing solution. We also show that axonal long-range projections that are EGFP-labelled by modified Rabies virus can be imaged throughout the brain using a purpose-built light-sheet fluorescence microscope. To demonstrate the viability of the technique, we determined a detailed map of the monosynaptic projections onto a target cell population in the lateral entorhinal cortex. This example demonstrates that our method permits the quantification of whole-brain connectivity patterns at the subcellular level in the uncut brain. PMID:25993380

The Father-Child Relationship, Parenting Styles, and Adolescent Risk Behaviors in Intact Families

ERIC Educational Resources Information Center

Bronte-Tinkew, Jacinta; Moore, Kristin A.; Carrano, Jennifer

2006-01-01

The father-child relationship and father's parenting style are examined as predictors of first delinquency and substance use, using data from the National Longitudinal Study of Youth 1997, Rounds 1 to 3 (N = 5,345), among adolescents in intact families. Discrete time logistic regressions indicate that a more positive father-child relationship…

Letter position coding across modalities: braille and sighted reading of sentences with jumbled words.

PubMed

Perea, Manuel; Jiménez, María; Martín-Suesta, Miguel; Gómez, Pablo

2015-04-01

This article explores how letter position coding is attained during braille reading and its implications for models of word recognition. When text is presented visually, the reading process easily adjusts to the jumbling of some letters (jugde-judge), with a small cost in reading speed. Two explanations have been proposed: One relies on a general mechanism of perceptual uncertainty at the visual level, and the other focuses on the activation of an abstract level of representation (i.e., bigrams) that is shared by all orthographic codes. Thus, these explanations make differential predictions about reading in a tactile modality. In the present study, congenitally blind readers read sentences presented on a braille display that tracked the finger position. The sentences either were intact or involved letter transpositions. A parallel experiment was conducted in the visual modality. Results revealed a substantially greater reading cost for the sentences with transposed-letter words in braille readers. In contrast with the findings with sighted readers, in which there is a cost of transpositions in the external (initial and final) letters, the reading cost in braille readers occurs serially, with a large cost for initial letter transpositions. Thus, these data suggest that the letter-position-related effects in visual word recognition are due to the characteristics of the visual stream.

The Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE

NASA Astrophysics Data System (ADS)

Vandenbroucke, B.; Wood, K.

2018-04-01

We present the public Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE, which can be used to simulate the self-consistent evolution of HII regions surrounding young O and B stars, or other sources of ionizing radiation. The code combines a Monte Carlo photoionization algorithm that uses a complex mix of hydrogen, helium and several coolants in order to self-consistently solve for the ionization and temperature balance at any given type, with a standard first order hydrodynamics scheme. The code can be run as a post-processing tool to get the line emission from an existing simulation snapshot, but can also be used to run full radiation hydrodynamical simulations. Both the radiation transfer and the hydrodynamics are implemented in a general way that is independent of the grid structure that is used to discretize the system, allowing it to be run both as a standard fixed grid code, but also as a moving-mesh code.

STATEQ: a nonlinear least-squares code for obtaining Martin thermodynamic representations of fluids in the gaseous and dense gaseous regions

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

Milora, S. L.

1976-02-01

The use of the code NLIN (IBM Share Program No. 1428) to obtain empirical thermodynamic pressure-volume-temperature (P-V-T) relationships for substances in the gaseous and dense gaseous states is described. When sufficient experimental data exist, the code STATEQ will provide least-squares estimates for the 21 parameters of the Martin model. Another code, APPROX, is described which also obtains parameter estimates for the model by making use of the approximate generalized behavior of fluids. Use of the codes is illustrated in obtaining thermodynamic representations for isobutane. (auth)

Phonological abilities in literacy-impaired children: Brain potentials reveal deficient phoneme discrimination, but intact prosodic processing.

PubMed

Männel, Claudia; Schaadt, Gesa; Illner, Franziska K; van der Meer, Elke; Friederici, Angela D

2017-02-01

Intact phonological processing is crucial for successful literacy acquisition. While individuals with difficulties in reading and spelling (i.e., developmental dyslexia) are known to experience deficient phoneme discrimination (i.e., segmental phonology), findings concerning their prosodic processing (i.e., suprasegmental phonology) are controversial. Because there are no behavior-independent studies on the underlying neural correlates of prosodic processing in dyslexia, these controversial findings might be explained by different task demands. To provide an objective behavior-independent picture of segmental and suprasegmental phonological processing in impaired literacy acquisition, we investigated event-related brain potentials during passive listening in typically and poor-spelling German school children. For segmental phonology, we analyzed the Mismatch Negativity (MMN) during vowel length discrimination, capturing automatic auditory deviancy detection in repetitive contexts. For suprasegmental phonology, we analyzed the Closure Positive Shift (CPS) that automatically occurs in response to prosodic boundaries. Our results revealed spelling group differences for the MMN, but not for the CPS, indicating deficient segmental, but intact suprasegmental phonological processing in poor spellers. The present findings point towards a differential role of segmental and suprasegmental phonology in literacy disorders and call for interventions that invigorate impaired literacy by utilizing intact prosody in addition to training deficient phonemic awareness. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Parent-child communication and adolescent self-esteem in separated, intercountry adoptive and intact non-adoptive families.

PubMed

Lanz, M; Iafrate, R; Rosnati, R; Scabini, E

1999-12-01

The purpose of the present study was to verify whether there are some differences in parent-child communication and in adolescent self-esteem among adoptive, separated and intact non-adoptive families and to investigate the extent to which parent-child communication is related to adolescent self-esteem in the three types of families. The study sample was composed of 450 adolescents aged between 11 and 17 years (160 from intact non-adoptive families, 140 from separated or divorced families and 150 from intercountry adoptive families). Subjects completed the Parent-Adolescent Communication Scale by Barnes and Olson, the Rosenberg Self-esteem Scale and some socio-demographic items. The results show that adolescents from separated families have more difficulties in their relationships with both the mother and the father than their peers, and that adoptive children perceive a more positive communication with their parents than biological children. Moreover, adoptees showed lower self-esteem than the other two groups of adolescents. Lastly, it emerged that male and female adolescents' self-esteem is related to positive communication with both parents in intact non-adoptive families, while no link was significant for male and female children of divorced parents or for adoptees. Copyright 1999 The Association for Professionals in Services for Adolescents.

Regulation of Sex Determination in Mice by a Non-coding Genomic Region

PubMed Central

Arboleda, Valerie A.; Fleming, Alice; Barseghyan, Hayk; Délot, Emmanuèle; Sinsheimer, Janet S.; Vilain, Eric

2014-01-01

To identify novel genomic regions that regulate sex determination, we utilized the powerful C57BL/6J-YPOS (B6-YPOS) model of XY sex reversal where mice with autosomes from the B6 strain and a Y chromosome from a wild-derived strain, Mus domesticus poschiavinus (YPOS), show complete sex reversal. In B6-YPOS, the presence of a 55-Mb congenic region on chromosome 11 protects from sex reversal in a dose-dependent manner. Using mouse genetic backcross designs and high-density SNP arrays, we narrowed the congenic region to a 1.62-Mb genomic region on chromosome 11 that confers 80% protection from B6-YPOS sex reversal when one copy is present and complete protection when two copies are present. It was previously believed that the protective congenic region originated from the 129S1/SviMJ (129) strain. However, genomic analysis revealed that this region is not derived from 129 and most likely is derived from the semi-inbred strain POSA. We show that the small 1.62-Mb congenic region that protects against B6-YPOS sex reversal is located within the Sox9 promoter and promotes the expression of Sox9, thereby driving testis development within the B6-YPOS background. Through 30 years of backcrossing, this congenic region was maintained, as it promoted male sex determination and fertility despite the female-promoting B6-YPOS genetic background. Our findings demonstrate that long-range enhancer regions are critical to developmental processes and can be used to identify the complex interplay between genome variants, epigenetics, and developmental gene regulation. PMID:24793290

Pathophysiology of preterm labor with intact membranes.

PubMed

Talati, Asha N; Hackney, David N; Mesiano, Sam

2017-11-01

Preterm labor with intact membranes is a major cause of spontaneous preterm birth (sPTB). To prevent sPTB a clear understanding is needed of the hormonal interactions that initiate labor. The steroid hormone progesterone acting via its nuclear progesterone receptors (PRs) in uterine cells is essential for the establishment and maintenance of pregnancy and disruption of PR signaling (i.e., functional progesterone/PR withdrawal) is key trigger for labor. The process of parturition is also associated with inflammation within the uterine tissues and it is now generally accepted that inflammatory stimuli from multiple extrinsic and intrinsic sources induce labor. Recent studies suggest inflammatory stimuli induce labor by affecting PR transcriptional activity in uterine cells to cause functional progesterone/PR withdrawal. Advances in understanding the functional interaction of inflammatory load on the pregnancy uterus and progesterone/PR signaling is opening novel areas of research and may lead to rational therapeutic strategies to effectively prevent sPTB. Copyright © 2017 Elsevier Inc. All rights reserved.

TRANSCRIPTION FACTOR ACTIVATION FOLLOWING EXPOSURE OF AN INTACT LUNG PREPARATION TO METALLIC PARTICULATE MATTER

EPA Science Inventory

TRANSCRIPTION FACTOR ACTIVATION FOLLOWING EXPOSURE OF AN INTACT LUNG PREPARATION TO METALLIC PARTICULATE MATTER

James M. Samet1,2, Robert Silbajoris1, Tony Huang1 and Ilona Jaspers3

1Human Studies Division, National Health and Environmental Effects Research Laborato...

Predicting water-holding capacity of intact chicken broiler breast fillets with Vis/NIR spectroscopy

USDA-ARS?s Scientific Manuscript database

The ability of using visible and near-infrared (Vis/NIR) spectroscopy to predict water-holding capacity (WHC) of intact chicken broiler breast fillets (pectoralis major) was assessed in this study. Boneless and skinless chicken fillets (214 in total) were procured from a commercial processing plant ...

Understanding Mixed Code and Classroom Code-Switching: Myths and Realities

ERIC Educational Resources Information Center

Li, David C. S.

2008-01-01

Background: Cantonese-English mixed code is ubiquitous in Hong Kong society, and yet using mixed code is widely perceived as improper. This paper presents evidence of mixed code being socially constructed as bad language behavior. In the education domain, an EDB guideline bans mixed code in the classroom. Teachers are encouraged to stick to…

Bioengineered human IAS reconstructs with functional and molecular properties similar to intact IAS

PubMed Central

Singh, Jagmohan

2012-01-01

Because of its critical importance in rectoanal incontinence, we determined the feasibility to reconstruct internal anal sphincter (IAS) from human IAS smooth muscle cells (SMCs) with functional and molecular attributes similar to the intact sphincter. The reconstructs were developed using SMCs from the circular smooth muscle layer of the human IAS, grown in smooth muscle differentiation media under sterile conditions in Sylgard-coated tissue culture plates with central Sylgard posts. The basal tone in the reconstructs and its changes were recorded following 0 Ca2+, KCl, bethanechol, isoproterenol, protein kinase C (PKC) activator phorbol 12,13-dibutyrate, and Rho kinase (ROCK) and PKC inhibitors Y-27632 and Gö-6850, respectively. Western blot (WB), immunofluorescence (IF), and immunocytochemical (IC) analyses were also performed. The reconstructs developed spontaneous tone (0.68 ± 0.26 mN). Bethanechol (a muscarinic agonist) and K+ depolarization produced contraction, whereas isoproterenol (β-adrenoceptor agonist) and Y-27632 produced a concentration-dependent decrease in the tone. Maximal decrease in basal tone with Y-27632 and Gö-6850 (each 10−5 M) was 80.45 ± 3.29 and 17.76 ± 3.50%, respectively. WB data with the IAS constructs′ SMCs revealed higher levels of RhoA/ROCK, protein kinase C-potentiated inhibitor or inhibitory phosphoprotein for myosin phosphatase (CPI-17), phospho-CPI-17, MYPT1, and 20-kDa myosin light chain vs. rectal smooth muscle. WB, IF, and IC studies of original SMCs and redispersed from the reconstructs for the relative distribution of different signal transduction proteins confirmed the feasibility of reconstruction of IAS with functional properties similar to intact IAS and demonstrated the development of myogenic tone with critical dependence on RhoA/ROCK. We conclude that it is feasible to bioengineer IAS constructs using human IAS SMCs that behave like intact IAS. PMID:22790596

Multicenter evaluation of a new immunoassay for intact PTH measurement on the Elecsys System 2010 and 1010.

PubMed

Hermsen, Derik; Franzson, Leifur; Hoffmann, Jean Paul; Isaksson, Anders; Kaufman, Jean M; Leary, Elizabeth; Müller, Christian; Nakatsuka, Kiyoshi; Nishizawa, Yoshiki; Reinauer, Hans; Riesen, Walter; Roth, Heinz-Jürgen; Steinmüller, Thomas; Troch, Tanja; Bergmann, Pierre

2002-01-01

The determination of parathyroid hormone (PTH) is of great clinical relevance in the assessment of calcium metabolic disorders. Although PTH was one of the first hormones measured by immunoassays, there are still many difficulties in its determination due to the low concentration of the hormone in blood and due to the heterogeneity of PTH resulting from different circulating hormone fragments. The aim of our multicenter-study was to evaluate the technical performance and the clinical validity of a new immunoassay for intact PTH measurement on the Elecsys Systems 2010 and 1010. The multicenter evaluation was performed in 11 clinical laboratories. The Elecsys PTH assay is a one step sandwich electrochemiluminescence immunoassay based upon the streptavidin-biotin technology. Two monoclonal antibodies are used in the assay providing detection of intact PTH. The imprecision study yielded within-run and between-days coefficients of variation of 3.1% - 6.6% and 3.4% - 15.6%, respectively using a three level control (PreciControl Bone, Roche Diagnostics) and human pool sera at two different concentrations (HS-low: 20 - 60 pg/ml, HS-high > 65 pg/ml). The analytical sensitivity calculated as the mean value plus 2 standard deviations of a within-run imprecision was below 2.70 pg/ml using zero calibrator matrix. Dilution linearity was observed up to 4890 pg/ml using zero calibrator matrix or human pool sera. Recoveries ranged between 85% - 115%. Serum, EDTA- and heparin plasma were evaluated for PTH measurement. Due to a better analyte stability (48h at 21 degrees C; 3d at 4 degrees C) EDTA plasma was recommended for PTH measurement. Results of the Elec sys PTH immunoassay correlated well (r = 0.926 - 0.994) with three different immunoradiometric assays (N-tact PTH SP, DiaSorin; Nichols Allegro Intact PTH, Nichols Institute Diagnostics; ELSA-PTH, CISBio International) and two different immunochemiluminometric assays (PTH-Intact-Immulite, DPC Biermann; Nichols Advantage Intact

Mapping leaf nitrogen and carbon concentrations of intact and fragmented indigenous forest ecosystems using empirical modeling techniques and WorldView-2 data

NASA Astrophysics Data System (ADS)

Omer, Galal; Mutanga, Onisimo; Abdel-Rahman, Elfatih M.; Peerbhay, Kabir; Adam, Elhadi

2017-09-01

Forest nitrogen (N) and carbon (C) are among the most important biochemical components of tree organic matter, and the estimation of their concentrations can help to monitor the nutrient uptake processes and health of forest trees. Traditionally, these tree biochemical components are estimated using costly, labour intensive, time-consuming and subjective analytical protocols. The use of very high spatial resolution multispectral data and advanced machine learning regression algorithms such as support vector machines (SVM) and artificial neural networks (ANN) provide an opportunity to accurately estimate foliar N and C concentrations over intact and fragmented forest ecosystems. In the present study, the utility of spectral vegetation indices calculated from WorldView-2 (WV-2) imagery for mapping leaf N and C concentrations of fragmented and intact indigenous forest ecosystems was explored. We collected leaf samples from six tree species in the fragmented as well as intact Dukuduku indigenous forest ecosystems. Leaf samples (n = 85 for each of the fragmented and intact forests) were subjected to chemical analysis for estimating the concentrations of N and C. We used 70% of samples for training our models and 30% for validating the accuracy of our predictive empirical models. The study showed that the N concentration was significantly higher (p = 0.03) in the intact forests than in the fragmented forest. There was no significant difference (p = 0.55) in the C concentration between the intact and fragmented forest strata. The results further showed that the foliar N and C concentrations could be more accurately estimated using the fragmented stratum data compared with the intact stratum data. Further, SVM achieved relatively more accurate N (maximum R2 Val = 0.78 and minimum RMSEVal = 1.07% of the mean) and C (maximum R2 Val = 0.67 and minimum RMSEVal = 1.64% of the mean) estimates compared with ANN (maximum R2Val = 0.70 for N and 0.51 for C and minimum RMSEVal = 5

QR Codes 101

ERIC Educational Resources Information Center

Crompton, Helen; LaFrance, Jason; van 't Hooft, Mark

2012-01-01

A QR (quick-response) code is a two-dimensional scannable code, similar in function to a traditional bar code that one might find on a product at the supermarket. The main difference between the two is that, while a traditional bar code can hold a maximum of only 20 digits, a QR code can hold up to 7,089 characters, so it can contain much more…

The random coding bound is tight for the average code.

NASA Technical Reports Server (NTRS)

Gallager, R. G.

1973-01-01

The random coding bound of information theory provides a well-known upper bound to the probability of decoding error for the best code of a given rate and block length. The bound is constructed by upperbounding the average error probability over an ensemble of codes. The bound is known to give the correct exponential dependence of error probability on block length for transmission rates above the critical rate, but it gives an incorrect exponential dependence at rates below a second lower critical rate. Here we derive an asymptotic expression for the average error probability over the ensemble of codes used in the random coding bound. The result shows that the weakness of the random coding bound at rates below the second critical rate is due not to upperbounding the ensemble average, but rather to the fact that the best codes are much better than the average at low rates.