41 CFR 60-1.10 - Foreign government practices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the basis of race, color, religion, sex, or national origin when hiring or making employee assignments... refusing to employ or assign any person because of race, color, religion, sex, or national origin... race, color, religion, sex, or national origin of the employee or potential employee, the contractor...

41 CFR 60-1.10 - Foreign government practices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the basis of race, color, religion, sex, or national origin when hiring or making employee assignments... refusing to employ or assign any person because of race, color, religion, sex, or national origin... race, color, religion, sex, or national origin of the employee or potential employee, the contractor...

41 CFR 60-1.10 - Foreign government practices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the basis of race, color, religion, sex, or national origin when hiring or making employee assignments... refusing to employ or assign any person because of race, color, religion, sex, or national origin... race, color, religion, sex, or national origin of the employee or potential employee, the contractor...

The nu(sub 6), nu(sub 7), nu(sub 8), and nu(sub 10) Bands of HO2NO2

NASA Technical Reports Server (NTRS)

Friedl, Randall R.; May, Randy D.; Duxbury, Geoffrey

1994-01-01

Two new fundamental vibration-rotation bands have been observed for HO2NO2 and assigned. They are nu(sub 7) at 648 1/cm and nu(sub 8) at 466 1/cm. On the basis of these assignments the previously observed bands at 722, 801.5, and 919 1/cm are assigned to nu(sub 10), nu(sub 7) + nu(sub 12), and 2 nu(sub 8), respectively. A partial rotational analysis of the atmospherically relevant nu(sub 6) band has been carried out, and the effects of tunneling, Coriolis interactions, and hot bands on the rotational structure have been characterized.The band origin derived from this analvsisis 8O2.54(sub 3) 1/cm.

Atomic Structure of Interface States in Silicon Heterojunction Solar Cells

NASA Astrophysics Data System (ADS)

George, B. M.; Behrends, J.; Schnegg, A.; Schulze, T. F.; Fehr, M.; Korte, L.; Rech, B.; Lips, K.; Rohrmüller, M.; Rauls, E.; Schmidt, W. G.; Gerstmann, U.

2013-03-01

Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism.

MESH2D Grid generator design and use

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

Flach, G. P.

Mesh2d is a Fortran90 program originally designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). x-coordinates depending only on index i implies strictly vertical x-grid lines, whereas the y-grid lines can undulate. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations. Since the original development effort, Mesh2d has been extended to more general two-dimensional structured grids of the form [x(i,j),(i,j)].

Origin of the computational hardness for learning with binary synapses.

PubMed

Huang, Haiping; Kabashima, Yoshiyuki

2014-11-01

Through supervised learning in a binary perceptron one is able to classify an extensive number of random patterns by a proper assignment of binary synaptic weights. However, to find such assignments in practice is quite a nontrivial task. The relation between the weight space structure and the algorithmic hardness has not yet been fully understood. To this end, we analytically derive the Franz-Parisi potential for the binary perceptron problem by starting from an equilibrium solution of weights and exploring the weight space structure around it. Our result reveals the geometrical organization of the weight space; the weight space is composed of isolated solutions, rather than clusters of exponentially many close-by solutions. The pointlike clusters far apart from each other in the weight space explain the previously observed glassy behavior of stochastic local search heuristics.

Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

PubMed

Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

2015-04-01

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci.

PubMed

Moore, Jean-Sébastien; Bourret, Vincent; Dionne, Mélanie; Bradbury, Ian; O'Reilly, Patrick; Kent, Matthew; Chaput, Gérald; Bernatchez, Louis

2014-12-01

Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America. © 2014 John Wiley & Sons Ltd.

The Social Security Administration's Youth Transition Demonstration Projects: Implementation Lessons from the Original Projects

ERIC Educational Resources Information Center

Martinez, John; Fraker, Thomas; Manno, Michelle; Baird, Peter; Mamun, Arif; O'Day, Bonnie; Rangarajan, Anu; Wittenburg, David

2010-01-01

This report focuses on the seven original Youth Transition Demonstration (YTD) projects selected for funding in 2003. Three of the original seven projects were selected for a national random assignment evaluation in 2005; however, this report only focuses on program operations prior to joining the random assignment evaluation for the three…

Extracting Country-of-Origin from Electronic Health Records for Gene- Environment Studies as Part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Study

PubMed Central

Farber-Eger, Eric; Goodloe, Robert; Boston, Jonathan; Bush, William S.; Crawford, Dana C.

2017-01-01

We describe here the extraction of country-of-origin, an acculturation variable relevant for gene-environment studies, in a biorepository linked to de-identified electronic health records (EHRs) assessed by the Epidemiologic Architecture for Genes Linked to Environment (EAGLE), a study site of the Population Architecture using Genomics and Epidemiology (PAGE) I study. We extracted country-of-origin from the unstructured clinical free text using regular expressions within the MySQL relational database system in a cohort of 15,863 subjects of mostly non-European descent (including 11,519 African Americans, 1,702 Hispanics, and 1,118 Asians). We performed searches for 231 world countries (including independent sovereign states, dependent areas, and disputed territories) and common misspellings in >14 gigabytes of data including >13 billion characters of clinical text. Manual review of a fraction of the initial country-of-origin assignments established rules for data cleaning and quality control to achieve final country-of-origin status for each subject. After data cleaning, a total of 1,911/15,893 (12.02%) subjects were assigned to a country-of-origin outside of the United States. Mexico was the most commonly assigned country outside of the United States (264 subjects; 13.8% of subjects with a foreign country-of-origin assignment). The distribution of the countries assigned followed expectations based on known migration patterns to the United States with an emphasis on the southeastern region. These data suggest country-of-origin can be successfully extracted from unstructured clinical text for downstream genetic association studies. PMID:28815105

Extracting Country-of-Origin from Electronic Health Records for Gene- Environment Studies as Part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Study.

PubMed

Farber-Eger, Eric; Goodloe, Robert; Boston, Jonathan; Bush, William S; Crawford, Dana C

2017-01-01

We describe here the extraction of country-of-origin, an acculturation variable relevant for gene-environment studies, in a biorepository linked to de-identified electronic health records (EHRs) assessed by the Epidemiologic Architecture for Genes Linked to Environment (EAGLE), a study site of the Population Architecture using Genomics and Epidemiology (PAGE) I study. We extracted country-of-origin from the unstructured clinical free text using regular expressions within the MySQL relational database system in a cohort of 15,863 subjects of mostly non-European descent (including 11,519 African Americans, 1,702 Hispanics, and 1,118 Asians). We performed searches for 231 world countries (including independent sovereign states, dependent areas, and disputed territories) and common misspellings in >14 gigabytes of data including >13 billion characters of clinical text. Manual review of a fraction of the initial country-of-origin assignments established rules for data cleaning and quality control to achieve final country-of-origin status for each subject. After data cleaning, a total of 1,911/15,893 (12.02%) subjects were assigned to a country-of-origin outside of the United States. Mexico was the most commonly assigned country outside of the United States (264 subjects; 13.8% of subjects with a foreign country-of-origin assignment). The distribution of the countries assigned followed expectations based on known migration patterns to the United States with an emphasis on the southeastern region. These data suggest country-of-origin can be successfully extracted from unstructured clinical text for downstream genetic association studies.

Synthesis and antitumor activity of quinonoid derivatives of cannabinoids.

PubMed

Kogan, Natalya M; Rabinowitz, Ruth; Levi, Paloma; Gibson, Dan; Sandor, Peter; Schlesinger, Michael; Mechoulam, Raphael

2004-07-15

Three cannabis constituents, cannabidiol (1), Delta(8)-tetrahydrocannabinol (3), and cannabinol (5), were oxidized to their respective para-quinones 2, 4, and 6. In the 1960s, the oxidized product 4 had been assigned a para-quinone structure, which was later modified to an ortho-quinone. To distinguish between the two possible quinone structures, a detailed NMR investigation was undertaken. The original para-quinone structure was confirmed. X-ray crystallography elucidated the structures of the crystalline 2 and 6. All three compounds displayed antiproliferative activity in several human cancer cell lines in vitro, and quinone 2 significantly reduced cancer growth of HT-29 cancer in nude mice.

THERMALLY STABLE PERFLUORINATED POLYMERS

DTIC Science & Technology

structure to cyclic product from perfluoroglutaronitrile and N2H4, opening of this cyclic product with polymerization to poly(N2-imidoyl perfluoroglutar ...Work on the 1,2,4-triazole polymer system, in which these heterocyclic groups are connected by perfluoroalkylene chains, included assignment of...hydrazidine), and synthesis of poly( perfluoropropylene - 1,2,4- triazole) both from the poly(imidoyl hydrazidine) and directly from the original cyclic

Molecular Origin of the Vibrational Structure of Ice Ih.

PubMed

Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

2017-06-15

An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

Investigating human geographic origins using dual-isotope (87Sr/86Sr, δ18O) assignment approaches.

PubMed

Laffoon, Jason E; Sonnemann, Till F; Shafie, Termeh; Hofman, Corinne L; Brandes, Ulrik; Davies, Gareth R

2017-01-01

Substantial progress in the application of multiple isotope analyses has greatly improved the ability to identify nonlocal individuals amongst archaeological populations over the past decades. More recently the development of large scale models of spatial isotopic variation (isoscapes) has contributed to improved geographic assignments of human and animal origins. Persistent challenges remain, however, in the accurate identification of individual geographic origins from skeletal isotope data in studies of human (and animal) migration and provenance. In an attempt to develop and test more standardized and quantitative approaches to geographic assignment of individual origins using isotopic data two methods, combining 87Sr/86Sr and δ18O isoscapes, are examined for the Circum-Caribbean region: 1) an Interval approach using a defined range of fixed isotopic variation per location; and 2) a Likelihood assignment approach using univariate and bivariate probability density functions. These two methods are tested with enamel isotope data from a modern sample of known origin from Caracas, Venezuela and further explored with two archaeological samples of unknown origin recovered from Cuba and Trinidad. The results emphasize both the potential and limitation of the different approaches. Validation tests on the known origin sample exclude most areas of the Circum-Caribbean region and correctly highlight Caracas as a possible place of origin with both approaches. The positive validation results clearly demonstrate the overall efficacy of a dual-isotope approach to geoprovenance. The accuracy and precision of geographic assignments may be further improved by better understanding of the relationships between environmental and biological isotope variation; continued development and refinement of relevant isoscapes; and the eventual incorporation of a broader array of isotope proxy data.

Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates.

PubMed

Jia, Jing; Wei, Yi-Liang; Qin, Cui-Jiao; Hu, Lan; Wan, Li-Hua; Li, Cai-Xia

2014-01-01

Inferring the ancestral origin of DNA samples can be helpful in correcting population stratification in disease association studies or guiding crime investigations. Populations throughout the world vary in appearance features and biological characteristics. Based on this idea, we performed a genome-wide scan for SNPs within genes that are related to physical and biological traits. Using the HapMap database, we screened 52 genes and their flanking regions. Thirty-five SNPs that displayed highly contrasting allele frequencies (F(st)>0.3, linkage disequilibrium r(2)<0.2, and Hardy-Weinberg equilibrium P>0.001) among Africans, Europeans, and East Asians were selected and validated. A multiplexed assay was developed to genotype these 35 SNPs in 357 individuals from 10 populations worldwide. This panel provided accurate estimates of individual ancestry proportions with balanced discriminatory power among the three continental ancestries: Africans, Europeans, and East Asians. It also proved very effective in evaluating admixed populations living in joint regions of continents (e.g., Uyghurs and Indians) and discriminating some subpopulations within each of the three continents. Structure analysis was performed to establish and evaluate the panel of ancestry-informative markers, and the components of each population were also described to indicate the structural composition. The 21 population structures in our study are consistent with geographic patterns, and individuals were properly assigned to their original ancestral populations with proportion analyses and random match probability calculations. Thus, the panel and its population information will be useful resources to minimize the effects of population stratification in association analyses and to assign the most likely origin of an unknown DNA contributor in forensic investigations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Mass fraction assignment of folic acid in a high purity material

NASA Astrophysics Data System (ADS)

Westwood, Steven; Josephs, Ralf; Choteau, Tiphaine; Daireaux, Adeline; Stoppacher, Norbert; Wielgosz, Robert; Davies, Stephen; de Rego, Eliane; Wollinger, Wagner; Garrido, Bruno; Fernandes, Jane; Lima, Jonathan; Oliveira, Rodrigo; de Sena, Rodrigo; Windust, Anthony; Huang, Ting; Dai, Xinhua; Quan, Can; He, Haihong; Zhang, Wei; Wei, Chao; Li, Na; Gao, Dexin; Liu, Zhao; Lo, Man-fung; Wong, Wai-fun; Pfeifer, Dietmar; Koch, Matthias; Dorgerloh, Ute; Rothe, Robert; Philip, Rosemary; Hirari, Nobuyasu; Fazlin Rezali, Mohd; Salazar Arzate, Claudia Marcela; Pedraza Evelina Berenice, Mercado; Serrano Caballero, Victor; Arce Osuna, Mariana; Krylov, A.; Kharitonov, S.; Lopushanskaya, E.; Liu, Qinde; Tang Lin, Teo; Fernandes-Whaley, Maria; Quinn, Laura; Nhlapo, Nontete; Prevoo-Franzsen, Desiree; Archer, Marcelle; Kim, Byungjoo; Baek, Song-Yee; Lee, Sunyoung; Lee, Joonhee; Marbumrung, Sornkrit; Kankaew, Ponhatai; Chaorenpornpukdee, Kanokrat; Chaipet, Thitiphan; Shearman, Kittiya; Ceyhan Goren, Ahmet; Gunduz, Simay; Yilmaz, Hasibe; Un, Ilker; Bilsel, Gokhan; Clarkson, Cailean; Bedner, Mary; Camara, Johanna E.; Lang, Brian E.; Lippa, Katrice A.; Nelson, Michael A.; Toman, Blaza; Yu, Lee L.

2018-01-01

The comparison required the assignment of the mass fraction of folic acid present as the main component in the comparison sample. Performance in the comparison is representative of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molecular weight range 300–500] and high polarity (pKOW < ‑2). Methods used by the eighteen participating NMIs or DIs were based on a mass balance (summation of impurities) or qNMR approach, or the combination of data obtained using both methods. The qNMR results tended to give slightly lower values for the content of folic acid, albeit with larger associated uncertainties, compared with the results obtained by mass balance procedures. Possible reasons for this divergence are discussed in the report, without reaching a definitive conclusion as to their origin. The comparison demonstrates that for a structurally complex polar organic compound containing a high water content and presenting a number of additional analytical challenges, the assignment of the mass fraction content property value of the main component can reasonably be achieved with an associated relative standard uncertainty in the assigned value of 0.5% Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

USGS Publications Warehouse

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

Use of Genetic Data to Infer Population-Specific Ecological and Phenotypic Traits from Mixed Aggregations

PubMed Central

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions. PMID:24905464

Laser spectroscopic study of β-estradiol and its monohydrated clusters in a supersonic jet.

PubMed

Morishima, Fumiya; Inokuchi, Yoshiya; Ebata, Takayuki

2012-08-09

The structures of 17β-estradiol (estradiol) and its 1:1 cluster with water have been investigated in supersonic jets. The S(1)-S(0) electronic spectrum of estradiol monomer shows four strong sharp bands in the 35050-35200 cm(-1) region. Ultraviolet-ultraviolet hole-burning (UV-UV HB) and infrared-ultraviolet double-resonance (IR-UV DR) spectra of these bands indicate that they are due to four different conformers of estradiol originating from the different orientation of the OH groups in the A- and D-rings. The addition of water vapor to the sample gas generates four new bands in the 34700-34800 cm(-1) region, which are assigned to the estradiol-H(2)O 1:1 cluster with the A-ring (phenyl ring) OH acting as a hydrogen(H)-bond donor. In addition, we found very weak bands near the origin bands of bare estradiol upon the addition of water vapor. These bands are assigned to the isomers of estradiol-H(2)O 1:1 cluster having an H-bond at the D-ring OH. We determine the conformation of bare estradiol and the structures of its monohydrated clusters with the aid of density functional theory calculation and discuss the relationship between the stability of hydrated clusters and the conformation of estradiol.

A test of geographic assignment using isotope tracers in feathers of known origin

USGS Publications Warehouse

Wunder, Michael B.; Kester, C.L.; Knopf, F.L.; Rye, R.O.

2005-01-01

We used feathers of known origin collected from across the breeding range of a migratory shorebird to test the use of isotope tracers for assigning breeding origins. We analyzed δD, δ13C, and δ15N in feathers from 75 mountain plover (Charadrius montanus) chicks sampled in 2001 and from 119 chicks sampled in 2002. We estimated parameters for continuous-response inverse regression models and for discrete-response Bayesian probability models from data for each year independently. We evaluated model predictions with both the training data and by using the alternate year as an independent test dataset. Our results provide weak support for modeling latitude and isotope values as monotonic functions of one another, especially when data are pooled over known sources of variation such as sample year or location. We were unable to make even qualitative statements, such as north versus south, about the likely origin of birds using both δD and δ13C in inverse regression models; results were no better than random assignment. Probability models provided better results and a more natural framework for the problem. Correct assignment rates were highest when considering all three isotopes in the probability framework, but the use of even a single isotope was better than random assignment. The method appears relatively robust to temporal effects and is most sensitive to the isotope discrimination gradients over which samples are taken. We offer that the problem of using isotope tracers to infer geographic origin is best framed as one of assignment, rather than prediction.

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania.

PubMed

Ballantyne, Kaye N; van Oven, Mannis; Ralf, Arwin; Stoneking, Mark; Mitchell, R John; van Oorschot, Roland A H; Kayser, Manfred

2012-07-01

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Secondary ion emission from phosphatidic acid sandwich films under atomic and molecular primary ion bombardment

NASA Astrophysics Data System (ADS)

Stapel, D.; Benninghoven, A.

2001-11-01

Secondary ion yields increase considerably when changing from atomic to molecular primary ions. Since secondary ion emission from deeper layers could result in a pronounced yield increase, the secondary ion emission depth of molecular fragments was investigated. A phosphatidic acid Langmuir-Blodgett (LB) sandwich system was applied. The well-defined layer structure of the applied sample allows the assignment of different depths of origin to the selected fragment ions. At least 93% of the detected characteristic molecular fragment ions originate from the first and second layers. This holds true for all applied atomic and molecular primary ions.

Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.

PubMed

Curk, Franck; Ancillo, Gema; Garcia-Lor, Andres; Luro, François; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Navarro, Luis; Ollitrault, Patrick

2014-12-29

The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2. 454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.

American woodcock migratory connectivity as indicated by hydrogen isotopes

USGS Publications Warehouse

Sullins, Daniel S.; Conway, Warren C.; Haukos, David A.; Hobson, Keith A.; Wassenaar, Leonard I; Comer, Christopher E.; Hung, I-Kuai

2016-01-01

To identify factors contributing to the long-term decline of American woodcock, a holistic understanding of range-wide population connectivity throughout the annual cycle is needed. We used band recovery data and isotopic composition of primary (P1) and secondary (S13) feathers to estimate population sources and connectivity among natal, early fall, and winter ranges of hunter-harvested juvenile American woodcock. We used P1 feathers from known-origin pre-fledged woodcock (n = 43) to create a hydrogenδ2Hf isoscape by regressing δ2Hf against expected growing-season precipitation (δ2Hp). Modeled δ2Hp values explained 79% of the variance in P1 δ2Hf values, indicating good model fit for estimating woodcock natal origins. However, a poor relationship (r2 = 0.23) between known-origin, S13 δ2Hf values, and expected δ2Hp values precluded assignment of early fall origins. We applied the δ2Hfisoscape to assign natal origins using P1 feathers from 494 hunter-harvested juvenile woodcock in the United States and Canada during 2010–2011 and 2011–2012 hunting seasons. Overall, 64% of all woodcock origins were assigned to the northernmost (>44°N) portion of both the Central and Eastern Management Regions. In the Eastern Region, assignments were more uniformly distributed along the Atlantic coast, whereas in the Central Region, most woodcock were assigned to origins within and north of the Great Lakes region. We compared our origin assignments to spatial coverage of the annual American woodcock Singing Ground Survey (SGS) and evaluated whether the survey effectively encompasses the entire breeding range. When we removed the inadequately surveyed Softwood shield Bird Conservation Region (BCR) from the northern portion of the SGS area, only 48% of juvenile woodcock originated in areas currently surveyed by the SGS. Of the individuals assigned to the northernmost portions of the breeding range, several were harvested in the southern extent of the wintering range. Based upon this latitudinal winter stratification, we examined whether woodcock employed a leapfrog migration strategy. Using δ2Hf values and band-recovery data, we found some support for this migration strategy hypothesis but not as a singular explanation. The large harvest derivation of individuals from the northernmost portions of the breeding range, and the difference in breeding distributions within each Management Region should be considered in future range-wide conservation and harvest management planning for American woodcock. 

Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

NASA Astrophysics Data System (ADS)

Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

2015-01-01

CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

[What gene and chromosomes say about the origin and evolution of insects and other arthropods].

PubMed

Lukhtanov, V A; Kuznetsova, V G

2010-09-01

At the turn of the 21st century, the use of molecular and molecular cytogenetic methods led to revolutionary advances in systematics of insects and other arthropods. Analysis of nuclear and mitochondrial genes, as well as investigation of structural rearrangements in the mitochondrial chromosome convincingly supported the Pancrustacea hypothesis, according to which insects originated directly from crustaceans, whereas myriapods are not closely related to them. The presence of the specific telomeric motif TTAGG confirmed the monophyletic origin of arthropods (Arthropoda) and the assignment of tongue worms (Pentastomida) to this type. Several different types of telomeric sequences have been found within the class of insects. Investigation of the molecular organization of these sequences may shed light on the relationships between the orders Diptera, Siphonaptera, and Mecoptera and on the origin of such enigmatic groups as the orders Strepsiptera, Zoraptera and suborder Coleorrhyncha.

DSSPcont: continuous secondary structure assignments for proteins

PubMed Central

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard

2003-01-01

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

2016-06-01

In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

Molecular origin of the vibrational structure of ice I h

DOE PAGES

Moberg, Daniel R.; Straight, Shelby C.; Knight, Christopher; ...

2017-05-25

Here, an unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the latticemore » vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.« less

Noachian and Hesperian modification of the original Chryse impact basin topography

NASA Technical Reports Server (NTRS)

Stockman, S. A.; Frey, H.

1995-01-01

We prospose a new center and ring assignment for the original Chryse impact basin based upon photogeologic mapping of Noachian outcrops and re-examination of the published geology using orthographic projections. While others have centered the Chryse impact on the topographic low associated with Hesperian volcanic and fluvial deposits, we suggest that the center of the Noachian-age excavation cavity was located approximately 800 km to the north, and that the basin topography was modified significantly from the Noachian into the Hesperian. Evolution of the topographic low included structural modification by a later impact centered in Acidalia, restricted volcanic deposition and loading, localized subsidence, and restricted deposition from the circum-Chryse outlfow channels.

The discovery of a new infrared emission feature at 1905 wavenumbers (5.25 microns) in the spectrum of BD + 30 deg 3639 and its relation to the polycyclic aromatic hydrocarbon model

NASA Technical Reports Server (NTRS)

Allamandola, L. J.; Bregman, J. D.; Sandford, S. A.; Tielens, A. G. G. M.; Witteborn, F. C.

1989-01-01

A new IR emission feature at 1905/cm (5.25 microns) has been discovered in the spectrum of BD + 30 deg 3639. This feature joins the family of well-known IR emission features at 3040, 2940, 1750, 1610, '1310', 1160, and 890/cm. The origin of this new feature is discussed and it is assigned to an overtone or combination band involving C-H bending modes of polycyclic aromatic hydrocarbons (PAHs). Laboratory work suggests that spectral studies of the 2000-1650/cm region may be very useful in elucidating the molecular structure of interstellar PAHs. The new feature, in conjunction with other recently discovered spectral structures, suggests that the narrow IR emission features originate in PAH molecules rather than large carbon grains.

Structural Case Assignment in Korean

ERIC Educational Resources Information Center

Koak, Heeshin

2012-01-01

In this dissertation, I aim to provide a theory on the distribution of structural Case in Korean. I propose the following Structural Case Assignment Hypothesis (SCAH) regarding the assignment of structural Case: "Structural Case is assigned by phase heads (C: nominative; v: accusative) to every argument in the c-command domain of the phase…

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

PubMed Central

Larson, Wesley A; Seeb, Lisa W; Everett, Meredith V; Waples, Ryan K; Templin, William D; Seeb, James E

2014-01-01

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure. PMID:24665338

Variation of Cats under Domestication: Genetic Assignment of Domestic Cats to Breeds and Worldwide Random Bred Populations

PubMed Central

Kurushima, J. D.; Lipinski, M. J.; Gandolfi, B.; Froenicke, L.; Grahn, J. C.; Grahn, R. A.; Lyons, L. A.

2012-01-01

Summary Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40–50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (accuracy single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the mis-assigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multi-step assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, i.e. race. PMID:23171373

Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers.

PubMed

Rafiei, Vahideh; Banihashemi, Ziaeddin; Bautista-Jalon, Laura S; Del Mar Jiménez-Gasco, Maria; Turgeon, B Gillian; Milgroom, Michael G

2018-06-01

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B 824 ; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B 824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B 824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

Assignment tests, telemetry and tag-recapture data converge to identify natal origins of leatherback turtles foraging in Atlantic Canadian waters.

PubMed

Stewart, Kelly R; James, Michael C; Roden, Suzanne; Dutton, Peter H

2013-07-01

Investigating migratory connectivity between breeding and foraging areas is critical to effective management and conservation of highly mobile marine taxa, particularly threatened, endangered, or economically important species that cross through regional, national and international boundaries. The leatherback turtle (Dermochelys coriacea, Vandelli 1761) is one such transboundary species that spends time at breeding areas at low latitudes in the northwest Atlantic during spring and summer. From there, they migrate widely throughout the North Atlantic, but many show fidelity to one region off eastern Canada, where critical foraging habitat has been proposed. Our goal was to identify nesting beach origins for turtles foraging here. Using genetics, we identified natal beaches for 288 turtles that were live-captured off the coast of Nova Scotia, Canada. Turtles were sampled (skin or blood) and genotyped using 17 polymorphic microsatellite markers. Results from three assignment testing programs (ONCOR, GeneClass2 and Structure) were compared. Our nesting population reference data set included 1417 individuals from nine Atlantic nesting assemblages. A supplementary data set for 83 foraging turtles traced to nesting beaches using flipper tags and/or PIT tags (n = 72), or inferred from satellite telemetry (n = 11), enabled ground-truthing of the assignments. We first assigned turtles using only genetic information and then used the supplementary recapture information to verify assignments. ONCOR performed best, assigning 64 of the 83 recaptured turtles to natal beaches (77·1%). Turtles assigned to Trinidad (164), French Guiana (72), Costa Rica (44), St. Croix (7), and Florida (1) reflect the relative size of those nesting populations, although none of the turtles were assigned to four other potential source nesting assemblages. Our results demonstrate the utility of genetic approaches for determining source populations of foraging marine animals and include the first identification of natal rookeries of male leatherbacks, identified through satellite telemetry and verified with genetics. This work highlights the importance of long-term monitoring and tagging programmes in nesting and high-use foraging areas. Moreover, it provides a scientific basis for evaluating stock-specific effects of fisheries on migratory marine species, thus identifying where coordinated international recovery efforts may be most effective. © 2013 NOAA ‐ National Marine Fisheries Service. Journal of Animal Ecology © 2013 British Ecological Society.

Latina/o or Mexicana/o?: The Relationship between Socially Assigned Race and Experiences with Discrimination

PubMed Central

Vargas, Edward D.; Winston, Nadia C.; Garcia, John A.; Sanchez, Gabriel R.

2016-01-01

Discrimination based on one’s racial or ethnic background is one of the oldest and most perverse practices in the United States. While much of this research has relied on self-reported racial categories, a growing body of research is attempting to measure race through socially-assigned race. Socially-assigned or ascribed race measures how individuals feel they are classified by other people. This paper draws on the socially assigned race literature and explores the impact of socially assigned race on experiences with discrimination using a 2011 nationally representative sample of Latina/os (n=1,200). While much of the current research on Latina/os has been focused on the aggregation across national origin group members, this paper marks a deviation by using socially-assigned race and national origin to understand how being ascribed as Mexican is associated with experiences of discrimination. We find evidence that being ascribed as Mexican increases the likelihood of experiencing discrimination relative to being ascribed as White or Latina/o. Furthermore, we find that being miss-classified as Mexican (ascribed as Mexican, but not of Mexican origin) is associated with a higher likelihood of experiencing discrimination compared to being ascribed as white, ascribed as Latina/o, and correctly ascribed as Mexican. We provide evidence that socially assigned race is a valuable complement to self-identified race/ethnicity for scholars interested in assessing the impact of race/ethnicity on a wide range of outcomes. PMID:27709119

Wildlife forensic science: A review of genetic geographic origin assignment.

PubMed

Ogden, Rob; Linacre, Adrian

2015-09-01

Wildlife forensic science has become a key means of enforcing legislation surrounding the illegal trade in protected and endangered species. A relatively new dimension to this area of forensic science is to determine the geographic origin of a seized sample. This review focuses on DNA testing, which relies on assignment of an unknown sample to its genetic population of origin. Key examples of this are the trade in timber, fish and ivory and these are used only to illustrate the large number of species for which this type of testing is potentially available. The role of mitochondrial and nuclear DNA markers is discussed, alongside a comparison of neutral markers with those exhibiting signatures of selection, which potentially offer much higher levels of assignment power to address specific questions. A review of assignment tests is presented along with detailed methods for evaluating error rates and considerations for marker selection. The availability and quality of reference data are of paramount importance to support assignment applications and ensure reliability of any conclusions drawn. The genetic methods discussed have been developed initially as investigative tools but comment is made regarding their use in courts. The potential to compliment DNA markers with elemental assays for greater assignment power is considered and finally recommendations are made for the future of this type of testing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Population variation in isotopic composition of shorebird feathers: Implications for determining molting grounds

USGS Publications Warehouse

Torres-Dowdall, J.; Farmer, A.H.; Bucher, E.H.; Rye, R.O.; Landis, G.

2009-01-01

Stable isotope analyses have revolutionized the study of migratory connectivity. However, as with all tools, their limitations must be understood in order to derive the maximum benefit of a particular application. The goal of this study was to evaluate the efficacy of stable isotopes of C, N, H, O and S for assigning known-origin feathers to the molting sites of migrant shorebird species wintering and breeding in Argentina. Specific objectives were to: 1) compare the efficacy of the technique for studying shorebird species with different migration patterns, life histories and habitat-use patterns; 2) evaluate the grouping of species with similar migration and habitat use patterns in a single analysis to potentially improve prediction accuracy; and 3) evaluate the potential gains in prediction accuracy that might be achieved from using multiple stable isotopes. The efficacy of stable isotope ratios to determine origin was found to vary with species. While one species (White-rumped Sandpiper, Calidris fuscicollis) had high levels of accuracy assigning samples to known origin (91% of samples correctly assigned), another (Collared Plover, Charadrius collaris) showed low levels of accuracy (52% of samples correctly assigned). Intra-individual variability may account for this difference in efficacy. The prediction model for three species with similar migration and habitat-use patterns performed poorly compared with the model for just one of the species (71% versus 91% of samples correctly assigned). Thus, combining multiple sympatric species may not improve model prediction accuracy. Increasing the number of stable isotopes in the analyses increased the accuracy of assigning shorebirds to their molting origin, but the best combination - involving a subset of all the isotopes analyzed - varied among species.

AB INITIO Investigations of the Magnetism in Diluted Magnetic Semiconductor Fe-DOPED GaN

NASA Astrophysics Data System (ADS)

Cheng, Jie; Zhou, Jing; Xu, Wei; Dong, Peng

2014-01-01

In this paper, we present a first principle investigation on Fe-doped GaN with wurtzite and zinc-blend structure using full potential density functional calculations. Data point out that the magnetic behavior of Fe-doped GaN system is strongly dependent on Fe doping configurations. In agreement with the experimental reports, and independently by doping, antiferromagnetism occurs in the zinc-blend structure, while in the wurtzite structure ferromagnetism depends on the Fe doping configurations. Detailed analyses combined with density of state calculations support the assignment that the ferromagnetism is closely related to the impurity band at the origin of the hybridization of Fe 3d and N 2p states in the Fe-doped GaN of wurtzite phase.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

PubMed Central

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

Reliability of routinely collected hospital data for child maltreatment surveillance.

PubMed

McKenzie, Kirsten; Scott, Debbie A; Waller, Garry S; Campbell, Margaret

2011-01-05

Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting.

Reliability of Routinely Collected Hospital Data for Child Maltreatment Surveillance

PubMed Central

2011-01-01

Background Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. Methods A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. Results In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Conclusion Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting. PMID:21208411

My Favorite Assignment: From the ABC 2010 Annual Convention, Chicago, Illinois

ERIC Educational Resources Information Center

Whalen, D. Joel

2011-01-01

The seven Favorite Assignments featured in this article were originally presented at the 2010 ABC Annual Convention, Chicago, Illinois. The reader can consider a variety of learning objectives from team building to persuasion, application of electronic media to face-to-face communication, and much more. Some Favorite Assignments take a full…

Towards Automated Structure-Based NMR Resonance Assignment

NASA Astrophysics Data System (ADS)

Jang, Richard; Gao, Xin; Li, Ming

We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

The structure of the NO(X (2)Pi)-N(2) complex: A joint experimental-theoretical study.

PubMed

Wen, B; Meyer, H; Kłos, J

2010-04-21

We report the first measurement of the spectrum of the NO-N(2) complex in the region of the first vibrational NO overtone transition. The origin band of the complex is blueshifted by 0.30 cm(-1) from the corresponding NO monomer frequency. The observed spectrum consists of three bands assigned to the origin band, the excitation of one quantum of z-axis rotation and one associated hot band. The spacing of the bands and the rotational structure indicate a T-shaped vibrationally averaged structure with the NO molecule forming the top of the T. These findings are confirmed by high level ab initio calculations of the potential energy surfaces in planar symmetry. The deepest minimum is found for a T-shaped geometry on the A(")-surface. As a result the sum potential also has the global minimum for this structure. The different potential surfaces show several additional local minima at slightly higher energies indicating that the complex most likely will perform large amplitude motion even in its ground vibrational state. Nevertheless, as suggested by the measured spectra, the complex must, on average, spend a substantial amount of time near the T-shaped configuration.

Tyrosine radicals are involved in the photosynthetic oxygen-evolving system.

PubMed Central

Barry, B A; Babcock, G T

1987-01-01

In addition to the reaction-center chlorophyll, at least two other organic cofactors are involved in the photosynthetic oxygen-evolution process. One of these cofactors, called "Z," transfers electrons from the site of water oxidation to the reaction center of photosystem II. The other species, "D," has an uncertain function but gives rise to the stable EPR signal known as signal II. Z+. and D+. have identical EPR spectra and are generally assumed to arise from species with the same chemical structure. Results from a variety of experiments have suggested that Z and D are plastoquinones or plastoquinone derivatives. In general, however, the evidence to support this assignment is indirect. To address this situation, we have developed more direct methods to assign the structure of the Z+./D+. radicals. By selective in vivo deuteration of the methyl groups of plastoquinone in cyanobacteria, we show that hyperfine couplings from the methyl protons cannot be responsible for the partially resolved structure seen in the D+. EPR spectrum. That is, we verify by extraction and mass spectrometry that quinones are labeled in algae fed deuterated methionine, but no change is observed in the line shape of signal II. Considering the spectral properties of the D+. radical, a tyrosine origin is a reasonable alternative. In a second series of experiments, we have found that deuteration of tyrosine does indeed narrow the D+. signal. Extraction and mass spectral analysis of the quinones in these cultures show that they are not labeled by tyrosine. These results eliminate a plastoquinone origin for D+.; we conclude instead that D+., and most likely Z+., are tyrosine radicals. PMID:3313386

Communicating with parents with full disclosure: a case of cloacal extrophy with genital ambiguity.

PubMed

Myers, Catherine; Lee, Peter A

2004-03-01

Full disclosure and complete involvement of parents in decisions concerning assignment of sex and genital surgery must be part of medical care for children presenting with findings consistent with disorders of intersex. Intersex most commonly involves disorders of steroidogenesis or gonadal function, but may include multiple cloacal anomalies, such as presented here. To describe full disclosure of medical findings, by a multi-disciplinary medical team, as they became available over a period of weeks, in an infant originally assigned male, but eventually assigned female. An infant born at 24 weeks of gestation, after prenatal ultrasound showing distended bladder, ascites, and bilateral hydroureters, found to have an imperforate anus and a tubular structure appearing as a thin penis, without palpable corpora. Events concerning this case are discussed in relation to full disclosure of medical information to parents, guidelines for management of intersex, and the diagnosis (cloacal anomaly, cloacal extrophy, ano-rectal anomalies or uro-rectal septum malformation sequence). Full disclosure with involvement of parents with medical decisions is not only mandated currently, but also can be an effective approach in intersex care.

"You Don't Have to Like Me, but You Have to Respect Me": The Impacts of Assertiveness, Cooperativeness, and Group Satisfaction in Collaborative Assignments

ERIC Educational Resources Information Center

Lambertz-Berndt, Megan M.; Blight, Michael G.

2016-01-01

This study investigates cooperativeness, assertiveness, group satisfaction, leader grade, and leadership negotiation in a collaborative assignment conducted in a small group. Researchers manipulated the assignment of team members who reported on measures of group satisfaction and original scales of assertiveness and cooperativeness. Respondents…

A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences

PubMed Central

Guo, Juan; Wang, Yunsheng; Song, Chi; Zhou, Jianfeng; Qiu, Lijuan; Huang, Hongwen; Wang, Ying

2010-01-01

Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K′ = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be ≈2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China contain tremendous genetic resources for cultivar improvement. PMID:20566681

Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission.

PubMed

Kittichai, Veerayuth; Koepfli, Cristian; Nguitragool, Wang; Sattabongkot, Jetsumon; Cui, Liwang

2017-10-01

Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins. Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination.

Dynamic stabilities of icosahedral-like clusters and their ability to form quasicrystals

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

Liang, Xiaogang; Hamid, Ilyar; Duan, Haiming, E-mail: dhm@xju.edu.cn

2016-06-15

The dynamic stabilities of the icosahedral-like clusters containing up to 2200 atoms are investigated for 15 metal elements. The clusters originate from five different initial structures (icosahedron, truncated decahedron, octahedron, closed-shell fragment of an HCP structure, and non-closed-shell fragment of an HCP structure). The obtained order of the dynamic stabilities of the icosahedral-like clusters can be assigned to three groups, from stronger to weaker, according to the size ranges involved: (Zr, Al, Ti) > (Cu, Fe, Co, Ni, Mg, Ag) > (Pb, Au, Pd, Pt, Rh, Ir), which correspond to the predicted formation ability of the quasicrystals. The differences ofmore » the sequences can be explained by analyzing the parameters of the Gupta-type many-body inter-atomic potentials.« less

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

PubMed Central

Kijas, James W.; Townley, David; Dalrymple, Brian P.; Heaton, Michael P.; Maddox, Jillian F.; McGrath, Annette; Wilson, Peter; Ingersoll, Roxann G.; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John; Cockett, Noelle; Oddy, V. Hutton; Nicholas, Frank W.; Raadsma, Herman

2009-01-01

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability. PMID:19270757

Amino acid fermentation at the origin of the genetic code.

PubMed

de Vladar, Harold P

2012-02-10

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

Arsenic-based Life: An active learning assignment for teaching scientific discourse.

PubMed

Jeremy Johnson, R

2017-01-02

Among recent high profile scientific debates was the proposal that life could exist with arsenic in place of phosphorous in its nucleic acids and other biomolecules. Soon after its initial publication, scientists across diverse disciplines began to question this extraordinary claim. Using the original article, its claims, its scientific support, and the ensuing counterarguments, a two-day, active learning classroom exercise was developed focusing on the presentation, evaluation, and discussion of scientific argumentation and discourse. In this culminating assignment of a first semester biochemistry course, undergraduate students analyze the scientific support from the original research articles and then present and discuss multiple scientific rebuttals in a lively, civil classroom debate. Through this assignment, students develop a sense of skepticism, especially for the original arsenic-based life claims, and learn to clearly articulate their counterarguments with scientific support and critical reasoning. With its direct integration into first-semester biochemistry curriculum and the excitement surrounding arsenic based life, this assignment provides a robust, simple, and stimulating framework for introducing scientific discourse and active learning into the undergraduate molecular science curriculum. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):40-45, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin.

PubMed

Degen, Bernd; Blanc-Jolivet, Céline; Stierand, Katrin; Gillet, Elizabeth

2017-03-01

During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin". In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genetic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120km by 120km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree species Entandrophragma cylindricum (Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5-7% for the Sapelli data set. Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genetic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

14 CFR 1203.800 - Delegations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... paragraph (b)(3) of the section are authorized to declassify top Secret security classification assignments... which NASA has original classification authority. (b) Designated officials—(1) TOP SECRET Classification... this section. (3) Declassification Authority, Top Secret Assignments over 25 years Old. (i) Agency...

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

PubMed Central

Jakob, Sabine S.; Rödder, Dennis; Engler, Jan O.; Shaaf, Salar; Özkan, Hakan; Blattner, Frank R.; Kilian, Benjamin

2014-01-01

Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included. PMID:24586028

High-resolution synchrotron-based Fourier transform spectroscopy of [image omitted] in the 120-350 cm-1 far-infrared region

NASA Astrophysics Data System (ADS)

Moruzzi, G.; Murphy, R. J.; Lees, R. M.; Predoi-Cross, A.; Billinghurst, B. E.

2010-09-01

The Fourier transform spectrum of the ? isotopologue of methanol has been recorded in the 120-350 cm-1 far-infrared region at a resolution of 0.00096 cm-1 using synchrotron source radiation at the Canadian Light Source. The study, motivated by astrophysical applications, is aimed at generating a sufficiently accurate set of energy level term values for the ground vibrational state to allow prediction of the centres of the quadrupole hyperfine multiplets for astronomically observable sub-millimetre transitions to within an uncertainty of a few MHz. To expedite transition identification, a new function was added to the Ritz program in which predicted spectral line positions were generated by an adjustable interpolation between the known assignments for the ? and ? isotopologues. By displaying the predictions along with the experimental spectrum on the computer monitor and adjusting the predictions to match observed features, rapid assignment of numerous ? sub-bands was possible. The least squares function of the Ritz program was then used to generate term values for the identified levels. For each torsion-K-rotation substate, the term values were fitted to a Taylor-series expansion in powers of J(J + 1) to determine the substate origin energy and effective B-value. In this first phase of the study we did not attempt a full global fit to the assigned transitions, but instead fitted the sub-band J-independent origins to a restricted Hamiltonian containing the principal torsional and K-dependent terms. These included structural and torsional potential parameters plus quartic distortional and torsion-rotation interaction terms.

A Comparative Cathodoluminescence Emission Study of Feldspathic Glasses in SNC Meteorites and Quenched Melts of These Glasses

NASA Astrophysics Data System (ADS)

Kubny, A.; Jagoutz, E.

2001-12-01

In this study the cathodoluminescence (electron-excited luminescence) emission spectra were measured in the range 200 to 900 nm of individual feldspathic glass grains in the SNC meteorites Shergotty 101, Shergotty 232, ALHA 84001, EETA 79001-47, EETA 79001-276, and Dar al Gani 476 and those of quenched melts of the feldspathic glass grains. The quenching experiments of the original feldspathic glasses were conducted at 1500° C and atmospheric pressure. The aim of this CL emission study was the characterization of feldspathic glasses of SNC meteorites by comparison of the diagnostic spectral features of the feldspathic glasses of SNC meteorites with those of their quenched melts. In the CL emission spectra of the studied feldspathic glasses generally broad bands in the blue (ca. 460 nm), green (ca. 560 nm), and red (ca. 700 nm) can appear. These emission bands are assigned to structural defects (Al-O--Al centers), and the structural incorporation of Mn2+ and Fe3+ , respectively. The blue emission band at about 460 nm attributed to Al-O--Al centers is observed in the spectra of the original feldspathic glasses whereas it is not present (or only in low relative intensity) in the spectra of the quenched melts. The green emission band at 550 to 575 nm assigned to electronic transitions of Mn2+ in M sites is observed in the spectra of the original feldspathic glasses. It is shifted to longer wavelengths of 590 to 605 nm in the spectra of the quenched melts. The occurrence of the red emission band at about 700 nm attributed to electronic transition of Fe3+ in the spectra of the quenched melts of the feldspathic glasses indicates the presence of structural units which allow the occupancy of Fe3+ on tetrahedral sites. The results obtained by CL emission spectroscopy confirm results of Raman spectroscopic studies that the stuctures of feldspathic glasses of the studied SNC meteorites are modified by melting and quenching at atmospheric pressure. Additionally, comparison with published work on CL emission of shocked oligoclases shows that the feldspathic glasses of the studied SNC meteorites are not diaplectic but melt glasses.

More reliable protein NMR peak assignment via improved 2-interval scheduling.

PubMed

Chen, Zhi-Zhong; Lin, Guohui; Rizzi, Romeo; Wen, Jianjun; Xu, Dong; Xu, Ying; Jiang, Tao

2005-03-01

Protein NMR peak assignment refers to the process of assigning a group of "spin systems" obtained experimentally to a protein sequence of amino acids. The automation of this process is still an unsolved and challenging problem in NMR protein structure determination. Recently, protein NMR peak assignment has been formulated as an interval scheduling problem (ISP), where a protein sequence P of amino acids is viewed as a discrete time interval I (the amino acids on P one-to-one correspond to the time units of I), each subset S of spin systems that are known to originate from consecutive amino acids from P is viewed as a "job" j(s), the preference of assigning S to a subsequence P of consecutive amino acids on P is viewed as the profit of executing job j(s) in the subinterval of I corresponding to P, and the goal is to maximize the total profit of executing the jobs (on a single machine) during I. The interval scheduling problem is max SNP-hard in general; but in the real practice of protein NMR peak assignment, each job j(s) usually requires at most 10 consecutive time units, and typically the jobs that require one or two consecutive time units are the most difficult to assign/schedule. In order to solve these most difficult assignments, we present an efficient 13/7-approximation algorithm for the special case of the interval scheduling problem where each job takes one or two consecutive time units. Combining this algorithm with a greedy filtering strategy for handling long jobs (i.e., jobs that need more than two consecutive time units), we obtain a new efficient heuristic for protein NMR peak assignment. Our experimental study shows that the new heuristic produces the best peak assignment in most of the cases, compared with the NMR peak assignment algorithms in the recent literature. The above algorithm is also the first approximation algorithm for a nontrivial case of the well-known interval scheduling problem that breaks the ratio 2 barrier.

Genomic characterisation of Arachis porphyrocalyx (Valls & C.E. Simpson, 2005) (Leguminosae): multiple origin of Arachis species with x = 9.

PubMed

Celeste, Silvestri María; Ortiz, Alejandra Marcela; Robledo, Germán Ariel; Valls, José Francisco Montenegro; Lavia, Graciela Inés

2017-01-01

The genus Arachis Linnaeus, 1753 comprises four species with x = 9, three belong to the section Arachis: Arachis praecox (Krapov. W.C. Greg. & Valls, 1994), Arachis palustris (Krapov. W.C. Greg. & Valls, 1994) and Arachis decora (Krapov. W.C. Greg. & Valls, 1994) and only one belongs to the section Erectoides: Arachis porphyrocalyx (Valls & C.E. Simpson, 2005). Recently, the x = 9 species of section Arachis have been assigned to G genome, the latest described so far. The genomic relationship of Arachis porphyrocalyx with these species is controversial. In the present work, we carried out a karyotypic characterisation of Arachis porphyrocalyx to evaluate its genomic structure and analyse the origin of all x = 9 Arachis species. Arachis porphyrocalyx showed a karyotype formula of 14m+4st, one pair of A chromosomes, satellited chromosomes type 8, one pair of 45S rDNA sites in the SAT chromosomes, one pair of 5S rDNA sites and pericentromeric C-DAPI+ bands in all chromosomes. Karyotype structure indicates that Arachis porphyrocalyx does not share the same genome type with the other three x = 9 species and neither with the remaining Erectoides species. Taking into account the geographic distribution, morphological and cytogenetic features, the origin of species with x = 9 of the genus Arachis cannot be unique; instead, they originated at least twice in the evolutionary history of the genus.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba 2In 2O 4(OH) 2 Structure and Dynamics

DOE PAGES

Dervisoglu, Riza; Middlemiss, Derek S.; Blanc, Frederic; ...

2015-05-01

Here, a structural characterization of the hydrated form of the brownmillerite-type phase Ba 2In 2O 5, Ba 2In 2O 4(OH) 2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics 2004, 170, 25–32) using X-ray and neutron studies. Calculationsmore » of possible proton arrangements within the partially occupied layer of Ba 2In 2O 4(OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H– 17O double resonance experiments.« less

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2015-06-09

A structural characterization of the hydrated form of the brownmillerite-type phase Ba 2 In 2 O 5 , Ba 2 In 2 O 4 (OH) 2 , is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2 O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25-32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba 2 In 2 O 4 (OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1 H and 17 O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1 H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1 H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17 O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1 H- 17 O double resonance experiments.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

PubMed Central

2015-01-01

A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

28 CFR 17.25 - Identification and markings.

Code of Federal Regulations, 2010 CFR

2010-07-01

... classified at a level equivalent to that level of classification assigned by the originating foreign government. (c) Information assigned a level of classification under predecessor Executive Orders shall be... ACCESS TO CLASSIFIED INFORMATION Classified Information § 17.25 Identification and markings. (a...

Laser spectroscopic study of the Rydberg state structure of atomic lithium

NASA Astrophysics Data System (ADS)

Ballard, M. Kent

1998-07-01

Pulsed laser induced fluorescence spectroscopy was performed on both isotopic species of atomic lithium. Nonresonant multiphoton excitation spectra were recorded. The laser induced fluorescence of the lithium vapor was measured following excitation with a tunable, pulsed, nanosecond laser. Both two- and three-photon allowed transitions were observed resulting in four different transition series originating from the 22S and 22P levels, the latter likely originating from photodissociation products of the lithium dimer, Li2. Forty-seven identifiable transitions were assigned for 6Li. Evidence for a parity forbidden multiphoton transition is also present. For 7Li, fifty-three identifiable transitions were assigned including an additional series of parity forbidden multiphoton transitions. Laser polarization and power dependencies were measured and found to be consistent with the multiphoton transition probabilities. Due to the intense laser fields needed to produce the nonresonant multiphoton excitations, the lithium vapor was subjected to the laser induced ac Stark effect. The Autler-Townes doublets observed for the nF gets 2P transition series were found to exhibit normal asymmetry. The observed asymmetrical Autler-Townes profiles are explained in terms of the two-level and the three-level atomic systems which are based on different excitation schemes. A new computerized data acquisition system was developed as well as associated computer programs needed to analyze spectra.

...And Kronos Ate His Sons

NASA Astrophysics Data System (ADS)

Vitiello, Giuseppe

In closed systems, energy is conserved. The origin of the time axis is completely arbitrary due to the invariance under continuous time-translations. The flowing of time swallows those fictitious origins one might assign on its axis, as Kronos ate his sons. Dissipation breaks such a scenario. It implies a non-forgettable origin of time. Open systems need their complement (their "double") in order to become, together, a closed system. Time emerges as an observable measured by the evolution of the open system complement, which acts as a clock. The conservation of the energy-momentum tensor in electrodynamics is considered and its relation with dissipative systems and self-similar fractal structures is discussed. The isomorphism with coherent states in quantum field theory (QFT) is established and the generator of transitions among unitarily inequivalent representations of the canonical commutation relations (CCR) is shown to provide sequences in time of phases, which defines the arrow of time. Merging properties of electrodynamics, fractal self-similarity, dissipation and coherent states point to an integrated vision of Nature.

Structural models of antibody variable fragments: A method for investigating binding mechanisms

NASA Astrophysics Data System (ADS)

Petit, Samuel; Brard, Frédéric; Coquerel, Gérard; Perez, Guy; Tron, François

1998-03-01

The value of comparative molecular modeling for elucidating structure-function relationships was demonstrated by analyzing six anti-nucleosome autoantibody variable fragments. Structural models were built using the automated procedure developed in the COMPOSER software, subsequently minimized with the AMBER force field, and validated according to several standard geometric and chemical criteria. Canonical class assignment from Chothia and Lesk's [Chottin and Lesk, J. Mol. Biol., 196 (1987) 901; Chothia et al., Nature, 342 (1989) 877] work was used as a supplementary validation tool for five of the six hypervariable loops. The analysis, based on the hypothesis that antigen binding could occur through electrostatic interactions, reveals a diversity of possible binding mechanisms of anti-nucleosome or anti-histone antibodies to their cognate antigen. These results lead us to postulate that anti-nucleosome autoantibodies could have different origins. Since both anti-DNA and anti-nculeosome autoantibodies are produced during the course of systemic lupus erythematosus, a non-organ specific autoimmune disease, a comparative structural and electrostatic analysis of the two populations of autoantibodies may constitute a way to elucidate their origin and the role of the antigen in tolerance breakdown. The present study illustrates some interests, advantages and limits of a methodology based on the use of comparative modeling and analysis of molecular surface properties.

Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

PubMed

Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

2016-02-18

Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

PubMed Central

Gilbey, John; Cauwelier, Eef; Coulson, Mark W.; Stradmeyer, Lee; Sampayo, James N.; Armstrong, Anja; Verspoor, Eric; Corrigan, Laura; Shelley, Jonathan; Middlemas, Stuart

2016-01-01

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations. PMID:27723810

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

Fourier Transform Microwave Spectroscopy of Multiconformational Molecules and Van Der Waals Complexes.

NASA Astrophysics Data System (ADS)

Hight Walker, Angela Renee

1995-01-01

With the use of a Fourier transform microwave (FTM) spectrometer, structural determinations of two types of species; multiconformational molecules and van der Waals complexes, have been performed. Presented in this thesis are three sections summarizing this research effort. The first section contains a detailed explanation of the FTM instrument. In Section II, the study of three multiconformational molecules is presented as two chapters. Finally, three chapters in Section III outline the work still in progress on many van der Waals complexes. Section I was written to be a "manual" for the FTM spectrometer and to aid new additions to the group in their understanding of the instrument. An instruction guide is necessary for home-built instruments such as this one due to their unique design and application. Vital techniques and theories are discussed and machine operation is outlined. A brief explanation of general microwave spectroscopy as performed on an FTM spectrometer is also given. Section II is composed of two chapters pertaining to multiconformational molecules. In Chapter 2, a complete structural analysis of dipropyl ether is reported. The only conformer assigned had C_{rm s} symmetry. Many transitions are yet unassigned. Chapter 3 summarizes an investigation of two nitrosamines; methyl ethyl and methyl propyl nitrosamine. Only one conformer was observed for methyl ethyl nitrosamine, but two were assigned to methyl propyl nitrosamine. Nuclear hyperfine structure and internal methyl rotation complicated the spectra. The final section, Section III, contains the ongoing progress on weakly bound van der Waals complexes. The analysis of the OCS--HBr complex identified the structure as quasi-linear with large amplitude bending motions. Five separate isotopomers were assigned. Transitions originating from the HBr--DBr complex were measured and presented in Chapter 5. Although early in the analysis, the structure was determined to be bent and deuterium bonded. The final chapter of this section is meant to be a permanent record of transition frequencies whose molecular carrier is still in question. Two different groups of transitions from two different samples are listed. Further work is needed to unambiguously assign the frequencies with a carrier and quantum numbers, however the complexes (H_2 O)--(HCl)_2 and NO--H _2O are considered possible suspects.

Origins of the plant chloroplasts and mitochondria based on comparisons of 5S ribosomal RNAs

NASA Technical Reports Server (NTRS)

Delihas, N.; Fox, G. E.

1987-01-01

In this paper, we provide macromolecular comparisons utilizing the 5S ribosomal RNA structure to suggest extant bacteria that are the likely descendants of chloroplast and mitochondria endosymbionts. The genetic stability and near universality of the 5S ribosomal gene allows for a useful means to study ancient evolutionary changes by macromolecular comparisons. The value in current and future ribosomal RNA comparisons is in fine tuning the assignment of ancestors to the organelles and in establishing extant species likely to be descendants of bacteria involved in presumed multiple endosymbiotic events.

Racemic alkaloids from the fungus Ganoderma cochlear.

PubMed

Wang, Xin-Long; Dou, Man; Luo, Qi; Cheng, Li-Zhi; Yan, Yong-Ming; Li, Rong-Tao; Cheng, Yong-Xian

2017-01-01

Seven pairs of new alkaloid enantiomers, ganocochlearines C-I (1, 3-8), and three pairs of known alkaloids were isolated from the fruiting bodies of Ganoderma cochlear. The chemical structures of new compounds were elucidated on the basis of 1D and 2D NMR data. The absolute configurations of compounds 1, 3-10 were assigned by ECD calculations. Biological activities of these isolates against renal fibrosis were accessed in rat normal or diseased renal interstitial fibroblast cells. Importantly, the plausible biosynthetic pathway for this class of alkaloids was originally proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

The discovery of a new infrared emission feature at 1905 wavenumbers (5.25 microns) in the spectrum of BD +30 degrees 3639 and its relation to the polycyclic aromatic hydrocarbon model

NASA Technical Reports Server (NTRS)

Allamandola, L. J.; Bregman, J. D.; Sandford, S. A.; Tielens, A. G.; Witteborn, F. C.; Wooden, D. H.; Rank, D.

1989-01-01

We have discovered a new IR emission feature at 1905 cm-1 (5.25 microns) in the spectrum of BD +30 degrees 3639. This feature joins the family of well-known IR emission features at 3040, 2940, 1750, 1610, "1310," 1160, and 890 cm-1 (3.3, 3.4, 5.7, 6.2, "7.7," 8.6, and 11.2 microns). The origin of this new feature is discussed and it is assigned to an overtone or combination band involving C-H bending modes of polycyclic aromatic hydrocarbons (PAHs). Laboratory work suggests that spectral studies of the 2000-1650 cm-1 (5.0-6.1 microns) region may be very useful in elucidating the molecular structure of interstellar PAHs. The new feature, in conjunction with other recently discovered spectral structure, suggests that the narrow IR emission features originate in PAH molecules rather than large carbon grains. Larger species are likely to be the source of the broad underlying "plateaus" seen in many of the spectra.

A comparative study of the origin, structure, and indexing language of the Persian and English keywords of articles indexed in the IranMedex database and their compliance with the Persian medical thesaurus and Medical Subject Headings

PubMed Central

Parsaei-Mohammadi, Parastoo; Ghasemi, Ali Hossein; Hassanzadeh-Beheshtabad, Raziyeh

2017-01-01

Introduction: In the present era, thesauri as tools in indexing play an effective role in integrating retrieval preventing fragmentation as well as a multiplicity of terminologies and also in providing information content of documents. Goals: This study aimed to investigate the keywords of articles indexed in IranMedex in terms of origin, structure and indexing situation and their Compliance with the Persian Medical Thesaurus and Medical Subject Headings (MeSH). Materials and Methods: This study is an applied research, and a survey has been conducted. Statistical population includes 32,850 Persian articles which are indexed in the IranMedex during the years 1385–1391. 379 cases were selected as sample of the study. Data collection was done using a checklist. In analyzing the findings, the SPSS Software were used. Findings: Although there was no significant difference in terms of indexing origin between the proportion of different types of the Persian and English keywords of articles indexed in the IranMedex, the compliance rates of the Persian and English keywords with the Persian medical thesaurus and MeSH were different in different years. In the meantime, the structure of keywords is leaning more towards phrase structure, and a single word structure and the majority of keywords are selected from the titles and abstracts. Conclusion: The authors’ familiarity with the thesauri and controlled tools causes homogeneity in assigning keywords and also provides more precise, faster, and easier retrieval of the keywords. It's suggested that a mixture of natural and control languages to be used in this database in order to reach more comprehensive results. PMID:28546967

A comparative study of the origin, structure, and indexing language of the Persian and English keywords of articles indexed in the IranMedex database and their compliance with the Persian medical thesaurus and Medical Subject Headings.

PubMed

Parsaei-Mohammadi, Parastoo; Ghasemi, Ali Hossein; Hassanzadeh-Beheshtabad, Raziyeh

2017-01-01

In the present era, thesauri as tools in indexing play an effective role in integrating retrieval preventing fragmentation as well as a multiplicity of terminologies and also in providing information content of documents. This study aimed to investigate the keywords of articles indexed in IranMedex in terms of origin, structure and indexing situation and their Compliance with the Persian Medical Thesaurus and Medical Subject Headings (MeSH). This study is an applied research, and a survey has been conducted. Statistical population includes 32,850 Persian articles which are indexed in the IranMedex during the years 1385-1391. 379 cases were selected as sample of the study. Data collection was done using a checklist. In analyzing the findings, the SPSS Software were used. Although there was no significant difference in terms of indexing origin between the proportion of different types of the Persian and English keywords of articles indexed in the IranMedex, the compliance rates of the Persian and English keywords with the Persian medical thesaurus and MeSH were different in different years. In the meantime, the structure of keywords is leaning more towards phrase structure, and a single word structure and the majority of keywords are selected from the titles and abstracts. The authors' familiarity with the thesauri and controlled tools causes homogeneity in assigning keywords and also provides more precise, faster, and easier retrieval of the keywords. It's suggested that a mixture of natural and control languages to be used in this database in order to reach more comprehensive results.

Investigations of protein structure and function using the scientific literature: an assignment for an undergraduate cell physiology course.

PubMed

Mulnix, Amy B

2003-01-01

Undergraduate biology curricula are being modified to model and teach the activities of scientists better. The assignment described here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College. Students work in small groups to read and present in poster format on the content of a single research article reporting on the structure and/or function of a protein. Goals of the assignment include highlighting the interdependence of protein structure and function; asking students to review, integrate, and apply previously acquired knowledge; and helping students see protein structure/function in a context larger than cell physiology. The assignment also is designed to build skills in reading scientific literature, oral and written communication, and collaboration among peers. Assessment of student perceptions of the assignment in two separate offerings indicates that the project successfully achieves these goals. Data specifically show that students relied heavily on their peers to understand their article. The assignment was also shown to require students to read articles more carefully than previously. In addition, the data suggest that the assignment could be modified and used successfully in other courses and at other institutions.

Amino acid fermentation at the origin of the genetic code

PubMed Central

2012-01-01

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eörs Szathmáry (nominated by Dr. Gáspár Jékely) and Dr. Ádám Kun (nominated by Dr. Sandor Pongor) PMID:22325238

Combating the illegal trade in African elephant ivory with DNA forensics.

PubMed

Wasser, Samuel K; Joseph Clark, William; Drori, Ofir; Stephen Kisamo, Emily; Mailand, Celia; Mutayoba, Benezeth; Stephens, Matthew

2008-08-01

International wildlife crime is burgeoning in this climate of global trade. We contend that the most effective way to contain this illegal trade is to determine where the wildlife is being removed. This allows authorities to direct law enforcement to poaching hot spots, potentially stops trade before the wildlife is actually killed, prevents countries from denying their poaching problems at home, and thwarts trade before it enters into an increasingly complex web of international criminal activity. Forensic tools have been limited in their ability to determine product origin because the information they can provide typically begins only at the point of shipment. DNA assignment analyses can determine product origin, but its use has been limited by the inability to assign samples to locations where reference samples do not exist. We applied new DNA assignment methods that can determine the geographic origin(s) of wildlife products from anywhere within its range. We used these methods to examine the geographic origin(s) of 2 strings of seizures involving large volumes of elephant ivory, 1 string seized in Singapore and Malawi and the other in Hong Kong and Cameroon. These ivory traffickers may comprise 2 of the largest poaching rings in Africa. In both cases all ivory seized in the string had common origins, which indicates that crime syndicates are targeting specific populations for intense exploitation. This result contradicts the dominant belief that dealers are using a decentralized plan of procuring ivory stocks as they became available across Africa. Large quantities of ivory were then moved, in multiple shipments, through an intermediate country prior to shipment to Asia, as a risk-reduction strategy that distances the dealer from the poaching locale. These smuggling strategies could not have been detected by forensic information, which typically begins only at the shipping source.

A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

NASA Astrophysics Data System (ADS)

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff-based computation is employed in the scoring function to evaluate the probability of side-chain resonance assignments to generate the observed NMR spectra. The complexity of the assignment problem is first reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is used to find a set of optimal side-chain resonance assignments that best fit the NMR data. We have tested our algorithm on NMR data for five proteins, including the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), human ubiquitin, the ubiquitin-binding zinc finger domain of the human Y-family DNA polymerase Eta (pol η UBZ), and the human Set2-Rpb1 interacting domain (hSRI). Our algorithm assigns resonances for more than 90% of the protons in the proteins, and achieves about 80% correct side-chain resonance assignments. The final structures computed using distance restraints resulting from the set of assigned side-chain resonances have backbone RMSD 0.5 - 1.4 Å and all-heavy-atom RMSD 1.0 - 2.2 Å from the reference structures that were determined by X-ray crystallography or traditional NMR approaches. These results demonstrate that our algorithm can be successfully applied to automate side-chain resonance assignment and high-quality protein structure determination. Since our algorithm does not require any specific NMR experiments for measuring the through-bond interactions with side-chain protons, it can save a significant amount of both experimental cost and spectrometer time, and hence accelerate the NMR structure determination process.

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2013 CFR

2013-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

48 CFR 252.211-7007 - Reporting of Government-Furnished Property.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and groups of products; or (iii) Formal designations assigned to products by customer or supplier (such as model number or model type, design differentiation, or specific design series or configuration). “Part or identifying number (PIN)” means the identifier assigned by the original design activity, or by...

28 CFR 345.35 - Assignments to FPI.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., color, religion, ethnic origin, age, or disability. (b) The SOI ordinarily makes assignments based on... course in pre-industrial training or on-the-job training (as available) before promotion to pay grade four. (2) An inmate who has not successfully completed pre-industrial or on-the-job training remains at...

Improving Preservice Elementary Teachers' Writing in a Science Context

ERIC Educational Resources Information Center

Everett, Susan; Luera, Gail; Otto, Charlotte

2008-01-01

The authors investigated whether a series of mini prewriting assignments linked to a formal paper describing an original research project would improve preservice elementary teachers' writing abilities in a science context. They compared 38 final reports from students who completed the prewriting assignments with 38 reports randomly selected from…

Just beneath the Surface.

ERIC Educational Resources Information Center

Greenman, Geri

2003-01-01

Describes an art assignment used in an oil painting class in which the students create a nonrepresentational painting using acrylic paint. Explains that the second stage of the assignment involves students in finding a face in this first painting and using oils to create the face on top of the original artwork. (CMK)

Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa.

PubMed

Hefke, Gwynneth; Davison, Sean; D'Amato, Maria Eugenia

2015-12-01

The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Matrix-isolation and computational study of the HXeY⋯H2O complexes (Y = Cl, Br, and I).

PubMed

Tsuge, Masashi; Berski, Sławomir; Räsänen, Markku; Latajka, Zdzisław; Khriachtchev, Leonid

2014-01-28

The HXeY⋯H2O complexes (Y = Cl, Br, and I) are studied theoretically and experimentally. The calculations at the CCSD(T)/def2-TZVPPD level of theory predict two stable structures for Y = Cl and Br and one structure for Y = I, with interaction energies up to about -7 kcal mol(-1). In the experiments, we have identified several infrared absorption bands originating from the H-Xe stretching mode of these complexes in a xenon matrix. The monomer-to-complex frequency shifts of this mode are up to +82 cm(-1) (Y = Cl), +101 cm(-1) (Y = Br), and +138 cm(-1) (Y = I), i.e., the shift is smaller for more strongly bound molecules. Based on the agreement of the experimental and theoretical results, the observed bands are assigned to the most stable planar structure with an O-H⋯Y-Xe hydrogen bond.

Rapid and Portable Methods for Identification of Bacterially Influenced Calcite: Application of Laser-Induced Breakdown Spectroscopy and AOTF Reflectance Spectroscopy, Fort Stanton Cave, New Mexico

NASA Astrophysics Data System (ADS)

McMillan, N. J.; Chavez, A.; Chanover, N.; Voelz, D.; Uckert, K.; Tawalbeh, R.; Gariano, J.; Dragulin, I.; Xiao, X.; Hull, R.

2014-12-01

Rapid, in-situ methods for identification of biologic and non-biologic mineral precipitation sites permit mapping of biological hot spots. Two portable spectrometers, Laser-Induced Breakdown Spectroscopy (LIBS) and Acoustic-Optic Tunable Filter Reflectance Spectroscopy (AOTFRS) were used to differentiate between bacterially influenced and inorganically precipitated calcite specimens from Fort Stanton Cave, NM, USA. LIBS collects light emitted from the decay of excited electrons in a laser ablation plasma; the spectrum is a chemical fingerprint of the analyte. AOTFRS collects light reflected from the surface of a specimen and provides structural information about the material (i.e., the presence of O-H bonds). These orthogonal data sets provide a rigorous method to determine the origin of calcite in cave deposits. This study used a set of 48 calcite samples collected from Fort Stanton cave. Samples were examined in SEM for the presence of biologic markers; these data were used to separate the samples into biologic and non-biologic groups. Spectra were modeled using the multivariate technique Partial Least Squares Regression (PLSR). Half of the spectra were used to train a PLSR model, in which biologic samples were assigned to the independent variable "0" and non-biologic samples were assigned the variable "1". Values of the independent variable were calculated for each of the training samples, which were close to 0 for the biologic samples (-0.09 - 0.23) and close to 1 for the non-biologic samples (0.57 - 1.14). A Value of Apparent Distinction (VAD) of 0.55 was used to numerically distinguish between the two groups; any sample with an independent variable value < 0.55 was classified as having a biologic origin; a sample with a value > 0.55 was determined to be non-biologic in origin. After the model was trained, independent variable values for the remaining half of the samples were calculated. Biologic or non-biologic origin was assigned by comparison to the VAD. Using LIBS data alone, the model has a 92% success rate, correctly identifying 23 of 25 samples. Modeling of AOTFRS spectra and the combined LIBS-AOTFRS data set have similar success rates. This study demonstrates that rapid, portable LIBS and AOTFRS instruments can be used to map the spatial distribution of biologic precipitation in caves.

Genomic characterisation of Arachis porphyrocalyx (Valls & C.E. Simpson, 2005) (Leguminosae): multiple origin of Arachis species with x = 9

PubMed Central

Celeste, Silvestri María; Ortiz, Alejandra Marcela; Robledo, Germán Ariel; Valls, José Francisco Montenegro; Lavia, Graciela Inés

2017-01-01

Abstract The genus Arachis Linnaeus, 1753 comprises four species with x = 9, three belong to the section Arachis: Arachis praecox (Krapov. W.C. Greg. & Valls, 1994), Arachis palustris (Krapov. W.C. Greg. & Valls, 1994) and Arachis decora (Krapov. W.C. Greg. & Valls, 1994) and only one belongs to the section Erectoides: Arachis porphyrocalyx (Valls & C.E. Simpson, 2005). Recently, the x = 9 species of section Arachis have been assigned to G genome, the latest described so far. The genomic relationship of Arachis porphyrocalyx with these species is controversial. In the present work, we carried out a karyotypic characterisation of Arachis porphyrocalyx to evaluate its genomic structure and analyse the origin of all x = 9 Arachis species. Arachis porphyrocalyx showed a karyotype formula of 14m+4st, one pair of A chromosomes, satellited chromosomes type 8, one pair of 45S rDNA sites in the SAT chromosomes, one pair of 5S rDNA sites and pericentromeric C-DAPI+ bands in all chromosomes. Karyotype structure indicates that Arachis porphyrocalyx does not share the same genome type with the other three x = 9 species and neither with the remaining Erectoides species. Taking into account the geographic distribution, morphological and cytogenetic features, the origin of species with x = 9 of the genus Arachis cannot be unique; instead, they originated at least twice in the evolutionary history of the genus. PMID:28919947

Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

PubMed

Ipek, M; Ipek, A; Seker, M; Gul, M K

2015-03-27

The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P < 0.001) between ssrOeUA-DCA14 and stearic acid and between GAPU71B and oleic acid indicated that these markers could be used for marker-assisted selection in olive.

Bioactive natural products from fungicolous Hawaiian isolates: secondary metabolites from a Phialemoniopsis sp.

PubMed Central

Kaur, Amninder; Rogers, Kristina D.; Swenson, Dale E.; Dowd, Patrick F.; Wicklow, Donald T.; Gloer, James B.

2014-01-01

Chemical investigations of two fungal isolates initially identified as members of the genus Phialemonium are described. Both isolates were obtained as colonists of other fungi collected on the island of Hawaii and were later assigned as P. curvatum. However, P. curvatum has recently been reclassified as a member of a new genus (Phialemoniopsis) and renamed as Phialemoniopsis curvata. Studies of solid–substrate fermentation cultures of one of these isolates afforded an oxirapentyn analogue and destruxin A4 as major components, while analysis of the second strain led to the isolation of several simple aromatic metabolites and a compound of mixed biogenetic origin called gabusectin that had previously been reported only in a patent. Structures were assigned mainly by detailed nuclear magnetic resonance and mass spectrometry analysis, and those of two of the major components were confirmed by X-ray crystallography. This report constitutes the first description of secondary metabolites from a member of the genus Phialemoniopsis. PMID:25379336

On a modification method of Lefschetz thimbles

NASA Astrophysics Data System (ADS)

Tsutsui, Shoichiro; Doi, Takahiro M.

2018-03-01

The QCD at finite density is not well understood yet, where standard Monte Carlo simulation suffers from the sign problem. In order to overcome the sign problem, the method of Lefschetz thimble has been explored. Basically, the original sign problem can be less severe in a complexified theory due to the constancy of the imaginary part of an action on each thimble. However, global phase factors assigned on each thimble still remain. Their interference is not negligible in a situation where a large number of thimbles contribute to the partition function, and this could also lead to a sign problem. In this study, we propose a method to resolve this problem by modifying the structure of Lefschetz thimbles such that only a single thimble is relevant to the partition function. It can be shown that observables measured in the original and modified theories are connected by a simple identity. We exemplify that our method works well in a toy model.

Mid-Infrared Spectroscopy of Persistent Leonid Trains

NASA Technical Reports Server (NTRS)

Russell, Ray W.; Rossano, George S.; Chatelain, Mark A.; Lynch, David K.; Tessensohn, Ted K.; Abendroth, Eric; Kim, Daryl; Jenniskens, Peter; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The first infrared spectroscopy in the 3-13 micron region has been obtained of several persistent Leonid meteor trains with two different instrument types, one at a desert ground-based site and the other on-board a high-flying aircraft. The spectra exhibit common structures assigned to enhanced emissions of warm CH4, CO2, CO and H2O which may originate from heated trace air compounds or materials created in the wake of the meteor. This is the first time that any of these molecules has been observed in the spectra of persistent trains. Hence, the mid-IR observations offer a new perspective on the physical processes that occur in the path of the meteor at some time after the meteor itself has passed by. Continuum emission is observed also, but its origin has not yet been established. No 10 micron dust emission feature has been observed.

Impact of Arthroscopic Lateral Acromioplasty on the Mechanical and Structural Integrity of the Lateral Deltoid Origin: A Cadaveric Study.

PubMed

Marchetti, Daniel Cole; Katthagen, J Christoph; Mikula, Jacob D; Montgomery, Scott R; Tahal, Dimitri S; Dahl, Kimi D; Turnbull, Travis Lee; Millett, Peter J

2017-03-01

To determine whether a 5-mm and/or 10-mm arthroscopic lateral acromioplasty (ALA) would weaken the structural and mechanical integrity of the lateral deltoid. The acromion and lateral deltoid origin were harvested from 15 pairs (n = 30) of fresh-frozen human cadaveric shoulder specimens. One side of each specimen pair (left or right) was randomly assigned to either a 5-mm (n = 7) or 10-mm (n = 8) ALA group, and the contralateral sides (n = 15) were used as matched controls. Acromion thickness and width were measured pre- and postoperatively. After ALA, specimens were inspected for damage to the lateral deltoid origin. Each specimen was secured within a dynamic testing machine, and the deltoid muscle was pulled to failure. Statistical analysis was performed to determine whether ALA reduced the lateral deltoid's failure load. There was no significant difference in failure load between the 5-mm ALA group (661 ± 207 N) and its matched control group (744 ± 212 N; mean difference = 83 N; 95% confidence interval [CI], -91 to 258; P = .285) nor between the 10-mm ALA group (544 ± 210 N) and its matched control group (598 ± 157 N; mean difference = 54 N; 95% CI, -141 to 250; P = .532). There was no correlation found between the amount of bone resected (measured by percent thickness and width of the acromion after ALA) and the failure load of the deltoid. Visual evaluation of the acromion after ALA revealed the lateral deltoid origin had no damage in any case. ALA did not weaken the structural or mechanical integrity of the lateral deltoid origin. Neither a 5-mm nor a 10-mm ALA significantly reduced the deltoid's failure load. The lateral deltoid origin was not macroscopically damaged in any case. ALA can be performed without the potential risk of macroscopically damaging the lateral deltoid origin or reducing its failure load. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Originality Detection Software in a Graduate Policy Course: A Mixed-Methods Evaluation of Plagiarism

ERIC Educational Resources Information Center

Dreuth Zeman, Laura; Steen, Julie A.; Metz Zeman, Natalie

2011-01-01

The authors used a mixed-methods approach to evaluate the use of Turnitin originality detection software in a graduate social work course. Qualitative analysis of student responses revealed positive and negative spent completing assignments, and the tone of the class. Quantitative analysis of students' originality scores indicated a short-term…

76 FR 47550 - Certain Tissue Paper Products From the People's Republic of China: Notice of Rescission of the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-05

... products produced from Chinese-origin jumbo rolls/ sheets.\\3\\ We determined in the Preliminary Results, as... paper products produced using Chinese-origin jumbo rolls/sheets. Further, based on AFA, we preliminarily... produced by MFVN from Chinese-origin jumbo rolls/sheets is China. Consequently, we assigned MFVN a cash...

Automated bond order assignment as an optimization problem.

PubMed

Dehof, Anna Katharina; Rurainski, Alexander; Bui, Quang Bao Anh; Böcker, Sebastian; Lenhof, Hans-Peter; Hildebrandt, Andreas

2011-03-01

Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach. We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods. The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.

Investigations of Protein Structure and Function Using the Scientific Literature: An Assignment for an Undergraduate Cell Physiology Course

PubMed Central

Mulnix, Amy B.

2003-01-01

Undergraduate biology curricula are being modified to model and teach the activities of scientists better. The assignment described here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College. Students work in small groups to read and present in poster format on the content of a single research article reporting on the structure and/or function of a protein. Goals of the assignment include highlighting the interdependence of protein structure and function; asking students to review, integrate, and apply previously acquired knowledge; and helping students see protein structure/function in a context larger than cell physiology. The assignment also is designed to build skills in reading scientific literature, oral and written communication, and collaboration among peers. Assessment of student perceptions of the assignment in two separate offerings indicates that the project successfully achieves these goals. Data specifically show that students relied heavily on their peers to understand their article. The assignment was also shown to require students to read articles more carefully than previously. In addition, the data suggest that the assignment could be modified and used successfully in other courses and at other institutions. PMID:14673490

An abbreviated SNP panel for ancestry assignment of honeybees (Apis mellifera)

USDA-ARS?s Scientific Manuscript database

This paper examines whether an abbreviated panel of 37 single nucleotide polymorphisms (SNPs) has the same power as a larger and more expensive panel of 95 SNPs to assign ancestry of honeybees (Apis mellifera) to three ancestral lineages. We selected 37 SNPs from the original 95 SNP panel using alle...

Assigned and unassigned distance geometry: applications to biological molecules and nanostructures

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

Billinge, Simon J. L.; Duxbury, Phillip M.; Gonçalves, Douglas S.

2016-04-04

Here, considering geometry based on the concept of distance, the results found by Menger and Blumenthal originated a body of knowledge called distance geometry. This survey covers some recent developments for assigned and unassigned distance geometry and focuses on two main applications: determination of three-dimensional conformations of biological molecules and nanostructures.

Using the Lesson Cycle in Teaching Composition: A Plan for Creativity.

ERIC Educational Resources Information Center

Robitaille, Marilyn M.

Designed to combine the science and the art of teaching composition, this series of assignments encourages junior high and high school writing students to explore tone, original visual images, point of view, and other literary techniques. One assignment asks students to write a number of paragraphs alternately using sarcasm, humor, melancholy, and…

Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations.

PubMed

Ben Halim, Nizar; Hsouna, Sana; Lasram, Khaled; Chargui, Mariem; Khemira, Laaroussi; Saidane, Rachid; Abdelhak, Sonia; Kefi, Rym

2018-02-01

Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (n = 4857) were compiled from previous studies. The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.

The experience of critiquing published research: learning from the student and researcher perspective.

PubMed

Knowles, Judie M; Gray, Morag A

2011-11-01

This paper commences with affirmation of the importance of research critique within academic programmes of study, and the context of this skill within the nursing profession. Judie (student) shares an experience from a Professional Doctorate in Education (EdD) assignment that involved selecting and critiquing a piece of published research. "The qualities of an effective mentor" (Gray and Smith, 2000) was critiqued using the Critical Appraisal Skills Programme (CASP, 2006) framework. Morag was the researcher and co-author (Gray and Smith, 2000) and was subsequently contacted by Judie for the purposes of validating her critique assignment. On the tenth anniversary since publication of her PhD research findings Morag reflects on the original article in the light of Judie's critique and shares evaluative comments. Some of the assignment critique is validated by Morag, whilst some of the evaluation demonstrates unreliability of critique shown by Judie. Discussion surrounding sufficiency of research critique through systematic examination of a published article, versus an original research report such as a thesis ensues. The student and researcher/author reveal their learning from this collaborative experience and conclude with recommendations for; setting critique assignments; authors publishing their research findings; and students undertaking critique assignments. Copyright © 2011 Elsevier Ltd. All rights reserved.

Object memory effects on figure assignment: conscious object recognition is not necessary or sufficient.

PubMed

Peterson, M A; de Gelder, B; Rapcsak, S Z; Gerhardstein, P C; Bachoud-Lévi, A

2000-01-01

In three experiments we investigated whether conscious object recognition is necessary or sufficient for effects of object memories on figure assignment. In experiment 1, we examined a brain-damaged participant, AD, whose conscious object recognition is severely impaired. AD's responses about figure assignment do reveal effects from memories of object structure, indicating that conscious object recognition is not necessary for these effects, and identifying the figure-ground test employed here as a new implicit test of access to memories of object structure. In experiments 2 and 3, we tested a second brain-damaged participant, WG, for whom conscious object recognition was relatively spared. Nevertheless, effects from memories of object structure on figure assignment were not evident in WG's responses about figure assignment in experiment 2, indicating that conscious object recognition is not sufficient for effects of object memories on figure assignment. WG's performance sheds light on AD's performance, and has implications for the theoretical understanding of object memory effects on figure assignment.

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

PubMed Central

Schneider, Thomas; Keiblinger, Katharina M; Schmid, Emanuel; Sterflinger-Gleixner, Katja; Ellersdorfer, Günther; Roschitzki, Bernd; Richter, Andreas; Eberl, Leo; Zechmeister-Boltenstern, Sophie; Riedel, Kathrin

2012-01-01

Leaf-litter decomposition is a central process in carbon cycling; however, our knowledge about the microbial regulation of this process is still scarce. Metaproteomics allows us to link the abundance and activity of enzymes during nutrient cycling to their phylogenetic origin based on proteins, the ‘active building blocks' in the system. Moreover, we employed metaproteomics to investigate the influence of environmental factors and nutrients on the decomposer structure and function during beech litter decomposition. Litter was collected at forest sites in Austria with different litter nutrient content. Proteins were analyzed by 1-D-SDS-PAGE followed by liquid-chromatography and tandem mass-spectrometry. Mass spectra were assigned to phylogenetic and functional groups by a newly developed bioinformatics workflow, assignments being validated by complementary approaches. We provide evidence that the litter nutrient content and the stoichiometry of C:N:P affect the decomposer community structure and activity. Fungi were found to be the main producers of extracellular hydrolytic enzymes, with no bacterial hydrolases being detected by our metaproteomics approach. Detailed investigation of microbial succession suggests that it is influenced by litter nutrient content. Microbial activity was stimulated at higher litter nutrient contents via a higher abundance and activity of extracellular enzymes. PMID:22402400

Tuning up mind's pattern to nature's own idea: Eddington's early twenties case for variational derivatives

NASA Astrophysics Data System (ADS)

Smadja, Ivahn

This paper sets out to show how Eddington's early twenties case for variational derivatives significantly bears witness to a steady and consistent shift in focus from a resolute striving for objectivity towards "selective subjectivism" and structuralism. While framing his so-called "Hamiltonian derivatives" along the lines of previously available variational methods allowing to derive gravitational field equations from an action principle, Eddington assigned them a theoretical function of his own devising in The Mathematical Theory of Relativity (1923). I make clear that two stages should be marked out in Eddington's train of thought if the meaning of such variational derivatives is to be adequately assessed. As far as they were originally intended to embody the mind's collusion with nature by linking atomicity of matter with atomicity of action, variational derivatives were at first assigned a dual role requiring of them not only to express mind's craving for permanence but also to tune up mind's privileged pattern to "Nature's own idea". Whereas at a later stage, as affine field theory would provide a framework for world-building, such "Hamiltonian differentiation" would grow out of tune through gauge-invariance and, by disregarding how mathematical theory might precisely come into contact with actual world, would be turned into a mere heuristic device for structural knowledge.

Longitudinal changes in health related quality of life in children with migrant backgrounds.

PubMed

Villalonga-Olives, Ester; Kawachi, Ichiro; Almansa, Josue; von Steinbüchel, Nicole

2017-01-01

Little is known about longitudinal changes in the Health Related Quality of Life (HRQoL) among children with migrant backgrounds. The sample comprised 350 children with predominantly migrant backgrounds enrolled in 7 kindergartens in Frankfurt and Darmstadt, Germany. At baseline, the participants' mean age was 4.4 years (SD 0.9). Data collection started in May 2009. Two waves of data were collected one year apart (94% response rate). HRQoL was evaluated with the Kiddy-KINDL. The other variables under study were sex, age, socioeconomic status, country of origin, developmental status (WET) and individual behavior (VBV). Data were collected from the children, parents and teachers. Structural equation modeling (SEM) was used to assess the Wilson and Cleary theoretical framework on changes in HRQoL and Generalized Estimated Equations (GEE) to model the longitudinal trend in HRQoL. Overall HRQoL remained stable between baseline and follow-up. SEM model fit was χ2 = 8.51; df = 5; p = 0.13; SRMR = 0.02 RMSEA = 0.06 and indicated that there were differences in kindergarten activities (p<0.05). The GEE model elucidated that the differences in HRQoL between the baseline and follow-up varied according to kindergarten activities that the children were assigned to (music, art, or no activities) (p<0.05), but that there were no differences in terms of country of origin. On average, girls reported better HRQoL. Overall HRQoL scores remained stable over follow-up in a sample of migrant children and there were no differences in terms of origin. However, there was heterogeneity in the results depending on the kindergarten activities that the children were assigned to.

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

The CoRR hypothesis for genes in organelles.

PubMed

Allen, John F

2017-12-07

Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separat from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function. Biochemistry and molecular biology now show that Sagan's proposal has an explanatory reach far beyond that originally envisaged. Prokaryotic origins of photosynthetic and respiratory mechanisms are apparent in protein structural insights into energy coupling. Genome sequencing confirms the underlying, prokaryotic architecture of chloroplasts and mitochondria and illustrates the profound influence of the original mergers of their ancestors' genes and proteins with those of their host cells. Peter Mitchell's 1961 chemiosmotic hypothesis applied the concept of vectorial catalysis that underlies biological energy transduction and cell structure, function, and origins. Continuity of electrical charge separation and membrane sidedness requires compartments within compartments, together with intricate mechanisms for transport within and between them. I suggest that the reason for the persistence of distinct genetic systems within bioenergetic organelles is the selective advantage of subcellular co-location of specific genes with their gene products. Co-location for Redox Regulation - CoRR - provides for a dialogue between chemical reduction-oxidation and the action of genes encoding its protein catalysts. These genes and their protein products are in intimate contact, and cannot be isolated from each other without loss of an essential mechanism of adaptation of electron transport to change in the external environment. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

5 CFR 1312.5 - Authority to classify.

Code of Federal Regulations, 2012 CFR

2012-01-01

... classify information or material under this part shall be limited to those officials concerned with matters..., to assign original classifications as indicated to information or material that is originated by OMB... International Affairs. (iv) Associate Director for Natural Resources, Energy and Science. (2) Secret and below...

5 CFR 1312.5 - Authority to classify.

Code of Federal Regulations, 2013 CFR

2013-01-01

... classify information or material under this part shall be limited to those officials concerned with matters..., to assign original classifications as indicated to information or material that is originated by OMB... International Affairs. (iv) Associate Director for Natural Resources, Energy and Science. (2) Secret and below...

5 CFR 1312.5 - Authority to classify.

Code of Federal Regulations, 2014 CFR

2014-01-01

... classify information or material under this part shall be limited to those officials concerned with matters..., to assign original classifications as indicated to information or material that is originated by OMB... International Affairs. (iv) Associate Director for Natural Resources, Energy and Science. (2) Secret and below...

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

76 FR 28499 - 30-Day Notice of Proposed Information Collection: Form DS-6561, Pre-Assignment for Overseas Duty...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... DEPARTMENT OF STATE [Public Notice 7459] 30-Day Notice of Proposed Information Collection: Form DS-6561, Pre-Assignment for Overseas Duty, OMB 1405-XXXX ACTION: Notice of request for public comments.... OMB Control Number: 1405-XXXX. Type of Request: New. Originating Office: Office of Medical Services, M...

Do Anti-Bredt Natural Products Exist? Olefin Strain Energy as a Predictor of Isolability.

PubMed

Krenske, Elizabeth H; Williams, Craig M

2015-09-01

Bredt's rule holds a special place in the realm of physical organic chemistry, but its application to natural products chemistry—the field in which the rule was originally formulated—is not well defined. Herein, the use of olefin strain (OS) energy as a readily calculated predictor of the stability of natural products containing a bridgehead alkene is introduced. Schleyer first used OS energies to classify parent bridgehead alkenes into "isolable", "observable", and "unstable" classes. OS calculations on natural products, using contemporary forcefield methods, unequivocally predict all structurally verified bridgehead alkene natural products to be "isolable". Thus, when one assigns the structure of a putative bridgehead alkene natural product, an OS in the "observable" or "unstable" ranges is a red flag for error. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Who was the agent? The neural correlates of reanalysis processes during sentence comprehension.

PubMed

Hirotani, Masako; Makuuchi, Michiru; Rüschemeyer, Shirley-Ann; Friederici, Angela D

2011-11-01

Sentence comprehension is a complex process. Besides identifying the meaning of each word and processing the syntactic structure of a sentence, it requires the computation of thematic information, that is, information about who did what to whom. The present fMRI study investigated the neural basis for thematic reanalysis (reanalysis of the thematic roles initially assigned to noun phrases in a sentence) and its interplay with syntactic reanalysis (reanalysis of the underlying syntactic structure originally constructed for a sentence). Thematic reanalysis recruited a network consisting of Broca's area, that is, the left pars triangularis (LPT), and the left posterior superior temporal gyrus, whereas only LPT showed greater sensitivity to syntactic reanalysis. These data provide direct evidence for a functional neuroanatomical basis for two linguistically motivated reanalysis processes during sentence comprehension. Copyright © 2010 Wiley-Liss, Inc.

Development of eighteen microsatellite loci in walleye (Sander vitreus)

USGS Publications Warehouse

Coykendall, D. Katharine; Morrison, Cheryl L.; Stott, Wendylee; Springmann, Marcus J.

2014-01-01

A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye (Sander vitreus) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis(sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

An Interactive Introduction to Protein Structure

ERIC Educational Resources Information Center

Lee, W. Theodore

2004-01-01

To improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer-generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail…

Evidence for an Elevated Aspartate pKa in the Active Site of Human Aromatase*

PubMed Central

Di Nardo, Giovanna; Breitner, Maximilian; Bandino, Andrea; Ghosh, Debashis; Jennings, Gareth K.; Hackett, John C.; Gilardi, Gianfranco

2015-01-01

Aromatase (CYP19A1), the enzyme that converts androgens to estrogens, is of significant mechanistic and therapeutic interest. Crystal structures and computational studies of this enzyme shed light on the critical role of Asp309 in substrate binding and catalysis. These studies predicted an elevated pKa for Asp309 and proposed that protonation of this residue was required for function. In this study, UV-visible absorption, circular dichroism, resonance Raman spectroscopy, and enzyme kinetics were used to study the impact of pH on aromatase structure and androstenedione binding. Spectroscopic studies demonstrate that androstenedione binding is pH-dependent, whereas, in contrast, the D309N mutant retains its ability to bind to androstenedione across the entire pH range studied. Neither pH nor mutation perturbed the secondary structure or heme environment. The origin of the observed pH dependence was further narrowed to the protonation equilibria of Asp309 with a parallel set of spectroscopic studies using exemestane and anastrozole. Because exemestane interacts with Asp309 based on its co-crystal structure with the enzyme, its binding is pH-dependent. Aromatase binding to anastrozole is pH-independent, consistent with the hypothesis that this ligand exploits a distinct set of interactions in the active site. In summary, we assign the apparent pKa of 8.2 observed for androstenedione binding to the side chain of Asp309. To our knowledge, this work represents the first experimental assignment of a pKa value to a residue in a cytochrome P450. This value is in agreement with theoretical calculations (7.7–8.1) despite the reliance of the computational methods on the conformational snapshots provided by crystal structures. PMID:25425647

Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

PubMed

Mura-Jornet, Isidora; Pimentel, Carolina; Dantas, Gisele P M; Petry, Maria Virginia; González-Acuña, Daniel; Barbosa, Andrés; Lowther, Andrew D; Kovacs, Kit M; Poulin, Elie; Vianna, Juliana A

2018-06-13

Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species' easternmost breeding colony (Bouvetøya). Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite F ST  = 0.002, p = 0.273; mtDNA F ST  = - 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP. The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

Origin of the 900 cm{sup −1} broad double-hump OH vibrational feature of strongly hydrogen-bonded carboxylic acids

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

Van Hoozen, Brian L.; Petersen, Poul B.

2015-03-14

Medium and strong hydrogen bonds are common in biological systems. Here, they provide structural support and can act as proton transfer relays to drive electron and/or energy transfer. Infrared spectroscopy is a sensitive probe of molecular structure and hydrogen bond strength but strongly hydrogen-bonded structures often exhibit very broad and complex vibrational bands. As an example, strong hydrogen bonds between carboxylic acids and nitrogen-containing aromatic bases commonly display a 900 cm{sup −1} broad feature with a remarkable double-hump structure. Although previous studies have assigned this feature to the OH, the exact origin of the shape and width of this unusualmore » feature is not well understood. In this study, we present ab initio calculations of the contributions of the OH stretch and bend vibrational modes to the vibrational spectrum of strongly hydrogen-bonded heterodimers of carboxylic acids and nitrogen-containing aromatic bases, taking the 7-azaindole—acetic acid and pyridine—acetic acid dimers as examples. Our calculations take into account coupling between the OH stretch and bend modes as well as how both of these modes are affected by lower frequency dimer stretch modes, which modulate the distance between the monomers. Our calculations reproduce the broadness and the double-hump structure of the OH vibrational feature. Where the spectral broadness is primarily caused by the dimer stretch modes strongly modulating the frequency of the OH stretch mode, the double-hump structure results from a Fermi resonance between the out of the plane OH bend and the OH stretch modes.« less

Keeping Kids Engaged Fights Plagiarism, Too

ERIC Educational Resources Information Center

Johnson, Doug

2004-01-01

Educators try to "catch" plagiarism, but their time is better spent creating assignments that require original, thoughtful research and, therefore, minimize plagiarism. In this article, the author presents two scenarios which exemplify projects that encourage students to do original work. Moreover, some qualities of projects carrying a low…

Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.

PubMed

Wasser, Samuel K; Mailand, Celia; Booth, Rebecca; Mutayoba, Benezeth; Kisamo, Emily; Clark, Bill; Stephens, Matthew

2007-03-06

The illegal ivory trade recently intensified to the highest levels ever reported. Policing this trafficking has been hampered by the inability to reliably determine geographic origin of contraband ivory. Ivory can be smuggled across multiple international borders and along numerous trade routes, making poaching hotspots and potential trade routes difficult to identify. This fluidity also makes it difficult to refute a country's denial of poaching problems. We extend an innovative DNA assignment method to determine the geographic origin(s) of large elephant ivory seizures. A Voronoi tessellation method is used that utilizes genetic similarities across tusks to simultaneously infer the origin of multiple samples that could have one or more common origin(s). We show that this joint analysis performs better than sample-by-sample methods in assigning sample clusters of known origin. The joint method is then used to infer the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. Wildlife authorities initially suspected that this ivory came from multiple locations across forest and savanna Africa. However, we show that the ivory was entirely from savanna elephants, most probably originating from a narrow east-to-west band of southern Africa, centered on Zambia. These findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes and led to changes within the Zambian government to improve antipoaching efforts. Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed.

Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban

PubMed Central

Wasser, Samuel K.; Mailand, Celia; Booth, Rebecca; Mutayoba, Benezeth; Kisamo, Emily; Clark, Bill; Stephens, Matthew

2007-01-01

The illegal ivory trade recently intensified to the highest levels ever reported. Policing this trafficking has been hampered by the inability to reliably determine geographic origin of contraband ivory. Ivory can be smuggled across multiple international borders and along numerous trade routes, making poaching hotspots and potential trade routes difficult to identify. This fluidity also makes it difficult to refute a country's denial of poaching problems. We extend an innovative DNA assignment method to determine the geographic origin(s) of large elephant ivory seizures. A Voronoi tessellation method is used that utilizes genetic similarities across tusks to simultaneously infer the origin of multiple samples that could have one or more common origin(s). We show that this joint analysis performs better than sample-by-sample methods in assigning sample clusters of known origin. The joint method is then used to infer the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. Wildlife authorities initially suspected that this ivory came from multiple locations across forest and savanna Africa. However, we show that the ivory was entirely from savanna elephants, most probably originating from a narrow east-to-west band of southern Africa, centered on Zambia. These findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes and led to changes within the Zambian government to improve antipoaching efforts. Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed. PMID:17360505

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

PubMed

Pupier, Marion; Nuzillard, Jean-Marc; Wist, Julien; Schlörer, Nils E; Kuhn, Stefan; Erdelyi, Mate; Steinbeck, Christoph; Williams, Antony J; Butts, Craig; Claridge, Tim D W; Mikhova, Bozhana; Robien, Wolfgang; Dashti, Hesam; Eghbalnia, Hamid R; Farès, Christophe; Adam, Christian; Kessler, Pavel; Moriaud, Fabrice; Elyashberg, Mikhail; Argyropoulos, Dimitris; Pérez, Manuel; Giraudeau, Patrick; Gil, Roberto R; Trevorrow, Paul; Jeannerat, Damien

2018-04-14

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases. Copyright © 2018 John Wiley & Sons, Ltd.

Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

DOE PAGES

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean -Christophe; ...

2017-11-15

In this paper, connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered CH 3NH 3more » + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R- and M-point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.« less

Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

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

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean -Christophe

In this paper, connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered CH 3NH 3more » + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R- and M-point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.« less

Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

NASA Astrophysics Data System (ADS)

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean-Christophe; Even, Jacky; Mohite, Aditya D.; Sfeir, Matthew Y.

2017-11-01

Connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered C H3N H3 + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R - and M -point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Quantum Optimal Multiple Assignment Scheme for Realizing General Access Structure of Secret Sharing

NASA Astrophysics Data System (ADS)

Matsumoto, Ryutaroh

The multiple assignment scheme is to assign one or more shares to single participant so that any kind of access structure can be realized by classical secret sharing schemes. We propose its quantum version including ramp secret sharing schemes. Then we propose an integer optimization approach to minimize the average share size.

Infrared and Raman spectroscopic characterization of the carbonate mineral huanghoite - And in comparison with selected rare earth carbonates

NASA Astrophysics Data System (ADS)

Frost, Ray L.; López, Andrés; Scholz, Ricardo; Xi, Yunfei; Belotti, Fernanda Maria

2013-11-01

Raman spectroscopy complimented with infrared spectroscopy has been used to study the rare earth based mineral huanghoite with possible formula given as BaCe(CO3)2F and compared with the Raman spectra of a series of selected natural halogenated carbonates from different origins including bastnasite, parisite and northupite. The Raman spectrum of huanghoite displays three bands are at 1072, 1084 and 1091 cm-1 attributed to the CO32- symmetric stretching vibration. The observation of three symmetric stretching vibrations is very unusual. The position of CO32- symmetric stretching vibration varies with mineral composition. Infrared spectroscopy of huanghoite show bands at 1319, 1382, 1422 and 1470 cm-1. No Raman bands of huanghoite were observed in these positions. Raman spectra of bastnasite, parisite and northupite show a single band at 1433, 1420 and 1554 cm-1 assigned to the ν3 (CO3)2- antisymmetric stretching mode. The observation of additional Raman bands for the ν3 modes for some halogenated carbonates is significant in that it shows distortion of the carbonate anion in the mineral structure. Four Raman bands for huanghoite are observed at 687, 704, 718 and 730 cm-1and assigned to the (CO3)2- ν2 bending modes. Raman bands are observed for huanghoite at around 627 cm-1 and are assigned to the (CO3)2- ν4 bending modes. Raman bands are observed for the carbonate ν4 in phase bending modes at 722 cm-1 for bastnasite, 736 and 684 cm-1 for parisite, 714 cm-1 for northupite. Raman bands for huanghoite observed at 3259, 3484 and 3589 cm-1 are attributed to water stretching bands. Multiple bands are observed in the OH stretching region for bastnasite and parisite indicating the presence of water and OH units in their mineral structure. Vibrational spectroscopy enables new information on the structure of huanghoite to be assessed.

Identification of ion-pair structures in solution by vibrational stark effects

DOE PAGES

Hack, John; Mani, Tomoyasu; Grills, David C.; ...

2016-01-25

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

Identification of ion-pair structures in solution by vibrational stark effects

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

Hack, John; Mani, Tomoyasu; Grills, David C.

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

Writing Assignments that Promote Active Learning

NASA Astrophysics Data System (ADS)

Narayanan, M.

2014-12-01

Encourage students to write a detailed, analytical report correlating classroom discussions to an important historical event or a current event. Motivate students interview an expert from industry on a topic that was discussed in class. Ask the students to submit a report with supporting sketches, drawings, circuit diagrams and graphs. Propose that the students generate a complete a set of reading responses pertaining to an assigned topic. Require each student to bring in one comment or one question about an assigned reading. The assignment should be a recent publication in an appropriate journal. Have the students conduct a web search on an assigned topic. Ask them to generate a set of ideas that can relate to classroom discussions. Provide the students with a study guide. The study guide should provide about 10 or 15 short topics. Quiz the students on one or two of the topics. Encourage the students to design or develop some creative real-world examples based on a chapter discussed or a topic of interest. Require that students originate, develop, support and defend a viewpoint using a specifically assigned material. Make the students practice using or utilizing a set of new technical terms they have encountered in an assigned chapter. Have students develop original examples explaining the different terms. Ask the students to select one important terminology from the previous classroom discussions. Encourage the students to explain why they selected that particular word. Ask them to talk about the importance of the terminology from the point of view of their educational objectives and future career. Angelo, T. A. (1991). Ten easy pieces: Assessing higher learning in four dimensions. In T. A. Angelo (Ed.), Classroom research: Early lessons from success (pp. 17-31). New Directions for Teaching and Learning, No. 46. San Francisco: Jossey-Bass.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

First observation of rotational structures in Re 168

DOE PAGES

Hartley, D. J.; Janssens, R. V. F.; Riedinger, L. L.; ...

2016-11-30

We assigned first rotational sequences to the odd-odd nucleus 168Re. Coincidence relationships of these structures with rhenium x rays confirm the isotopic assignment, while arguments based on the γ-ray multiplicity (K-fold) distributions observed with the new bands lead to the mass assignment. Configurations for the two bands were determined through analysis of the rotational alignments of the structures and a comparison of the experimental B(M1)/B(E2) ratios with theory. Tentative spin assignments are proposed for the πh 11/2νi 13/2 band, based on energy level systematics for other known sequences in neighboring odd-odd rhenium nuclei, as well as on systematics seen formore » the signature inversion feature that is well known in this region. Furthermore, the spin assignment for the πh 11/2ν(h 9/2/f 7/2) structure provides additional validation of the proposed spins and configurations for isomers in the 176Au → 172Ir → 168Re α-decay chain.« less

Teaching Engaged Research Literacy: A Description and Assessment of the Research Ripped from the Headlines Project

ERIC Educational Resources Information Center

Hosek, Angela M.

2016-01-01

This assignment serves to increase students' information literacy related to research gathering, critique, analysis, and implementation. For this assignment, students will: (a) identify and examine a news article that uses research; (b) trace the origins and conduct an analysis of the research study cited in the news article or a related research…

Herpesvirus papio contains a plasmid origin of replication that acts in cis interspecies with an Epstein-Barr virus trans-acting function.

PubMed Central

Pesano, R L; Pagano, J S

1986-01-01

Herpesvirus papio (HVP) and Epstein-Barr virus (EBV) are closely related biologically and biochemically; lymphoblastoid cells infected with either virus contain episomal viral DNA. The putative origin of replication for EBV plasmids (oriP) has been assigned to a 1,790-base-pair fragment (cis) in the short unique region of the genome which requires a viral function supplied in trans from elsewhere in the genome (J. Yates, N. Warren, D. Reisman, and B. Sugden, Proc. Natl. Acad. Sci. USA 81:3806-3810, 1984). We report here the identification of the putative origin of replication (cis) in HVP; we assigned it to the HVP EcoRI K fragment. The results indicate that the HVP replication process requires both a cis and a trans-acting function, analogous to that found in EBV. Images PMID:3023667

Optimization of controllability and robustness of complex networks by edge directionality

NASA Astrophysics Data System (ADS)

Liang, Man; Jin, Suoqin; Wang, Dingjie; Zou, Xiufen

2016-09-01

Recently, controllability of complex networks has attracted enormous attention in various fields of science and engineering. How to optimize structural controllability has also become a significant issue. Previous studies have shown that an appropriate directional assignment can improve structural controllability; however, the evolution of the structural controllability of complex networks under attacks and cascading has always been ignored. To address this problem, this study proposes a new edge orientation method (NEOM) based on residual degree that changes the link direction while conserving topology and directionality. By comparing the results with those of previous methods in two random graph models and several realistic networks, our proposed approach is demonstrated to be an effective and competitive method for improving the structural controllability of complex networks. Moreover, numerical simulations show that our method is near-optimal in optimizing structural controllability. Strikingly, compared to the original network, our method maintains the structural controllability of the network under attacks and cascading, indicating that the NEOM can also enhance the robustness of controllability of networks. These results alter the view of the nature of controllability in complex networks, change the understanding of structural controllability and affect the design of network models to control such networks.

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

PubMed Central

Hong, Mei

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ~94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools. PMID:26787537

Improving target coverage and organ-at-risk sparing in intensity-modulated radiotherapy for cervical oesophageal cancer using a simple optimisation method.

PubMed

Lu, Jia-Yang; Cheung, Michael Lok-Man; Huang, Bao-Tian; Wu, Li-Li; Xie, Wen-Jia; Chen, Zhi-Jian; Li, De-Rui; Xie, Liang-Xi

2015-01-01

To assess the performance of a simple optimisation method for improving target coverage and organ-at-risk (OAR) sparing in intensity-modulated radiotherapy (IMRT) for cervical oesophageal cancer. For 20 selected patients, clinically acceptable original IMRT plans (Original plans) were created, and two optimisation methods were adopted to improve the plans: 1) a base dose function (BDF)-based method, in which the treatment plans were re-optimised based on the original plans, and 2) a dose-controlling structure (DCS)-based method, in which the original plans were re-optimised by assigning additional constraints for hot and cold spots. The Original, BDF-based and DCS-based plans were compared with regard to target dose homogeneity, conformity, OAR sparing, planning time and monitor units (MUs). Dosimetric verifications were performed and delivery times were recorded for the BDF-based and DCS-based plans. The BDF-based plans provided significantly superior dose homogeneity and conformity compared with both the DCS-based and Original plans. The BDF-based method further reduced the doses delivered to the OARs by approximately 1-3%. The re-optimisation time was reduced by approximately 28%, but the MUs and delivery time were slightly increased. All verification tests were passed and no significant differences were found. The BDF-based method for the optimisation of IMRT for cervical oesophageal cancer can achieve significantly better dose distributions with better planning efficiency at the expense of slightly more MUs.

Theoretical study on the sound absorption of electrolytic solutions. II. Assignments of relaxations.

PubMed

Yamaguchi, T; Matsuoka, T; Koda, S

2007-08-14

The theory on the ultrasonic absorption spectrum of electrolytic solutions recently proposed by us is applied to the model system that resembles to the aqueous solution of MgSO4. The charges on ions are reduced to +/-1.5e in order to obtain the equilibrium structure by the integral equation theory. The theory reproduces the existence of two relaxations around 100 kHz and 1 GHz. The physical origin of the relaxation is analyzed based on the theoretical expression. The slower relaxation is shown to originate in the formation of contact ion pair, in harmony with the conventional assignment. The amplitude of this relaxation agrees with the experimental one fairly well. The absorption cross section is a weakly increasing function of the concentration of the salt in theory, whereas it depends little on the concentration in experiment, which is ascribed to the weaker association of the pair in the theory. The deviation from the Debye relaxation is found for the faster process, and the concentration dependence is small. The analysis shows that this relaxation stems from the coupling between the pressure and the long-range concentration fluctuation, and the concentration independence and the non-Debye relaxation are explained based on the theoretical analysis. In particular, the theory demonstrates that this process has the t(-3/2) tail in the time domain, which is confirmed by numerical calculation. The deviation of the theoretical relaxation amplitude from the experimental one is elucidated in terms of the theoretical expression of the coefficient.

Fourier transform spectroscopy of the CO-stretching band of O-18 methanol

NASA Astrophysics Data System (ADS)

Lees, R. M.; Murphy, Reba-Jean; Moruzzi, Giovanni; Predoi-Cross, Adriana; Xu, Li-Hong; Appadoo, D. R. T.; Billinghurst, B.; Goulding, R. R. J.; Zhao, Saibei

2009-07-01

The high-resolution Fourier transform spectrum of the ν8 CO-stretching band of CH 318OH between 900 and 1100 cm -1 has been recorded at the Canadian Light Source (CLS) synchrotron facility in Saskatoon, and the majority of the torsion-rotation structure has been analyzed. For the ν t = 0 torsional ground state, subbands have been identified for K values from 0 to 11 for A and E torsional symmetries up to J values typically well over 30. For ν t = 1, A and E subbands have been assigned up to K = 7, and several ν t = 2 subbands have also been identified. Upper-state term values determined from the assigned transitions using the Ritz program have been fitted to J( J + 1) power-series expansions to obtain substate origins and sets of state-specific parameters giving a compact representation of the substate J-dependence. The ν t = 0 subband origins have been fitted to effective molecular constants for the excited CO-stretching state and a torsional barrier of 377.49(32) cm -1 is found, representing a 0.89% increase over the ground-state value. The vibrational energy for the CO-stretch state was found to be 1007.49(7) cm -1. A number of subband-wide and J-localized perturbations have been seen in the spectrum, arising both from anharmonic and Coriolis interactions, and several of the interacting states have been identified.

Geographic origin and individual assignment of Shorea platyclados (Dipterocarpaceae) for forensic identification

PubMed Central

Diway, Bibian; Khoo, Eyen

2017-01-01

The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases. A haplotype map was generated from chloroplast DNA sequencing for population identification, resulting in 29 multilocus haplotypes, based on 39 informative intraspecific variable sites. Subsequently, a DNA profiling database was developed from 15 STRs allowing for individual identification in Malaysia. Cluster analysis divided the 27 populations into two genetic clusters, corresponding to the region of Eastern and Western Malaysia. The conservativeness tests showed that the Malaysia database is conservative after removal of bias from population subdivision and sampling effects. Independent self-assignment tests correctly assigned individuals to the database in an overall 60.60−94.95% of cases for identified populations, and in 98.99−99.23% of cases for identified regions. Both the chloroplast DNA database and the STRs appear to be useful for tracking timber originating in Malaysia. Hence, this DNA-based method could serve as an effective addition tool to the existing forensic timber identification system for ensuring the sustainably management of this species into the future. PMID:28430826

Determining origin in a migratory marine vertebrate: a novel method to integrate stable isotopes and satellite tracking

USGS Publications Warehouse

Vander Zanden, Hannah B.; Tucker, Anton D.; Hart, Kristen M.; Lamont, Margaret M.; Fujisaki, Ikuko; Addison, David S.; Mansfield, Katherine L.; Phillips, Katrina F.; Wunder, Michael B.; Bowen, Gabriel J.; Pajuelo, Mariela; Bolten, Alan B.; Bjorndal, Karen A.

2015-01-01

Stable isotope analysis is a useful tool to track animal movements in both terrestrial and marine environments. These intrinsic markers are assimilated through the diet and may exhibit spatial gradients as a result of biogeochemical processes at the base of the food web. In the marine environment, maps to predict the spatial distribution of stable isotopes are limited, and thus determining geographic origin has been reliant upon integrating satellite telemetry and stable isotope data. Migratory sea turtles regularly move between foraging and reproductive areas. Whereas most nesting populations can be easily accessed and regularly monitored, little is known about the demographic trends in foraging populations. The purpose of the present study was to examine migration patterns of loggerhead nesting aggregations in the Gulf of Mexico (GoM), where sea turtles have been historically understudied. Two methods of geographic assignment using stable isotope values in known-origin samples from satellite telemetry were compared: 1) a nominal approach through discriminant analysis and 2) a novel continuous-surface approach using bivariate carbon and nitrogen isoscapes (isotopic landscapes) developed for this study. Tissue samples for stable isotope analysis were obtained from 60 satellite-tracked individuals at five nesting beaches within the GoM. Both methodological approaches for assignment resulted in high accuracy of foraging area determination, though each has advantages and disadvantages. The nominal approach is more appropriate when defined boundaries are necessary, but up to 42% of the individuals could not be considered in this approach. All individuals can be included in the continuous-surface approach, and individual results can be aggregated to identify geographic hotspots of foraging area use, though the accuracy rate was lower than nominal assignment. The methodological validation provides a foundation for future sea turtle studies in the region to inexpensively determine geographic origin for large numbers of untracked individuals. Regular monitoring of sea turtle nesting aggregations with stable isotope sampling can be used to fill critical data gaps regarding habitat use and migration patterns. Probabilistic assignment to origin with isoscapes has not been previously used in the marine environment, but the methods presented here could also be applied to other migratory marine species.

Determining origin in a migratory marine vertebrate: a novel method to integrate stable isotopes and satellite tracking.

PubMed

Zanden, Hannah B Vander; Tucker, Anton D; Hart, Kristen M; Lamont, Margaret M; Fuisaki, Ikuko; Addison, David; Mansfield, Katherine L; Phillips, Katrina F; Wunder, Michael B; Bowen, Gabriel J; Pajuelo, Mariela; Bolten, Alan B; Bjorndal, Karen A

2015-03-01

Stable isotope analysis is a useful tool to track animal movements in both terrestrial and marine environments. These intrinsic markers are assimilated through the diet and may exhibit spatial gradients as a result of biogeochemical processes at the base of the food web. In the marine environment, maps to predict the spatial distribution of stable isotopes are limited, and thus determining geographic origin has been reliant upon integrating satellite telemetry and stable isotope data. Migratory sea turtles regularly move between foraging and reproductive areas. Whereas most nesting populations can be easily accessed and regularly monitored, little is known about the demographic trends in foraging populations. The purpose of the present study was to examine migration patterns of loggerhead nesting aggregations in the Gulf of Mexico (GoM), where sea turtles have been historically understudied. Two methods of geographic assignment using stable isotope values in known-origin samples from satellite telemetry were compared: (1) a nominal approach through discriminant analysis and (2) a novel continuous-surface approach using bivariate carbon and nitrogen isoscapes (isotopic landscapes) developed for this study. Tissue samples for stable isotope analysis were obtained from 60 satellite-tracked individuals at five nesting beaches within the GoM. Both methodological approaches for assignment resulted in high accuracy of foraging area determination, though each has advantages and disadvantages. The nominal approach is more appropriate when defined boundaries are necessary, but up to 42% of the individuals could not be considered in this approach. All individuals can be included in the continuous-surface approach, and individual results can be aggregated to identify geographic hotspots of foraging area use, though the accuracy rate was lower than nominal assignment. The methodological validation provides a foundation for future sea turtle studies in the region to inexpensively determine geographic origin for large numbers of untracked individuals. Regular monitoring of sea turtle nesting aggregations with stable isotope sampling can be used to fill critical data gaps regarding habitat use and migration patterns. Probabilistic assignment to origin with isoscapes has not been previously used in the marine environment, but the methods presented here could also be applied to other migratory marine species.

The solid-state terahertz spectrum of MDMA (Ecstasy) - A unique test for molecular modeling assignments

NASA Astrophysics Data System (ADS)

Allis, Damian G.; Hakey, Patrick M.; Korter, Timothy M.

2008-10-01

The terahertz (THz, far-infrared) spectrum of 3,4-methylene-dioxymethamphetamine hydrochloride (Ecstasy) is simulated using solid-state density functional theory. While a previously reported isolated-molecule calculation is noteworthy for the precision of its solid-state THz reproduction, the solid-state calculation predicts that the isolated-molecule modes account for only half of the spectral features in the THz region, with the remaining structure arising from lattice vibrations that cannot be predicted without solid-state molecular modeling. The molecular origins of the internal mode contributions to the solid-state THz spectrum, as well as the proper consideration of the protonation state of the molecule, are also considered.

THE tilde{A}-tilde{X} AND tilde{B}-tilde{X} ABSORPTIONS OF NO_3 TRAPPED IN SOLID NEON

NASA Astrophysics Data System (ADS)

Jacox, Marilyn E.; Thompson, Warren E.

2009-06-01

Absorptions arising from the tilde{A}-tilde{X} transition of normal and isotopically substituted NO_3 have been observed between 7500 and 9500 cm^{-1}. Details of the spectra will be discussed and assignments will be proposed. Absorptions arising from the tilde{B}-tilde{X} transition of NO_3, with band origin near 15 000 cm^{-1}, have also been observed for the normal species and two of its isotopologues which possess D_{3h} symmetry. As in the gas phase, the absorptions are broadened because of predissociation. The observed band structure corresponds closely with that reported for the gas-phase molecule.

"Anomalous" excitation in hydrogen-bonded molecular crystals - a Raman scattering study of specifically deuterated acetanilide (C 6D 5-CONH-CD 3)

NASA Astrophysics Data System (ADS)

Sauvajol, J. L.; De Nunzio, G.; Almairac, R.; Moret, J.; Barthés, M.; Bataillon, Place E.

1991-01-01

The focus of experimental and theoretical works about crystalline Acetanilide has been the "anomalous" temperature-dependent ir absorption and Raman peaks at about 1650 cm -1 and the multiband structure in the N-H stretch region. A lively discussion about the assignment of these "anomalous" bands has arisen and is still in progress. The present Raman experiments should be placed in this context as an attempt to identify the molecular degrees of freedom which originate the "anomalous" bands. In this aim Raman experiments have been performed on specifically deuterated Acetanilide [C 6D 5-CONH-CD 3] single crystal in the low-frequency (phonon) and C=O stretching regions. On cooling a distinct band at about 1495 cm -1 increases in intensity. We assign this peak to the equivalent of the 1650 cm -1 band in Acetanilide. The temperature dependence of this Raman line was studied. The results are discussed in the light of the models proposed to explain the anomalous behaviour of the 1650 cm -1 Raman line in Acetanilide.

On the problem of resonance assignments in solid state NMR of uniformly 15N, 13C-labeled proteins

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

PubMed Central

Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

2014-01-01

Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

Exploration of ICD-9-CM Coding of Chronic Disease within the Elixhauser Comorbidity Measure in Patients with Chronic Heart Failure

PubMed Central

Garvin, Jennifer Hornung; Redd, Andrew; Bolton, Dan; Graham, Pauline; Roche, Dominic; Groeneveld, Peter; Leecaster, Molly; Shen, Shuying; Weiner, Mark G.

2013-01-01

Introduction International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes capture comorbidities that can be used to risk adjust nonrandom patient groups. We explored the accuracy of capturing comorbidities associated with one risk adjustment method, the Elixhauser Comorbidity Measure (ECM), in patients with chronic heart failure (CHF) at one Veterans Affairs (VA) medical center. We explored potential reasons for the differences found between the original codes assigned and conditions found through retrospective review. Methods This descriptive, retrospective study used a cohort of patients discharged with a principal diagnosis coded as CHF from one VA medical center in 2003. One admission per patient was used in the study; with multiple admissions, only the first admission was analyzed. We compared the assignment of original codes assigned to conditions found in a retrospective, manual review of the medical record conducted by an investigator with coding expertise as well as by physicians. Members of the team experienced with assigning ICD-9-CM codes and VA coding processes developed themes related to systemic reasons why chronic conditions were not coded in VA records using applied thematic techniques. Results In the 181-patient cohort, 388 comorbid conditions were identified; 305 of these were chronic conditions, originally coded at the time of discharge with an average of 1.7 comorbidities related to the ECM per patient. The review by an investigator with coding expertise revealed a total of 937 comorbidities resulting in 618 chronic comorbid conditions with an average of 3.4 per patient; physician review found 872 total comorbidities with 562 chronic conditions (average 3.1 per patient). The agreement between the original and the retrospective coding review was 88 percent. The kappa statistic for the original and the retrospective coding review was 0.375 with a 95 percent confidence interval (CI) of 0.352 to 0.398. The kappa statistic for the retrospective coding review and physician review was 0.849 (CI, 0.823–0.875). The kappa statistic for the original coding and the physician review was 0.340 (CI, 0.316–0.364). Several systemic factors were identified, including familiarity with inpatient VA and non-VA guidelines, the quality of documentation, and operational requirements to complete the coding process within short time frames and to identify the reasons for movement within a given facility. Conclusion Comorbidities within the ECM representing chronic conditions were significantly underrepresented in the original code assignment. Contributing factors potentially include prioritization of codes related to acute conditions over chronic conditions; coders’ professional training, educational level, and experience; and the limited number of codes allowed in initial coding software. This study highlights the need to evaluate systemic causes of underrepresentation of chronic conditions to improve the accuracy of risk adjustment used for health services research, resource allocation, and performance measurement. PMID:24159270

Diversity in C-Xanes Spectra Obtained from Carbonaceous Solid Inclusions from Monahans Halite

NASA Technical Reports Server (NTRS)

Kebukawa, Y.; Zolensky, M. E.; Fries, M.; Kilcoyne, A. L. D.; Rahman, Z.; Cody, G. D.

2014-01-01

Monahans meteorite (H5) contains fluid inclusion- bearing halite (NaCl) crystals [1]. Microthermometry and Raman spectroscopy showed that the fluid in the inclusions is an aqueous brine and they were trapped near 25degC [1]. Their continued presence in the halite grains requires that their incorporation into the H chondrite asteroid was post metamorphism [2]. Abundant solid inclusions are also present in the halites. The solid inclusions include abundant and widely variable organics [2]. Analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction and TEM reveal that these grains include macromolecular carbon similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, magnetite, sulfides, lepidocrocite, carbonates, diamond, apatite and possibly the zeolite phillipsite [3]. Here we report organic analyses of these carbonaceous residues in Monahans halite using C-, N-, and O- X-ray absorption near edge structure (XANES). Samples and Methods: Approximately 100 nm-thick sections were extracted with a focused ion beam (FIB) at JSC from solid inclusions from Monahans halite. The sections were analyzed using the scanning transmission X-ray microscope (STXM) on beamline 5.3.2.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory for XANES spectroscopy. Results and Discussion: C-XANES spectra of the solid inclusions show micrometer-scale heterogeneity, indicating that the macromolecular carbon in the inclusions have complex chemical variations. C-XANES features include 284.7 eV assigned to aromatic C=C, 288.4-288.8 eV assigned to carboxyl, and 290.6 eV assigned to carbonate. The carbonyl features obtained by CXANES might have been caused by the FIB used in sample preparation. No specific N-XANES features are observed. The CXANES spectra obtained from several areas in the FIB sections include type 1&2 chondritic IOM like, type 3 chondritic IOM like, and none of the above. The natures of the macromolecular carbon in the solid inclusions observed by C-XANES are consistent with the previous studies showing that the carbonaceous solid inclusions have not originated from Monahans parent body [1-3], and have various origins, including various chondritic meteorite parent bodies as well as other unknown source(s).

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

PubMed

Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

2010-04-30

Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity.

Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping.

PubMed

Pariset, L; Mariotti, M; Nardone, A; Soysal, M I; Ozkan, E; Williams, J L; Dunner, S; Leveziel, H; Maróti-Agóts, A; Bodò, I; Valentini, A

2010-12-01

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure. © 2010 Blackwell Verlag GmbH.

Fire behavior, fuel treatments, and fire suppression on the Hayman Fire - Part 5: Fire suppression activities

Treesearch

Charles W. McHugh; Paul Gleason

2003-01-01

The purpose of this report is to document the suppression actions taken during the Hayman Fire. The long duration of suppression activities (June 8 through July 18), and multiple incident management teams assigned to the fire, makes this a challenging task. Original records and reports produced independently by the various teams assigned to different portions of the...

Operating System Support for Shared Hardware Data Structures

DTIC Science & Technology

2013-01-31

Carbon [73] uses hardware queues to improve fine-grained multitasking for Recognition, Mining , and Synthesis. Compared to software ap- proaches...web transaction processing, data mining , and multimedia. Early work in database processors [114, 96, 79, 111] reduce the costs of relational database...assignment can be solved statically or dynamically. Static assignment deter- mines offline which data structures are assigned to use HWDS resources and at

Gibberellin Receptor GID1: Gibberellin Recognition and Molecular Evolution

NASA Astrophysics Data System (ADS)

Kato, Hiroaki; Sato, Tomomi; Ueguchi-Tanaka, Miyako

Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. We analyzed the crystal structure of a nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF 1 (GID1) from Oryza sativa. As it was proposed from the sequence similarity, the overall structure of GID1 shows an α/β-hydrolase fold similar to that of the hormone-sensitive lipases (HSLs) except for an amino-terminal lid. The GA-binding site corresponds to the substrate-binding site of HSLs. Almost residues assigned for GA binding showed very little or no activity when they were replaced with Ala. The substitution of the residues corresponding to those of the lycophyte GID1s caused an increase in the binding affinity for GA34, a 2β-hydroxylated GA4. These findings indicate that GID1 originated from HSL and was tinkered to have the specificity for bioactive GAs in the course of plant evolution.

Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge.

PubMed

Kundu, Kunal; Pal, Lipika R; Yin, Yizhou; Moult, John

2017-09-01

The use of gene panel sequence for diagnostic and prognostic testing is now widespread, but there are so far few objective tests of methods to interpret these data. We describe the design and implementation of a gene panel sequencing data analysis pipeline (VarP) and its assessment in a CAGI4 community experiment. The method was applied to clinical gene panel sequencing data of 106 patients, with the goal of determining which of 14 disease classes each patient has and the corresponding causative variant(s). The disease class was correctly identified for 36 cases, including 10 where the original clinical pipeline did not find causative variants. For a further seven cases, we found strong evidence of an alternative disease to that tested. Many of the potentially causative variants are missense, with no previous association with disease, and these proved the hardest to correctly assign pathogenicity or otherwise. Post analysis showed that three-dimensional structure data could have helped for up to half of these cases. Over-reliance on HGMD annotation led to a number of incorrect disease assignments. We used a largely ad hoc method to assign probabilities of pathogenicity for each variant, and there is much work still to be done in this area. © 2017 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction

NASA Astrophysics Data System (ADS)

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-05-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.

Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction

PubMed Central

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-01-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 – 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. PMID:25863893

CHEM-Based Self-Deploying Spacecraft Radar Antennas

NASA Technical Reports Server (NTRS)

Sokolowski, Witold; Huang, John; Ghaffarian, Reza

2004-01-01

A document proposes self-deploying spacecraft radar antennas based on cold hibernated elastic memory (CHEM) structures. Described in a number of prior NASA Tech Briefs articles, the CHEM concept is one of utilizing open-cell shape-memory-polymer (SMP) foams to make lightweight structures that can be compressed for storage and can later be expanded, then rigidified for use. A CHEM-based antenna according to the proposal would comprise three layers of microstrip patches and transmission lines interspersed with two flat layers of SMP foam, which would serve as both dielectric spacers and as means of deployment. The SMP foam layers would be fabricated at full size at a temperature below the SMP glass-transition temperature (Tg). The layers would be assembled into a unitary structure, which, at temperature above Tg, would be compacted to much smaller thickness, then rolled up for storage. Next, the structure would be cooled to below Tg and kept there during launch. Upon reaching the assigned position in outer space, the structure would be heated above Tg to make it rebound to its original size and shape. The structure as thus deployed would then be rigidified by natural cooling to below Tg

Preparing transition-metal clusters in known structural forms: the mass-analyzed threshold ionization spectrum of V3.

PubMed

Ford, Mark S; Mackenzie, Stuart R

2005-08-22

The first results are presented of a new experiment designed both to generate and characterize spectroscopically individual isomers of transition-metal cluster cations. As a proof of concept the one-photon mass-analyzed threshold ionization (MATI) spectrum of V3 has been recorded in the region of 44,000-45,000 cm-1. This study extends the range of a previous zero-kinetic-energy (ZEKE) photoelectron study of Yang et al. [Chem. Phys. Lett. 231, 177 (1994)] with which the current results are compared. The MATI spectra reported here exhibit surprisingly high resolution (0.2 cm-1) for this technique despite the use of large discrimination and extraction fields. Analysis of the rotational profile of the origin band allows assignment of the V3 ground state as and the V3+ ground state as , both with D3h geometry, in agreement with the density-functional theory study of the V3 ZEKE spectrum by Calaminici et al. [J. Chem. Phys. 114, 4036 (2001)]. There is also some evidence in the spectrum of transitions to the low-lying excited state of the ion. The vibrational structure observed in the MATI spectrum is, however, significantly different to and less extensive than that predicted in the density-functional theory study. Possible reasons for the discrepancies are discussed and an alternative assignment is proposed which results in revised values for the vibrational wave numbers of both the neutral and ionic states. These studies demonstrate the efficient generation of cluster ions in known structural (isomeric) forms and pave the way for the study of cluster reactivity as a function of geometrical structure.

Evaluation of 3D-Jury on CASP7 models.

PubMed

Kaján, László; Rychlewski, Leszek

2007-08-21

3D-Jury, the structure prediction consensus method publicly available in the Meta Server http://meta.bioinfo.pl/, was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature http://meta.bioinfo.pl/compare_your_model_example.pl available in the Meta Server.

Evaluation of 3D-Jury on CASP7 models

PubMed Central

Kaján, László; Rychlewski, Leszek

2007-01-01

Background 3D-Jury, the structure prediction consensus method publicly available in the Meta Server , was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. Results The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. Conclusion The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature available in the Meta Server. PMID:17711571

Creating Masterpieces: How Course Structures and Routines Enable Student Performance

ERIC Educational Resources Information Center

Dean, Kathy Lund; Fornaciari, Charles J.

2014-01-01

Over a five-year period, we made a persistent observation: Course structures and routines, such as assignment parameters, student group process rules, and grading schemes were being consistently ignored. As a result, we got distracted by correcting these structural issues and were spending less time on student assignment performance. In this…

Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin.

PubMed

Rynkiewicz, Michael J; Schott, Veronika; Orzechowski, Marek; Lehman, William; Fischer, Stefan

2015-12-01

Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimuthal transitions. However, a new model based on cryo-EM of troponin- and myosin-free filaments proposes that the interacting-face of tropomyosin can differ significantly from that in the original model. Because resolution was insufficient to assign tropomyosin side-chains, the interacting-face could not be unambiguously determined. Here, we use structural analysis and energy landscapes to further examine the proposed models. The observed bend in seven crystal structures of tropomyosin is much closer in direction and extent to the original model than to the new model. Additionally, we computed the interaction map for repositioning tropomyosin over the F-actin surface, but now extended over a much larger surface than previously (using the original interacting-face). This map shows two energy minima-one corresponding to the "blocked-state" as in the original model, and the other related by a simple 24 Å translation of tropomyosin parallel to the F-actin axis. The tropomyosin-actin complex defined by the second minimum fits perfectly into the recent cryo-EM density, without requiring any change in the interacting-face. Together, these data suggest that movement of tropomyosin between regulatory states does not require interacting-face rotation. Further, they imply that thin filament assembly may involve an interplay between initially seeded tropomyosin molecules growing from distinct binding-site regions on actin.

Original Language Subtitles: Their Effects on the Native and Foreign Viewer

ERIC Educational Resources Information Center

Kruger, Jan-Louis; Doherty, Stephen; Soto-Sanfiel, María-T.

2017-01-01

This study investigates the impact of same-language subtitles on the immersion into audiovisual narratives as a function of the viewer's language (native or foreigner). Students from two universities in Australia and one in Spain were assigned randomly to one of two experimental groups, in which they saw a drama with the original English…

77 FR 32034 - Policies To Promote Rural Radio Service and To Streamline Allotment and Assignment Procedures

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-31

... Qualifications Window (``TQ Window''). During the TQ Window, any Tribe or Tribal entity that could qualify to add... filed Form 301 application to be considered at this stage, then during the TQ Window the original Tribal... acceptable application is filed during the TQ Window, whether by the original Tribal allotment proponent...

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

PubMed

Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

2011-06-15

PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

Assigning African elephant DNA to geographic region of origin: Applications to the ivory trade

PubMed Central

Wasser, Samuel K.; Shedlock, Andrew M.; Comstock, Kenine; Ostrander, Elaine A.; Mutayoba, Benezeth; Stephens, Matthew

2004-01-01

Resurgence of illicit trade in African elephant ivory is placing the elephant at renewed risk. Regulation of this trade could be vastly improved by the ability to verify the geographic origin of tusks. We address this need by developing a combined genetic and statistical method to determine the origin of poached ivory. Our statistical approach exploits a smoothing method to estimate geographic-specific allele frequencies over the entire African elephants' range for 16 microsatellite loci, using 315 tissue and 84 scat samples from forest (Loxodonta africana cyclotis) and savannah (Loxodonta africana africana) elephants at 28 locations. These geographic-specific allele frequency estimates are used to infer the geographic origin of DNA samples, such as could be obtained from tusks of unknown origin. We demonstrate that our method alleviates several problems associated with standard assignment methods in this context, and the absolute accuracy of our method is high. Continent-wide, 50% of samples were located within 500 km, and 80% within 932 km of their actual place of origin. Accuracy varied by region (median accuracies: West Africa, 135 km; Central Savannah, 286 km; Central Forest, 411 km; South, 535 km; and East, 697 km). In some cases, allele frequencies vary considerably over small geographic regions, making much finer discriminations possible and suggesting that resolution could be further improved by collection of samples from locations not represented in our study. PMID:15459317

Method for protein structure alignment

DOEpatents

Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

2005-02-22

This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

Evaluation of a Modified User Guide for Hearing Aid Management.

PubMed

Caposecco, Andrea; Hickson, Louise; Meyer, Carly; Khan, Asaduzzaman

2016-01-01

This study investigated if a hearing aid user guide modified using best practice principles for health literacy resulted in superior ability to perform hearing aid management tasks, compared with the user guide in the original form. This research utilized a two-arm study design to compare the original manufacturer's user guide with a modified user guide for the same hearing aid--an Oticon Acto behind-the-ear aid with an open dome. The modified user guide had a lower reading grade level (4.2 versus 10.5), used a larger font size, included more graphics, and had less technical information. Eighty-nine adults ages 55 years and over were included in the study; none had experience with hearing aid use or management. Participants were randomly assigned either the modified guide (n = 47) or the original guide (n = 42). All participants were administered the Hearing Aid Management test, designed for this study, which assessed their ability to perform seven management tasks (e.g., change battery) with their assigned user guide. The regression analysis indicated that the type of user guide was significantly associated with performance on the Hearing Aid Management test, adjusting for 11 potential covariates. In addition, participants assigned the modified guide required significantly fewer prompts to perform tasks and were significantly more likely to perform four of the seven tasks without the need for prompts. The median time taken by those assigned the modified guide was also significantly shorter for three of the tasks. Other variables associated with performance on the Hearing Aid Management test were health literacy level, finger dexterity, and age. Findings indicate that the need to design hearing aid user guides in line with best practice principles of health literacy as a means of facilitating improved hearing aid management in older adults.

Surname lists to identify South Asian and Chinese ethnicity from secondary data in Ontario, Canada: a validation study

PubMed Central

2010-01-01

Background Surname lists are useful for identifying cohorts of ethnic minority patients from secondary data sources. This study sought to develop and validate lists to identify people of South Asian and Chinese origin. Methods Comprehensive lists of South Asian and Chinese surnames were reviewed to identify those that uniquely belonged to the ethnic minority group. Surnames that were common in other populations, communities or ethnic groups were specifically excluded. These surname lists were applied to the Registered Persons Database, a registry of the health card numbers assigned to all residents of the Canadian province of Ontario, so that all residents were assigned to South Asian ethnicity, Chinese ethnicity or the General Population. Ethnic assignment was validated against self-identified ethnicity through linkage with responses to the Canadian Community Health Survey. Results The final surname lists included 9,950 South Asian surnames and 1,133 Chinese surnames. All 16,688,384 current and former residents of Ontario were assigned to South Asian ethnicity, Chinese ethnicity or the General Population based on their surnames. Among 69,859 respondents to the Canadian Community Health Survey, both lists performed extremely well when compared against self-identified ethnicity: positive predictive value was 89.3% for the South Asian list, and 91.9% for the Chinese list. Because surnames shared with other ethnic groups were deliberately excluded from the lists, sensitivity was lower (50.4% and 80.2%, respectively). Conclusions These surname lists can be used to identify cohorts of people with South Asian and Chinese origins from secondary data sources with a high degree of accuracy. These cohorts could then be used in epidemiologic and health service research studies of populations with South Asian and Chinese origins. PMID:20470433

Surname lists to identify South Asian and Chinese ethnicity from secondary data in Ontario, Canada: a validation study.

PubMed

Shah, Baiju R; Chiu, Maria; Amin, Shubarna; Ramani, Meera; Sadry, Sharon; Tu, Jack V

2010-05-15

Surname lists are useful for identifying cohorts of ethnic minority patients from secondary data sources. This study sought to develop and validate lists to identify people of South Asian and Chinese origin. Comprehensive lists of South Asian and Chinese surnames were reviewed to identify those that uniquely belonged to the ethnic minority group. Surnames that were common in other populations, communities or ethnic groups were specifically excluded. These surname lists were applied to the Registered Persons Database, a registry of the health card numbers assigned to all residents of the Canadian province of Ontario, so that all residents were assigned to South Asian ethnicity, Chinese ethnicity or the General Population. Ethnic assignment was validated against self-identified ethnicity through linkage with responses to the Canadian Community Health Survey. The final surname lists included 9,950 South Asian surnames and 1,133 Chinese surnames. All 16,688,384 current and former residents of Ontario were assigned to South Asian ethnicity, Chinese ethnicity or the General Population based on their surnames. Among 69,859 respondents to the Canadian Community Health Survey, both lists performed extremely well when compared against self-identified ethnicity: positive predictive value was 89.3% for the South Asian list, and 91.9% for the Chinese list. Because surnames shared with other ethnic groups were deliberately excluded from the lists, sensitivity was lower (50.4% and 80.2%, respectively). These surname lists can be used to identify cohorts of people with South Asian and Chinese origins from secondary data sources with a high degree of accuracy. These cohorts could then be used in epidemiologic and health service research studies of populations with South Asian and Chinese origins.

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

Hartley, D. J.; Janssens, R. V. F.; Riedinger, L. L.

We assigned first rotational sequences to the odd-odd nucleus 168Re. Coincidence relationships of these structures with rhenium x rays confirm the isotopic assignment, while arguments based on the γ-ray multiplicity (K-fold) distributions observed with the new bands lead to the mass assignment. Configurations for the two bands were determined through analysis of the rotational alignments of the structures and a comparison of the experimental B(M1)/B(E2) ratios with theory. Tentative spin assignments are proposed for the πh 11/2νi 13/2 band, based on energy level systematics for other known sequences in neighboring odd-odd rhenium nuclei, as well as on systematics seen formore » the signature inversion feature that is well known in this region. Furthermore, the spin assignment for the πh 11/2ν(h 9/2/f 7/2) structure provides additional validation of the proposed spins and configurations for isomers in the 176Au → 172Ir → 168Re α-decay chain.« less

An Implementation of Active Learning: Assessing the Effectiveness of the Team Infomercial Assignment

ERIC Educational Resources Information Center

Matveev, Alexei V.; Milter, Richard G.

2010-01-01

This article examines the effectiveness of the team infomercial assignment as an active learning tool in undergraduate courses. The structure and three phases of the team infomercial assignment, as well as student evaluations and feedback, are presented. We investigated student experiences working on the team infomercial assignment, the common…

Moving beyond "Bookish Knowledge": Using Film-Based Assignments to Promote Deep Learning

ERIC Educational Resources Information Center

Olson, Joann S.; Autry, Linda; Moe, Jeffry

2016-01-01

This article investigates the effectiveness of a film-based assignment given to adult learners in a graduate-level group counseling class. Semi-structured interviews were conducted with four students; data analysis suggested film-based assignments may promote deep approaches to learning (DALs). Participants indicated the assignment helped them…

Identification of Scoliosis Research Society-22r Health-Related Quality of Life questionnaire domains using factor analysis methodology.

PubMed

Lai, Sue-Min; Asher, Marc A; Burton, Douglas C; Carlson, Brandon B

2010-05-20

Cross-sectional mail questionnaire. Examination of the underlying construct validity of the Scoliosis Research Society-22r (SRS-22r) Health-Related Quality of Life (HRQoL) Questionnaire using factor analysis. The original SRS-24 HRQoL questionnaire has undergone a series of modifications in an effort to further improve its psychometric properties and validate its use in patients from 10 years of age until well into adulthood. The SRS-22r questionnaire is the result of this effort. To date, the underlying construct validity of the original English version has not been analyzed by factor analysis. A questionnaire including all questions on the SRS-24, -23, -22, and -22r questionnaires (49 total questions) was mailed to a consecutive series of 235 patients who had received primary posterior or anterior instrumentation and arthrodesis. Domain structure of the SRS-22r questions was analyzed using iterated principal factor analysis with orthogonal rotation. One hundred twenty-one (51%) of the patients, age 23.34 +/- 4.52 years (range, 14.16-34.57 years), returned the questionnaire at 8.63 +/- 4.00 years (range, 2.32-15.94 years) following surgery. Factor analysis using all 22 questions resulted in 3 factors with many shared items because of significant collinearity of the satisfaction/dissatisfaction with management questions with the others. After 18 iterations, factor analysis using the 20 nonmanagement questions revealed 4 factors that explained 98% of the variance. These factors parallel the assigned domains of the SRS-22r questionnaire. Three questions (2 self-image and 1 function) were identified that had high loading in 2 factors. However, internal consistency was best when 2 of the questions (1 self-image and 1 function) were retained in their assigned SRS-22r domains and the third decreased self-image internal consistency by only 0.01%. The internal consistencies (Cronbach alpha) of the assigned SRS-22r nonmanagement domains were excellent or very good: function 0.83, pain 0.87, self-image 0.80, and mental health 0.90. For the management domain it was good: 0.73. Factor analysis of the SRS-22r HRQoL confirms placement of the 20 nonmanagement domain questions in the assigned 4 domains, all with excellent or very good internal consistency.

“C.R.E.A.T.E.”-ing Unique Primary-Source Research Paper Assignments for a Pleasure and Pain Course Teaching Neuroscientific Principles in a Large General Education Undergraduate Course

PubMed Central

Bodnar, Richard J.; Rotella, Francis M.; Loiacono, Ilyssa; Coke, Tricia; Olsson, Kerstin; Barrientos, Alicia; Blachorsky, Lauren; Warshaw, Deena; Buras, Agata; Sanchez, Ciara M.; Azad, Raihana; Stellar, James R.

2016-01-01

A large (250 registrants) General Education lecture course, Pleasure and Pain, presented basic neuroscience principles as they related to animal and human models of pleasure and pain by weaving basic findings related to food and drug addiction and analgesic states with human studies examining empathy, social neuroscience and neuroeconomics. In its first four years, the course grade was based on weighted scores from two multiple-choice exams and a five-page review of three unique peer-reviewed research articles. Although well-registered and well-received, 18% of the students received Incomplete grades, primarily due to failing to submit the paper that went largely unresolved and eventually resulted in a failing grade. To rectify this issue, a modified version of the C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method replaced the paper with eight structured assignments focusing on an initial general-topic article, the introduction-methods, and results-discussion of each of three related peer-review neuroscience-related articles, and a final summary. Compliance in completing these assignments was very high, resulting in only 11 INC grades out of 228 students. Thus, use of the C.R.E.A.T.E. method reduced the percentage of problematic INC grades from 18% to 4.8%, a 73% decline, without changing the overall grade distribution. Other analyses suggested the students achieved a deeper understanding of the scientific process using the C.R.E.A.T.E. method relative to the original term paper assignment. PMID:27385918

"C.R.E.A.T.E."-ing Unique Primary-Source Research Paper Assignments for a Pleasure and Pain Course Teaching Neuroscientific Principles in a Large General Education Undergraduate Course.

PubMed

Bodnar, Richard J; Rotella, Francis M; Loiacono, Ilyssa; Coke, Tricia; Olsson, Kerstin; Barrientos, Alicia; Blachorsky, Lauren; Warshaw, Deena; Buras, Agata; Sanchez, Ciara M; Azad, Raihana; Stellar, James R

2016-01-01

A large (250 registrants) General Education lecture course, Pleasure and Pain, presented basic neuroscience principles as they related to animal and human models of pleasure and pain by weaving basic findings related to food and drug addiction and analgesic states with human studies examining empathy, social neuroscience and neuroeconomics. In its first four years, the course grade was based on weighted scores from two multiple-choice exams and a five-page review of three unique peer-reviewed research articles. Although well-registered and well-received, 18% of the students received Incomplete grades, primarily due to failing to submit the paper that went largely unresolved and eventually resulted in a failing grade. To rectify this issue, a modified version of the C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method replaced the paper with eight structured assignments focusing on an initial general-topic article, the introduction-methods, and results-discussion of each of three related peer-review neuroscience-related articles, and a final summary. Compliance in completing these assignments was very high, resulting in only 11 INC grades out of 228 students. Thus, use of the C.R.E.A.T.E. method reduced the percentage of problematic INC grades from 18% to 4.8%, a 73% decline, without changing the overall grade distribution. Other analyses suggested the students achieved a deeper understanding of the scientific process using the C.R.E.A.T.E. method relative to the original term paper assignment.

SSR analysis of genetic diversity and structure of the germplasm of faba bean (Vicia faba L.).

PubMed

El-Esawi, Mohamed A

Assessing the diversity and genetic structure of faba bean (Vicia faba L.) germplasm is essential to improve the quality and yield of this economically important crop. In this study, simple sequence repeats (SSRs) were utilized to evaluate the diversity and structure of 35 faba bean genotypes originating from three different geographical regions (Northern Africa, Eastern Africa, and Near East). All 15 SSR loci generated a total of 100 alleles. The allele number per locus varied from 4 to 11, with a mean of 6.67. The expected heterozygosity (H e ) of SSR loci ranged between 0.51 and 0.81, with a mean of 0.63. The PIC value also varied from 0.44 to 0.78, with an average of 0.58. The expected heterozygosity of 22 faba bean genotypes was higher than the observed one. Interestingly, AMOVA analysis showed that much of variability resided within accessions (79.2%). A highly significant difference among regions was also evidenced, and represented 5.3% of the total variation. Moreover, cluster analysis divided the 35 faba bean genotypes into two main clusters. The first main cluster comprised all faba bean genotypes originating from the Near East region, whereas the second main cluster comprised all the genotypes originating from the Northern and Eastern Africa regions, indicating that the Northern and Eastern African faba bean genotypes were more closely related to each other than to the Near East genotypes. Structure analysis also revealed that the 35 faba bean genotypes might be assigned to two populations, in complete accordance with cluster analysis data. In conclusion, this study showed high levels of diversity in the analysed genotypes of faba bean, and could be utilized in future breeding programmes to develop new cultivars of high yield. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant.

PubMed

Lu, Ling; Li, Chunhua; Yuan, Jie; Lu, Teng; Okamoto, Hiroaki; Murphy, Donald G

2013-03-01

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots

PubMed Central

Wasser, S. K.; Brown, L.; Mailand, C.; Mondol, S.; Clark, W.; Laurie, C.; Weir, B. S.

2017-01-01

Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa’s major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime. PMID:26089357

On the modified Mercalli intensities and magnitudes of the 1811-1812 New Madrid earthquakes

USGS Publications Warehouse

Hough, S.E.; Armbruster, J.G.; Seeber, L.; Hough, J.F.

2000-01-01

We reexamine original felt reports from the 1811-1812 New Madrid earthquakes and determine revised isoseismal maps for the three principal mainshocks. In many cases we interpret lower values than those assigned by earlier studies. In some cases the revisions result from an interpretation of original felt reports with an appreciation for site response issues. Additionally, earlier studies had assigned modified Mercalli intensity (MMI) values of V-VII to a substantial number of reports that we conclude do not describe damage commensurate with intensities this high. We investigate several approaches to contouring the MMI values using both analytical and subjective methods. For the first mainshock on 02:15 LT December 16, 1811, our preferred contouring yields M??7.2-7.3 using the area-moment regressions of Johnston [1996]. For the 08:00 LT on January 23, 1812, and 03:45 LT on February 7, 1812, mainshocks, we obtain M??7.0 and M??7.4-7.5, respectively. Our magnitude for the February mainshock is consistent with the established geometry of the Reelfoot fault, which all evidence suggests to have been the causative structure for this event. We note that the inference of lower magnitudes for the New Madrid events implies that site response plays a significant role in controlling seismic hazard at alluvial sites in the central and eastern United States. We also note that our results suggest that thrusting may have been the dominant mechanism of faulting associated with the 1811-1812 sequence. Copyright 2000 by the American Geophysical Union.

DNATCO: assignment of DNA conformers at dnatco.org.

PubMed

Černý, Jiří; Božíková, Paulína; Schneider, Bohdan

2016-07-08

The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Revision of middle Proterozoic Yellowjacket Formation, central Idaho, and revision of Cretaceous Slim Sam Formation, Elkhorn mountains area, Montana

USGS Publications Warehouse

Tysdal, Russell G.

2000-01-01

The Yellowjacket Formation is restricted to the strata originally assigned to it by Ross (1934). The Yellowjacket, the conformably overlying Hoodoo Quartzite, and succeeding unnamed argillaceous quartzite unit form a genetically related sequence that lies in a structural block delimited on the northeast by the Iron Lake fault. Directly northeast of the fault, strata currently assigned by others to the lower subunit of the Yellowjacket are correlated with the Apple Creek Formation in the Lemhi Range. Mapping in the western part of the Lemhi Range shows that the Apple Creek Formation lies depositionally above the Big Creek Formation and that no rocks of the Yellowjacket-Hoodoo unnamed unit stratigraphic sequence are present. In contrast, in the area of the Yellowjacket mapped by Ross (1934) and the area directly northeast of the Iron Lake Fault, the Big Creek Formation is absent, even though it is 2,700 m thick in the Lemhi Range. These data indicate that the Iron Lake Fault juxtaposed the Yellowjacket-Hoodoo-unnamed unit sequence against non-Yellowjacket strata to the northeast. The Upper Cretaceous Slim Sam Formation of the Elkhorn Mountains area is revised. Strata of the lower part are correlated with the regionally recognized marine Telegraph Creek Formation and the overlying marine to marginal marine Eagle Sandstone. Only lower strata of the Eagle are present in the study area and they are preserved discontinously. The nonmarine volcanic and volcaniclastic rocks of the upper part of the Slim Sam as originally defined retain the name Slim Sam Formation. These rocks, mainly of sedimentary origin, are genetically related to the Elkhorn Mountains Volcanics. The lower contact of the Slim Sam (restricted) is unconformable above the Eagle Sandstone or more commonly above the Telegraph Creek Formation. The upper contact is conformable with the Elkhorn Mountains Volcanics.

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS

NASA Astrophysics Data System (ADS)

Nilsson, Jonas; Noborn, Fredrik; Gomez Toledo, Alejandro; Nasir, Waqas; Sihlbom, Carina; Larson, Göran

2017-02-01

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl- O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na+ ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides.

50 CFR 679.50 - Groundfish Observer Program.

Code of Federal Regulations, 2010 CFR

2010-10-01

... following: (A) Identification of the management, organizational structure, and ownership structure of the.../processors. A catcher/processor will be assigned to a fishery category based on the retained groundfish catch... in Federal waters will be assigned to a fishery category based on the retained groundfish catch...

Undergraduates Improve upon Published Crystal Structure in Class Assignment

ERIC Educational Resources Information Center

Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

2014-01-01

Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

Consistent assignment of nursing staff to residents in nursing homes: a critical review of conceptual and methodological issues.

PubMed

Roberts, Tonya; Nolet, Kimberly; Bowers, Barbara

2015-06-01

Consistent assignment of nursing staff to residents is promoted by a number of national organizations as a strategy for improving nursing home quality and is included in pay for performance schedules in several states. However, research has shown inconsistent effects of consistent assignment on quality outcomes. In order to advance the state of the science of research on consistent assignment and inform current practice and policy, a literature review was conducted to critique conceptual and methodological understandings of consistent assignment. Twenty original research reports of consistent assignment in nursing homes were found through a variety of search strategies. Consistent assignment was conceptualized and operationalized in multiple ways with little overlap from study to study. There was a lack of established methods to measure consistent assignment. Methodological limitations included a lack of control and statistical analyses of group differences in experimental-level studies, small sample sizes, lack of attention to confounds in multicomponent interventions, and outcomes that were not theoretically linked. Future research should focus on developing a conceptual understanding of consistent assignment focused on definition, measurement, and links to outcomes. To inform current policies, testing consistent assignment should include attention to contexts within and levels at which it is most effective. Published by Oxford University Press on behalf of the Gerontological Society of America 2013.

Revision of “Balaena” belgica reveals a new right whale species, the possible ancestry of the northern right whale, Eubalaena glacialis, and the ages of divergence for the living right whale species

PubMed Central

Bosselaers, Mark

2017-01-01

In 1941, Abel established Balaena belgica based on a series of fused cervical vertebrae and citing other cranial fragments from the late Neogene of the Antwerp harbor (northern Belgium). Later, Plisnier-Ladame & Quinet (1969) added a neurocranium and other skeletal remains from the same area to this species. Recently, the neurocranium was re-assigned to the genus Eubalaena thanks to newer phylogenetic analyses. Here, a new description is provided of materials previously assigned to “Balaena” belgica together with taxonomic revisions. Our work suggests that the cervical complex originally designated as the type of “Balaena” belgica is too poorly preserved to be used as such and is assigned to Balaenidae gen. et sp. indet., thus making “Balaena” belgica a nomen dubium. In addition to the neurocranium, the other remains consist in a fragment of maxilla assigned to Balaenidae gen. et sp. indet. and in a humerus assigned to Eubalaena sp. Discovered in the Kruisschans Sands Member of the Lillo Formation (3.2–2.8 Ma, Piacenzian, Late Pliocene), the neurocranium is designated as the holotype of the new species Eubalaena ianitrix. Our phylogenetic analysis supports a sister-group relationship of Eubalaena ianitrix and Eubalaena glacialis, and helps constraining the ages of origin for balaenid clades. Ecological and phylogenetic data suggest that Eubalaena ianitrix may represent the direct ancestor of Eubalaena glacialis, the latter having evolved through phyletic transformation including body size increase during the temperature decline of the Late Pliocene. PMID:28663936

Assessing the Ability of Chloroplast and Nuclear DNA Gene Markers to Verify the Geographic Origin of Jatoba (Hymenaea courbaril L.) Timber.

PubMed

Chaves, Camila L; Degen, Bernd; Pakull, Birte; Mader, Malte; Honorio, Euridice; Ruas, Paulo; Tysklind, Niklas; Sebbenn, Alexandre M

2018-06-27

Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber.

Revision of "Balaena" belgica reveals a new right whale species, the possible ancestry of the northern right whale, Eubalaena glacialis, and the ages of divergence for the living right whale species.

PubMed

Bisconti, Michelangelo; Lambert, Olivier; Bosselaers, Mark

2017-01-01

In 1941, Abel established Balaena belgica based on a series of fused cervical vertebrae and citing other cranial fragments from the late Neogene of the Antwerp harbor (northern Belgium). Later, Plisnier-Ladame & Quinet (1969) added a neurocranium and other skeletal remains from the same area to this species. Recently, the neurocranium was re-assigned to the genus Eubalaena thanks to newer phylogenetic analyses. Here, a new description is provided of materials previously assigned to " Balaena " belgica together with taxonomic revisions. Our work suggests that the cervical complex originally designated as the type of " Balaena " belgica is too poorly preserved to be used as such and is assigned to Balaenidae gen. et sp. indet., thus making " Balaena " belgica a nomen dubium. In addition to the neurocranium, the other remains consist in a fragment of maxilla assigned to Balaenidae gen. et sp. indet. and in a humerus assigned to Eubalaena sp. Discovered in the Kruisschans Sands Member of the Lillo Formation (3.2-2.8 Ma, Piacenzian, Late Pliocene), the neurocranium is designated as the holotype of the new species Eubalaena ianitrix . Our phylogenetic analysis supports a sister-group relationship of Eubalaena ianitrix and Eubalaena glacialis , and helps constraining the ages of origin for balaenid clades. Ecological and phylogenetic data suggest that Eubalaena ianitrix may represent the direct ancestor of Eubalaena glacialis , the latter having evolved through phyletic transformation including body size increase during the temperature decline of the Late Pliocene.

Model-based morphological segmentation and labeling of coronary angiograms.

PubMed

Haris, K; Efstratiadis, S N; Maglaveras, N; Pappas, C; Gourassas, J; Louridas, G

1999-10-01

A method for extraction and labeling of the coronary arterial tree (CAT) using minimal user supervision in single-view angiograms is proposed. The CAT structural description (skeleton and borders) is produced, along with quantitative information for the artery dimensions and assignment of coded labels, based on a given coronary artery model represented by a graph. The stages of the method are: 1) CAT tracking and detection; 2) artery skeleton and border estimation; 3) feature graph creation; and iv) artery labeling by graph matching. The approximate CAT centerline and borders are extracted by recursive tracking based on circular template analysis. The accurate skeleton and borders of each CAT segment are computed, based on morphological homotopy modification and watershed transform. The approximate centerline and borders are used for constructing the artery segment enclosing area (ASEA), where the defined skeleton and border curves are considered as markers. Using the marked ASEA, an artery gradient image is constructed where all the ASEA pixels (except the skeleton ones) are assigned the gradient magnitude of the original image. The artery gradient image markers are imposed as its unique regional minima by the homotopy modification method, the watershed transform is used for extracting the artery segment borders, and the feature graph is updated. Finally, given the created feature graph and the known model graph, a graph matching algorithm assigns the appropriate labels to the extracted CAT using weighted maximal cliques on the association graph corresponding to the two given graphs. Experimental results using clinical digitized coronary angiograms are presented.

Development of a genetic tool for product regulation in the diverse British pig breed market.

PubMed

Wilkinson, Samantha; Archibald, Alan L; Haley, Chris S; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Groenen, Martien A M; Wiener, Pamela; Ogden, Rob

2012-11-15

The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.

Development of a genetic tool for product regulation in the diverse British pig breed market

PubMed Central

2012-01-01

Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. Results The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. Conclusion The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. PMID:23150935

¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

PubMed

Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

2016-04-15

Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

New measurements and analysis of the far-infrared spectrum of CH2DOH in the lowest torsional vibrational state (e0)

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Indra

2016-05-01

In this work the far infrared (FIR) absorption spectrum has been measured for the asymmetrically mono deuterated Methanol (CH2DOH) species in the wavenumber range of 15-1200 cm-1 better accuracy and signal/noise ratio than known before. Assignments have been made for b-type transitions in the lowest lying torsional vibrational state trans-(e0) for a wide range of rotational angular momentum. The assignments have been rigorously confirmed by the residual loop defect methods. The rR-branch wavenumbers are analyzed by the usual state dependent expansion parameters and the Q-Branch origins. These origins have been used to calculate the torsional and torsional-rotation interaction contributions. These findings are in good agreement with predicted from the Hamiltonian model described in recent publications. A large number of assignments have also been made in the millimeter wave spectrum recorded earlier and thereby evaluated the asymmetry splitting parameters for 4 different axial rotational angular momentum quantum numbers. The analysis and interpretation of the spectra are reported. New assignments for about 260 transitions are included the text and a catalog of about 1500 transitions belonging to the e0 species is prepared (Appendix 1) and is made available through the open server in "Research Gate" and will be freely available to others.

Impact of sequencing depth on the characterization of the microbiome and resistome.

PubMed

Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E; Morley, Paul S; McAllister, Tim A

2018-04-12

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

Hierarchy effect on electronic structure and core-to-valence transitions in bone tissue: perspectives in medical nanodiagnostics of mineralized bone

NASA Astrophysics Data System (ADS)

Samoilenko, Dmitrii O.; Avrunin, Alexander S.; Pavlychev, Andrey A.

2017-06-01

Electronic structure and core-to-valence transitions in bone tissue are examined in the framework of the morphological 3DSL model that takes into account (i) structural and functional organization of the skeleton in the normal and pathological conditions and (ii) peculiarities of electron wave propagation in a three-dimensional superlattice of "black-nanocrystallites-in-muddy-waters". Our focus is on the HAP-to-bone red shifts of core-to-valence transitions near Ca and P 2p and O 1s edges in single-crystal hydroxyapatite (HAP) Ca10(PO4)6(OH)2. The origin of the HAP-to-bone shift is discussed and the extended comparative analysis of the experimental data is performed. The detected spectral shift is assigned with the effect of hierarchical organization of bone tissue. This hierarchy effect on the core-to-valence transition energies is regarded as a promising tool for medical imaging and perspective pathway for nanodiagnostics of mineralized bone. Contribution to the Topical Issue "Dynamics of Systems at the Nanoscale", edited by Andrey Solov'yov and Andrei Korol.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

PubMed

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]^{+} and [YGPAA+H]^{+} Ions: a Stereochemical "twist" on the β-HAIRPIN Turn

NASA Astrophysics Data System (ADS)

DeBlase, Andrew F.; Harrilal, Christopher P.; Lawler, John T.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

2017-06-01

Incorporation of the unnatural D-proline (^{D}P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of β-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (10 K) gas-phase ions, we probe the inherent conformational preferences of the ^{D}P and ^{L}P diastereomers in the protonated peptide [YAPAA+H]^{+}, where only intramolecular interactions are possible. Consistent with the solution phase studies, one of the conformers of [YADPAA+H]^{+} is folded into a charge-stabilized β-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the ^{L}P diastereomer, [YALPAA+H]^{+}, is found and assigned to a structure that is not the anticipated "mirror image" β-turn. Instead, the ^{L}P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the ^{D}P diastereomer to support a trans-amide bond and the proclivity of ^{L}P for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]^{+}. These results provide a basis for understanding the residue-specific and stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of β-hairpin formation.

Automated and assisted RNA resonance assignment using NMR chemical shift statistics

PubMed Central

Aeschbacher, Thomas; Schmidt, Elena; Blatter, Markus; Maris, Christophe; Duss, Olivier; Allain, Frédéric H.-T.; Güntert, Peter; Schubert, Mario

2013-01-01

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs. PMID:23921634

Within-Site Variation in Feather Stable Hydrogen Isotope (δ2Hf) Values of Boreal Songbirds: Implications for Assignment to Molt Origin.

PubMed

Nordell, Cameron J; Haché, Samuel; Bayne, Erin M; Sólymos, Péter; Foster, Kenneth R; Godwin, Christine M; Krikun, Richard; Pyle, Peter; Hobson, Keith A

2016-01-01

Understanding bird migration and dispersal is important to inform full life-cycle conservation planning. Stable hydrogen isotope ratios from feathers (δ2Hf) can be linked to amount-weighted long-term, growing season precipitation δ2H (δ2Hp) surfaces to create δ2Hf isoscapes for assignment to molt origin. However, transfer functions linking δ2Hp with δ2Hf are influenced by physiological and environmental processes. A better understanding of the causes and consequences of variation in δ2Hf values among individuals and species will improve the predictive ability of geographic assignment tests. We tested for effects of species, land cover, forage substrate, nest substrate, diet composition, body mass, sex, and phylogenetic relatedness on δ2Hf from individuals at least two years old of 21 songbird species captured during the same breeding season at a site in northeastern Alberta, Canada. For four species, we also tested for a year × species interaction effect on δ2Hf. A model including species as single predictor received the most support (AIC weight = 0.74) in explaining variation in δ2Hf. A species-specific variance parameter was part of all best-ranked models, suggesting variation in δ2Hf was not consistent among species. The second best-ranked model included a forage substrate × diet interaction term (AIC weight = 0.16). There was a significant year × species interaction effect on δ2Hf suggesting that interspecific differences in δ2Hf can differ among years. Our results suggest that within- and among-year interspecific variation in δ2Hf is the most important source of variance typically not being explicitly quantified in geographic assignment tests using non-specific transfer functions to convert δ2Hp into δ2Hf. However, this source of variation is consistent with the range of variation from the transfer functions most commonly being propagated in assignment tests of geographic origins for passerines breeding in North America.

Assigning Main Orientation to an EOH Descriptor on Multispectral Images.

PubMed

Li, Yong; Shi, Xiang; Wei, Lijun; Zou, Junwei; Chen, Fang

2015-07-01

This paper proposes an approach to compute an EOH (edge-oriented histogram) descriptor with main orientation. EOH has a better matching ability than SIFT (scale-invariant feature transform) on multispectral images, but does not assign a main orientation to keypoints. Alternatively, it tends to assign the same main orientation to every keypoint, e.g., zero degrees. This limits EOH to matching keypoints between images of translation misalignment only. Observing this limitation, we propose assigning to keypoints the main orientation that is computed with PIIFD (partial intensity invariant feature descriptor). In the proposed method, SIFT keypoints are detected from images as the extrema of difference of Gaussians, and every keypoint is assigned to the main orientation computed with PIIFD. Then, EOH is computed for every keypoint with respect to its main orientation. In addition, an implementation variant is proposed for fast computation of the EOH descriptor. Experimental results show that the proposed approach performs more robustly than the original EOH on image pairs that have a rotation misalignment.

Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints.

PubMed

Degen, B; Ward, S E; Lemes, M R; Navarro, C; Cavers, S; Sebbenn, A M

2013-01-01

Illegal logging is one of the main causes of ongoing worldwide deforestation and needs to be eradicated. The trade in illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, there is a lack of practical mechanisms for identifying the origin of timber and wood products. In this study, six nuclear microsatellites were used to generate DNA fingerprints for a genetic reference database characterising the populations of origin of a large set of mahogany (Swietenia macrophylla King, Meliaceae) samples. For the database, leaves and/or cambium from 1971 mahogany trees sampled in 31 stands from Mexico to Bolivia were genotyped. A total of 145 different alleles were found, showing strong genetic differentiation (δ(Gregorious)=0.52, F(ST)=0.18, G(ST(Hedrick))=0.65) and clear correlation between genetic and spatial distances among stands (r=0.82, P<0.05). We used the genetic reference database and Bayesian assignment testing to determine the geographic origins of two sets of mahogany wood samples, based on their multilocus genotypes. In both cases the wood samples were assigned to the correct country of origin. We discuss the overall applicability of this methodology to tropical timber trading. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

CONSERVATION. Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots.

PubMed

Wasser, S K; Brown, L; Mailand, C; Mondol, S; Clark, W; Laurie, C; Weir, B S

2015-07-03

Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime. Copyright © 2015, American Association for the Advancement of Science.

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

Ford, Michael J.; Williamson, Kevin S.

We investigated differences in the statistical power to assign parentage between an artificially propagated and wild salmon population. The propagated fish were derived from the wild population, and are used to supplement its abundance. Levels of genetic variation were similar between the propagated and wild groups at 11 microsatellite loci, and exclusion probabilities were >0.999999 for both groups. The ability to unambiguously identify a pair of parents for each sampled progeny was much lower than expected, however. Simulations demonstrated that the proportion of cases the most likely pair of parents were the true parents was lower for propagated parents thanmore » for wild parents. There was a clear relationship between parentage assignment ability and the degree of linkage disequilibrium, the estimated effective number of breeders that produced the parents, and the size of the largest family within the potential parents. If a stringent threshold for parentage assignment was used, estimates of relative fitness were biased downward for the propagated fish. The bias appeared to be largely eliminated by either fractionally assigning progeny among parents in proportion to their likelihood of parentage, or by assigning progeny to the most likely set of parents without using a statistical threshold. We used a DNA-based parentage analysis to measure the relative reproductive success of hatchery- and natural-origin spring Chinook salmon in the natural environment. Both male and female hatchery-origin fish produced far fewer juvenile progeny per parent when spawning naturally than did natural origin fish. Differences in age structure, spawning location, weight and run timing were responsible for some of the difference in fitness. Male size and age had a large influence on fitness, with larger and older males producing more offspring than smaller or younger individuals. Female size had a significant effect on fitness, but the effect was much smaller than the effect of size on male fitness. For both sexes, run time had a smaller but still significant effect on fitness, with earlier returning fish favored. Spawning location within the river had a significant effect on fitness for both males and females, and for females explained most of the reduced fitness observed for hatchery fish in this population. While differences have been reported in the relative reproductive success of hatchery and naturally produced salmonids Oncorhynchus spp., factors explaining the differences are often confounded. We examined the spawning site habitat and redd structure variables of hatchery and naturally produced spring Chinook salmon O. tshawytscha of known size that spawned in two tributaries of the Wenatchee River. We controlled for variability in spawning habitat by limiting our analysis to redds found within four selected reaches. No difference in the instantaneous spawner density or location of the redd in the stream channel was detected between reaches. Within each reach, no difference in the fork length or weight of hatchery and naturally produced fish was detected. While most variables differed between reaches, we found no difference in redd characteristics within a reach between hatchery and naturally produced females. Correlation analysis of fish size and redd characteristics found several weak but significant relationships suggesting larger fish contract larger redds in deeper water. Spawner density was inversely related to several redd structure variables suggesting redd size may decrease as spawner density increases. Results should be considered preliminary until samples size and statistical power goals are reached in future years. Trends in relative reproductive success of hatchery and naturally produced spring Chinook salmon Oncorhynchus tshawytscha in the Wenatchee Basins suggest females that spawn in the upper reaches of the tributaries produced a great number of offspring compared to females that spawn in the lower reaches of the tributaries. To better understand this trend, redd microhabitat data was collected from spring Chinook salmon that spawned in the Chiwawa River and Nason Creek, the primary spawning tributaries in the Wenatchee Basin. The objective of the study was to examine the influence of habitat and spawner density on spawning site and redd structure characteristics. We analyzed 27 variables of redd microhabitat data collected from the upper and lower most reaches of each study stream. In both streams, we found redds in the upper most reaches to be significantly larger (length and width) and deeper (bowl depth). Spawner density was significantly greater in the lower Chiwawa River compared to the upper reach. No difference in spawner density was detected between reaches in Nason Creek (P = 0.54). Data should be considered preliminary until sample size goals are achieved.« less

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

Pease, J.H.

The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometrymore » calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.« less

Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data.

PubMed

Benigni, Paolo; Marin, Rebecca; Fernandez-Lima, Francisco

2015-10-01

With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MS n and IMS n measurements for faster and more accurate tridimensional structural assignment.

20 CFR 655.20 - Applications for temporary employment certification.

Code of Federal Regulations, 2012 CFR

2012-04-01

... charge or deposit charge, all tools, supplies, and equipment required to perform the duties assigned. (l..., color, national origin, age, sex, religion, disability, or citizenship. Rejections of any U.S. workers...

Legislative Process in the U.S. Congress.

ERIC Educational Resources Information Center

Ray, Bruce A.

1981-01-01

Describes a college course which studies the U.S. House of Representatives. The course examines the origins of the House, life on the hill, rules, committee assignments, leadership, legislators, and the bureaucracy. (RM)

The Nature of the Dielectric Response of Methanol Revealed by the Terahertz Kerr Effect.

PubMed

Kampfrath, Tobias; Campen, R Kramer; Wolf, Martin; Sajadi, Mohsen

2018-03-15

The dielectric response of liquids in the terahertz (THz) and sub-THz frequency range arises from low-energy collective molecular motions, which are often strongly influenced by intermolecular interactions. To shed light on the microscopic origin of the THz dielectric response of the simplest alcohol, methanol, we resonantly excite this liquid with an intense THz electric-field pulse and monitor the relaxation of the induced optical birefringence. We find a unipolar THz-Kerr-effect signal which, in contrast to aprotic polar liquids, shows a weak coupling between the THz electric field and the permanent molecular dipole moment of the liquid. We assign this weak coupling to the restricted translational rather than rotational nature of the excited mode. Our approach opens a new avenue to the assignment of the dielectric spectrum of liquids to a microscopic origin.

Marking Student Programs Using Graph Similarity

ERIC Educational Resources Information Center

Naude, Kevin A.; Greyling, Jean H.; Vogts, Dieter

2010-01-01

We present a novel approach to the automated marking of student programming assignments. Our technique quantifies the structural similarity between unmarked student submissions and marked solutions, and is the basis by which we assign marks. This is accomplished through an efficient novel graph similarity measure ("AssignSim"). Our experiments…

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715

Ancestry estimation and control of population stratification for sequence-based association studies.

PubMed

Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y; Branham, Kari E; Heckenlively, John; Fulton, Robert; Wilson, Richard K; Mardis, Elaine R; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R

2014-04-01

Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

A Self-Instructional Approach To the Teaching of Enzymology Involving Computer-Based Sequence Analysis and Molecular Modelling.

ERIC Educational Resources Information Center

Attwood, Paul V.

1997-01-01

Describes a self-instructional assignment approach to the teaching of advanced enzymology. Presents an assignment that offers a means of teaching enzymology to students that exposes them to modern computer-based techniques of analyzing protein structure and relates structure to enzyme function. (JRH)

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Font group identification using reconstructed fonts

NASA Astrophysics Data System (ADS)

Cutter, Michael P.; van Beusekom, Joost; Shafait, Faisal; Breuel, Thomas M.

2011-01-01

Ideally, digital versions of scanned documents should be represented in a format that is searchable, compressed, highly readable, and faithful to the original. These goals can theoretically be achieved through OCR and font recognition, re-typesetting the document text with original fonts. However, OCR and font recognition remain hard problems, and many historical documents use fonts that are not available in digital forms. It is desirable to be able to reconstruct fonts with vector glyphs that approximate the shapes of the letters that form a font. In this work, we address the grouping of tokens in a token-compressed document into candidate fonts. This permits us to incorporate font information into token-compressed images even when the original fonts are unknown or unavailable in digital format. This paper extends previous work in font reconstruction by proposing and evaluating an algorithm to assign a font to every character within a document. This is a necessary step to represent a scanned document image with a reconstructed font. Through our evaluation method, we have measured a 98.4% accuracy for the assignment of letters to candidate fonts in multi-font documents.

Origin of the magnetoresistance in oxide tunnel junctions determined through electric polarization control of the interface

DOE PAGES

Inoue, Hisashi; Swartz, Adrian G.; Harmon, Nicholas J.; ...

2015-11-11

The observed magnetoresistance (MR) in three-terminal (3T) ferromagnet-nonmagnet (FM-NM) tunnel junctions has historically been assigned to ensemble dephasing (Hanle effect) of a spin accumulation, thus offering a powerful approach for characterizing the spin lifetime of candidate materials for spintronics applications. However, due to crucial discrepancies of the extracted spin parameters with known materials properties, this interpretation has come under intense scrutiny. By employing epitaxial artificial dipoles as the tunnel barrier in oxide heterostructures, the band alignments between the FM and NM channels can be controllably engineered, providing an experimental platform for testing the predictions of the various spin accumulation models.more » Using this approach, we have been able to definitively rule out spin accumulation as the origin of the 3T MR. Instead, we assign the origin of the magnetoresistance to spin-dependent hopping through defect states in the barrier, a fundamental phenomenon seen across diverse systems. In conclusion, a theoretical framework is developed that can account for the signal amplitude, linewidth, and anisotropy.« less

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

A Survey of Automated Assessment Approaches for Programming Assignments

ERIC Educational Resources Information Center

Ala-Mutka, Kirsti M.

2005-01-01

Practical programming is one of the basic skills pursued in computer science education. On programming courses, the coursework consists of programming assignments that need to be assessed from different points of view. Since the submitted assignments are executable programs with a formal structure, some features can be assessed automatically. The…

Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.

PubMed

Barnwal, Ravi Pratap; Rout, Ashok K; Chary, Kandala V R; Atreya, Hanudatta S

2007-12-01

We present two NMR experiments, (3,2)D HNHA and (3,2)D HNHB, for rapid and accurate measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides based on the principle of G-matrix Fourier transform NMR spectroscopy and quantitative J-correlation. These experiments, which facilitate fast acquisition of three-dimensional data with high spectral/digital resolution and chemical shift dispersion, will provide renewed opportunities to utilize them for sequence specific resonance assignments, estimation/characterization of secondary structure with/without prior knowledge of resonance assignments, stereospecific assignment of prochiral groups and 3D structure determination, refinement and validation. Taken together, these experiments have a wide range of applications from structural genomics projects to studying structure and folding in polypeptides.

Use of a Spreadsheet to Help Students Understand the Origin of the Empirical Equation that Allows Estimation of the Extinction Coefficients of Proteins

ERIC Educational Resources Information Center

Sims, Paul A.

2012-01-01

A brief history of the development of the empirical equation that is used by prominent, Internet-based programs to estimate (or calculate) the extinction coefficients of proteins is presented. In addition, an overview of a series of related assignments designed to help students understand the origin of the empirical equation is provided. The…

20 CFR 655.20 - Assurances and obligations of H-2B employers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... charge, all tools, supplies, and equipment required to perform the duties assigned. (l) Disclosure of job..., color, national origin, age, sex, religion, disability, or citizenship. Rejections of any U.S. workers...

29 CFR 503.16 - Assurances and obligations of H-2B employers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... charge or deposit charge, all tools, supplies, and equipment required to perform the duties assigned. (l....S. worker regardless of race, color, national origin, age, sex, religion, disability, or citizenship...

29 CFR 503.16 - Assurances and obligations of H-2B employers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... charge or deposit charge, all tools, supplies, and equipment required to perform the duties assigned. (l....S. worker regardless of race, color, national origin, age, sex, religion, disability, or citizenship...

29 CFR 503.16 - Assurances and obligations of H-2B employers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... charge or deposit charge, all tools, supplies, and equipment required to perform the duties assigned. (l....S. worker regardless of race, color, national origin, age, sex, religion, disability, or citizenship...

20 CFR 655.20 - Assurances and obligations of H-2B employers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... charge, all tools, supplies, and equipment required to perform the duties assigned. (l) Disclosure of job..., color, national origin, age, sex, religion, disability, or citizenship. Rejections of any U.S. workers...

5 CFR 1312.2 - Responsibilities.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., DECLASSIFICATION AND SAFEGUARDING OF NATIONAL SECURITY INFORMATION Classification and Declassification of National Security Information § 1312.2 Responsibilities. The effectiveness of the classification and... originate classified information are responsible for proper assignment of a classification to that material...

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

PubMed

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

Ethnicity and Population Structure in Personal Naming Networks

PubMed Central

Mateos, Pablo; Longley, Paul A.; O'Sullivan, David

2011-01-01

Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how ‘naming networks’, constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply ‘emerge’ from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new understandings of migration, identity, integration and social interaction across the world. PMID:21909399

Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers.

PubMed

Liu, Dongqi; Hou, Feixia; Liu, Qin; Zhang, Xiuyue; Yan, Taiming; Song, Zhaobin

2015-02-01

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.

Long-distance autumn migration across the Sahara by painted lady butterflies: exploiting resource pulses in the tropical savannah.

PubMed

Stefanescu, Constantí; Soto, David X; Talavera, Gerard; Vila, Roger; Hobson, Keith A

2016-10-01

The painted lady, Vanessa cardui, is a migratory butterfly that performs an annual multi-generational migration between Europe and North Africa. Its seasonal appearance south of the Sahara in autumn is well known and has led to the suggestion that it results from extremely long migratory flights by European butterflies to seasonally exploit the Sahel and the tropical savannah. However, this possibility has remained unproven. Here, we analyse the isotopic composition of butterflies from seven European and seven African countries to provide new support for this hypothesis. Each individual was assigned a geographical natal origin, based on its wing stable hydrogen isotope (δ 2 H w ) value and a predicted δ 2 H w basemap for Europe and northern Africa. Natal assignments of autumn migrants collected south of the Sahara confirmed long-distance movements (of 4000 km or more) starting in Europe. Samples from Maghreb revealed a mixed origin of migrants, with most individuals with a European origin, but others having originated in the Sahel. Therefore, autumn movements are not only directed to northwestern Africa, but also include southward and northward flights across the Sahara. Through this remarkable behaviour, the productive but highly seasonal region south of the Sahara is incorporated into the migratory circuit of V. cardui. © 2016 The Author(s).

Sex assessment using clavicle measurements: inter- and intra-population comparisons.

PubMed

Králík, Miroslav; Urbanová, Petra; Wagenknechtová, Martina

2014-01-01

We studied sexual dimorphism of the human clavicle in order to describe size variation and create population-specific discriminant tools for morphometric sex assessment. The studied sample consisted of 200 skeletons of adult individuals obtained from the University of Athens Human Skeletal Reference Collection, Athens, Greece. The specimens were well-documented and represented a modern population from cemeteries in the Athens area. Six dimensions typically used for clavicle measurements were recorded. For sexing clavicles, we used both traditional univariate (limiting, demarking and sectioning points) and multivariate discriminant function analysis. The accuracy of the best five classification equations/functions ranged from 91.62% to 92.55% of correctly assigned specimens. By testing new and previously published sexing functions (Greeks, Polynesians, Guatemalans) on four available population samples (English, Indians from Amritsar, Indians from Varanasi, and data from the present study) we found that, for some combinations of tested and reference samples, the accuracy of the sex assessment may decrease even below the probability given by random sex assignment. Therefore, measurements of the clavicle should not be used for sex assessment of individual cases (both forensic and archeological) whose population origin is unknown. However, significant metric differences were also recorded among three different Greek samples (i.e. within a population). As a consequence, application of a sexing method generated from one Greek sample and applied to another Greek sample led to negligible reduction in the success of sex assessment, despite general similarities in ethnic origin (Greeks), generation structure and presumed social background of the samples. Therefore, we believe that future studies should focus on understanding the nature of the differences among within-population reference samples. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Influences of the propyl group on the van der Waals structures of 4-propylaniline complexes with one and two argon atoms studied by electronic and cationic spectroscopy

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

Yang, Zhijun; Gu, Quanli; Department of Chemistry, University of Oklahoma, Norman, Oklahoma 73019

2015-07-21

4-propylaniline complexes with one and two argon atoms formed in the molecular beam were studied in the first excited electronic state, S{sub 1}, using resonance enhanced two-photon ionization spectroscopy and in the cation ground state, D{sub 0}, using mass analyzed threshold ionization spectroscopy. The combination of electronic and cationic spectra of the clusters allows two conformations to be identified in both aniline-Ar{sub 1} and aniline-Ar{sub 2}, which are assigned to either the gauche configuration or anti-configuration of 4-propylaniline. The gauche isomer exhibits complex bands shifted 29 cm{sup −1} and 89 cm{sup −1} from the S{sub 1} origin bands and 83more » cm{sup −1} and 148 cm{sup −1} from the ionization potential assigned to the Ar{sub 1} and Ar{sub 2} complexes, respectively. For the anti-rotamer, the corresponding shifts actually become nearly additive, 53 cm{sup −1} and 109 cm{sup −1} for the S{sub 1} origin bands, and 61 cm{sup −1} and 125 cm{sup −1} for the ionization potentials. Ab initio calculations provide insights into the influences of the propyl and amino groups on the positions of the argon atoms within the clusters. In addition, the binding energy of one argon with the gauche isomer of 4-propylaniline has been measured to be 550 ± 5 cm{sup −1} in the D{sub 0} state, 496 ± 5 cm{sup −1} in the S{sub 1} state, and 467 ± 5 cm{sup −1} in the neutral ground state, S{sub 0}.« less

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.

PubMed

Brunak, S; Engelbrecht, J

1996-06-01

A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome.

Protein domain assignment from the recurrence of locally similar structures

PubMed Central

Tai, Chin-Hsien; Sam, Vichetra; Gibrat, Jean-Francois; Garnier, Jean; Munson, Peter J.

2010-01-01

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6,373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. PMID:21287617

A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians.

PubMed

Hwa, Hsiao-Lin; Lin, Chih-Peng; Huang, Tsun-Ying; Kuo, Po-Hsiu; Hsieh, Wei-Hsin; Lin, Chun-Yen; Yin, Hsiang-I; Tseng, Li-Hui; Lee, James Chun-I

2017-06-01

Ancestry informative single-nucleotide polymorphism (AISNP) panels for differentiating between East and Southeast Asian populations are scarce. This study aimed to identify AISNPs for ancestry assignment of five East and Southeast Asian populations, and Caucasians. We analyzed 145 autosomal SNPs of the 627 DNA samples from individuals of six populations (234 Taiwanese Han, 91 Filipinos, 79 Indonesians, 60 Thais, 71 Vietnamese, and 92 Caucasians) using arrays. The multiple logistic regression model and a multi-tier approach were used for ancestry classification. We observed that 130 AISNPs were effective for classifying the ethnic origins with fair accuracy. Among the 130 AISNPs, 122 were useful for stratification between these five Asian populations and 64 were effective for differentiating between Caucasians and these Asian populations. For differentiation between Caucasians and Asians, an accuracy rate of 100% was achieved in these 627 subjects with 50 optimal AISNPs among the 64 effective SNPs. For classification of the five Asian populations, the accuracy rates of ancestry inference using 20 to 57 SNPs for each of the two Asian populations ranged from 74.1% to 100%. Another 14 degraded DNA samples with incomplete profiling were analyzed, and the ancestry of 12 (85.7%) of those subjects was accurately assigned. We developed a 130-AISNP panel for ethnic origin differentiation between the five East and Southeast Asian populations and Caucasians. This AISNP set may be helpful for individual ancestral assignment of these populations in forensic casework.

Range-wide patterns of migratory connectivity in the western sandpiper Calidris mauri

USGS Publications Warehouse

Franks, Samantha E.; Norris, D. Ryan; Kyser, T. Kurt; Fernández, Guillermo; Schwarz, Birgit; Carmona, Roberto; Colwell, Mark A.; Sandoval, Jorge Correa; Dondua, Alexey; Gates, H. River; Haase, Ben; Hodkinson, David J.; Jiménez, Ariam; Lanctot, Richard B.; Ortego, Brent; Sandercock, Brett K.; Sanders, Felicia J.; Takekawa, John Y.; Warnock, Nils; Ydenberg, Ron C.; Lank, David B.

2012-01-01

Understanding the population dynamics of migratory animals and predicting the consequences of environmental change requires knowing how populations are spatially connected between different periods of the annual cycle. We used stable isotopes to examine patterns of migratory connectivity across the range of the western sandpiper Calidris mauri. First, we developed a winter isotope basemap from stable-hydrogen (δD), -carbon (δ13C), and -nitrogen (δ15N) isotopes of feathers grown in wintering areas. δD and δ15N values from wintering individuals varied with the latitude and longitude of capture location, while δ13C varied with longitude only. We then tested the ability of the basemap to assign known-origin individuals. Sixty percent of wintering individuals were correctly assigned to their region of origin out of seven possible regions. Finally, we estimated the winter origins of breeding and migrant individuals and compared the resulting empirical distribution against the distribution that would be expected based on patterns of winter relative abundance. For breeding birds, the distribution of winter origins differed from expected only among males in the Yukon-Kuskokwim (Y-K) Delta and Nome, Alaska. Males in the Y-K Delta originated overwhelmingly from western Mexico, while in Nome, there were fewer males from western North America and more from the Baja Peninsula than expected. An unexpectedly high proportion of migrants captured at a stopover site in the interior United States originated from eastern and southern wintering areas, while none originated from western North America. In general, we document substantial mixing between the breeding and wintering populations of both sexes, which will buffer the global population of western sandpipers from the effects of local habitat loss on both breeding and wintering grounds.

Fifty years after Welles and Welles: Distribution and genetic structure of Desert Bighorn Sheep in Death Valley National Park

USGS Publications Warehouse

Epps, Clinton W.; Wehausen, John D.; Sloan, William B.; Holt, Stacy; Creech, Tyler G.; Crowhurst, Rachel S.; Jaeger, Jef R.; Longshore, Kathleen M.; Monello, Ryan J.

2013-01-01

Where possible, we revisited many of the water sources and other locations originally investigated by Welles and Welles (1961) and earlier researchers. We extracted DNA from fecal pellets, carcass tissue samples, and blood samples archived from earlier captures and genotyped them using highly variable genetic markers (15 microsatellite loci) with sufficient power to distinguish individuals and characterize gene flow and genetic structure. We also analyzed DNA samples collected from other bighorn sheep populations extending north to the White Mountains, west to the Inyo Mountains, south to the Avawatz Mountains, and southeast to the Clark Mountain Range, Kingston Range, and Spring Mountains of Nevada. We estimated genetic structure and recent gene flow among nearly all known populations of bighorn sheep in and around Death Valley National Park (DEVA), and used assignment tests to evaluate individual and population-level genetic structure to infer connectivity across the region. We found that bighorn sheep are still widely distributed in mountain ranges throughout DEVA, including many of the areas described by Welles and Welles (1961), although some use patterns appear to have changed and other areas still require resurvey. Gene flow was relatively high through some sections of fairly continuous habitat, such as the Grapevine and Funeral Mountains along the eastern side of Death Valley, but other populations were more isolated. Genetic diversity was relatively high throughout the park. Although southern Death Valley populations were genetically distinct from populations to the southeast, population assignment tests and recent gene flow estimates suggested that individuals occasionally migrate between those regions, indicating the potential for the recent outbreak of respiratory disease in the southern Mojave Desert to spread into the Death Valley system. We recommend careful monitoring of bighorn sheep using remote cameras to check for signs of respiratory disease in southeastern DEVA and ground surveys in the still-understudied southwestern part of DEVA.

A "Journey in Feminist Theory Together": The "Doing Feminist Theory through Digital Video" Project

ERIC Educational Resources Information Center

Hurst, Rachel Alpha Johnston

2014-01-01

"Doing Feminist Theory Through Digital Video" is an assignment I designed for my undergraduate feminist theory course, where students created a short digital video on a concept in feminist theory. I outline the assignment and the pedagogical and epistemological frameworks that structured the assignment (digital storytelling,…

Confirmed assignments of isomeric dimethylbenzyl radicals generated by corona discharge.

PubMed

Yoon, Young Wook; Lee, Sang Kuk

2011-12-07

The controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By employing corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of 1,2,4-trimethylbenzene. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion, we revised previous assignments of the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. Spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of 1,2,4-trimethylbenzene. © 2011 American Institute of Physics

Raman spectra of ruthenium and tantalum trimers in argon matrices

NASA Astrophysics Data System (ADS)

Fang, Li; Shen, Xiaole; Chen, Xiaoyu; Lombardi, John R.

2000-12-01

The resonance Raman spectra of ruthenium trimers (Ru 3) in argon matrices have been obtained. Three resonance Raman transitions were observed between 570 and 590 nm. Two of them (303.4 and 603.7 cm -1) are assigned to the totally symmetric vibrational progression, giving k e=1.86 mdyne/ Å. The line at 581.5 cm-1 is assigned as the origin of a low-lying electronic state. We also report on the observation of a resonance Raman spectrum of tantalum trimers (Ta 3). Observed lines include 251.2 and 501.9 cm-1 which we assign to the fundamental and the first overtone of the symmetric stretch in Ta 3. This gives k e=2.25 mdyne/ Å.

Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state.

PubMed

Malik, Nikita; Kumar, Ashutosh

2016-09-01

NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled (13)C,(15)N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (Acer saccharum Marshall).

PubMed

Graignic, Noémie; Tremblay, Francine; Bergeron, Yves

2018-03-01

Due to climate change, the ranges of many North American tree species are expected to shift northward. Sugar maple ( Acer saccharum Marshall) reaches its northern continuous distributional limit in northeastern North America at the transition between boreal mixed-wood and temperate deciduous forests. We hypothesized that marginal fragmented northern populations from the boreal mixed wood would have a distinct pattern of genetic structure and diversity. We analyzed variation at 18 microsatellite loci from 23 populations distributed along three latitudinal transects (west, central, and east) that encompass the continuous-discontinuous species range. Each transect was divided into two zones, continuous (temperate deciduous) and discontinuous (boreal mixed wood), based on sugar maple stand abundance. Respective positive and negative relationships were found between the distance of each population to the northern limit (D_north), and allelic richness ( A R ) and population differentiation ( F ST ). These relations were tested for each transect separately; the pattern (discontinuous-continuous) remained significant only for the western transect. structure analysis revealed the presence of four clusters. The most northern populations of each transect were assigned to a distinct group. Asymmetrical gene flow occurred from the southern into the four northernmost populations. Southern populations in Québec may have originated from two different postglacial migration routes. No evidence was found to validate the hypothesis that northern populations were remnants of a larger population that had migrated further north of the species range after the retreat of the ice sheet. The northernmost sugar maple populations possibly originated from long-distance dispersal.

Changes in area affect figure-ground assignment in pigeons.

PubMed

Castro, Leyre; Lazareva, Olga F; Vecera, Shaun P; Wasserman, Edward A

2010-03-05

A critical cue for figure-ground assignment in humans is area: smaller regions are more likely to be perceived as figures than are larger regions. To see if pigeons are similarly sensitive to this cue, we trained birds to report whether a target appeared on a colored figure or on a differently colored background. The initial training figure was either smaller than (Experiments 1 and 2) or the same area as (Experiment 2) the background. After training, we increased or decreased the size of the figure. When the original training shape was smaller than the background, pigeons' performance improved with smaller figures (and worsened with larger figures); when the original training shape was the same area as the background, pigeons' performance worsened when they were tested with smaller figures. A smaller figural region appeared to improve the figure-ground discrimination only when size was a relevant cue in the initial discrimination.

An alternative design for a sparse distributed memory

NASA Technical Reports Server (NTRS)

Jaeckel, Louis A.

1989-01-01

A new design for a Sparse Distributed Memory, called the selected-coordinate design, is described. As in the original design, there are a large number of memory locations, each of which may be activated by many different addresses (binary vectors) in a very large address space. Each memory location is defined by specifying ten selected coordinates (bit positions in the address vectors) and a set of corresponding assigned values, consisting of one bit for each selected coordinate. A memory location is activated by an address if, for all ten of the locations's selected coordinates, the corresponding bits in the address vector match the respective assigned value bits, regardless of the other bits in the address vector. Some comparative memory capacity and signal-to-noise ratio estimates for the both the new and original designs are given. A few possible hardware embodiments of the new design are described.

Changes in Area Affect Figure-Ground Assignment in Pigeons

PubMed Central

Castro, Leyre; Lazareva, Olga F.; Vecera, Shaun P.; Wasserman, Edward A.

2010-01-01

A critical cue for figure-ground assignment in humans is area: Smaller regions are more likely to be perceived as figures than are larger regions. To see if pigeons are similarly sensitive to this cue, we trained birds to report whether a target appeared on a colored figure or on a differently colored background. The initial training figure was either smaller than (Experiments 1 and 2) or the same area as (Experiment 2) the background. After training, we increased or decreased the size of the figure. When the original training shape was smaller than the background, pigeons’ performance improved with smaller figures (and worsened with larger figures); when the original training shape was the same area as the background, pigeons’ performance worsened when they were tested with smaller figures. A smaller figural region appeared to improve the figure-ground discrimination only when size was a relevant cue in the initial discrimination. PMID:20060406

Seismicity map of the State of Illinois

USGS Publications Warehouse

Stover, C.W.; Reagor, B.G.; Algermissen, S.T.

1979-01-01

The earthquake data shown on this map and listed in table 1 are a list of earthquakes that were originally used in preparing the Seismic Risk Studies in the United States (Algermissen, 1969) which have been recompiled and updated through 1977. The data have been reexamined and intensities assigned where none had been assigned before, on the basis of available data. Other intensity values were updated from new and additional data sources that were not available at the time of original compilation. Some epicenters were relocated on the basis of new information. The data shown in table 1 are estimates of the most accurate epicenter, magnitude, and intensity of teach earthquake, on the basis of historical and current information. Some of the aftershocks from large earthquakes are listed but are incomplete in many instances, especially for the ones that occurred before seismic instruments were in universal usage. 

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

PubMed

Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

2015-02-01

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

Polish Translation and Validation of the Tinnitus Handicap Inventory and the Tinnitus Functional Index

PubMed Central

Wrzosek, Małgorzata; Szymiec, Eugeniusz; Klemens, Wiesława; Kotyło, Piotr; Schlee, Winfried; Modrzyńska, Małgorzata; Lang-Małecka, Agnieszka; Preis, Anna; Bulla, Jan

2016-01-01

Objective: The need for validated measures enabling clinicians to classify tinnitus patients according to the severity of tinnitus and screen the progress of therapies in our country led us to translate into Polish and to validate two tinnitus questionnaires, namely the Tinnitus Handicap Inventory (THI) and the Tinnitus Functional Index (TFI). Design: The original English versions of the questionnaires were translated into Polish and translated back to English by three independent translators. These versions were then finalized by the authors into a Polish THI (THI-Pl) and a Polish TFI (TFI-Pl). Participants from three laryngological centers in Poland anonymously answered the THI-Pl (N = 98) and the TFI-Pl (N = 108) in addition to the Polish versions of the Center for Epidemiologic Studies Depression Scale as a measure of self-perceived level of depression, and the Satisfaction With Life Scale to assess self-perceived quality of life. Both were used to determine discriminant validity. Two Visual Analog Scales were used to measure tinnitus annoyance and tinnitus loudness in order to determine convergent validity. Results: Similar to the original version of the THI, the THI-Pl showed a high internal consistency (Cronbach’s α = 0.93). The exploratory factor analysis revealed that the questionnaire has a three-factorial structure that does not correspond to the original division for functional, catastrophic, and emotional subscales. Convergent and discriminant validities were confirmed. The TFI-Pl showed high internal consistency (Cronbach’s α = 0.96) with the reliability ranging from 0.82 to 0.95 for its different subscales. Factor analysis confirmed an eight-factorial structure with factors assigning all items to appropriate subscales reported in the original version of the questionnaire. Discriminant and convergent validities were also confirmed for the TFI-Pl. Conclusion: We translated and validated the Polish versions of the THI and the TFI to make them suitable for clinical use in Poland. PMID:27965609

The PAH Emission Characteristics of the Reflection Nebula NGC 2023

NASA Astrophysics Data System (ADS)

Peeters, Els; Bauschlicher, Charles W., Jr.; Allamandola, Louis J.; Tielens, Alexander G. G. M.; Ricca, Alessandra; Wolfire, Mark G.

2017-02-01

We present 5-20 μm spectral maps of the reflection nebula NGC 2023 obtained with the Infrared Spectrograph SL and SH modes on board the Spitzer Space Telescope, which reveal emission from polycyclic aromatic hydrocarbons (PAHs), C60, and H2 superposed on a dust continuum. We show that several PAH emission bands correlate with each other and exhibit distinct spatial distributions that reveal a spatial sequence with distance from the illuminating star. We explore the distinct morphology of the 6.2, 7.7, and 8.6 μm PAH bands and find that at least two spatially distinct components contribute to the 7-9 μm PAH emission in NGC 2023. We report that the PAH features behave independently of the underlying plateaus. We present spectra of compact, oval PAHs ranging in size from C66 to C210, determined computationally using density functional theory, and we investigate trends in the band positions and relative intensities as a function of PAH size, charge, and geometry. Based on the NASA Ames PAH database, we discuss the 7-9 μm components in terms of band assignments and relative intensities. We assign the plateau emission to very small grains with possible contributions from PAH clusters and identify components in the 7-9 μm emission that likely originate in these structures. Based on the assignments and the observed spatial sequence, we discuss the photochemical evolution of the interstellar PAH family as the PAHs are more and more exposed to the radiation field of the central star in the evaporative flows associated with the Photo-Dissociation Regions in NGC 2023.

Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

PubMed

Al Hasan, Naila M; Johnson, Grant E; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy(n-) and VxOyCl(n-) ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N(+), tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCl(n-) and VxOyCl(L)((n-1)-) clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl((1-2)-) and VxOy ((1-2)-) anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

PubMed

Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

2015-10-01

Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

PubMed

von Grotthuss, Marcin; Plewczynski, Dariusz; Ginalski, Krzysztof; Rychlewski, Leszek; Shakhnovich, Eugene I

2006-02-06

The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF.

Complete structure of the polysaccharide from Streptococcus sanguis J22

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

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1990-01-09

The cell wall polysaccharides of certain oral streptococci such as Streptococcus sanguis strains 34 and J22, although immunologically distinct, act as receptors for the fimbrial lectins of Actinomyces viscosus T14V. The authors report the complete covalent structure of the polysaccharide from S. sanguis J22 which is composed of a heptasaccharide subunit linked by phosphodiester bonds. The repeating subunit, which contains {alpha}-GalNAc, {alpha}-rhamnose, {beta}-rhamnose, {beta}-glucose, and {beta}-galactose all in the pyranoside form and {beta}-galactofuranose, is compared with the previously published structure of the polysaccharide from strain 34. The structure has been determined almost exclusively by high-resolution nuclear magnetic resonance methods. Themore » {sup 1}H and {sup 13}C NMR spectra of the polysaccharides from both strains 34 and J22 have been completely assigned. The stereochemistry of pyranosides was assigned from J{sub H-H} values determined from phase-sensitive COSY spectra, and acetamido sugars were assigned by correlation of the resonances of the amide {sup 1}H with the sugar ring protons. The {sup 13}C spectra were assigned by {sup 1}H-detected multiple-quantum correlation (HMQC) spectra, and the assignments were confirmed by {sup 1}H-detected multiple-bond correlation (HMBC) spectra. The positions of the glycosidic linkages were assigned by detection of three-bond {sup 1}H-{sup 13}C correlation across the glycosidic linkage in the HMBC spectra. The positions of the phosphodiester linkages were determined by splittings observed in the {sup 13}C resonances due to {sup 31}P coupling and also by {sup 1}H-detected {sup 31}P correlation spectroscopy.« less

Assigning crystallographic electron densities with free energy calculations—The case of the fluoride channel Fluc

PubMed Central

2018-01-01

Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps. PMID:29771936

Using hydrogen isotopes to assign origins of bats in the eastern United States

Treesearch

Eric R. Britzke; Susan C. Loeb; Keith A. Hobson; Christopher S. Romanek; Maarten J. Vonhof

2009-01-01

Stable hydrogen isotopes (dDs) in metabolically inert tissues such as feathers and hair provide a set of endogenous markers that may be useful for establishing migratory connectivity in animals. We tested the assumption...

14 CFR 1203.800 - Delegations.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Secret and Confidential security classification assignments to information under their jurisdiction for... Information. (2) SECRET and CONFIDENTIAL Classification Authority. Officials listed in paragraph (b)(1) of... Authority To Make Determinations in Original Classification Matters § 1203.800 Delegations. (a) The NASA...

14 CFR 1203.800 - Delegations.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Secret and Confidential security classification assignments to information under their jurisdiction for... Information. (2) SECRET and CONFIDENTIAL Classification Authority. Officials listed in paragraph (b)(1) of... Authority To Make Determinations in Original Classification Matters § 1203.800 Delegations. (a) The NASA...

Processor Would Find Best Paths On Map

NASA Technical Reports Server (NTRS)

Eberhardt, Silvio P.

1990-01-01

Proposed very-large-scale integrated (VLSI) circuit image-data processor finds path of least cost from specified origin to any destination on map. Cost of traversal assigned to each picture element of map. Path of least cost from originating picture element to every other picture element computed as path that preserves as much as possible of signal transmitted by originating picture element. Dedicated microprocessor at each picture element stores cost of traversal and performs its share of computations of paths of least cost. Least-cost-path problem occurs in research, military maneuvers, and in planning routes of vehicles.

Different Structural Changes Occur in the Blue- and Green-Absorbing Proteorhodopsin During the Primary Photoreaction†

PubMed Central

Amsden, Jason J.; Kralj, Joel M.; Bergo, Vladislav B.; Spudich, Elena N.; Spudich, John L.; Rothschild, Kenneth J.

2013-01-01

We examine the structural changes during the primary photoreaction in blue-absorbing proteorhodopsin (BPR), a light-driven retinylidene proton pump, using low-temperature FTIR difference spectroscopy. Comparison of the light induced BPR difference spectrum recorded at 80 K to that of green-absorbing proteorhodopsin (GPR) reveals that there are several differences in the BPR and GPR primary photoreactions despite the similar structure of the retinal chromophore and all-trans → 13-cis isomerization. Strong bands near 1700 cm−1 assigned previously to a change in hydrogen bonding of Asn230 in GPR are still present in BPR but in addition bands in the same region are assigned on the basis of site-directed mutagenesis to changes occurring in Gln105. In the amide II region bands are assigned on the basis of total-N15 labeling to structural changes of the protein backbone, although no such bands were previously observed for GPR. A band at 3642 cm−1 in BPR, assigned to the OH stretching mode of a water molecule on the basis of H218O substitution, appears at a different frequency than a band at 3626 cm−1 previously assigned to a water molecule in GPR. However, the substitution of Gln105 for Leu105 in BPR leads to the appearance of both bands at 3642 and 3626 cm−1 indicating the waters assigned in BPR and GPR exist in separate distinct locations and can coexist in the GPR-like Q105L mutant of BPR. These results indicate that there exist significant differences in the conformational changes occurring in these two types proteorhodopsin during the initial photoreaction despite their similar chromophores structures, which might reflect a different arrangement of water in the active site as well as substitution of a hydrophilic for hydrophobic residue at residue 105. PMID:18842006

Raman study of HgBa 2Ca n-1 Cu nO 2 n+2+ δ ( n=1,2,3,4 and 5) superconductors

NASA Astrophysics Data System (ADS)

Zhou, Xingjiang; Cardona, M.; Chu, C. W.; Lin, Q. M.; Loureiro, S. M.; Marezio, M.

1996-02-01

Polarized micro-Raman scattering measurements have been performed on the five members of the HgBa 2Ca n-1 Cu nO 2 n+2+ δ ( n=1,2,3,4 and 5) high- Tc superconductor family using different laser frequencies. Local laser annealing measurements were carried out to investigate the variation of the Raman spectra with the excess oxygen content, δ. A systematic evolution of the spectra, which display mainly peaks near 590, 570, 540 and 470 cm -1, with increasing number of CuO 2 layers has been observed; its origin has been shown to lie in the variation of the interstitial oxygen content. In addition to confirming that the 590 cm -1 mode represents vibration of apical oxygens in the absence of neighboring excess oxygen, the 570 cm -1 mode, which may be composed of some finer structures, has been assigned to the vibration of the apical oxygen modified by the presence of the neighboring excess oxygens. The 540 and 470 cm -1 modes may represent the direct vibration of excess oxygens. The implication of possible different distribution sites of excess oxygens is discussed. All other observed lower-frequency modes are also assigned.

Multivariate analysis of matrix-assisted laser desorption/ionization mass spectrometric data related to glycoxidation products of human globins in nephropathic patients.

PubMed

Lapolla, Annunziata; Ragazzi, Eugenio; Andretta, Barbara; Fedele, Domenico; Tubaro, Michela; Seraglia, Roberta; Molin, Laura; Traldi, Pietro

2007-06-01

To clarify the possible pathogenetic role of oxidation products originated from the glycation of proteins, human globins from nephropathic patients have been studied by matrix-assisted laser desorption/ionization mass spectrometry (MALDI), revealing not only unglycated and monoglycated globins, but also a series of different species. For the last ones, structural assignments were tentatively done on the basis of observed masses and expectations for the Maillard reaction pattern. Consequently, they must be considered only propositive, and the discussion which will follow must be considered in this view. In our opinion this approach does not seem to compromise the intended diagnostic use of the data because distinctions are valid even if the assignments are uncertain. We studied nine healthy subjects and 19 nephropathic patients and processed the data obtained from the MALDI spectra using a multivariate analysis. Our results showed that multivariate analytical techniques enable differential aspects of the profile of molecular species to be identified in the blood of end stage nephropathic patients. A correct grouping can be achieved by principal component analysis (PCA) and the results suggest that several products involved in carbonyl stress exist in nephropathic patients. These compounds may have a relevant role as specific markers of the pathological state.

Boosting Sensitivity in Liquid Chromatography–Fourier Transform Ion Cyclotron Resonance–Tandem Mass Spectrometry for Product Ion Analysis of Monoterpene Indole Alkaloids

PubMed Central

Nakabayashi, Ryo; Tsugawa, Hiroshi; Kitajima, Mariko; Takayama, Hiromitsu; Saito, Kazuki

2015-01-01

In metabolomics, the analysis of product ions in tandem mass spectrometry (MS/MS) is noteworthy to chemically assign structural information. However, the development of relevant analytical methods are less advanced. Here, we developed a method to boost sensitivity in liquid chromatography–Fourier transform ion cyclotron resonance–tandem mass spectrometry analysis (MS/MS boost analysis). To verify the MS/MS boost analysis, both quercetin and uniformly labeled 13C quercetin were analyzed, revealing that the origin of the product ions is not the instrument, but the analyzed compounds resulting in sensitive product ions. Next, we applied this method to the analysis of monoterpene indole alkaloids (MIAs). The comparative analyses of MIAs having indole basic skeleton (ajmalicine, catharanthine, hirsuteine, and hirsutine) and oxindole skeleton (formosanine, isoformosanine, pteropodine, isopteropodine, rhynchophylline, isorhynchophylline, and mitraphylline) identified 86 and 73 common monoisotopic ions, respectively. The comparative analyses of the three pairs of stereoisomers showed more than 170 common monoisotopic ions in each pair. This method was also applied to the targeted analysis of MIAs in Catharanthus roseus and Uncaria rhynchophylla to profile indole and oxindole compounds using the product ions. This analysis is suitable for chemically assigning features of the metabolite groups, which contributes to targeted metabolome analysis. PMID:26734034

The Personal Computer in Mechanical Engineering Thermodynamics Courses.

ERIC Educational Resources Information Center

Romer, I. C., Jr.; Balmer, R. T.

1986-01-01

Describes experiences over several semesters with microcomputers in a mechanical engineering applied thermodynamics course. Includes course objectives, computer assignment structure, typical assignments, prewritten versus student-written software, and other topic areas. (JN)

Raman and infrared spectroscopy of α and β phases of thin nickel hydroxide films electrochemically formed on nickel.

PubMed

Hall, David S; Lockwood, David J; Poirier, Shawn; Bock, Christina; MacDougall, Barry R

2012-06-28

The present work utilizes Raman and infrared (IR) spectroscopy, supported by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) to re-examine the fine structural details of Ni(OH)(2), which is a key material in many energy-related applications. This work also unifies the large body of literature on the topic. Samples were prepared by the galvanostatic basification of nickel salts and by aging the deposits in hot KOH solutions. A simplified model is presented consisting of two fundamental phases (α and β) of Ni(OH)(2) and a range of possible structural disorder arising from factors such as impurities, hydration, and crystal defects. For the first time, all of the lattice modes of β-Ni(OH)(2) have been identified and assigned using factor group analysis. Ni(OH)(2) films can be rapidly identified in pure and mixed samples using Raman or IR spectroscopy by measuring their strong O-H stretching modes, which act as fingerprints. Thus, this work establishes methods to measure the phase, or phases, and disorder at a Ni(OH)(2) sample surface and to correlate desired chemical properties to their structural origins.

Fe model predicting the increase in seismic resistance induced by the progressive FRP strengthening on already damaged masonry arches subjected to settlement

NASA Astrophysics Data System (ADS)

Stockdale, G.; Milani, G.

2017-11-01

In seismic regions, the retrofitting of masonry structures subjected to differential foundation settlements is of the upmost importance. This practice however poses significant challenges, most notably in the consideration of historical monuments where the integrity of the original structure must be weighted alongside public safety. Fiber reinforced polymers (FRPs), when appropriately applied, provide the potential to balance this duality of heritage preservation and modern safety. Using an advanced FE point of view, this work studies the seismic response of a progressive reinforcement strategy aimed at strengthening and controlling the failure mechanism for masonry arches that exist in a damaged state induced through a differential abutment settlement. A heterogeneous FE approach of a semi-circular block and mortar arch on continuously spreading supports is examined. In this model hinge formation is obtained by assigning a damage plasticity behavior to the mortar joints. Strategically placed FRPs, designed through the utilization of the Italian CNR recommendations for externally bonded FRP systems, are applied through the Abaqus birth and death approach and introduced to the spreading support model after settlement. Finally, the structural behavior of the reinforced and unreinforced models are examined for a seismic response.

Using CRANID to test the population affinity of known crania.

PubMed

Kallenberger, Lauren; Pilbrow, Varsha

2012-11-01

CRANID is a statistical program used to infer the source population of a cranium of unknown origin by comparing its cranial dimensions with a worldwide craniometric database. It has great potential for estimating ancestry in archaeological, forensic and repatriation cases. In this paper we test the validity of CRANID in classifying crania of known geographic origin. Twenty-three crania of known geographic origin but unknown sex were selected from the osteological collections of the University of Melbourne. Only 18 crania showed good statistical match with the CRANID database. Without considering accuracy of sex allocation, 11 crania were accurately classified into major geographic regions and nine were correctly classified to geographically closest available reference populations. Four of the five crania with poor statistical match were nonetheless correctly allocated to major geographical regions, although none was accurately assigned to geographically closest reference samples. We conclude that if sex allocations are overlooked, CRANID can accurately assign 39% of specimens to geographically closest matching reference samples and 48% to major geographic regions. Better source population representation may improve goodness of fit, but known sex-differentiated samples are needed to further test the utility of CRANID. © 2012 The Authors Journal of Anatomy © 2012 Anatomical Society.

Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes.

PubMed

Hvilsom, C; Frandsen, P; Børsting, C; Carlsen, F; Sallé, B; Simonsen, B T; Siegismund, H R

2013-06-01

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.

Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

PubMed Central

Hvilsom, C; Frandsen, P; Børsting, C; Carlsen, F; Sallé, B; Simonsen, B T; Siegismund, H R

2013-01-01

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies. PMID:23531981

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Millán, Judith; Basterretxea, Francisco; Fernández, José A; Castaño, Fernando

2011-04-28

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).

Unique determination of "subatomic" contrast by imaging covalent backbonding.

PubMed

Sweetman, Adam; Rahe, Philipp; Moriarty, Philip

2014-05-14

The origin of so-called "subatomic" resolution in dynamic force microscopy has remained controversial since its first observation in 2000. A number of detailed experimental and theoretical studies have identified different possible physicochemical mechanisms potentially giving rise to subatomic contrast. In this study, for the first time we are able to assign the origin of a specific instance of subatomic contrast as being due to the back bonding of a surface atom in the tip-sample junction.

Neonatal Sex Assignment in Disorders of Sex Development: A Philosophical Introspection

PubMed Central

Raveenthiran, V.

2017-01-01

Management of ambiguous genitalia is highly controversial. This condition was known previously as intersex and presently as disorders of sex development (DSD). There is no consensus regarding the choice, timing and method of sex assignment in neonates with DSD. Consensus conferences could not unify the views of various stakeholders and third parties. This article philosophically examines the nature and origin of such controversies. Misconception, bias and conflicting priorities are identified as the three cardinal sources of controversies. Conceptual duality of sexes, confused notion of sex and gender, bias towards penetrative intercourse, conflict between utopian ideals and reality, unwillingness to compromise are identified as perpetuators of controversies. Suggestions are made regarding sex assignment in various types of DSD based on the understanding of published literature and the author’s personal experience. PMID:28920018

Assigning king eiders to wintering regions in the Bering Sea using stable isotopes of feathers and claws

USGS Publications Warehouse

Oppel, S.; Powell, A.N.

2008-01-01

Identification of wintering regions for birds sampled during the breeding season is crucial to understanding how events outside the breeding season may affect populations. We assigned king eiders captured on breeding grounds in northern Alaska to 3 broad geographic wintering regions in the Bering Sea using stable carbon and nitrogen isotopes obtained from head feathers. Using a discriminant function analysis of feathers obtained from birds tracked with satellite transmitters, we estimated that 88 % of feathers were assigned to the region in which they were grown. We then assigned 84 birds of unknown origin to wintering regions based on their head feather isotope ratios, and tested the utility of claws for geographic assignment. Based on the feather results, we estimated that similar proportions of birds in our study area use each of the 3 wintering regions in the Bering Sea. These results are in close agreement with estimates from satellite telemetry and show the usefulness of stable isotope signatures of feathers in assigning marine birds to geographic regions. The use of claws is currently limited by incomplete understanding of claw growth rates. Data presented here will allow managers of eiders, other marine birds, and marine mammals to assign animals to regions in the Bering Sea based on stable isotope signatures of body tissues. ?? Inter-Research 2008.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Unifying Temporal and Structural Credit Assignment Problems

NASA Technical Reports Server (NTRS)

Agogino, Adrian K.; Tumer, Kagan

2004-01-01

Single-agent reinforcement learners in time-extended domains and multi-agent systems share a common dilemma known as the credit assignment problem. Multi-agent systems have the structural credit assignment problem of determining the contributions of a particular agent to a common task. Instead, time-extended single-agent systems have the temporal credit assignment problem of determining the contribution of a particular action to the quality of the full sequence of actions. Traditionally these two problems are considered different and are handled in separate ways. In this article we show how these two forms of the credit assignment problem are equivalent. In this unified frame-work, a single-agent Markov decision process can be broken down into a single-time-step multi-agent process. Furthermore we show that Monte-Carlo estimation or Q-learning (depending on whether the values of resulting actions in the episode are known at the time of learning) are equivalent to different agent utility functions in a multi-agent system. This equivalence shows how an often neglected issue in multi-agent systems is equivalent to a well-known deficiency in multi-time-step learning and lays the basis for solving time-extended multi-agent problems, where both credit assignment problems are present.

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.

PubMed

Lütteke, Thomas; von der Lieth, Claus-W

2004-06-04

Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported. Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.

Contact replacement for NMR resonance assignment.

PubMed

Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

2008-07-01

Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor.

PubMed Central

Fairbrother, W. J.; Champe, M. A.; Christinger, H. W.; Keyt, B. A.; Starovasnik, M. A.

1997-01-01

Nearly complete sequence-specific 1H, 13C, and 15N resonance assignments are reported for the backbone atoms of the receptor-binding domain of vascular endothelial growth factor (VEGF), a 23-kDa homodimeric protein that is a major regulator of both normal and pathological angiogenesis. The assignment strategy relied on the use of seven 3D triple-resonance experiments [HN(CO)CA, HNCA, HNCO, (HCA)CONH, HN(COCA)HA, HN(CA)HA, and CBCA-(CO)NH] and a 3D 15N-TOCSY-HSQC experiment recorded on a 0.5 mM (12 mg/mL) sample at 500 MHz, pH 7.0, 45 degrees C. Under these conditions, 15N relaxation data show that the protein has a rotational correlation time of 15.0 ns. Despite this unusually long correlation time, assignments were obtained for 94 of the 99 residues; 8 residues lack amide 1H and 15N assignments, presumably due to rapid exchange of the amide 1H with solvent under the experimental conditions used. The secondary structure of the protein was deduced from the chemical shift indices of the 1H alpha, 13C alpha, 13C beta, and 13CO nuclei, and from analysis of backbone NOEs observed in a 3D 15N-NOESY-HSQC spectrum. Two helices and a significant amount of beta-sheet structure were identified, in general agreement with the secondary structure found in a recently determined crystal structure of a similar VEGF construct [Muller YA et al., 1997, Proc Natl Acad Sci USA 94:7192-7197]. PMID:9336848

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

PubMed Central

2010-01-01

Background The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results Our results show that dispersal in C. australis is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females. PMID:20109219

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

Sadjadi, Seyedabdolreza; Zhang, Yong; Kwok, Sun, E-mail: sunkwok@hku.hk

The 3.3 μ m unidentified infrared emission feature is commonly attributed to the C–H stretching band of aromatic molecules. Astronomical observations have shown that this feature is composed of two separate bands at 3.28 and 3.30 μ m, and the origin of these two bands is unclear. In this paper, we perform vibrational analyses based on quantum mechanical calculations of 153 organic molecules, including both pure aromatic molecules and molecules with mixed aromatic/olefinic/aliphatic hydridizations. We find that many of the C–H stretching vibrational modes in polycyclic aromatic hydrocarbon (PAH) molecules are coupled. Even considering the uncoupled modes only, the correlationmore » between the band intensity ratios and the structure of the PAH molecule is not observed, and the 3.28 and 3.30 μ m features cannot be directly interpreted in the PAH model. Based on these results, the possible aromatic, olefinic, and aliphatic origins of the 3.3 μ m feature are discussed. We suggest that the 3.28 μ m feature is assigned to aromatic C–H stretch whereas the 3.30 μ m feature is olefinic. From the ratio of these two features, the relative olefinic to aromatic content of the carrier can be determined.« less

Density Functional Theory Study of Cyanoetheneselenol: A Molecule of Astrobiological Interest

NASA Astrophysics Data System (ADS)

Surajbali, P.; Ramanah, D. Kodi; Rhyman, L.; Alswaidan, I. A.; Fun, H.-K.; Somanah, R.; Ramasami, P.

2015-12-01

The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6-311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array.

Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers

PubMed Central

Paschou, Peristera

2010-01-01

Recent large-scale studies of European populations have demonstrated the existence of population genetic structure within Europe and the potential to accurately infer individual ancestry when information from hundreds of thousands of genetic markers is used. In fact, when genomewide genetic variation of European populations is projected down to a two-dimensional Principal Components Analysis plot, a surprising correlation with actual geographic coordinates of self-reported ancestry has been reported. This substructure can hamper the search of susceptibility genes for common complex disorders leading to spurious correlations. The identification of genetic markers that can correct for population stratification becomes therefore of paramount importance. Analyzing 1,200 individuals from 11 populations genotyped for more than 500,000 SNPs (Population Reference Sample), we present a systematic exploration of the extent to which geographic coordinates of origin within Europe can be predicted, with small panels of SNPs. Markers are selected to correlate with the top principal components of the dataset, as we have previously demonstrated. Performing thorough cross-validation experiments we show that it is indeed possible to predict individual ancestry within Europe down to a few hundred kilometers from actual individual origin, using information from carefully selected panels of 500 or 1,000 SNPs. Furthermore, we show that these panels can be used to correctly assign the HapMap Phase 3 European populations to their geographic origin. The SNPs that we propose can prove extremely useful in a variety of different settings, such as stratification correction or genetic ancestry testing, and the study of the history of European populations. PMID:20805874

SEM, EDX and Raman and infrared spectroscopic study of brianyoungite Zn3(CO3,SO4)(OH)4 from Esperanza Mine, Laurion District, Greece

NASA Astrophysics Data System (ADS)

Frost, Ray L.; López, Andrés; Wang, Lina; Scholz, Ricardo; Sampaio, Ney Pinheiro

2015-10-01

The mineral brianyoungite, a carbonate-sulphate of zinc, has been studied by scanning electron microscopy (SEM) with chemical analysis using energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Multiple carbonate stretching modes are observed and support the concept of non-equivalent carbonate units in the brianyoungite structure. Intense Raman band at 1056 cm-1 with shoulder band at 1038 cm-1 is assigned to the CO32- ν1 symmetric stretching mode. Two intense Raman bands at 973 and 984 cm-1 are assigned to the symmetric stretching modes of the SO42- anion. The observation of two bands supports the concept of the non-equivalence of sulphate units in the brianyoungite structure. Raman bands at 704 and 736 cm-1 are assigned to the CO32- ν4 bending modes and Raman bands at 507, 528, 609 and 638 cm-1 are assigned to the CO32- ν2 bending modes. Multiple Raman and infrared bands in the OH stretching region are observed, proving the existence of water and hydroxyl units in different molecular environments in the structure of brianyoungite. Vibrational spectroscopy enhances our knowledge of the molecular structure of brianyoungite.

9 CFR 327.15 - Outside containers of foreign products; marking and labeling; application of official inspection...

Code of Federal Regulations, 2010 CFR

2010-01-01

... to the United States shall bear, in English, in a prominent and legible manner: (1) The name or... country of origin; and (3) The establishment number assigned by the foreign meat inspection system and...

7 CFR 2.24 - Assistant Secretary for Administration.

Code of Federal Regulations, 2010 CFR

2010-01-01

.... (iii) Maintain overall responsibility and control over the Hearing Clerk's activities which include the custody of and responsibility for the control, maintenance, and servicing of the original and permanent..., maintaining, and disposing of real and personal property, including control of space assignments; (B...

50 CFR Table 31 to Part 679 - List of Amendment 80 Vessels and LLP Licenses Originally Assigned to an Amendment 80 Vessel

Code of Federal Regulations, 2010 CFR

2010-10-01

... FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 679, Table 31 Table 31 to Part...

49 CFR 599.200 - Registration of participating dealers.

Code of Federal Regulations, 2011 CFR

2011-10-01

... franchise agreement to sell new automobiles with an original equipment manufacturer of automobiles; (4) A...) Dealer's Federal Tax Identification Number (TIN) and OEM assigned dealer franchise number; (ii) Legal.... (e) Revocation of Dealer Registration. (1) Termination or Discontinuance of Franchise. (i) A dealer...

49 CFR 599.200 - Registration of participating dealers.

Code of Federal Regulations, 2013 CFR

2013-10-01

... franchise agreement to sell new automobiles with an original equipment manufacturer of automobiles; (4) A...) Dealer's Federal Tax Identification Number (TIN) and OEM assigned dealer franchise number; (ii) Legal.... (e) Revocation of Dealer Registration. (1) Termination or Discontinuance of Franchise. (i) A dealer...

49 CFR 599.200 - Registration of participating dealers.

Code of Federal Regulations, 2010 CFR

2010-10-01

... franchise agreement to sell new automobiles with an original equipment manufacturer of automobiles; (4) A...) Dealer's Federal Tax Identification Number (TIN) and OEM assigned dealer franchise number; (ii) Legal.... (e) Revocation of Dealer Registration. (1) Termination or Discontinuance of Franchise. (i) A dealer...

49 CFR 599.200 - Registration of participating dealers.

Code of Federal Regulations, 2014 CFR

2014-10-01

... franchise agreement to sell new automobiles with an original equipment manufacturer of automobiles; (4) A...) Dealer's Federal Tax Identification Number (TIN) and OEM assigned dealer franchise number; (ii) Legal.... (e) Revocation of Dealer Registration. (1) Termination or Discontinuance of Franchise. (i) A dealer...

49 CFR 599.200 - Registration of participating dealers.

Code of Federal Regulations, 2012 CFR

2012-10-01

... franchise agreement to sell new automobiles with an original equipment manufacturer of automobiles; (4) A...) Dealer's Federal Tax Identification Number (TIN) and OEM assigned dealer franchise number; (ii) Legal.... (e) Revocation of Dealer Registration. (1) Termination or Discontinuance of Franchise. (i) A dealer...

Drug-induced uveitis

PubMed Central

2013-01-01

A number of medications have been associated with uveitis. This review highlights both well-established and recently reported systemic, topical, intraocular, and vaccine-associated causes of drug-induced uveitis, and assigns a quantitative score to each medication based upon criteria originally described by Naranjo and associates. PMID:23522744

Cross-cultural adaptation of the Health Education Impact Questionnaire: experimental study showed expert committee, not back-translation, added value.

PubMed

Epstein, Jonathan; Osborne, Richard H; Elsworth, Gerald R; Beaton, Dorcas E; Guillemin, Francis

2015-04-01

To assess the contribution of back-translation and expert committee to the content and psychometric properties of a translated multidimensional questionnaire. Recommendations for questionnaire translation include back-translation and expert committee, but their contribution to measurement properties is unknown. Four English to French translations of the Health Education Impact Questionnaire were generated with and without committee or back-translation. Face validity, acceptability, and structural properties were compared after random assignment to people with rheumatoid arthritis (N = 1,168), chronic renal failure (N = 2,368), and diabetes (N = 538). For face validity, 15 bilingual people compared translations quality with the original. Psychometric properties were examined using confirmatory factor analysis (metric and scalar invariance) and item response theory. Qualitatively, there were five types of translation errors: style, intensity, frequency/time frame, breadth, and meaning. Bilingual assessors ranked best the translations with committee (P = 0.0026). All translations had good structural properties (root mean square error of approximation <0.05; comparative fit index [CFI], ≥0.899; and Tucker-Lewis index, ≥0.889). Full measurement invariance was observed between translations (ΔCFI ≤ 0.01) with metric invariance between translations and original (lowest ΔCFI = 0.022 between fully constrained models and models with free intercepts). Item characteristic curve analyses revealed no significant differences. This is the first experimental evidence that back-translation has moderate impact, whereas expert committee helps to ensure accurate content. Copyright © 2015 Elsevier Inc. All rights reserved.

Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

PubMed Central

2009-01-01

Background Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture. Results Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates. Conclusion The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations. PMID:19538757

The Same or Separate? An Exploration of Teachers' Perceptions of the Classroom Assignment of Twins in Prior to School and Kindergarten to Year Two School Settings

ERIC Educational Resources Information Center

Jones, Laura; De Gioia, Katey

2010-01-01

This article investigates the perceptions of 12 teachers from New South Wales, Australia, regarding the classroom assignment of twins. Analysis of semi-structured interviews with each of the teachers revealed four key findings: 1) teachers' perceptions about the classroom assignment of twins vary according to their previous experience and…

Case Study: A Step-by-Step Guide to Students Writing Case Studies (and Tools for Novice Case Authors)

ERIC Educational Resources Information Center

Prud'homme-Genereux, Annie

2015-01-01

In experimenting with ways of structuring the assignment and providing guidance to students, the author developed a series of tools that may be of interest to instructors wishing to implement a case-writing assignment in their course. This assignment is more suited for instructors experienced in case writing, as their knowledge of how to design a…

Epoxy-based hydrogels investigated by high-frequency dielectric relaxation spectroscopy.

PubMed

Krakovský, Ivan; Shikata, Toshiyuki; Hasegawa, Ryuta

2013-11-14

Using high-frequency dielectric relaxation spectroscopy, nanophase-separated structures of epoxy-based hydrogels were investigated as a function of water content at 25 °C. The dielectric spectra resulting from the hydrogels were reasonably decomposed into two Debye-type and two Cole-Cole-type relaxation modes. The fastest Debye-type mode, found at 8.3 ps, was attributed to the rotational relaxation process of free water molecules in the bulk state. The other Debye-type mode, at ca. 20-34 ps, originates from the exchange process of water molecules that are hydrogen-bonded to the hydrophilic epoxy network portions for free bulk ones. The first Cole-Cole-type mode observed, at ca. 20-370 ps, was assigned to the complicated dynamics for electric dipole moments of the hydrophilic groups in the epoxy networks (mainly monomeric oxyethylene units). The slowest major Cole-Cole-type mode, at 5-29 ns, was attributed to the Maxwell-Wagner-Sillars polarization process and confirmed the presence of the nanophase-separated structures as revealed by the previous small-angle neutron scattering experiments.

Infrared and Raman Study of the Recluse Spider Silk

NASA Astrophysics Data System (ADS)

Wang, S. L.; Wang, Qijue; Xing, Zhen; Schniepp, H. C.; Qazilbash, M. M.

Spider silk exhibits remarkable mechanical properties, such as high tensile strength and toughness. We want to gain insight into the composition and structure of spider silk to discover the origin of these properties. We are especially interested in the organization of the crystalline beta sheets that are expected to contribute to the high strength of the silk from the recluse spider, Loxosceles laeta. The recluse spider produces a silk that has a unique geometry amongst arachnids. We measure the silk's optical properties, particularly the infrared-active and Raman-active vibrations. Broadband infrared transmission spectra were collected in the spectral range between 600 cm-1 and 4000 cm-1, with light polarized parallel and perpendicular to the long axis of the silk. Raman micro-spectroscopy was performed in the spectral range 500 cm-1 and 4000 cm- 1 with a 514 nm laser. The infrared and Raman vibrational modes are fit with Lorentzian and pseudo-Voigt functions. The vibrational modes are assigned to specific structures and electronic bonds in the silk. This work was supported by NASA/ Virginia Space Grant Consortium.

Factor Structure, Internal Consistency, and Screening Sensitivity of the GARS-2 in a Developmental Disabilities Sample

PubMed Central

Volker, Martin A.; Dua, Elissa H.; Lopata, Christopher; Thomeer, Marcus L.; Toomey, Jennifer A.; Smerbeck, Audrey M.; Rodgers, Jonathan D.; Popkin, Joshua R.; Nelson, Andrew T.; Lee, Gloria K.

2016-01-01

The Gilliam Autism Rating Scale-Second Edition (GARS-2) is a widely used screening instrument that assists in the identification and diagnosis of autism. The purpose of this study was to examine the factor structure, internal consistency, and screening sensitivity of the GARS-2 using ratings from special education teaching staff for a sample of 240 individuals with autism or other significant developmental disabilities. Exploratory factor analysis yielded a correlated three-factor solution similar to that found in 2005 by Lecavalier for the original GARS. Though the three factors appeared to be reasonably consistent with the intended constructs of the three GARS-2 subscales, the analysis indicated that more than a third of the GARS-2 items were assigned to the wrong subscale. Internal consistency estimates met or exceeded standards for screening and were generally higher than those in previous studies. Screening sensitivity was .65 and specificity was .81 for the Autism Index using a cut score of 85. Based on these findings, recommendations are made for instrument revision. PMID:26981279

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

Bréchignac, Philippe, E-mail: philippe.brechignac@u-psud.fr; Falvo, Cyril; Parneix, Pascal

Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail.more » Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory.« less

Operation Market Garden: Case Study for Analyzing Senior Leader Responsibilities

DTIC Science & Technology

2009-05-04

late-July 1944 Brest Undetermined Seize ports TRANSFIGURE 17 August 1944 Paris - Orleans gap 101st (US), 1st (UK), Polish BDE Trap 7th Army (German...committed to more than one full lift per day. Had troop carrier forces been committed as was originally intended, i.e., to make a quick turn around to...mission assigned to us in the original plan.”28 While his airborne divisions fought as hard and held out as long as they were capable of doing, their

Sequential /sup 1/H NMR assignments and secondary structure of hen egg white lysozyme in solution

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

Redfield, C.; Dobson, C.M.

Assignments of /sup 1/H NMR resonances of 121 of the 129 residues of hen egg white lysozyme have been obtained by sequence-specific methods. Spin systems were identified with phase-sensitive two-dimensional (2-D) correlated spectroscopy and single and double relayed coherence transfer spectroscopy. For key types of amino acid residues, particularly alanine, threonine, valine, and glycine, complete spin systems were identified. For other residues a less complete definition of the spin system was found to be adequate for the purpose of sequential assignment. Sequence-specific assignments were achieved by phase-sensitive 2-D nuclear Overhauser enhancement spectroscopy (NOESY). Exploitation of the wide range of hydrogenmore » exchange rates found in lysozyme was a useful approach to overcoming the problem of spectral overlap. The sequential assignment was built up from 21 peptide segments ranging in length from 2 to 13 residues. The NOESY spectra were also used to provide information about the secondary structure of the protein in solution. Three helical regions and two regions of ..beta..-sheet were identified from the NOESY data; these regions are identical with those found in the X-ray structure of hen lysozyme. Slowly exchanging amides are generally correlated with hydrogen bonding identified in the X-ray structure; a number of exceptions to this general trend were, however, found. The results presented in this paper indicate that highly detailed information can be obtained from 2-D NMR spectra of a protein that is significantly larger than those studies previously.« less

Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking

USGS Publications Warehouse

White, Shannon L.; Miller, William L.; Dowell, Stephanie A.; Bartron, Meredith L.; Wagner, Tyler

2018-01-01

Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive‐raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long‐term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential, and contribute to local population extirpation. However, low survival and fitness of captive‐raised individuals can minimize the long‐term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed, and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive‐raised) for 1742 wild‐caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild‐caught individuals probabilistically assigned to wild origin, and only 5.6% of wild‐caught fish assigned to introgressed. Models examining environmental drivers of introgression explained less than 3% of the among‐population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery‐derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.

Synchrotron Spectroscopy and Torsional Structure of the Csh-Bending and CH3-ROCKING Bands of Methyl Mercaptan

NASA Astrophysics Data System (ADS)

Lees, Ronald M.; Xu, Li-Hong; Billinghurst, Brant E.

2016-06-01

The Fourier transform spectra of the CSH-bending and CH3-rocking infrared bands of CH3SH have been investigated at 0.001 cm-1 resolution employing synchrotron radiation at the Canadian Light Source in Saskatoon. The relative band strengths and structures are remarkably different from those for the analogous CH3OH relative, with the CSH bend being very weak and both the in-plane and out-of-plane CH3 rocks being strong with comparable intensities. The CSH bend, centered at 801.5 cm-1, has parallel a-type character with no detectable b-type component. The out-of-plane CH3 rock at 957.0 cm-1 is a purely c-type perpendicular band, whereas the in-plane rock around 1074 cm-1 is of mixed a/b character. The K-reduced vt = 0 sub-state origins for the CSH bend follow the normal oscillatory torsional pattern as a function of K with an amplitude of 0.362 cm-1, as compared to 0.653 cm-1 for the ground state and 0.801 cm-1 for the C-S stretching mode. The torsional energy curves for the out-of-plane rock are also well-behaved but are inverted, with an amplitude of 1.33 cm-1. In contrast, the sub-state origins for the in-plane rock do not display a clear oscillatory structure but are scattered over a range of about 2 cm-1, with indications of some significant perturbations. The assignments for the three bands all extend up to about K = 10 and are well-determined from GSCD relations, particularly for the a/b in-plane rock for which ΔK = 0, +1 and -1 transitions are all observed.

Multimodal analysis of pretreated biomass species highlights generic markers of lignocellulose recalcitrance.

PubMed

Herbaut, Mickaël; Zoghlami, Aya; Habrant, Anouck; Falourd, Xavier; Foucat, Loïc; Chabbert, Brigitte; Paës, Gabriel

2018-01-01

Biomass recalcitrance to enzymatic hydrolysis has been assigned to several structural and chemical factors. However, their relative importance remains challenging to evaluate. Three representative biomass species (wheat straw, poplar and miscanthus) were submitted to four standard pretreatments (dilute acid, hot water, ionic liquid and sodium chlorite) in order to generate a set of contrasted samples. A large array of techniques, including wet chemistry analysis, porosity measurements using NMR spectroscopy, electron and fluorescence microscopy, were used in order to determine possible generic factors of biomass recalcitrance. The pretreatment conditions selected allowed obtaining samples displaying different susceptibility to enzymatic hydrolysis (from 3 up to 98% of the initial glucose content released after 96 h of saccharification). Generic correlation coefficients were calculated between the measured chemical and structural features and the final saccharification rates. Increases in porosity displayed overall strong positive correlations with saccharification efficiency, but different porosity ranges were concerned depending on the considered biomass. Lignin-related factors displayed highly negative coefficients for all biomasses. Lignin content, which is likely involved in the correlations observed for porosity, was less detrimental to enzymatic hydrolysis than lignin composition. Lignin influence was highlighted by the strong negative correlation with fluorescence intensity which mainly originates from monolignols in mature tissues. Our results provide a better understanding of the factors responsible for biomass recalcitrance that can reasonably be considered as generic. The correlations with specific porosity ranges are biomass species-dependent, meaning that enzymes cocktails with fitted enzyme size are likely to be needed to optimise saccharification depending on the biomass origin. Lignin composition, which probably influences its structure, is the most important parameter to overcome to enhance enzymes access to the polysaccharides. Accordingly, fluorescence intensity was found to be a rapid and simple method to assess recalcitrance after pretreatment.

Structural confirmation of regioisomers of Lopinavir impurities using MS and gradient COSY (1H and 13C NMR assignment of Lopinavir impurities).

PubMed

Siva Lakshmi Devi, A; Srinivasa Rao, Y; Suresh, Y; Yogeswar Reddy, M; Jyothi, G; Rajababu, B; Prasad, V S R; Umamaheswar Rao, V

2007-05-01

We report the complete (1)H and (13)C NMR assignment of impurities of six Lopinavir (2S)-N-[(2S, 4S, 5S)-5-{[2-(2,6-dimethylphenoxy)acetyl]amino}-4-hydroxy-1,6-diphenyl hexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butan- amide. Two of the impurities are regioisomers and GCOSY used to differentiate the two structures. The spectral assignments for all six impurities were achieved by concerted application of one and two-dimensional NMR techniques ((1)H NMR, (13)C NMR, DEPT, GCOSY, GHSQC and GHMBC). Copyright (c) 2007 John Wiley & Sons, Ltd.

Vibrational spectroscopic study of the antimonate mineral bindheimite Pb 2Sb 2O 6(O,OH)

NASA Astrophysics Data System (ADS)

Bahfenne, Silmarilly; Frost, Ray L.

2009-09-01

Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the antimonate mineral bindheimite Pb 2Sb 2O 6(O,OH). The mineral is characterised by an intense Raman band at 656 cm -1 assigned to SbO stretching vibrations. Other lower intensity bands at 664, 749 and 814 cm -1 are also assigned to stretching vibrations. This observation suggests the non-equivalence of SbO units in the structure. Low intensity Raman bands at 293, 312 and 328 cm -1 are assigned to the OSbO bending vibrations. Infrared bands at 979, 1008, 1037 and 1058 cm -1 may be assigned to δOH deformation modes of SbOH units. Infrared bands at 1603 and 1640 cm -1 are assigned to water bending vibrations, suggesting that water is involved in the bindheimite structure. Broad infrared bands centred upon 3250 cm -1 supports this concept. Thus the true formula of bindheimite is questioned and probably should be written as Pb 2Sb 2O 6(O,OH,H 2O).

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

PubMed

Turcot, Valérie; Lu, Yingchang; Highland, Heather M; Schurmann, Claudia; Justice, Anne E; Fine, Rebecca S; Bradfield, Jonathan P; Esko, Tõnu; Giri, Ayush; Graff, Mariaelisa; Guo, Xiuqing; Hendricks, Audrey E; Karaderi, Tugce; Lempradl, Adelheid; Locke, Adam E; Mahajan, Anubha; Marouli, Eirini; Sivapalaratnam, Suthesh; Young, Kristin L; Alfred, Tamuno; Feitosa, Mary F; Masca, Nicholas G D; Manning, Alisa K; Medina-Gomez, Carolina; Mudgal, Poorva; Ng, Maggie C Y; Reiner, Alex P; Vedantam, Sailaja; Willems, Sara M; Winkler, Thomas W; Abecasis, Gonçalo; Aben, Katja K; Alam, Dewan S; Alharthi, Sameer E; Allison, Matthew; Amouyel, Philippe; Asselbergs, Folkert W; Auer, Paul L; Balkau, Beverley; Bang, Lia E; Barroso, Inês; Bastarache, Lisa; Benn, Marianne; Bergmann, Sven; Bielak, Lawrence F; Blüher, Matthias; Boehnke, Michael; Boeing, Heiner; Boerwinkle, Eric; Böger, Carsten A; Bork-Jensen, Jette; Bots, Michiel L; Bottinger, Erwin P; Bowden, Donald W; Brandslund, Ivan; Breen, Gerome; Brilliant, Murray H; Broer, Linda; Brumat, Marco; Burt, Amber A; Butterworth, Adam S; Campbell, Peter T; Cappellani, Stefania; Carey, David J; Catamo, Eulalia; Caulfield, Mark J; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der I; Chowdhury, Rajiv; Christensen, Cramer; Chu, Audrey Y; Cocca, Massimiliano; Collins, Francis S; Cook, James P; Corley, Janie; Corominas Galbany, Jordi; Cox, Amanda J; Crosslin, David S; Cuellar-Partida, Gabriel; D'Eustacchio, Angela; Danesh, John; Davies, Gail; Bakker, Paul I W; Groot, Mark C H; Mutsert, Renée; Deary, Ian J; Dedoussis, George; Demerath, Ellen W; Heijer, Martin; Hollander, Anneke I; Ruijter, Hester M; Dennis, Joe G; Denny, Josh C; Di Angelantonio, Emanuele; Drenos, Fotios; Du, Mengmeng; Dubé, Marie-Pierre; Dunning, Alison M; Easton, Douglas F; Edwards, Todd L; Ellinghaus, David; Ellinor, Patrick T; Elliott, Paul; Evangelou, Evangelos; Farmaki, Aliki-Eleni; Farooqi, I Sadaf; Faul, Jessica D; Fauser, Sascha; Feng, Shuang; Ferrannini, Ele; Ferrieres, Jean; Florez, Jose C; Ford, Ian; Fornage, Myriam; Franco, Oscar H; Franke, Andre; Franks, Paul W; Friedrich, Nele; Frikke-Schmidt, Ruth; Galesloot, Tessel E; Gan, Wei; Gandin, Ilaria; Gasparini, Paolo; Gibson, Jane; Giedraitis, Vilmantas; Gjesing, Anette P; Gordon-Larsen, Penny; Gorski, Mathias; Grabe, Hans-Jörgen; Grant, Struan F A; Grarup, Niels; Griffiths, Helen L; Grove, Megan L; Gudnason, Vilmundur; Gustafsson, Stefan; Haessler, Jeff; Hakonarson, Hakon; Hammerschlag, Anke R; Hansen, Torben; Harris, Kathleen Mullan; Harris, Tamara B; Hattersley, Andrew T; Have, Christian T; Hayward, Caroline; He, Liang; Heard-Costa, Nancy L; Heath, Andrew C; Heid, Iris M; Helgeland, Øyvind; Hernesniemi, Jussi; Hewitt, Alex W; Holmen, Oddgeir L; Hovingh, G Kees; Howson, Joanna M M; Hu, Yao; Huang, Paul L; Huffman, Jennifer E; Ikram, M Arfan; Ingelsson, Erik; Jackson, Anne U; Jansson, Jan-Håkan; Jarvik, Gail P; Jensen, Gorm B; Jia, Yucheng; Johansson, Stefan; Jørgensen, Marit E; Jørgensen, Torben; Jukema, J Wouter; Kahali, Bratati; Kahn, René S; Kähönen, Mika; Kamstrup, Pia R; Kanoni, Stavroula; Kaprio, Jaakko; Karaleftheri, Maria; Kardia, Sharon L R; Karpe, Fredrik; Kathiresan, Sekar; Kee, Frank; Kiemeney, Lambertus A; Kim, Eric; Kitajima, Hidetoshi; Komulainen, Pirjo; Kooner, Jaspal S; Kooperberg, Charles; Korhonen, Tellervo; Kovacs, Peter; Kuivaniemi, Helena; Kutalik, Zoltán; Kuulasmaa, Kari; Kuusisto, Johanna; Laakso, Markku; Lakka, Timo A; Lamparter, David; Lange, Ethan M; Lange, Leslie A; Langenberg, Claudia; Larson, Eric B; Lee, Nanette R; Lehtimäki, Terho; Lewis, Cora E; Li, Huaixing; Li, Jin; Li-Gao, Ruifang; Lin, Honghuang; Lin, Keng-Hung; Lin, Li-An; Lin, Xu; Lind, Lars; Lindström, Jaana; Linneberg, Allan; Liu, Ching-Ti; Liu, Dajiang J; Liu, Yongmei; Lo, Ken S; Lophatananon, Artitaya; Lotery, Andrew J; Loukola, Anu; Luan, Jian'an; Lubitz, Steven A; Lyytikäinen, Leo-Pekka; Männistö, Satu; Marenne, Gaëlle; Mazul, Angela L; McCarthy, Mark I; McKean-Cowdin, Roberta; Medland, Sarah E; Meidtner, Karina; Milani, Lili; Mistry, Vanisha; Mitchell, Paul; Mohlke, Karen L; Moilanen, Leena; Moitry, Marie; Montgomery, Grant W; Mook-Kanamori, Dennis O; Moore, Carmel; Mori, Trevor A; Morris, Andrew D; Morris, Andrew P; Müller-Nurasyid, Martina; Munroe, Patricia B; Nalls, Mike A; Narisu, Narisu; Nelson, Christopher P; Neville, Matt; Nielsen, Sune F; Nikus, Kjell; Njølstad, Pål R; Nordestgaard, Børge G; Nyholt, Dale R; O'Connel, Jeffrey R; O'Donoghue, Michelle L; Olde Loohuis, Loes M; Ophoff, Roel A; Owen, Katharine R; Packard, Chris J; Padmanabhan, Sandosh; Palmer, Colin N A; Palmer, Nicholette D; Pasterkamp, Gerard; Patel, Aniruddh P; Pattie, Alison; Pedersen, Oluf; Peissig, Peggy L; Peloso, Gina M; Pennell, Craig E; Perola, Markus; Perry, James A; Perry, John R B; Pers, Tune H; Person, Thomas N; Peters, Annette; Petersen, Eva R B; Peyser, Patricia A; Pirie, Ailith; Polasek, Ozren; Polderman, Tinca J; Puolijoki, Hannu; Raitakari, Olli T; Rasheed, Asif; Rauramaa, Rainer; Reilly, Dermot F; Renström, Frida; Rheinberger, Myriam; Ridker, Paul M; Rioux, John D; Rivas, Manuel A; Roberts, David J; Robertson, Neil R; Robino, Antonietta; Rolandsson, Olov; Rudan, Igor; Ruth, Katherine S; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J; Sapkota, Yadav; Sattar, Naveed; Schoen, Robert E; Schreiner, Pamela J; Schulze, Matthias B; Scott, Robert A; Segura-Lepe, Marcelo P; Shah, Svati H; Sheu, Wayne H-H; Sim, Xueling; Slater, Andrew J; Small, Kerrin S; Smith, Albert V; Southam, Lorraine; Spector, Timothy D; Speliotes, Elizabeth K; Starr, John M; Stefansson, Kari; Steinthorsdottir, Valgerdur; Stirrups, Kathleen E; Strauch, Konstantin; Stringham, Heather M; Stumvoll, Michael; Sun, Liang; Surendran, Praveen; Swift, Amy J; Tada, Hayato; Tansey, Katherine E; Tardif, Jean-Claude; Taylor, Kent D; Teumer, Alexander; Thompson, Deborah J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Thuesen, Betina H; Tönjes, Anke; Tromp, Gerard; Trompet, Stella; Tsafantakis, Emmanouil; Tuomilehto, Jaakko; Tybjaerg-Hansen, Anne; Tyrer, Jonathan P; Uher, Rudolf; Uitterlinden, André G; Uusitupa, Matti; Laan, Sander W; Duijn, Cornelia M; Leeuwen, Nienke; van Setten, Jessica; Vanhala, Mauno; Varbo, Anette; Varga, Tibor V; Varma, Rohit; Velez Edwards, Digna R; Vermeulen, Sita H; Veronesi, Giovanni; Vestergaard, Henrik; Vitart, Veronique; Vogt, Thomas F; Völker, Uwe; Vuckovic, Dragana; Wagenknecht, Lynne E; Walker, Mark; Wallentin, Lars; Wang, Feijie; Wang, Carol A; Wang, Shuai; Wang, Yiqin; Ware, Erin B; Wareham, Nicholas J; Warren, Helen R; Waterworth, Dawn M; Wessel, Jennifer; White, Harvey D; Willer, Cristen J; Wilson, James G; Witte, Daniel R; Wood, Andrew R; Wu, Ying; Yaghootkar, Hanieh; Yao, Jie; Yao, Pang; Yerges-Armstrong, Laura M; Young, Robin; Zeggini, Eleftheria; Zhan, Xiaowei; Zhang, Weihua; Zhao, Jing Hua; Zhao, Wei; Zhao, Wei; Zhou, Wei; Zondervan, Krina T; Rotter, Jerome I; Pospisilik, John A; Rivadeneira, Fernando; Borecki, Ingrid B; Deloukas, Panos; Frayling, Timothy M; Lettre, Guillaume; North, Kari E; Lindgren, Cecilia M; Hirschhorn, Joel N; Loos, Ruth J F

2018-05-01

In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA) was incorrectly assigned to author Wei Zhou. The errors have been corrected in the HTML and PDF versions of the article.

Improved tissue assignment using dual-energy computed tomography in low-dose rate prostate brachytherapy for Monte Carlo dose calculation

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

Côté, Nicolas; Bedwani, Stéphane; Carrier, Jean-François, E-mail: jean-francois.carrier.chum@ssss.gouv.qc.ca

Purpose: An improvement in tissue assignment for low-dose rate brachytherapy (LDRB) patients using more accurate Monte Carlo (MC) dose calculation was accomplished with a metallic artifact reduction (MAR) method specific to dual-energy computed tomography (DECT). Methods: The proposed MAR algorithm followed a four-step procedure. The first step involved applying a weighted blend of both DECT scans (I {sub H/L}) to generate a new image (I {sub Mix}). This action minimized Hounsfield unit (HU) variations surrounding the brachytherapy seeds. In the second step, the mean HU of the prostate in I {sub Mix} was calculated and shifted toward the mean HUmore » of the two original DECT images (I {sub H/L}). The third step involved smoothing the newly shifted I {sub Mix} and the two original I {sub H/L}, followed by a subtraction of both, generating an image that represented the metallic artifact (I {sub A,(H/L)}) of reduced noise levels. The final step consisted of subtracting the original I {sub H/L} from the newly generated I {sub A,(H/L)} and obtaining a final image corrected for metallic artifacts. Following the completion of the algorithm, a DECT stoichiometric method was used to extract the relative electronic density (ρ{sub e}) and effective atomic number (Z {sub eff}) at each voxel of the corrected scans. Tissue assignment could then be determined with these two newly acquired physical parameters. Each voxel was assigned the tissue bearing the closest resemblance in terms of ρ{sub e} and Z {sub eff}, comparing with values from the ICRU 42 database. A MC study was then performed to compare the dosimetric impacts of alternative MAR algorithms. Results: An improvement in tissue assignment was observed with the DECT MAR algorithm, compared to the single-energy computed tomography (SECT) approach. In a phantom study, tissue misassignment was found to reach 0.05% of voxels using the DECT approach, compared with 0.40% using the SECT method. Comparison of the DECT and SECT D {sub 90} dose parameter (volume receiving 90% of the dose) indicated that D {sub 90} could be underestimated by up to 2.3% using the SECT method. Conclusions: The DECT MAR approach is a simple alternative to reduce metallic artifacts found in LDRB patient scans. Images can be processed quickly and do not require the determination of x-ray spectra. Substantial information on density and atomic number can also be obtained. Furthermore, calcifications within the prostate are detected by the tissue assignment algorithm. This enables more accurate, patient-specific MC dose calculations.« less

A review of the volatiles from the healthy human body.

PubMed

de Lacy Costello, B; Amann, A; Al-Kateb, H; Flynn, C; Filipiak, W; Khalid, T; Osborne, D; Ratcliffe, N M

2014-03-01

A compendium of all the volatile organic compounds (VOCs) emanating from the human body (the volatolome) is for the first time reported. 1840 VOCs have been assigned from breath (872), saliva (359), blood (154), milk (256), skin secretions (532) urine (279), and faeces (381) in apparently healthy individuals. Compounds were assigned CAS registry numbers and named according to a common convention where possible. The compounds have been grouped into tables according to their chemical class or functionality to permit easy comparison. Some clear differences are observed, for instance, a lack of esters in urine with a high number in faeces. Careful use of the database is needed. The numbers may not be a true reflection of the actual VOCs present from each bodily excretion. The lack of a compound could be due to the techniques used or reflect the intensity of effort e.g. there are few publications on VOCs from blood compared to a large number on VOCs in breath. The large number of volatiles reported from skin is partly due to the methodologies used, e.g. collecting excretions on glass beads and then heating to desorb VOCs. All compounds have been included as reported (unless there was a clear discrepancy between name and chemical structure), but there may be some mistaken assignations arising from the original publications, particularly for isomers. It is the authors' intention that this database will not only be a useful database of VOCs listed in the literature, but will stimulate further study of VOCs from healthy individuals. Establishing a list of volatiles emanating from healthy individuals and increased understanding of VOC metabolic pathways is an important step for differentiating between diseases using VOCs.

Exploring total cardiac variability in healthy and pathophysiological subjects using improved refined multiscale entropy.

PubMed

Marwaha, Puneeta; Sunkaria, Ramesh Kumar

2017-02-01

Multiscale entropy (MSE) and refined multiscale entropy (RMSE) techniques are being widely used to evaluate the complexity of a time series across multiple time scales 't'. Both these techniques, at certain time scales (sometimes for the entire time scales, in the case of RMSE), assign higher entropy to the HRV time series of certain pathologies than that of healthy subjects, and to their corresponding randomized surrogate time series. This incorrect assessment of signal complexity may be due to the fact that these techniques suffer from the following limitations: (1) threshold value 'r' is updated as a function of long-term standard deviation and hence unable to explore the short-term variability as well as substantial variability inherited in beat-to-beat fluctuations of long-term HRV time series. (2) In RMSE, entropy values assigned to different filtered scaled time series are the result of changes in variance, but do not completely reflect the real structural organization inherited in original time series. In the present work, we propose an improved RMSE (I-RMSE) technique by introducing a new procedure to set the threshold value by taking into account the period-to-period variability inherited in a signal and evaluated it on simulated and real HRV database. The proposed I-RMSE assigns higher entropy to the age-matched healthy subjects than that of patients suffering from atrial fibrillation, congestive heart failure, sudden cardiac death and diabetes mellitus, for the entire time scales. The results strongly support the reduction in complexity of HRV time series in female group, old-aged, patients suffering from severe cardiovascular and non-cardiovascular diseases, and in their corresponding surrogate time series.

The PAH Emission Characteristics of the Reflection Nebula NGC 2023

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

Peeters, Els; Bauschlicher, Charles W. Jr.; Allamandola, Louis J.

We present 5–20 μ m spectral maps of the reflection nebula NGC 2023 obtained with the Infrared Spectrograph SL and SH modes on board the Spitzer Space Telescope, which reveal emission from polycyclic aromatic hydrocarbons (PAHs), C{sub 60}, and H{sub 2} superposed on a dust continuum. We show that several PAH emission bands correlate with each other and exhibit distinct spatial distributions that reveal a spatial sequence with distance from the illuminating star. We explore the distinct morphology of the 6.2, 7.7, and 8.6 μ m PAH bands and find that at least two spatially distinct components contribute to themore » 7–9 μ m PAH emission in NGC 2023. We report that the PAH features behave independently of the underlying plateaus. We present spectra of compact, oval PAHs ranging in size from C{sub 66} to C{sub 210}, determined computationally using density functional theory, and we investigate trends in the band positions and relative intensities as a function of PAH size, charge, and geometry. Based on the NASA Ames PAH database, we discuss the 7–9 μ m components in terms of band assignments and relative intensities. We assign the plateau emission to very small grains with possible contributions from PAH clusters and identify components in the 7–9 μ m emission that likely originate in these structures. Based on the assignments and the observed spatial sequence, we discuss the photochemical evolution of the interstellar PAH family as the PAHs are more and more exposed to the radiation field of the central star in the evaporative flows associated with the Photo-Dissociation Regions in NGC 2023.« less

78 FR 1101 - Hazardous Materials: Harmonization With the United Nations Recommendations on the Transport of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-07

... packaging maintains an equivalent level of performance to the originally tested packaging design must be... material, packing group assignments, special provisions, packaging authorizations, packaging sections, air... responsibilities related to packaging design variation, manufacturer notification, and recordkeeping requirements...

Introduction to School Business Management.

ERIC Educational Resources Information Center

Miles, F. Mike

This chapter of "Principles of School Business Management" reviews the historical development of the school business management process and the role, responsibilities, and training of the administrators assigned to carry out the process. The origins of school management in colonial America and the subsequent growth and increasing…

28 CFR 544.101 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Library Services § 544.101 Procedures. (a) The Warden shall assign a staff member (ordinarily the Supervisor of Education) responsibility for the inmate library. (b) The inmate library shall offer an inmate... origin, staff shall attempt to provide reading materials in the inmates' language. (d) Inmate library...

28 CFR 544.101 - Procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Library Services § 544.101 Procedures. (a) The Warden shall assign a staff member (ordinarily the Supervisor of Education) responsibility for the inmate library. (b) The inmate library shall offer an inmate... origin, staff shall attempt to provide reading materials in the inmates' language. (d) Inmate library...

28 CFR 544.101 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Library Services § 544.101 Procedures. (a) The Warden shall assign a staff member (ordinarily the Supervisor of Education) responsibility for the inmate library. (b) The inmate library shall offer an inmate... origin, staff shall attempt to provide reading materials in the inmates' language. (d) Inmate library...

28 CFR 544.101 - Procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Library Services § 544.101 Procedures. (a) The Warden shall assign a staff member (ordinarily the Supervisor of Education) responsibility for the inmate library. (b) The inmate library shall offer an inmate... origin, staff shall attempt to provide reading materials in the inmates' language. (d) Inmate library...

28 CFR 544.101 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Library Services § 544.101 Procedures. (a) The Warden shall assign a staff member (ordinarily the Supervisor of Education) responsibility for the inmate library. (b) The inmate library shall offer an inmate... origin, staff shall attempt to provide reading materials in the inmates' language. (d) Inmate library...

38 CFR 3.340 - Total and permanent total ratings and unemployability.

Code of Federal Regulations, 2012 CFR

2012-07-01

... assigned, generally, for temporary exacerbations or acute infectious diseases except where specifically... any incapacity from acute infectious disease, accident, or injury, unless there is present one of the... incapacitating exacerbations since incurrence of the original disease or injury, and to periods of...

38 CFR 3.340 - Total and permanent total ratings and unemployability.

Code of Federal Regulations, 2013 CFR

2013-07-01

... assigned, generally, for temporary exacerbations or acute infectious diseases except where specifically... any incapacity from acute infectious disease, accident, or injury, unless there is present one of the... incapacitating exacerbations since incurrence of the original disease or injury, and to periods of...

38 CFR 3.340 - Total and permanent total ratings and unemployability.

Code of Federal Regulations, 2011 CFR

2011-07-01

... assigned, generally, for temporary exacerbations or acute infectious diseases except where specifically... any incapacity from acute infectious disease, accident, or injury, unless there is present one of the... incapacitating exacerbations since incurrence of the original disease or injury, and to periods of...

38 CFR 3.340 - Total and permanent total ratings and unemployability.

Code of Federal Regulations, 2014 CFR

2014-07-01

... assigned, generally, for temporary exacerbations or acute infectious diseases except where specifically... any incapacity from acute infectious disease, accident, or injury, unless there is present one of the... incapacitating exacerbations since incurrence of the original disease or injury, and to periods of...

Astronaut Gregory Jarvis during KC-135 zero gravity training

NASA Image and Video Library

1985-01-25

S85-26106 (25 Jan. 1985) --- Astronaut Gregory Jarvis gets a familiarization session in weightlessness aboard a KC-135 "zero gravity" aircraft. Jarvis was originally assigned as payload specialist to STS-51D but was reassigned to STS-51L. Photo credit: NASA

Time-series oligonucleotide count to assign antiviral siRNAs with long utility fit in the big data era.

PubMed

Wada, K; Wada, Y; Iwasaki, Y; Ikemura, T

2017-10-01

Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes. Reflecting their high mutation rates, occurrences of target oligonucleotides evidently fluctuate in viral populations and often disappear. Time-series analysis of the one-base changed sequences derived from each original target identified the oligonucleotide that shows a compensatory increase and will potentially become the 'awaiting-type oligonucleotide'; the combined use of this oligonucleotide with the original can provide therapeutics with long utility. This strategy is also useful for assigning diagnostic reverse transcription-PCR primers with long utility.

Time-series oligonucleotide count to assign antiviral siRNAs with long utility fit in the big data era

PubMed Central

Wada, K; Wada, Y; Iwasaki, Y; Ikemura, T

2017-01-01

Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes. Reflecting their high mutation rates, occurrences of target oligonucleotides evidently fluctuate in viral populations and often disappear. Time-series analysis of the one-base changed sequences derived from each original target identified the oligonucleotide that shows a compensatory increase and will potentially become the ‘awaiting-type oligonucleotide’ the combined use of this oligonucleotide with the original can provide therapeutics with long utility. This strategy is also useful for assigning diagnostic reverse transcription-PCR primers with long utility. PMID:28905886

sup 1 H assignments and secondary structure determination of the soybean trypsin/chymotrypsin Bowman-Birk inhibitor

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

Werner, M.H.; Wemmer, D.E.

1991-04-09

The {sup 1}H resonance assignments and secondary structure of the trypsin/chymotrypsin Bowman-Birk inhibitor from soybeans were determined by nuclear magnetic resonance spectroscopy (NMR) at 600 MHz in an 18% acetonitrile-d{sub 3}/aqueous cosolvent. Resonances from 69 to 71 amino acids were assigned sequence specifically. Residues Q11-T15 form an antiparallel {beta}-sheet with residues Q21-S25 in the tryptic inhibitory domain and an analogous region of antiparallel sheet forms between residues S38-A42 and Q48-V52 in the chymotryptic inhibitory domain. The inhibitory sites of each fragment (K16-S17 for trypsin, L43-S44 for chymotrypsin) are each part of a type VI like turn at one end ofmore » their respective region of the antiparallel {beta}-sheet. These structural elements are compared to those found in other Bowman-Birk inhibitors.« less

The Concept of Oxidation States in Metal Complexes

ERIC Educational Resources Information Center

Steinborn, Dirk

2004-01-01

The concepts of oxidation numbers when applied means electrons that are shared between atoms in molecules are assigned to a specific atom. Oxidation numbers are assigned from the Lewis structure of a molecule, with knowledge of the electronegativities of elements.

Relationship auditing of the FMA ontology

PubMed Central

Gu, Huanying (Helen); Wei, Duo; Mejino, Jose L.V.; Elhanan, Gai

2010-01-01

The Foundational Model of Anatomy (FMA) ontology is a domain reference ontology based on a disciplined modeling approach. Due to its large size, semantic complexity and manual data entry process, errors and inconsistencies are unavoidable and might remain within the FMA structure without detection. In this paper, we present computable methods to highlight candidate concepts for various relationship assignment errors. The process starts with locating structures formed by transitive structural relationships (part_of, tributary_of, branch_of) and examine their assignments in the context of the IS-A hierarchy. The algorithms were designed to detect five major categories of possible incorrect relationship assignments: circular, mutually exclusive, redundant, inconsistent, and missed entries. A domain expert reviewed samples of these presumptive errors to confirm the findings. Seven thousand and fifty-two presumptive errors were detected, the largest proportion related to part_of relationship assignments. The results highlight the fact that errors are unavoidable in complex ontologies and that well designed algorithms can help domain experts to focus on concepts with high likelihood of errors and maximize their effort to ensure consistency and reliability. In the future similar methods might be integrated with data entry processes to offer real-time error detection. PMID:19475727

Identification of oxidative coupling products of xylenols arising from laboratory-scale phytoremediation.

PubMed

Poerschmann, J; Schultze-Nobre, L; Ebert, R U; Górecki, T

2015-01-01

Oxidative coupling reactions take place during the passage of xylenols through a laboratory-scale helophyte-based constructed wetland system. Typical coupling product groups including tetramethyl-[1,1'-biphenyl] diols and tetramethyl diphenylether monools as stable organic intermediates could be identified by a combination of pre-chromatographic derivatization and GC/MS analysis. Structural assignment of individual analytes was performed by an increment system developed by Zenkevich to pre-calculate retention sequences. The most abundant analyte turned out to be 3,3',5,5'-tetramethyl-[1,1'-biphenyl]-4,4'-diol, which can be formed by a combination of radicals based on 2,6-xylenol or by an attack of a 2,6-xylenol-based radical on 2,6-xylenol. Organic intermediates originating from oxidative coupling could also be identified in anaerobic constructed wetland systems. This finding suggested the presence of (at least partly) oxic conditions in the rhizosphere. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

Characterizing visible and invisible cell wall mutant phenotypes

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

Carpita, Nicholas C.; McCann, Maureen C.

2015-04-06

About 10% of a plant's genome is devoted to generating the protein machinery to synthesize, remodel, and deconstruct the cell wall. High-throughput genome sequencing technologies have enabled a reasonably complete inventory of wall-related genes that can be assembled into families of common evolutionary origin. Assigning function to each gene family member has been aided immensely by identification of mutants with visible phenotypes or by chemical and spectroscopic analysis of mutants with ‘invisible’ phenotypes of modified cell wall composition and architecture that do not otherwise affect plant growth or development. This review connects the inference of gene function on the basismore » of deviation from the wild type in genetic functional analyses to insights provided by modern analytical techniques that have brought us ever closer to elucidating the sequence structures of the major polysaccharide components of the plant cell wall.« less

International disaster research

NASA Technical Reports Server (NTRS)

Silverstein, Martin Elliot

1991-01-01

No existing telecommunications system can be expected to provide strategy and tactics appropriate to the complex, many faceted problem of disaster. Despite the exciting capabilities of space, communications, remote sensing, and the miracles of modern medicine, complete turnkey transfers to the disaster problem do not make the fit, and cannot be expected to do so. In 1980, a Presidential team assigned the mission of exploring disaster response within the U.S. Federal Government encountered an unanticipated obstacle: disaster was essentially undefined. In the absence of a scientifically based paradigm of disaster, there can be no measure of cost effectiveness, optimum design of manpower structure, or precise application of any technology. These problems spawned a 10-year, multidisciplinary study designed to define the origins, anatomy, and necessary management techniques for catastrophes. The design of the study necessarily reflects interests and expertise in disaster medicine, emergency medicine, telecommunications, computer communications, and forencsic sciences. This study is described.

Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering

NASA Astrophysics Data System (ADS)

Gallina, M. E.; Comez, L.; Morresi, A.; Paolantoni, M.; Perticaroli, S.; Sassi, P.; Fioretto, D.

2010-06-01

High resolution depolarized light scattering spectra, extended from 0.5 to 2×104 GHz by the combined used of a dispersive and an interferometric setup, give evidence of separated solute and solvent dynamics in diluted trehalose aqueous solutions. The slow relaxation process, located in the gigahertz frequency region, is analyzed as a function of temperature and concentration and assigned to the rotational diffusion of the sugar molecule. The results are discussed in comparison with the data obtained on glucose solutions and they are used to clarify the molecular origin of some among the several relaxation processes reported in literature for oligosaccharides solutions. The concentration dependence of relaxation time and of shear viscosity are also discussed, suggesting that the main effect of carbohydrate molecules on the structural relaxation of diluted aqueous solutions is the perturbation induced on the dynamics of the first hydration shell of each solute molecule.

Enzymatic detoxification of jojoba meal and effect of the resulting meal on food intake in rats.

PubMed

Bouali, Abderrahime; Bellirou, Ahmed; Boukhatem, Noureddin; Hamal, Abdellah; Bouammali, Boufelja

2008-05-10

When defatted jojoba meal is used as animal food, it causes food-intake reduction and growth retardation. Detoxification procedures by chemical, microbiological, and solvent extraction methods are reported by several authors. Here we report a successful detoxification of jojoba meal using enzymes. We establish reaction conditions that yield new meal which has the same nutritional qualities in proteins as the original meal. The enzymatic reaction gives rise to one major compound to which the structure of an amide is assigned on the basis of IR, 1H and 13C NMR spectra. The effect of the resulting jojoba meal on the food intake in rats is checked. In contrast, the detoxified meal containing the amide derivatives shows no toxicological activity since rats receiving oral administration of the obtained meal show normal growth. Thus, it is expected that this meal could be used as an animal feed ingredient.

Loss for photoemission versus gain for Auger: Direct experimental evidence of crystal-field splitting and charge transfer in photoelectron spectroscopy

DOE PAGES

Woicik, J. C.; Weiland, C.; Rumaiz, A. K.

2015-05-29

Here, we find a 5 eV satellite in the Ti1s photoelectron spectrum of the transition-metal oxide SrTiO 3. This satellite appears in addition to the well-studied 13 eV structure that is typically associated with the Ti2p core line. We give direct experimental evidence that the presence of two satellites is due to the crystal-field splitting of the metal 3d orbitals. They originate from ligand 2pt 2g → metal3dt 2g and ligand 2pe g → metal 3de g monopole charge-transfer excitations within the sudden approximation of quantum mechanics. This assignment is made by the energetics of the resonant and high-energy thresholdmore » behaviors of the TiK–L 2L 3 Auger decay that follows Ti1s photoionization.« less

Hibonite: Crystal Chemistry and Origin of Blue Coloration in Meteoritic Assemblages

NASA Technical Reports Server (NTRS)

Burns, R. G.; Burns, V. M.

1985-01-01

The blue color and optical spectra of hibonite, a common constituent of refractory inclusions in carbonaceous chondrites, are discussed. Because they may be manifestations of exotic cation species stabilized in unusual coordination sites in the hibonite crystalstructure. Hibonite, ideally CaAl12O19, is conducive to atomic substitution of host Ca2+ and Al3+ ions by a variety of lanthanide and first series transition elements. The latter cations are responsible for the colors of many rock-forming minerals as a result of intraelectronic or intervalence transitions. The visible-region spectra of most oxide and silicate minerals are generally well understood. Assignments of absorption bands in meteoritic hibonite optical spectra due to uncertainties of cation valencies and complexities in the crystal structure are examined. The crystal chemistry of hibonite is reviewed, Mossbauer spectral measurements of iron-bearing hibonite and electronic transitions that may be responsible for the blue coloration of meteoritic hibonites are discussed.

Swelling-induced and controlled curving in layered gel beams

PubMed Central

Lucantonio, A.; Nardinocchi, P.; Pezzulla, M.

2014-01-01

We describe swelling-driven curving in originally straight and non-homogeneous beams. We present and verify a structural model of swollen beams, based on a new point of view adopted to describe swelling-induced deformation processes in bilayered gel beams, that is based on the split of the swelling-induced deformation of the beam at equilibrium into two components, both depending on the elastic properties of the gel. The method allows us to: (i) determine beam stretching and curving, once assigned the characteristics of the solvent bath and of the non-homogeneous beam, and (ii) estimate the characteristics of non-homogeneous flat gel beams in such a way as to obtain, under free-swelling conditions, three-dimensional shapes. The study was pursued by means of analytical, semi-analytical and numerical tools; excellent agreement of the outcomes of the different techniques was found, thus confirming the strength of the method. PMID:25383031

Critical Race Theory, Race Equity, and Public Health: Toward Antiracism Praxis

PubMed Central

Airhihenbuwa, Collins O.

2010-01-01

Racial scholars argue that racism produces rates of morbidity, mortality, and overall well-being that vary depending on socially assigned race. Eliminating racism is therefore central to achieving health equity, but this requires new paradigms that are responsive to structural racism's contemporary influence on health, health inequities, and research. Critical Race Theory is an emerging transdisciplinary, race-equity methodology that originated in legal studies and is grounded in social justice. Critical Race Theory's tools for conducting research and practice are intended to elucidate contemporary racial phenomena, expand the vocabulary with which to discuss complex racial concepts, and challenge racial hierarchies. We introduce Critical Race Theory to the public health community, highlight key Critical Race Theory characteristics (race consciousness, emphases on contemporary societal dynamics and socially marginalized groups, and praxis between research and practice) and describe Critical Race Theory's contribution to a study on racism and HIV testing among African Americans. PMID:20147679

A computer-aided design system geared toward conceptual design in a research environment. [for hypersonic vehicles

NASA Technical Reports Server (NTRS)

STACK S. H.

1981-01-01

A computer-aided design system has recently been developed specifically for the small research group environment. The system is implemented on a Prime 400 minicomputer linked with a CDC 6600 computer. The goal was to assign the minicomputer specific tasks, such as data input and graphics, thereby reserving the large mainframe computer for time-consuming analysis codes. The basic structure of the design system consists of GEMPAK, a computer code that generates detailed configuration geometry from a minimum of input; interface programs that reformat GEMPAK geometry for input to the analysis codes; and utility programs that simplify computer access and data interpretation. The working system has had a large positive impact on the quantity and quality of research performed by the originating group. This paper describes the system, the major factors that contributed to its particular form, and presents examples of its application.

First record of Ginkgo-related fertile organs (Hamshawvia, Stachyopitys) and leaves (Baiera, Sphenobaiera) in the Triassic of Brazil, Santa Maria formation

NASA Astrophysics Data System (ADS)

Barboni, Ronaldo; Dutra, Tânia Lindner

2015-11-01

This paper describes new ginkgophytes recently discovered in a new exposure of the original type section of the Passo das Tropas Member, Santa Maria Formation, linked to Paraná Basin succession. The well-preserved fossils come from a very fine red laminated mudstone representing a lacustrine interval, within a broader low-sinuosity fluvial succession. The material occurs in a Dicroidium-dominated assemblage and is represented by the leaves Baiera and Sphenobaiera, accompanied by the fertile structures Hamshawvia and Stachyopytis. Cuticle fragments preserved on leaf impressions of Sphenobaiera schenkii show xeromorphic features. The geology, paleogeography and paleoclimate of the Passo das Tropas Member (PTM), Santa Maria Formation, is discussed. By comparing these ginkgophytes with those from other Gondwanan assemblages, the Brazilian deposits earlier assigned to Anisian-Ladinian age can now be extended to the Carnian age.

Neutron star equation of state and QPO observations

NASA Astrophysics Data System (ADS)

Urbanec, Martin; Stuchlík, Zdeněk; Török, Gabriel; Bakala, Pavel; Čermák, Petr

2007-12-01

Assuming a resonant origin of the twin peak quasiperiodic oscillations observed in the X-ray neutron star binary systems, we apply a genetic algorithm method for selection of neutron star models. It was suggested that pairs of kilohertz peaks in the X-ray Fourier power density spectra of some neutron stars reflect a non-linear resonance between two modes of accretion disk oscillations. We investigate this concept for a specific neutron star source. Each neutron star model is characterized by the equation of state (EOS), rotation frequency Ω and central energy density rho_{c}. These determine the spacetime structure governing geodesic motion and position dependent radial and vertical epicyclic oscillations related to the stable circular geodesics. Particular kinds of resonances (KR) between the oscillations with epicyclic frequencies, or the frequencies derived from them, can take place at special positions assigned ambiguously to the spacetime structure. The pairs of resonant eigenfrequencies relevant to those positions are therefore fully given by KR, rho_{c}, Ω, EOS and can be compared to the observationally determined pairs of eigenfrequencies in order to eliminate the unsatisfactory sets (KR, rho_{c}, Ω, EOS). For the elimination we use the advanced genetic algorithm. Genetic algorithm comes out from the method of natural selection when subjects with the best adaptation to assigned conditions have most chances to survive. The chosen genetic algorithm with sexual reproduction contains one chromosome with restricted lifetime, uniform crossing and genes of type 3/3/5. For encryption of physical description (KR, rho_{c}, Ω, EOS) into the chromosome we use the Gray code. As a fitness function we use correspondence between the observed and calculated pairs of eigenfrequencies.

Microwave Spectrum of the Ethanol-Methanol Dimer

NASA Astrophysics Data System (ADS)

Finneran, Ian A.; Carroll, Brandon; Mead, Griffin; Blake, Geoffrey

2016-06-01

The hydrogen bond donor/acceptor competition in mixed alcohol clusters remains a fundamental question in physical chemistry. Previous theoretical work on the prototype ethanol-methanol dimer has been inconclusive in predicting the energetically preferred structure. Here, we report the microwave spectrum of the ethanol-methanol dimer between 8-18 GHz, using a chirped pulse Fourier transform microwave spectrometer. With the aid of ab initio calculations, 36 transitions have been fit and assigned to a t-ethanol-acceptor, methanol-donor structure in an argon-backed expansion. In a helium-backed expansion, a second excited conformer has been observed, and tentatively assigned to a g-ethanol-acceptor, methanol-donor structure. No ethanol-donor, methanol-acceptor structures have been found, suggesting such structures are energetically disfavored.

Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail

USGS Publications Warehouse

Fournier, Auriel M. V.; Sullivan, Alexis R.; Bump, Joseph K.; Perkins, Marie; Shieldcastle, Mark C.; King, Sammy L.

2017-01-01

Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments.We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America.Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments.Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana.Synthesis and applications. In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.

Multilocus Sequence Typing of Cronobacter Strains Isolated from Retail Foods and Environmental Samples.

PubMed

Killer, Jiří; Skřivanová, Eva; Hochel, Igor; Marounek, Milan

2015-06-01

Cronobacter spp. are bacterial pathogens that affect children and immunocompromised adults. In this study, we used multilocus sequence typing (MLST) to determine sequence types (STs) in 11 Cronobacter spp. strains isolated from retail foods, 29 strains from dust samples obtained from vacuum cleaners, and 4 clinical isolates. Using biochemical tests, species-specific polymerase chain reaction, and MLST analysis, 36 strains were identified as Cronobacter sakazakii, and 6 were identified as Cronobacter malonaticus. In addition, one strain that originated from retail food and one from a dust sample from a vacuum cleaner were identified on the basis of MLST analysis as Cronobacter dublinensis and Cronobacter turicensis, respectively. Cronobacter spp. strains isolated from the retail foods were assigned to eight different MLST sequence types, seven of which were newly identified. The strains isolated from the dust samples were assigned to 7 known STs and 14 unknown STs. Three clinical isolates and one household dust isolate were assigned to ST4, which is the predominant ST associated with neonatal meningitis. One clinical isolate was classified based on MLST analysis as Cronobacter malonaticus and belonged to an as-yet-unknown ST. Three strains isolated from the household dust samples were assigned to ST1, which is another clinically significant ST. It can be concluded that Cronobacter spp. strains of different origin are genetically quite variable. The recovery of C. sakazakii strains belonging to ST1 and ST4 from the dust samples suggests the possibility that contamination could occur during food preparation. All of the novel STs and alleles for C. sakazakii, C. malonaticus, C. dublinensis, and C. turicensis determined in this study were deposited in the Cronobacter MLST database available online ( http://pubmlst.org/cronobacter/).

Responding to Misinformation about Climate Change

ERIC Educational Resources Information Center

Lawrence, Eva K.; Estow, Sarah

2017-01-01

This study examined responses to climate change misinformation and messages designed to counter misinformation. Participants (N = 406) first responded to a social media post denying the existence of global warming and then were randomly assigned to read one of three responses to the original post (correction, collaboration, control). Participants…

47 CFR 36.141 - General.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false General. 36.141 Section 36.141.../termination (iot) Equipment § 36.141 General. (a) Information Origination/Termination Equipment is maintained... regulation, pursuant to § 61.41 of this chapter, shall assign the average balance of Account 2310 to the...

[Criteria of quality of structure in rehabilitation units with inpatient treatment].

PubMed

Klein, K; Farin, E; Jäckel, W H; Blatt, O; Schliehe, F

2004-04-01

The structure of a rehabilitation unit is an important feature of the quality of care. Adequate and qualitatively good structures provide the basis for appropriate therapy offers and treatment and eventually, a better health for rehabilitants. The quality of structures is generally recorded without any evaluation of the aspects in particular. The definition of standards is the basis for such an evaluation. The project presented is aimed at the definition of relevant structural standards for rehab units with inpatient treatment for musculoskeletal, cardiac, neurological, gastroenterological, oncological, pneumological and dermatological diseases. Here, the distinction between basal criteria which have to be fulfilled by every rehab unit with inpatient treatment and criteria important for a well-aimed assignment of patients with specific needs ("assignment criteria") should be made. Apart from the documentation of structural attributes, the structural quality of a rehab unit can be described individually as well as in comparison with other units. Relevant structural criteria were defined in expert meetings by means of a modified Delphi-technique with five inquiries. Overall, 199 "basal criteria" and "assignment criteria" were defined. All criteria can be assigned to the two domains general structural characteristics (general characteristics and equipment of rooms; medical/technical equipment; therapy, education, care; staff) and process-related structures (conceptual frames; internal quality management; internal communication and personnel development). The structural standards are applicable to units for musculoskeletal, cardiac, neurological, oncological, gastroenterological, dermatological and pneumological rehabilitation financed by the two main providers of rehabilitation, the statutory pension insurance scheme and the statutory health insurance scheme for all other five indications. The definition of structural standards agreed by experts in a formal consensus process, provides comprehensive and concrete requirements for German rehab units with inpatient medical rehabilitation. If the two main providers of rehabilitation both use the standards this can be regarded as a hallmark on the path to a unitary programme for quality management. The results enable units to analyse their weak points not just on an individual basis but allow also for a comparison between units, along with contributing to optimizing the structural quality of rehab units.

Assignment of the structural gene for human beta glucuronidase to chromosome 7 and tetrameric association of subunits in the enzyme molecule.

PubMed Central

Chern, C J; Croce, C M

1976-01-01

The structural locus for human beta glucuronidase is assigned to chromosome 7, a localization based upon concordant segregation of the expression of the human enzyme and the presence of human chromosome 7 in somatic cell hybrid clones derived independently from fusions of different human and mouse cells. Hybrid clones containing only human chromosome 7 are included in this study. Electrophoresis of beta glucuronidase also has revealed that human beta glucuronidase has a tetrametric structure. Images Fig. 1 Fig. 2 Fig. 3 PMID:941902

Measured Laboratory and In-Use Fuel Economy Observed over Targeted Drive Cycles for Comparable Hybrid and Conventional Package Delivery Vehicles

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

Lammert, M. P.; Walkowicz, K.; Duran, A.

2012-10-01

In-use and laboratory-derived fuel economies were analyzed for a medium-duty hybrid electric drivetrain with 'engine off at idle' capability and a conventional drivetrain in a typical commercial package delivery application. Vehicles studied included eleven 2010 Freightliner P100H hybrids in service at a United Parcel Service facility in Minneapolis during the first half of 2010. The hybrids were evaluated for 18 months against eleven 2010 Freightliner P100D diesels at the same facility. Both vehicle groups use the same 2009 Cummins ISB 200-HP engine. In-use fuel economy was evaluated using UPS's fueling and mileage records, periodic ECM image downloads, and J1939 CANmore » bus recordings during the periods of duty cycle study. Analysis of the in-use fuel economy showed 13%-29% hybrid advantage depending on measurement method, and a delivery route assignment analysis showed 13%-26% hybrid advantage on the less kinetically intense original diesel route assignments and 20%-33% hybrid advantage on the more kinetically intense original hybrid route assignments. Three standardized laboratory drive cycles were selected that encompassed the range of real-world in-use data. The hybrid vehicle demonstrated improvements in ton-mi./gal fuel economy of 39%, 45%, and 21% on the NYC Comp, HTUF Class 4, and CARB HHDDT test cycles, respectively.« less

Optimal processor assignment for pipeline computations

NASA Technical Reports Server (NTRS)

Nicol, David M.; Simha, Rahul; Choudhury, Alok N.; Narahari, Bhagirath

1991-01-01

The availability of large scale multitasked parallel architectures introduces the following processor assignment problem for pipelined computations. Given a set of tasks and their precedence constraints, along with their experimentally determined individual responses times for different processor sizes, find an assignment of processor to tasks. Two objectives are of interest: minimal response given a throughput requirement, and maximal throughput given a response time requirement. These assignment problems differ considerably from the classical mapping problem in which several tasks share a processor; instead, it is assumed that a large number of processors are to be assigned to a relatively small number of tasks. Efficient assignment algorithms were developed for different classes of task structures. For a p processor system and a series parallel precedence graph with n constituent tasks, an O(np2) algorithm is provided that finds the optimal assignment for the response time optimization problem; it was found that the assignment optimizing the constrained throughput in O(np2log p) time. Special cases of linear, independent, and tree graphs are also considered.

PICKY: a novel SVD-based NMR spectra peak picking method.

PubMed

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-06-15

Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 A. PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

A vibrational spectroscopic study of tengerite-(Y) Y2(CO3)3 2-3H2O

NASA Astrophysics Data System (ADS)

Frost, Ray L.; López, Andrés; Wang, Lina; Scholz, Ricardo; Sampaio, Ney Pinheiro; de Oliveira, Fernando A. N.

2015-02-01

The mineral tengerite-(Y) has been studied by vibrational spectroscopy. Multiple carbonate stretching modes are observed and support the concept of non-equivalent carbonate units in the tengerite-(Y) structure. Intense sharp bands at 464, 479 and 508 cm-1 are assigned to YO stretching modes. Raman bands at 765 and 775 cm-1 are assigned to the CO32- ν4 bending modes and Raman bands at 589, 611, 674 and 689 cm-1 are assigned to the CO32- ν2 bending modes. Multiple Raman and infrared bands in the OH stretching region are observed, proving the existence of water in different molecular environments in the structure of tengerite-(Y).

Data-assisted protein structure modeling by global optimization in CASP12.

PubMed

Joo, Keehyoung; Heo, Seungryong; Joung, InSuk; Hong, Seung Hwan; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

In CASP12, 2 types of data-assisted protein structure modeling were experimented. Either SAXS experimental data or cross-linking experimental data was provided for a selected number of CASP12 targets that the CASP12 predictor could utilize for better protein structure modeling. We devised 2 separate energy terms for SAXS data and cross-linking data to drive the model structures into more native-like structures that satisfied the given experimental data as much as possible. In CASP11, we successfully performed protein structure modeling using simulated sparse and ambiguously assigned NOE data and/or correct residue-residue contact information, where the only energy term that folded the protein into its native structure was the term which was originated from the given experimental data. However, the 2 types of experimental data provided in CASP12 were far from being sufficient enough to fold the target protein into its native structure because SAXS data provides only the overall shape of the molecule and the cross-linking contact information provides only very low-resolution distance information. For this reason, we combined the SAXS or cross-linking energy term with our regular modeling energy function that includes both the template energy term and the de novo energy terms. By optimizing the newly formulated energy function, we obtained protein models that fit better with provided SAXS data than the X-ray structure of the target. However, the improvement of the model relative to the 1 modeled without the SAXS data, was not significant. Consistent structural improvement was achieved by incorporating cross-linking data into the protein structure modeling. © 2018 Wiley Periodicals, Inc.

Using structural damage statistics to derive macroseismic intensity within the Kathmandu valley for the 2015 M7.8 Gorkha, Nepal earthquake

NASA Astrophysics Data System (ADS)

McGowan, S. M.; Jaiswal, K. S.; Wald, D. J.

2017-09-01

We make and analyze structural damage observations from within the Kathmandu valley following the 2015 M7.8 Gorkha, Nepal earthquake to derive macroseismic intensities at several locations including some located near ground motion recording sites. The macroseismic intensity estimates supplement the limited strong ground motion data in order to characterize the damage statistics. This augmentation allows for direct comparisons between ground motion amplitudes and structural damage characteristics and ultimately produces a more constrained ground shaking hazard map for the Gorkha earthquake. For systematic assessments, we focused on damage to three specific building categories: (a) low/mid-rise reinforced concrete frames with infill brick walls, (b) unreinforced brick masonry bearing walls with reinforced concrete slabs, and (c) unreinforced brick masonry bearing walls with partial timber framing. Evaluating dozens of photos of each construction type, assigning each building in the study sample to a European Macroseismic Scale (EMS)-98 Vulnerability Class based upon its structural characteristics, and then individually assigning an EMS-98 Damage Grade to each building allows a statistically derived estimate of macroseismic intensity for each of nine study areas in and around the Kathmandu valley. This analysis concludes that EMS-98 macroseismic intensities for the study areas from the Gorkha mainshock typically were in the VII-IX range. The intensity assignment process described is more rigorous than the informal approach of assigning intensities based upon anecdotal media or first-person accounts of felt-reports, shaking, and their interpretation of damage. Detailed EMS-98 macroseismic assessments in urban areas are critical for quantifying relations between shaking and damage as well as for calibrating loss estimates. We show that the macroseismic assignments made herein result in fatality estimates consistent with the overall and district-wide reported values.

Using structural damage statistics to derive macroseismic intensity within the Kathmandu valley for the 2015 M7.8 Gorkha, Nepal earthquake

USGS Publications Warehouse

McGowan, Sean; Jaiswal, Kishor; Wald, David J.

2017-01-01

We make and analyze structural damage observations from within the Kathmandu valley following the 2015 M7.8 Gorkha, Nepal earthquake to derive macroseismic intensities at several locations including some located near ground motion recording sites. The macroseismic intensity estimates supplement the limited strong ground motion data in order to characterize the damage statistics. This augmentation allows for direct comparisons between ground motion amplitudes and structural damage characteristics and ultimately produces a more constrained ground shaking hazard map for the Gorkha earthquake. For systematic assessments, we focused on damage to three specific building categories: (a) low/mid-rise reinforced concrete frames with infill brick walls, (b) unreinforced brick masonry bearing walls with reinforced concrete slabs, and (c) unreinforced brick masonry bearing walls with partial timber framing. Evaluating dozens of photos of each construction type, assigning each building in the study sample to a European Macroseismic Scale (EMS)-98 Vulnerability Class based upon its structural characteristics, and then individually assigning an EMS-98 Damage Grade to each building allows a statistically derived estimate of macroseismic intensity for each of nine study areas in and around the Kathmandu valley. This analysis concludes that EMS-98 macroseismic intensities for the study areas from the Gorkha mainshock typically were in the VII–IX range. The intensity assignment process described is more rigorous than the informal approach of assigning intensities based upon anecdotal media or first-person accounts of felt-reports, shaking, and their interpretation of damage. Detailed EMS-98 macroseismic assessments in urban areas are critical for quantifying relations between shaking and damage as well as for calibrating loss estimates. We show that the macroseismic assignments made herein result in fatality estimates consistent with the overall and district-wide reported values.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

PubMed Central

Watson, Mick; Minot, Samuel S.; Rivera, Maria C.; Franklin, Rima B.

2017-01-01

Abstract Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error rate reduction, this platform shows great promise for precise real-time analysis of the composition and structure of more complex microbial communities. PMID:28327976

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

PubMed

Brown, Bonnie L; Watson, Mick; Minot, Samuel S; Rivera, Maria C; Franklin, Rima B

2017-03-01

Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error rate reduction, this platform shows great promise for precise real-time analysis of the composition and structure of more complex microbial communities. © The Author 2017. Published by Oxford University Press.

Group galaxy number density profiles far out: Is the `one-halo' term NFW out to >10 virial radii?

NASA Astrophysics Data System (ADS)

Trevisan, M.; Mamon, G. A.; Stalder, D. H.

2017-10-01

While the density profiles (DPs) of Lambda cold dark matter haloes obey the Navarro, Frenk & White (NFW) law out to roughly one virial radius, rvir, the structure of their outer parts is still poorly understood, because the one-halo term describing the halo itself is dominated by the two-halo term representing the other haloes picked up. Using a semi-analytical model, we measure the real-space one-halo number DP of groups out to 20rvir by assigning each galaxy to its nearest group above mass Ma, in units of the group rvir. If Ma is small (large), the outer DP of groups falls rapidly (slowly). We find that there is an optimal Ma for which the stacked DP resembles the NFW model to 0.1 dex accuracy out to 13 virial radii. We find similar long-range NFW surface DPs (out to 10rvir) in the Sloan Digital Sky Survey observations using a galaxy assignment scheme that combines the non-linear virialized regions of groups with their linear outer parts. The optimal Ma scales as the minimum mass of the groups that are stacked to a power 0.25-0.3. The NFW model thus does not solely originate from violent relaxation. Moreover, populating haloes with galaxies using halo occupation distribution models must proceed out to much larger radii than usually done.

34 CFR 270.3 - What definitions apply to these programs?

Code of Federal Regulations, 2014 CFR

2014-07-01

... U.S.C. 2000c(d)) Sex desegregation means the assignment of students to public schools and within... SECONDARY EDUCATION, DEPARTMENT OF EDUCATION DESEGREGATION OF PUBLIC EDUCATION § 270.3 What definitions... (including training) in the areas of race, sex, and national origin desegregation of public elementary and...

34 CFR 270.3 - What definitions apply to these programs?

Code of Federal Regulations, 2012 CFR

2012-07-01

... U.S.C. 2000c(d)) Sex desegregation means the assignment of students to public schools and within... SECONDARY EDUCATION, DEPARTMENT OF EDUCATION DESEGREGATION OF PUBLIC EDUCATION § 270.3 What definitions... (including training) in the areas of race, sex, and national origin desegregation of public elementary and...

34 CFR 270.3 - What definitions apply to these programs?

Code of Federal Regulations, 2013 CFR

2013-07-01

... U.S.C. 2000c(d)) Sex desegregation means the assignment of students to public schools and within... SECONDARY EDUCATION, DEPARTMENT OF EDUCATION DESEGREGATION OF PUBLIC EDUCATION § 270.3 What definitions... (including training) in the areas of race, sex, and national origin desegregation of public elementary and...

34 CFR 270.3 - What definitions apply to these programs?

Code of Federal Regulations, 2011 CFR

2011-07-01

... U.S.C. 2000c(d)) Sex desegregation means the assignment of students to public schools and within... SECONDARY EDUCATION, DEPARTMENT OF EDUCATION DESEGREGATION OF PUBLIC EDUCATION § 270.3 What definitions... (including training) in the areas of race, sex, and national origin desegregation of public elementary and...

39 CFR 241.3 - Discontinuance of post offices.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... These rules are designed to ensure that the reasons leading a district manager, Customer Service and... originally assigned to the discontinued post office may be changed if the responsible district manager... to the discontinued post office. (ii) If the ZIP Code is changed and the parent post office covers...

Use of Inpatient Mental Health Services by Members of Ethnic Minority Groups.

ERIC Educational Resources Information Center

Snowden, Lonnie R.; Cheung, Freda K.

1990-01-01

Discusses the ethnic-related differences in mental hospitalization admittance rates, diagnoses, and length of treatment. Explores reasons other than ethnic origin that may account for these differences, including socioeconomic standing, access to alternative services, bias in practitioners' assignment of diagnostic labels, and differential stigma…

Lesekurse fuer Anfaenger-Fachbereich Psychologie (Reading Courses for Beginners-Psychology)

ERIC Educational Resources Information Center

Armaleo-Popper, Lore

1976-01-01

Describes a German course for psychologists, given in Italy by the author, using eight original texts by Freud and Mitscherlich. These were assigned for 40-50 hours' continuation reading at home, or were discussed in the 100-120 hours in the classroom. (Text is in German.) (IFS/WGA)

Sticky-Note Murals

ERIC Educational Resources Information Center

Sands, Ian

2011-01-01

In this article, the author describes a sticky-note mural project that originated from his desire to incorporate contemporary materials into his assignments as well as to inspire collaboration between students. The process takes much more than sticking sticky notes to the wall. It takes critical thinking skills and teamwork to design and complete…

41 CFR 302-9.142 - What will I be reimbursed if I transport a POV from a point of origin that is different from the...

Code of Federal Regulations, 2013 CFR

2013-07-01

...? 302-9.142 Section 302-9.142 Public Contracts and Property Management Federal Travel Regulation System... TEMPORARY STORAGE OF A PRIVATELY OWNED VEHICLE Transportation Pov Transportation at Time of Assignment § 302...

41 CFR 302-9.142 - What will I be reimbursed if I transport a POV from a point of origin that is different from the...

Code of Federal Regulations, 2012 CFR

2012-07-01

...? 302-9.142 Section 302-9.142 Public Contracts and Property Management Federal Travel Regulation System... TEMPORARY STORAGE OF A PRIVATELY OWNED VEHICLE Transportation Pov Transportation at Time of Assignment § 302...

41 CFR 302-9.142 - What will I be reimbursed if I transport a POV from a point of origin that is different from the...

Code of Federal Regulations, 2014 CFR

2014-07-01

...? 302-9.142 Section 302-9.142 Public Contracts and Property Management Federal Travel Regulation System... TEMPORARY STORAGE OF A PRIVATELY OWNED VEHICLE Transportation Pov Transportation at Time of Assignment § 302...

41 CFR 302-9.142 - What will I be reimbursed if I transport a POV from a point of origin that is different from the...

Code of Federal Regulations, 2011 CFR

2011-07-01

...? 302-9.142 Section 302-9.142 Public Contracts and Property Management Federal Travel Regulation System... STORAGE OF A PRIVATELY OWNED VEHICLE Transportation Pov Transportation at Time of Assignment § 302-9.142...

41 CFR 302-9.142 - What will I be reimbursed if I transport a POV from a point of origin that is different from the...

Code of Federal Regulations, 2010 CFR

2010-07-01

...? 302-9.142 Section 302-9.142 Public Contracts and Property Management Federal Travel Regulation System... STORAGE OF A PRIVATELY OWNED VEHICLE Transportation Pov Transportation at Time of Assignment § 302-9.142...

A Collaboration in Care: Re-Visioning Teacher-Student Dialogue in Dance Education

ERIC Educational Resources Information Center

Gose, Rebecca; Siemietkowski, Grace

2018-01-01

The following narrative recounts a collaborative reflective investigation into pedagogical care using a teacher-student dyad approach. Originating from the student's inquiry that fulfilled her teacher's assignment, the ensuing exploration investigates care from both teacher and student perspectives in the classroom and choreographic settings. This…

The Effects of Elaboration on Self-Learning Procedures from Text.

ERIC Educational Resources Information Center

Yang, Fu-mei

This study investigated the effects of augmenting and deleting elaborations in an existing self-instructional text for a micro-computer database application, "Microsoft Works User's Manual." A total of 60 undergraduate students were randomly assigned to the original, elaborated, or unelaborated text versions. The elaborated version…

Learning to Create Ad Strategies for "Different" Target Audiences.

ERIC Educational Resources Information Center

Treise, Debbie; Wagner, Elaine

1999-01-01

Describes a focus group exercise used with advertising creative- and strategy-development students that was designed to cultivate awareness of the ethnic consumers' purchase-decision process. Offers an overview of the project's stages, describes the assignment, and notes that members of the original-product focus group also reviewed students'…

How to Do Things with Words: Speech Acts in Education

ERIC Educational Resources Information Center

Gasparatou, Renia

2018-01-01

Originating from philosophy and science, many different ideas have made their way into educational policies. Educational policies often take such ideas completely out of context, and enforce them as general norms to every aspect of education; even opposing ideals make their way into school's curricula, teaching techniques, assignments, and…

Performance evaluation of distributed wavelength assignment in WDM optical networks

NASA Astrophysics Data System (ADS)

Hashiguchi, Tomohiro; Wang, Xi; Morikawa, Hiroyuki; Aoyama, Tomonori

2004-04-01

In WDM wavelength routed networks, prior to a data transfer, a call setup procedure is required to reserve a wavelength path between the source-destination node pairs. A distributed approach to a connection setup can achieve a very high speed, while improving the reliability and reducing the implementation cost of the networks. However, along with many advantages, several major challenges have been posed by the distributed scheme in how the management and allocation of wavelength could be efficiently carried out. In this thesis, we apply a distributed wavelength assignment algorithm named priority based wavelength assignment (PWA) that was originally proposed for the use in burst switched optical networks to the problem of reserving wavelengths of path reservation protocols in the distributed control optical networks. Instead of assigning wavelengths randomly, this approach lets each node select the "safest" wavelengths based on the information of wavelength utilization history, thus unnecessary future contention is prevented. The simulation results presented in this paper show that the proposed protocol can enhance the performance of the system without introducing any apparent drawbacks.

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

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

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2002-06-01

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis.

PubMed

Cui, Licong; Xu, Rong; Luo, Zhihui; Wentz, Susan; Scarberry, Kyle; Zhang, Guo-Qiang

2014-08-03

Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration. We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface. Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F₁ measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness' original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision. Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method, combining term-strength, FCA, and information retrieval techniques, significantly improved recall and performed well according to example-based metrics.

Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis

PubMed Central

2014-01-01

Background Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration. Methods We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface. Results Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F1 measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness’ original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision. Conclusion Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method, combining term-strength, FCA, and information retrieval techniques, significantly improved recall and performed well according to example-based metrics. PMID:25086916

Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

PubMed

Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

2015-04-15

A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.

Tracing Asian Seabass Individuals to Single Fish Farms Using Microsatellites

PubMed Central

Yue, Gen Hua; Xia, Jun Hong; Liu, Peng; Liu, Feng; Sun, Fei; Lin, Grace

2012-01-01

Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass. PMID:23285169

Application of firefly algorithm to the dynamic model updating problem

NASA Astrophysics Data System (ADS)

Shabbir, Faisal; Omenzetter, Piotr

2015-04-01

Model updating can be considered as a branch of optimization problems in which calibration of the finite element (FE) model is undertaken by comparing the modal properties of the actual structure with these of the FE predictions. The attainment of a global solution in a multi dimensional search space is a challenging problem. The nature-inspired algorithms have gained increasing attention in the previous decade for solving such complex optimization problems. This study applies the novel Firefly Algorithm (FA), a global optimization search technique, to a dynamic model updating problem. This is to the authors' best knowledge the first time FA is applied to model updating. The working of FA is inspired by the flashing characteristics of fireflies. Each firefly represents a randomly generated solution which is assigned brightness according to the value of the objective function. The physical structure under consideration is a full scale cable stayed pedestrian bridge with composite bridge deck. Data from dynamic testing of the bridge was used to correlate and update the initial model by using FA. The algorithm aimed at minimizing the difference between the natural frequencies and mode shapes of the structure. The performance of the algorithm is analyzed in finding the optimal solution in a multi dimensional search space. The paper concludes with an investigation of the efficacy of the algorithm in obtaining a reference finite element model which correctly represents the as-built original structure.

Evidence for a Role of VIPP1 in the Structural Organization of the Photosynthetic Apparatus in Chlamydomonas[W][OA

PubMed Central

Nordhues, André; Schöttler, Mark Aurel; Unger, Ann-Katrin; Geimer, Stefan; Schönfelder, Stephanie; Schmollinger, Stefan; Rütgers, Mark; Finazzi, Giovanni; Soppa, Barbara; Sommer, Frederik; Mühlhaus, Timo; Roach, Thomas; Krieger-Liszkay, Anja; Lokstein, Heiko; Crespo, José Luis; Schroda, Michael

2012-01-01

The vesicle-inducing protein in plastids (VIPP1) was suggested to play a role in thylakoid membrane formation via membrane vesicles. As this functional assignment is under debate, we investigated the function of VIPP1 in Chlamydomonas reinhardtii. Using immunofluorescence, we localized VIPP1 to distinct spots within the chloroplast. In VIPP1-RNA interference/artificial microRNA cells, we consistently observed aberrant, prolamellar body-like structures at the origin of multiple thylakoid membrane layers, which appear to coincide with the immunofluorescent VIPP1 spots and suggest a defect in thylakoid membrane biogenesis. Accordingly, using quantitative shotgun proteomics, we found that unstressed vipp1 mutant cells accumulate 14 to 20% less photosystems, cytochrome b6f complex, and ATP synthase but 30% more light-harvesting complex II than control cells, while complex assembly, thylakoid membrane ultrastructure, and bulk lipid composition appeared unaltered. Photosystems in vipp1 mutants are sensitive to high light, which coincides with a lowered midpoint potential of the QA/QA− redox couple and increased thermosensitivity of photosystem II (PSII), suggesting structural defects in PSII. Moreover, swollen thylakoids, despite reduced membrane energization, in vipp1 mutants grown on ammonium suggest defects in the supermolecular organization of thylakoid membrane complexes. Overall, our data suggest a role of VIPP1 in the biogenesis/assembly of thylakoid membrane core complexes, most likely by supplying structural lipids. PMID:22307852

Mealybug species from Chilean agricultural landscapes and main factors influencing the genetic structure of Pseudococcus viburni

PubMed Central

Correa, Margarita C. G.; Lombaert, Eric; Malausa, Thibaut; Crochard, Didier; Alvear, Andrés; Zaviezo, Tania; Palero, Ferran

2015-01-01

The present study aimed to characterize the distribution of mealybug species along Chilean agro-ecosystems and to determine the relative impact of host plant, management strategy, geography and micro-environment on shaping the distribution and genetic structure of the obscure mealybug Pseudococcus viburni. An extensive survey was completed using DNA barcoding methods to identify Chilean mealybugs to the species level. Moreover, a fine-scale study of Ps. viburni genetic diversity and population structure was carried out, genotyping 529 Ps. viburni individuals with 21 microsatellite markers. Samples from 16 localities were analyzed using Bayesian and spatially-explicit methods and the genetic dataset was confronted to host-plant, management and environmental data. Chilean crops were found to be infested by Ps. viburni, Pseudococcus meridionalis, Pseudococcus longispinus and Planococcus citri, with Ps. viburni and Ps. meridionalis showing contrasting distribution and host-plant preference patterns. Ps. viburni samples presented low genetic diversity levels but high genetic differentiation. While no significant genetic variance could be assigned to host-plant or management strategy, climate and geography were found to correlate significantly with genetic differentiation levels. The genetic characterization of Ps. viburni within Chile will contribute to future studies tracing back the origin and improving the management of this worldwide invader. PMID:26559636

Multifunctional Deployment Hinges Rigidified by Ultraviolet

NASA Technical Reports Server (NTRS)

Kerslake, Thomas W.; Simburger, Edward J.; Matusmoto, James; Giants, Thomas W.; Garcia, Alexander; Perry, Alan; Rawal, Suraj; Marshall, Craig; Lin, John Kun Hung; Day, Jonathan Robert;

Reinterpretation of the Vibrational Spectroscopy of the Medicinal Bioinorganic Synthon c,c,t-[Pt(NH3)2Cl2(OH)2]†

PubMed Central

Johnstone, Timothy C.

2014-01-01

The Pt(IV) complex c,c,t-[Pt(NH3)2Cl2(OH)2] is an important intermediate in the synthesis of Pt(IV) anticancer prodrugs and has been investigated as an anticancer agent in its own right. An analysis of the vibrational spectroscopy of this molecule was previously reported [Faggiani et al., 1982, Can. J. Chem. 60, 529] in which crystallographic determination of the structure of the complex permitted a site group approach. The space group, however, was incorrectly assigned. In the present study we have redetermined at high resolution crystal structures of c,c,t-[Pt(NH3)2Cl2(OH)2] and c,c,t-[Pt(NH3)2Cl2(OH)2]·H2O2, which enable discussion of the effect of hydrogen bonding on the N–H and O–H vibrational bands. The correct crystallographic site symmetry of the platinum complex in the c,c,t-[Pt(NH3)2Cl2(OH)2] structure is employed to conduct a new vibrational analysis using both group theoretical and modern DFT methods. This analysis reveals the nature and symmetry of the “missing band” described in the original publication and suggests a possible explanation for its disappearance. PMID:24515615

Jet-cooled laser-induced fluorescence spectroscopy of ScH: Observation of an Ω‧=2-Ω″=1 transition

NASA Astrophysics Data System (ADS)

Mukund, Sheo; Bhattacharyya, Soumen; Nakhate, S. G.

2014-11-01

New bands of scandium monohydride at origins 17,914.5 and 17,942.3 cm-1 have been observed in a jet-cooled beam with laser-induced fluorescence spectroscopy. Mass-selected resonant photoionization spectroscopy also confirmed the carrier of the band as ScH. The rotational analysis indicated that both transitions at 17,914.5 and 17,942.3 cm-1 are of Ω‧=2-Ω″=1 type with vibrational assignments (0,0) and (1,1) respectively. The assigned g3Φ2-a3Δ1 excitation is the first observed triplet-triplet transition in ScH.

Long-range anisotropic effects in a V-shaped Tröger's base diformanilide: Conformational study by NMR assignment and DFT calculations

NASA Astrophysics Data System (ADS)

Trupp, Leandro; Laurella, Sergio L.; Tettamanzi, M. Cristina; Barja, Beatriz C.; Bruttomesso, Andrea C.

2018-04-01

Herein we describe the synthesis and conformational analysis of a Tröger's base diformanilide whose distinctive NMR spectra was fully assigned via DFT calculations. The complexity of the spectra originated by the presence of three conformers in equilibrium shows that the nuclei in each side of the molecule are sensitive to the configuration not only of the closest formamide moiety but also of the farthest one, due to long-range anisotropic effects. The temperature and the solvent polarity influence were analyzed to determine the different conformer populations and the corresponding rotational activation parameters.

Phenotypic variation of Leptodactylus cupreus Caramaschi, São-Pedro and Feio, 2008 (Anura, Leptodactylidae).

PubMed

Cassini, Carla S; Orrico, Victor G D; Dias, Iuri Ribeiro; Solé, Mirco; Haddad, Célio F B

2013-02-17

This study describes for the first time the female of Leptodactylus cupreus and provides new information concerning its geographical distribution, male's morphology and bioacustics. Leptodactylus cupreus, a poorly known species from the Brazilian Atlantic Forest, was originally allocated in the L. mystaceus complex of the L. fuscus species group. Based on morphological observations, we infer that L. cupreus should be in fact related to L. mystacinus, a species that, although assigned to the L. fuscus species group, is not assigned to the L. mystaceus complex. Therefore, we comment the phylogenetic relationships concerning L. cupreus, L. mystaceus and L. mystacinus.

Glacial Geology and Stratigraphy of Fort Richardson, Alaska. A Review of Available Data on the Hydrogeology

DTIC Science & Technology

2000-04-01

Alaska.) Stricker, G.D., M.E. Brownfield, L.A. Yehle, and J.A. Wolfe (1988) Mineralogy and stage assign- ment of some Tertiary coal from the Tikishla... originates at the mouth of the Eagle River Valley near the city of Eagle River (Fig. 1, Plate 1). The fan slopes gently to the west– southwest, underlying...south, several low hills of ground moraine protrude through younger glacial depos- its of various origins from the most recent glacia- tion of this area

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

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

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-07-02

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including V xO y n– and V xO yCl n– ions (x = 1–14, y = 2–36, n = 1–3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V 14O 36Cl(L) 5 (L = Et 4N +, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged V xO yCl n– and V xOmore » yCl(L) (n–1)– clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller V xO yCl (1–2)– and V xO y (1–2)– anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged V xO yCl and V xO y species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of V xO yCl and V xO y anions through low-energy CID. Finally and furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.« less

The Enzyme Function Initiative†

PubMed Central

Gerlt, John A.; Allen, Karen N.; Almo, Steven C.; Armstrong, Richard N.; Babbitt, Patricia C.; Cronan, John E.; Dunaway-Mariano, Debra; Imker, Heidi J.; Jacobson, Matthew P.; Minor, Wladek; Poulter, C. Dale; Raushel, Frank M.; Sali, Andrej; Shoichet, Brian K.; Sweedler, Jonathan V.

2011-01-01

The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily-specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include: 1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation); 2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia; 3) computational and bioinformatic tools for using the strategy; 4) provision of experimental protocols and/or reagents for enzyme production and characterization; and 5) dissemination of data via the EFI’s website, enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal and pharmaceutical efforts. PMID:21999478

The Enzyme Function Initiative.

PubMed

Gerlt, John A; Allen, Karen N; Almo, Steven C; Armstrong, Richard N; Babbitt, Patricia C; Cronan, John E; Dunaway-Mariano, Debra; Imker, Heidi J; Jacobson, Matthew P; Minor, Wladek; Poulter, C Dale; Raushel, Frank M; Sali, Andrej; Shoichet, Brian K; Sweedler, Jonathan V

2011-11-22

The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic, we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include (1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation), (2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia, (3) computational and bioinformatic tools for using the strategy, (4) provision of experimental protocols and/or reagents for enzyme production and characterization, and (5) dissemination of data via the EFI's Website, http://enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal, and pharmaceutical efforts. © 2011 American Chemical Society

Thermal response to firefighting activities in residential structure fires: impact of job assignment and suppression tactic.

PubMed

Horn, Gavin P; Kesler, Richard M; Kerber, Steve; Fent, Kenneth W; Schroeder, Tad J; Scott, William S; Fehling, Patricia C; Fernhall, Bo; Smith, Denise L

2018-03-01

Firefighters' thermal burden is generally attributed to high heat loads from the fire and metabolic heat generation, which may vary between job assignments and suppression tactic employed. Utilising a full-sized residential structure, firefighters were deployed in six job assignments utilising two attack tactics (1. Water applied from the interior, or 2. Exterior water application before transitioning to the interior). Environmental temperatures decreased after water application, but more rapidly with transitional attack. Local ambient temperatures for inside operation firefighters were higher than other positions (average ~10-30 °C). Rapid elevations in skin temperature were found for all job assignments other than outside command. Neck skin temperatures for inside attack firefighters were ~0.5 °C lower when the transitional tactic was employed. Significantly higher core temperatures were measured for the outside ventilation and overhaul positions than the inside positions (~0.6-0.9 °C). Firefighters working at all fireground positions must be monitored and relieved based on intensity and duration. Practitioner Summary: Testing was done to characterise the thermal burden experienced by firefighters in different job assignments who responded to controlled residential fires (with typical furnishings) using two tactics. Ambient, skin and core temperatures varied based on job assignment and tactic employed, with rapid elevations in core temperature in many roles.

Introducing chemical biology applications to introductory organic chemistry students using series of weekly assignments.

PubMed

Kanin, Maralee R; Pontrello, Jason K

2016-01-01

Calls to bring interdisciplinary content and examples into introductory science courses have increased, yet strategies that involve course restructuring often suffer from the need for a significant faculty commitment to motivate change. Minimizing the need for dramatic course reorganization, the structure, reactivity, and chemical biology applications of classes of biological monomers and polymers have been integrated into introductory organic chemistry courses through three series of semester-long weekly assignments that explored (a) Carbohydrates and Oligosaccharides, (b) Amino Acids, Peptides, and Proteins, and (c) Nucleosides, Nucleotides, and Nucleic Acids. Comparisons of unannounced pre- and post tests revealed improved understanding of a reaction introduced in the assignments, and course examinations evaluated cumulative assignment topics. Course surveys revealed that demonstrating biologically relevant applications consistently throughout the semesters enhanced student interest in the connection between basic organic chemistry content and its application to new and unfamiliar bio-related examples. Covering basic material related to these classes of molecules outside of the classroom opened lecture time to allow the instructor to further build on information developed through the weekly assignments, teaching advanced topics and applications typically not covered in an introductory organic chemistry lecture course. Assignments were implemented as homework, either with or without accompanying discussion, in both laboratory and lecture organic courses within the context of the existing course structures. © 2015 The International Union of Biochemistry and Molecular Biology.

Nickel-catalyzed proton-deuterium exchange (HDX) for linkage analysis of complex carbohydrates

USDA-ARS?s Scientific Manuscript database

The structural assignment of complex carbohydrates typically requires the analysis of at least three parameters: 1. composition; 2. linkage; and 3. substituents. These are often assigned on a small scale by gas chromatography/mass spectrometry (GC/MS). Linkage positions are determined by permethylat...

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

PubMed Central

Zivanovic, Yvan; Confalonieri, Fabrice; Ponchon, Luc; Lurz, Rudi; Chami, Mohamed; Flayhan, Ali; Renouard, Madalena; Huet, Alexis; Decottignies, Paulette; Davidson, Alan R.; Breyton, Cécile

2014-01-01

Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm. PMID:24198424

Molecular Basis of the Bohr Effect in Arthropod Hemocyanin

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

Hirota, S.; Kawahara, T; Beltramini, M

2008-01-01

Flash photolysis and K-edge x-ray absorption spectroscopy (XAS) were used to investigate the functional and structural effects of pH on the oxygen affinity of three homologous arthropod hemocyanins (Hcs). Flash photolysis measurements showed that the well-characterized pH dependence of oxygen affinity (Bohr effect) is attributable to changes in the oxygen binding rate constant, kon, rather than changes in koff. In parallel, coordination geometry of copper in Hc was evaluated as a function of pH by XAS. It was found that the geometry of copper in the oxygenated protein is unchanged at all pH values investigated, while significant changes were observedmore » for the deoxygenated protein as a function of pH. The interpretation of these changes was based on previously described correlations between spectral lineshape and coordination geometry obtained for model compounds of known structure A pH-dependent change in the geometry of cuprous copper in the active site of deoxyHc, from pseudotetrahedral toward trigonal was assigned from the observed intensity dependence of the 1s ? 4pz transition in x-ray absorption near edge structure (XANES) spectra. The structural alteration correlated well with increase in oxygen affinity at alkaline pH determined in flash photolysis experiments. These results suggest that the oxygen binding rate in deoxyHc depends on the coordination geometry of Cu(I) and suggest a structural origin for the Bohr effect in arthropod Hcs.« less

Deep transfer learning for automatic target classification: MWIR to LWIR

NASA Astrophysics Data System (ADS)

Ding, Zhengming; Nasrabadi, Nasser; Fu, Yun

2016-05-01

Publisher's Note: This paper, originally published on 5/12/2016, was replaced with a corrected/revised version on 5/18/2016. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance. When dealing with sparse or no labeled data in the target domain, transfer learning shows its appealing performance by borrowing the supervised knowledge from external domains. Recently deep structure learning has been exploited in transfer learning due to its attractive power in extracting effective knowledge through multi-layer strategy, so that deep transfer learning is promising to address the cross-domain mismatch. In general, cross-domain disparity can be resulted from the difference between source and target distributions or different modalities, e.g., Midwave IR (MWIR) and Longwave IR (LWIR). In this paper, we propose a Weighted Deep Transfer Learning framework for automatic target classification through a task-driven fashion. Specifically, deep features and classifier parameters are obtained simultaneously for optimal classification performance. In this way, the proposed deep structures can extract more effective features with the guidance of the classifier performance; on the other hand, the classifier performance is further improved since it is optimized on more discriminative features. Furthermore, we build a weighted scheme to couple source and target output by assigning pseudo labels to target data, therefore we can transfer knowledge from source (i.e., MWIR) to target (i.e., LWIR). Experimental results on real databases demonstrate the superiority of the proposed algorithm by comparing with others.

Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification.

PubMed

Verhoeven, Jacobus Th J; Meekes, Ellis T M; Roenhorst, Johanna W; Flores, Ricardo; Serra, Pedro

2013-04-01

A viroid-like RNA has been detected in two asymptomatic dahlia accessions by return and double PAGE. It appeared smaller than Chrysanthemum stunt viroid and Potato spindle tuber viroid, the two members of the genus Pospiviroid, family Pospiviroidae, reported in this ornamental previously. RT-PCR with primers designed for amplifying all pospiviroids produced no amplicons, but RT-PCR with random primers revealed a 342 nt RNA. The sequence of this RNA was confirmed with specific primers, which additionally revealed its presence in many dahlia cultivars. The RNA was named Dahlia latent viroid (DLVd) because it replicates autonomously, but symptomlessly, in dahlia and shares maximum sequence identity with other viroids of less than 56 %. Furthermore, DLVd displays characteristic features of the family Pospiviroidae: a predicted rod-like secondary structure of minimum free energy with a central conserved region (CCR), and the ability to form the metastable structures hairpins I and II. Its CCR is identical to that of Hop stunt viroid (HSVd, genus Hostuviroid). However, DLVd: (i) has the terminal conserved region present in members of the genus Pospiviroid, but absent in HSVd, and (ii) lacks the terminal conserved hairpin present in HSVd. Phylogenetic reconstructions indicate that HSVd and Pepper chat fruit viroid (genus Pospiviroid) are the closest relatives of DLVd, but DLVd differs from these viroids in its host range, restricted to dahlia so far. Therefore, while DLVd fulfils the criteria to be a novel species of the family Pospiviroidae, its recombinant origin makes assignment to the genera Pospiviroid or Hostuviroid problematic.

High-resolution Fourier transform synchrotron spectroscopy of the C-S stretching band of methyl mercaptan, CH332SH

NASA Astrophysics Data System (ADS)

Lees, R. M.; Xu, Li-Hong; Billinghurst, B. E.

2016-01-01

The C-S stretching fundamental band of 12CH332SH, the principal isotopologue of methyl mercaptan, has been investigated by Fourier transform infrared spectroscopy on the Far-Infrared beamline at the Canadian Light Source synchrotron. The band is centered around 710 cm-1 and shows well-resolved a-type parallel structure. Most of the A and E spectral sub-bands have been assigned up to K = 12 for the vt = 0 torsional state and K = 9 for the vt = 1 state, along with a smaller variety of sub-bands for vt = 2. C-S stretching energy term values have been determined employing known ground-state energies, and have been fitted to series expansions in powers of J(J + 1) to determine the substate origins. The origins have in turn been fitted to a Fourier model to characterize the oscillatory torsional energy structure of the C-S stretching state. The amplitude of oscillation of the vt = 0 torsional curves is significantly larger for the C-S stretch state compared to the ground state. A strategy devised to relate this amplitude to an effective torsional barrier height indicates a decrease of about 7% in the effective V3 for the C-S stretch. The vibrational frequency determined for the stretching fundamental from the Fourier fit is 710.3 cm-1. The C-S stretching manifold is crossed by excited vt = 4 torsional levels of the ground state, and strong torsion-vibrational resonant coupling is observed via perturbations in the spectrum together with forbidden sub-bands induced by mixing and intensity borrowing.

A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment

PubMed Central

Mobli, Mehdi; Stern, Alan S.; Bermel, Wolfgang; King, Glenn F.; Hoch, Jeffrey C.

2010-01-01

One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives. PMID:20299257

The evolving market structures of gambling: case studies modelling the socioeconomic assignment of gaming machines in Melbourne and Sydney, Australia.

PubMed

Marshall, David C; Baker, Robert G V

2002-01-01

The expansion of gambling industries worldwide is intertwined with the growing government dependence on gambling revenue for fiscal assignments. In Australia, electronic gaming machines (EGMs) have dominated recent gambling industry growth. As EGMs have proliferated, growing recognition has emerged that EGM distribution closely reflects levels of socioeconomic disadvantage. More machines are located in less advantaged regions. This paper analyses time-series socioeconomic distributions of EGMs in Melbourne, Australia, an immature EGM market, and then compares the findings with the mature market in Sydney. Similar findings in both cities suggest that market assignment of EGMs transcends differences in historical and legislative environments. This indicates that similar underlying structures are evident in both markets. Modelling the spatial structures of gambling markets provides an opportunity to identify regions most at risk of gambling related problems. Subsequently, policies can be formulated which ensure fiscal revenue from gambling can be better targeted towards regions likely to be most afflicted by excessive gambling-related problems.

Interfacial assignment of branched-alkyl benzene sulfonates: A molecular simulation

NASA Astrophysics Data System (ADS)

Liu, Zi-Yu; Wei, Ning; Wang, Ce; Zhou, He; Zhang, Lei; Liao, Qi; Zhang, Lu

2015-11-01

A molecular dynamics simulation was conducted to analyze orientations of sodium branched-alkyl benzene sulfonates molecules at nonane/water interface, which is helpful to design optimal surfactant structures to achieve ultralow interfacial tension (IFT). Through the two dimensional density profiles, monolayer collapses are found when surfactant concentration continues to increase. Thus the precise scope of monolayer is certain and orientation can be analyzed. Based on the simulated results, we verdict the interfacial assignment of branched-alkyl benzene sulfonates at the oil-water interface, and discuss the effect of hydrophobic tail structure on surfactant assignment. Bigger hydrophobic size can slow the change rate of surfactant occupied area as steric hindrance, and surfactant meta hydrophobic tails have a stronger tendency to stretch to the oil phase below the collapsed concentration. Furthermore, an interfacial model with reference to collapse, increasing steric hindrance and charge repulsive force between interfacial surfactant molecules, responsible for effecting of surfactant concentration and structure has been supposed.

1H, 15N and 13C resonance assignments for free and IEEVD peptide-bound forms of the tetratricopeptide repeat domain from the human E3 ubiquitin ligase CHIP.

PubMed

Zhang, Huaqun; McGlone, Cameron; Mannion, Matthew M; Page, Richard C

2017-04-01

The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the 1 H, 13 C, and 15 N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

NASA Astrophysics Data System (ADS)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

Evaluation of different derivatisation approaches for gas chromatographic-mass spectrometric analysis of carbohydrates in complex matrices of biological and synthetic origin.

PubMed

Becker, M; Zweckmair, T; Forneck, A; Rosenau, T; Potthast, A; Liebner, F

2013-03-15

Gas chromatographic analysis of complex carbohydrate mixtures requires highly effective and reliable derivatisation strategies for successful separation, identification, and quantitation of all constituents. Different single-step (per-trimethylsilylation, isopropylidenation) and two-step approaches (ethoximation-trimethylsilylation, ethoximation-trifluoroacetylation, benzoximation-trimethylsilylation, benzoximation-trifluoroacetylation) have been comprehensively studied with regard to chromatographic characteristics, informational value of mass spectra, ease of peak assignment, robustness toward matrix effects, and quantitation using a set of reference compounds that comprise eight monosaccharides (C(5)-C(6)), glycolaldehyde, and dihydroxyacetone. It has been shown that isopropylidenation and the two oximation-trifluoroacetylation approaches are least suitable for complex carbohydrate matrices. Whereas the former is limited to compounds that contain vicinal dihydroxy moieties in cis configuration, the latter two methods are sensitive to traces of trifluoroacetic acid which strongly supports decomposition of ketohexoses. It has been demonstrated for two "real" carbohydrate-rich matrices of biological and synthetic origin, respectively, that two-step ethoximation-trimethylsilylation is superior to other approaches due to the low number of peaks obtained per carbohydrate, good peak separation performance, structural information of mass spectra, low limits of detection and quantitation, minor relative standard deviations, and low sensitivity toward matrix effects. Copyright © 2013 Elsevier B.V. All rights reserved.

Phototaxis and the origin of visual eyes

PubMed Central

Randel, Nadine

2016-01-01

Vision allows animals to detect spatial differences in environmental light levels. High-resolution image-forming eyes evolved from low-resolution eyes via increases in photoreceptor cell number, improvements in optics and changes in the neural circuits that process spatially resolved photoreceptor input. However, the evolutionary origins of the first low-resolution visual systems have been unclear. We propose that the lowest resolving (two-pixel) visual systems could initially have functioned in visual phototaxis. During visual phototaxis, such elementary visual systems compare light on either side of the body to regulate phototactic turns. Another, even simpler and non-visual strategy is characteristic of helical phototaxis, mediated by sensory–motor eyespots. The recent mapping of the complete neural circuitry (connectome) of an elementary visual system in the larva of the annelid Platynereis dumerilii sheds new light on the possible paths from non-visual to visual phototaxis and to image-forming vision. We outline an evolutionary scenario focusing on the neuronal circuitry to account for these transitions. We also present a comprehensive review of the structure of phototactic eyes in invertebrate larvae and assign them to the non-visual and visual categories. We propose that non-visual systems may have preceded visual phototactic systems in evolution that in turn may have repeatedly served as intermediates during the evolution of image-forming eyes. PMID:26598725

Intraclass Correlation Values for Planning Group-Randomized Trials in Education

ERIC Educational Resources Information Center

Hedges, Larry V.; Hedberg, E. C.

2007-01-01

Experiments that assign intact groups to treatment conditions are increasingly common in social research. In educational research, the groups assigned are often schools. The design of group-randomized experiments requires knowledge of the intraclass correlation structure to compute statistical power and sample sizes required to achieve adequate…

Distributed Collaborative Homework Activities in a Problem-Based Usability Engineering Course

ERIC Educational Resources Information Center

Carroll, John M.; Jiang, Hao; Borge, Marcela

2015-01-01

Teams of students in an upper-division undergraduate Usability Engineering course used a collaborative environment to carry out a series of three distributed collaborative homework assignments. Assignments were case-based analyses structured using a jigsaw design; students were provided a collaborative software environment and introduced to a…

Appropriate Technology and Journal Writing: Structured Dialogues that Enhance Learning

ERIC Educational Resources Information Center

Longhurst, James; Sandage, Scott A.

2004-01-01

Of the many available options, instructors should choose "appropriate technology" that meets pedagogical goals with minimum disruption. Student journal assignments follow many teaching "best practices" but consume time and energy; we recommend e-mail as the most appropriate choice for journal assignments. E-mail encourages fast and personalized…

Correction of spin diffusion during iterative automated NOE assignment

NASA Astrophysics Data System (ADS)

Linge, Jens P.; Habeck, Michael; Rieping, Wolfgang; Nilges, Michael

2004-04-01

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus β-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.

PICKY: a novel SVD-based NMR spectra peak picking method

PubMed Central

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-01-01

Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 Å. Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking. Contact: mli@uwaterloo.ca PMID:19477998

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.

PubMed

Gold, Nicola D; Jackson, Richard M

2006-02-03

The rapid growth in protein structural data and the emergence of structural genomics projects have increased the need for automatic structure analysis and tools for function prediction. Small molecule recognition is critical to the function of many proteins; therefore, determination of ligand binding site similarity is important for understanding ligand interactions and may allow their functional classification. Here, we present a binding sites database (SitesBase) that given a known protein-ligand binding site allows rapid retrieval of other binding sites with similar structure independent of overall sequence or fold similarity. However, each match is also annotated with sequence similarity and fold information to aid interpretation of structure and functional similarity. Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known. Alternatively, the resource can provide valuable information for detailed studies of molecular recognition including structure-based ligand design and in understanding ligand cross-reactivity. Here, we show examples of atomic similarity between superfamily or more distant fold relatives as well as between seemingly unrelated proteins. Assignment of unclassified proteins to structural superfamiles is also undertaken and in most cases substantiates assignments made using sequence similarity. Correct assignment is also possible where sequence similarity fails to find significant matches, illustrating the potential use of binding site comparisons for newly determined proteins.

Collaborative group work: effects of group size and assignment structure on learning gain, student satisfaction and perceived participation.

PubMed

Kooloos, Jan G M; Klaassen, Tim; Vereijken, Mayke; Van Kuppeveld, Sascha; Bolhuis, Sanneke; Vorstenbosch, Marc

2011-01-01

Collaborative group sessions in Nijmegen include 15 students who work all together on a group assignment. Sometimes, the group is split-up in three and every subgroup elaborates a part of the assignment. At the end, they peer-teach each other. It is believed that the split-up enhances participation and therefore learning gain. To establish the effect of group size and structure of the assignment on the perceived participation, the satisfaction and learning gain of collaborative group sessions. In this study, 27 groups of 15 students were equally divided into: A-group: all 15 students working on the complete assignment. B-group: subgroups of 5 students working on the complete assignment. C-group: subgroups of 5 students working on a smaller part, and peer-teaching each other at the end of the group session. All students took a pre-test, a post-test and a follow-up test and completed a questionnaire. Questionnaires were analyzed with a one-way analysis of variance (ANOVA) and post hoc by multiple comparisons. Learning gain was analyzed using a repeated measures ANOVA. A group size effect is observed in favor of working in subgroups. Perceived participation of the students differs between A and B (p ≤ 0.001) and between A and C (p ≤ 0.001), but not between B and C. Also, an assignment effect is found in favor of the smaller assignment combined with peer-teaching. The students' satisfaction differs between A and C (p ≤ 0.003) and between B and C (p ≤ 0.001), but not between A and B. The C-group also shows higher test results (p ≤ 0.043). The students prefer smaller groups as well as smaller assignments including peer-teaching. A possible larger learning gain of this format needs to be re-investigated.

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

PubMed Central

Krishnarjuna, B.; Jaipuria, Garima; Thakur, Anushikha

2010-01-01

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective ‘unlabeling’ or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly 13C/15N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {12COi–15Ni+1}-filtered HSQC, which aids in linking the 1HN/15N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i − 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to 2H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of 14N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies. Electronic supplementary material The online version of this article (doi:10.1007/s10858-010-9459-z) contains supplementary material, which is available to authorized users. PMID:21153044

Arsenic-Based Life: An Active Learning Assignment for Teaching Scientific Discourse

ERIC Educational Resources Information Center

Johnson, R. Jeremy

2017-01-01

Among recent high profile scientific debates was the proposal that life could exist with arsenic in place of phosphorous in its nucleic acids and other biomolecules. Soon after its initial publication, scientists across diverse disciplines began to question this extraordinary claim. Using the original article, its claims, its scientific support,…

46 CFR 151.10-1 - Barge hull classifications.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 5 2011-10-01 2011-10-01 false Barge hull classifications. 151.10-1 Section 151.10-1... classifications. (a) Each barge constructed or converted in conformance with this subpart shall be assigned a hull... the hull type classification for the service for which they were originally approved. Changes in...

"My Lesson Plan Was Perfect Until I Tried to Teach": Care Ethics into Practice in Classroom Management

ERIC Educational Resources Information Center

Rabin, Colette; Smith, Grinell

2016-01-01

As teacher educators, the authors developed an assignment focused on care ethics to prepare teacher candidates to design classroom-management procedures aimed at cultivating caring community. The teacher candidates revised traditional classroom-management processes, such as class rules, into cocreated norms. They also designed original management…

A meta-analysis of bacterial diversity in the feces of cattle

USDA-ARS?s Scientific Manuscript database

In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13447 sequences were assigned t...

77 FR 72349 - SBI International, Inc. v. Mr. Howard Finkel c/o Cosco Container Lines; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-05

... Cosco Container Lines; Notice of Filing of Complaint and Assignment Notice is given that a complaint has... registered in Florida, hereinafter ``Complainant,'' against Mr. Howard Finkel c/o Cosco Container Lines, hereinafter ``Respondent.'' Complainant alleges that ``4 refrigerated containers originating from the USA port...

Approaches to Studying the Enacted Mathematics Curriculum. Research in Mathematics Education

ERIC Educational Resources Information Center

Heck, Dan, Ed.; Chval, Kathryn, Ed.; Weiss, Iris, Ed.; Ziebarth, Steven W., Ed.

2012-01-01

Curriculum materials are among the most pervasive and powerful influences on school mathematics. In many mathematics classes, student assignments, the questions the teacher asks, the ways students are grouped, the forms of assessment, and much more originate in curriculum materials. At the same time, teachers have considerable latitude in how they…

Variability in expression of anadromy by female Oncorhynchus mykiss within a river network

Treesearch

Justin S. Mills; Jason B. Dunham; Gordon H. Reeves; John R. McMillan; Christian E. Zimmerman; Chris E. Jordan

2012-01-01

We described and predicted spatial variation in marine migration (anadromy) of female Oncorhynchus mykiss in the John Day River watershed, Oregon. We collected 149 juvenile O. mykiss across 72 sites and identified locations used by anadromous females by assigning maternal origin (anadromous versus non-anadromous) to each...

Hot Band Analysis and Kinetics Measurements for Ethynyl Radical, C_2H, in the 1.49 μm Region

NASA Astrophysics Data System (ADS)

Le, Anh T.; Hall, Gregory; Sears, Trevor

2017-06-01

Ethynyl, C_2H, is an important intermediate in combustion processes and has been widely observed in interstellar space. Spectroscopically, it is of particular interest because it possesses three low-lying electronic surfaces: a ground ^2Σ^+state, and a low-lying ^2Π excited electronic state, which splits due to the Renner-Teller effect. Vibronic coupling among these states leads to a complicated, mixed-character, energy level structure. We have previously reported work on three bands originating from the ˜{X}(0,0,0) ^2Σ ground state to excited vibronic states: two ^2Σ - ^2 Σ transitions at 6696 and 7088 \\wn and a ^2Π - ^2Σ transition at 7108 \\wn. In this work, the radicals were formed in a hot, non-thermal, population distribution by u.v. pulsed laser photolysis of a precursor. Kinetic measurements of the time-evolution of the ground state populations following collisional relaxation and reactive loss were also made, using some of the stronger rotational lines observed. Time-dependent signals in mixtures containing a variable concentration of precursor in argon suggested that vibronically hot C_2H radicals were less reactive than the relaxed, thermalized, radical. Two additional hot bands originating in states ˜{X}(0,1^1,0) ^2Π and ˜{X}(0,2^0,0) ^2Σ, have now been identified in the same spectral region. In a new series of experiments, we have measured the kinetics of formation and decay of representative levels involving all the assigned transitions, i.e. originating in ˜{X}(0,v_2,0), with v_2 =0 ,1, and 2, in various concentrations of mixtures of precursor, inert gas and hydrogen. The new spectra also show greatly improved signal-to-noise ratio in comparison to our previous work, due to the use of a transient FM detection scheme, and additional spectral assignments seem likely. Both kinetics and spectroscopic results will be described in the talk. Acknowledgments: Work at Brookhaven National Laboratory was carried out under Contract No. DE-SC0012704 with the U.S. Department of Energy, Office of Science, and supported by its Division of Chemical Sciences, Geosciences and Biosciences within the Office of Basic Energy Sciences. A. T. Le, G. E. Hall, T. J. Sears, J. Chem. Phys. 145 074306, 2016

Morality Principles for Risk Modelling: Needs and Links with the Origins of Plausible Inference

NASA Astrophysics Data System (ADS)

Solana-Ortega, Alberto; Solana, Vicente

2009-12-01

In comparison with the foundations of probability calculus, the inescapable and controversial issue of how to assign probabilities has only recently become a matter of formal study. The introduction of information as a technical concept was a milestone, but the most promising entropic assignment methods still face unsolved difficulties, manifesting the incompleteness of plausible inference theory. In this paper we examine the situation faced by risk analysts in the critical field of extreme events modelling, where the former difficulties are especially visible, due to scarcity of observational data, the large impact of these phenomena and the obligation to assume professional responsibilities. To respond to the claim for a sound framework to deal with extremes, we propose a metafoundational approach to inference, based on a canon of extramathematical requirements. We highlight their strong moral content, and show how this emphasis in morality, far from being new, is connected with the historic origins of plausible inference. Special attention is paid to the contributions of Caramuel, a contemporary of Pascal, unfortunately ignored in the usual mathematical accounts of probability.

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

PubMed

Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

2011-12-01

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms.

Single Stage Tandem Mass Spectrometry Assignment of the C-5 Uronic Acid Stereochemistry in Heparan Sulfate Tetrasaccharides using Electron Detachment Dissociation

NASA Astrophysics Data System (ADS)

Agyekum, Isaac; Zong, Chengli; Boons, Geert-Jan; Amster, I. Jonathan

2017-09-01

The analysis of heparan sulfate (HS) glycosaminoglycans presents many challenges, due to the high degree of structural heterogeneity arising from their non-template biosynthesis. Complete structural elucidation of glycosaminoglycans necessitates the unambiguous assignments of sulfo modifications and the C-5 uronic acid stereochemistry. Efforts to develop tandem mass spectrometric-based methods for the structural analysis of glycosaminoglycans have focused on the assignment of sulfo positions. The present work focuses on the assignment of the C-5 stereochemistry of the uronic acid that lies closest to the reducing end. Prior work with electron-based tandem mass spectrometry methods, specifically electron detachment dissociation (EDD), have shown great promise in providing stereo-specific product ions, such as the B3 ´ -CO2, which has been found to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) in some HS tetrasaccharides. The previously observed diagnostic ions are generally not observed with 2- O-sulfo uronic acids or for more highly sulfated heparan sulfate tetrasaccharides. A recent study using electron detachment dissociation and principal component analysis revealed a series of ions that correlate with GlcA versus IdoA for a set of 2- O-sulfo HS tetrasaccharide standards. The present work comprehensively investigates the efficacy of these ions for assigning the C-5 stereochemistry of the reducing end uronic acid in 33 HS tetrasaccharides. A diagnostic ratio can be computed from the sum of the ions that correlate to GlcA to those that correlate to IdoA. [Figure not available: see fulltext.

33 CFR 67.01-15 - Classification of structures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Classification of structures. 67... AIDS TO NAVIGATION AIDS TO NAVIGATION ON ARTIFICIAL ISLANDS AND FIXED STRUCTURES General Requirements § 67.01-15 Classification of structures. (a) When will structures be assigned to a Class? The District...

Redefining the modular organization of the core Mediator complex.

PubMed

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-07-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.

Redefining the modular organization of the core Mediator complex

PubMed Central

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-01-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation. PMID:24810298

Differently Structured Advance Organizers Lead to Different Initial Schemata and Learning Outcomes

ERIC Educational Resources Information Center

Gurlitt, Johannes; Dummel, Sebastian; Schuster, Silvia; Nuckles, Matthias

2012-01-01

Does the specific structure of advance organizers influence learning outcomes? In the first experiment, 48 psychology students were randomly assigned to three differently structured advance organizers: a well-structured, a well-structured and key-concept emphasizing, and a less structured advance organizer. These were followed by a sorting task, a…

Molecular and Morphological Evidence Challenges the Records of the Extant Liverwort Ptilidium pulcherrimum in Eocene Baltic Amber.

PubMed

Heinrichs, Jochen; Scheben, Armin; Lee, Gaik Ee; Váňa, Jiří; Schäfer-Verwimp, Alfons; Krings, Michael; Schmidt, Alexander R

2015-01-01

Preservation of liverworts in amber, a fossilized tree resin, is often exquisite. Twenty-three fossil species of liverworts have been described to date from Eocene (35-50 Ma) Baltic amber. In addition, two inclusions have been assigned to the extant species Ptilidium pulcherrimum (Ptilidiales or Porellales). However, the presence of the boreal P. pulcherrimum in the subtropical or warm-temperate Baltic amber forest challenges the phytogeographical interpretation of the Eocene flora. A re-investigation of one of the fossils believed to be P. pulcherrimum reveals that this specimen in fact represents the first fossil evidence of the genus Tetralophozia, and thus is re-described here as Tetralophozia groehnii sp. nov. A second fossil initially assigned to P. pulcherrimum is apparently lost, and can be reassessed only based on the original description and illustrations. This fossil is morphologically similar to the extant North Pacific endemic Ptilidium californicum, rather than P. pulcherrimum. Divergence time estimates based on chloroplast DNA sequences provide evidence of a Miocene origin of P. pulcherrimum, and thus also argue against the presence of this taxon in the Eocene. Ptilidium californicum originated 25-43 Ma ago. As a result, we cannot rule out that the Eocene fossil belongs to P. californicum. Alternatively, the fossil might represent a stem lineage element of Ptilidium or an early crown group species with morphological similarities to P. californicum.

Establishing the 3-D finite element solid model of femurs in partial by volume rendering.

PubMed

Zhang, Yinwang; Zhong, Wuxue; Zhu, Haibo; Chen, Yun; Xu, Lingjun; Zhu, Jianmin

2013-01-01

It remains rare to report three-dimensional (3-D) finite element solid model of femurs in partial by volume rendering method, though several methods of femoral 3-D finite element modeling are already available. We aim to analyze the advantages of the modeling method by establishing the 3-D finite element solid model of femurs in partial by volume rendering. A 3-D finite element model of the normal human femurs, made up of three anatomic structures: cortical bone, cancellous bone and pulp cavity, was constructed followed by pretreatment of the CT original image. Moreover, the finite-element analysis was carried on different material properties, three types of materials given for cortical bone, six assigned for cancellous bone, and single for pulp cavity. The established 3-D finite element of femurs contains three anatomical structures: cortical bone, cancellous bone, and pulp cavity. The compressive stress primarily concentrated in the medial surfaces of femur, especially in the calcar femorale. Compared with whole modeling by volume rendering method, the 3-D finite element solid model created in partial is more real and fit for finite element analysis. Copyright © 2013 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Study of the β- decay of 116m1In: A new interpretation of low-lying 0+ states in 116Sn

NASA Astrophysics Data System (ADS)

Pore, J. L.; Cross, D. S.; Andreoiu, C.; Ashley, R.; Ball, G. C.; Bender, P. C.; Chester, A. S.; Diaz Varela, A.; Demand, G. A.; Dunlop, R.; Garnsworthy, A. B.; Garrett, P. E.; Hackman, G.; Hadinia, B.; Jigmeddorj, B.; Laffoley, A. T.; Liblong, A.; Kanungo, R.; Noakes, B.; Petrache, C. M.; Rajabali, M. M.; Starosta, K.; Svensson, C. E.; Voss, P. J.; Wang, Z. M.; Wood, J. L.; Yates, S. W.

2017-02-01

The 116Sn nucleus contains a collective rotational band originating from proton π 2 p-2 h excitations across the proton Z=50 shell gap. Even though this nucleus has been extensively investigated in the past, there was still missing information on the low-energy interband transitions connecting the intruder and normal structures. The low-lying structure of 116Sn was investigated through a high-statistics study of the β- decay of 116m1In with the 8π spectrometer and its ancillary detectors at TRIUMF. These measurements are critical in order to properly characterize the π 2 p-2 h rotational band. Weak γ-decay branches are observed utilizing γ-γ coincidence spectroscopy methods, leading to the first direct observation of the 85 keV 22+→ 03+ γ ray with a transition strength of B(E2) = 99.7(84) W.u. The analysis of these results strongly suggests that the 2027 keV 03+ state should replace the previously assigned 1757 keV 02+ state as the band-head of the π 2 p-2 h rotational band.

Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

2013-01-01

In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

Genome structure of Rosa multiflora, a wild ancestor of cultivated roses

PubMed Central

Nakamura, Noriko; Hirakawa, Hideki; Sato, Shusei; Otagaki, Shungo; Matsumoto, Shogo; Tabata, Satoshi; Tanaka, Yoshikazu

2018-01-01

Abstract The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses. PMID:29045613

Skeletons in confusion: a review of astrophorid sponges with (dicho–)calthrops as structural megascleres (Porifera, Demospongiae, Astrophorida)

PubMed Central

Van Soest, Rob W.M.; Beglinger, Elly J.; De Voogd, Nicole J.

2010-01-01

Abstract We present a review of astrophorid species possessing calthrops megascleres as structural megascleres (including species with dichotriaene modifications, but excluding mesotriaene and trichotriaene bearing species). Radiating oxeas characteristic of most astrophorids are lacking in such sponges, but auxiliary oxeas are apparently present in some species. These sponges are currently assigned to two families, Pachastrellidae with four nominal genera Dercitus, Stoeba, Dercitancorina, Halinastra (the latter two generally considered junior synonyms of Stoeba), and Calthropellidae with nominal genera Calthropella, Corticellopsis (usually considered a junior synonym), Pachataxa and Pachastrissa. Our review of many original specimens and extensive new material demonstrates the existence of considerable morphological similarity in megasclere shape and arrangement, and possible overlap of some microscleres of these sponges: pseudasters in Dercitus resembling euasters in Calthropella, ataxasters and other modified types in Calthropellidae resembling rhabds in a species of Dercitus. Pachastrellid representatives are proposed to be united in a single genus Dercitus, recognizable as (dicho–)calthrops bearing sponges with sanidaster–like microrhabds. Three subgenera, Dercitus s.s., Stoeba and the revived Halinastra are distinguished to accommodate species groups sharing additional characters. Dercitancorina is merged with Dercitus (Stoeba), because the type species, Dercitus lesinensis was found to be barely distinct from Dercitus (Stoeba) plicatus. Similarly, the calthropellid representatives are proposed to be united in a single genus Calthropella recognizable as calthrops bearing sponges with oxyasters. Three subgenera, Calthropella s.s., Pachataxa and Corticellopsis are distinguished to accommodate species groups sharing additional characters. The calthropellid genus Pachastrissa is considered a junior synonym of Calthropella s.s. because its type species, Pachastrella geodioides, is barely distinct from the type species of Calthropella, Calthropella simplex. Two species previously assigned to Dercitus or Stoeba (Dercitus loricatus and Stoeba natalensis) are excluded from the genus Dercitus as they do not fit with the emended and improved definition of the genus. One species assigned to Calthropella, Calthropella digitata, is excluded from that genus and assigned to the ancorinid genus Stelletta. Based on the similarity of the megascleres and their structure-less arrangement, we predict that the two reviewed genera will be found to be closely related and eventually will need to be accomodated in a single family, but independent molecular evidence is awaited before changes in the family classification, including a verdict on the validity of the family Calthropellidae, will be proposed. Our review included 38 valid species among which fourteen species and one subspecies appear to be new to science. Four of these were represented by insufficient material for a proper description, but the remaining ten are described as new species: Dercitus (Stoeba) senegalensis sp. n., Dercitus (Stoeba) verdensis sp. n., Dercitus (Stoeba) fijiensis sp. n., Dercitus (Stoeba) bahamensis sp. n., Dercitus (Halinastra) berau sp. n., Dercitus (Halinastra) japonensis sp. n., Dercitus (Halinastra) arubensis sp. n., Dercitus (Halinastra) sibogae sp. n., Calthropella (Calthropella) xavierae sp. n., and Calthropella (Pachataxa) pyrifera sp. n. The new subspecies, Dercitus (Dercitus) bucklandi lusitanicus ssp. n. is described for southern East Atlantic populations of the nominal species. Several specimens assigned to existing species were found to be deviating to the extent that they are likely members of further undescribed species. These are briefly discussed to facilitate further studies of the diversity of the two genera. Species of both genera and the six subgenera, including deviating or insufficiently characterized specimens belonging to species not yet properly described, are keyed out. Distribution patterns are discussed. PMID:21594036

On the design of high-rise buildings with a specified level of reliability

NASA Astrophysics Data System (ADS)

Dolganov, Andrey; Kagan, Pavel

2018-03-01

High-rise buildings have a specificity, which significantly distinguishes them from traditional buildings of high-rise and multi-storey buildings. Steel structures in high-rise buildings are advisable to be used in earthquake-proof regions, since steel, due to its plasticity, provides damping of the kinetic energy of seismic impacts. These aspects should be taken into account when choosing a structural scheme of a high-rise building and designing load-bearing structures. Currently, modern regulatory documents do not quantify the reliability of structures. Although the problem of assigning an optimal level of reliability has existed for a long time. The article shows the possibility of designing metal structures of high-rise buildings with specified reliability. Currently, modern regulatory documents do not quantify the reliability of high-rise buildings. Although the problem of assigning an optimal level of reliability has existed for a long time. It is proposed to establish the value of reliability 0.99865 (3σ) for constructions of buildings and structures of a normal level of responsibility in calculations for the first group of limiting states. For increased (construction of high-rise buildings) and reduced levels of responsibility for the provision of load-bearing capacity, it is proposed to assign respectively 0.99997 (4σ) and 0.97725 (2σ). The coefficients of the use of the cross section of a metal beam for different levels of security are given.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Phylogeographic Structure in Benthic Marine Invertebrates of the Southeast Pacific Coast of Chile with Differing Dispersal Potential

PubMed Central

Haye, Pilar A.; Segovia, Nicolás I.; Muñoz-Herrera, Natalia C.; Gálvez, Francisca E.; Martínez, Andrea; Meynard, Andrés; Pardo-Gandarillas, María C.; Poulin, Elie; Faugeron, Sylvain

2014-01-01

The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure. PMID:24586356

Learning by Identification of Mistakes in Workings in Engineering Modules

ERIC Educational Resources Information Center

Chian, S. C.

2018-01-01

Conventional graded assignments are commonly structured in a format where students attempt a prescribed question and are graded based on the completeness of their workings rather than the understanding of concepts. An alternative assignment format was proposed which requires students to identify and explain mistakes in a given set of workings…

Characterizing dispersal patterns in a threatened seabird with limited genetic structure

Treesearch

Laurie A. Hall; Per J. Palsboll; Steven R. Beissinger; James T. Harvey; Martine Berube; Martin G. Raphael; Kim Nelson; Richard T. Golightly; Laura McFarlane-Tranquilla; Scott H. Newman; M. Zachariah Peery

2009-01-01

Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used...

42 CFR 23.4 - How must an entity apply for assignment?

Code of Federal Regulations, 2010 CFR

2010-10-01

... applicant's overall organizational structure; (2) A justification of the request for the assignment of personnel based upon the needs of the health manpower shortage area; (3) A description of the applicant's..., equipment and supplies; (4) A list of the proposed fees and discounted fees to be charged for the provision...

Cue Conflicts in Context: Interplay between Morphosyntax and Discourse Context in Danish Preschoolers' Semantic Role Assignment

ERIC Educational Resources Information Center

Thomsen, Ditte Boeg; Poulsen, Mads

2015-01-01

When learning their first language, children develop strategies for assigning semantic roles to sentence structures, depending on morphosyntactic cues such as case and word order. Traditionally, comprehension experiments have presented transitive clauses in isolation, and cross-linguistically children have been found to misinterpret object-first…

Rotational Spectroscopy and Conformational Studies of 4-PENTYNENITRILE, 4-PENTENENITRILE, and Glutaronitrile

NASA Astrophysics Data System (ADS)

Hays, Brian M.; Mehta-Hurt, Deepali; Jawad, Khadija M.; Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Zhang, Di; Zwier, Timothy S.

2017-06-01

The pure rotational spectra of 4-pentynenitrile, 4-pentenenitrile, and glutaronitrile were acquired using chirped pulse Fouirer transform microwave spectroscopy. 4-pentynenitrile and 4-pentenenitrile are the recombination products of two resonance stabilized radicals, propargyl + cyanomethyl or allyl + cyanomethyl, respectively, and are thus anticipated to be significant among the more complex nitriles in Titan's atmosphere. Indeed, these partially unsaturated alkyl cyanides have been found in laboratory analogs of tholins and are also expected to have interesting photochemistry. The optimized structures of all conformers below predicted energies of 500 \\wn were calculated for each molecule. Both of the conformers, trans and gauche, for 4-pentynenitrile have been identified and assigned. Five conformers were assigned in 4-pentenenitrile. The eclipsed conformers, with respect to the vinyl group, dominate the spectrum but some population was found in the syn conformers including the syn-gauche conformer, calculated to be 324 \\wn above the global minimum. The glutaronitrile spectrum contained only the two conformers below 500 \\wn, with reduced amount of the gauche trans conformer. The assigned spectra and structural assignments will be presented.

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

Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.

Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure ofmore » Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.« less

Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates.

PubMed

Southan, Christopher; Williams, Antony J; Ekins, Sean

2013-01-01

There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structural assignment of poecillastrins B and C, macrolide lactams from the deep-water Caribbean sponge Poecillastra species.

PubMed

Takada, Kentaro; Choi, Byoung W; Rashid, Mohammad A; Gamble, William R; Cardellina, John H; Van, Que N; Lloyd, John R; McMahon, James B; Gustafson, Kirk R

2007-03-01

Two new chondropsin-type macrolide lactams, poecillastrins B (1) and C (2), were isolated from aqueous extracts of the marine sponge Poecillastra sp. These trace metabolites were isolated in low yield (400-600 microg), and their structures were determined primarily by analysis of NMR data acquired using a cyrogenically cooled probe. High-quality 1D and 2D NMR data sets allowed complete assignment of the spectroscopic data and defined the new structures as 35-membered ring analogues of poecillastrin A (3). Compounds 1 and 2 showed potent cytotoxic activity against a human melanoma tumor cell line (LOX) with an IC50 value of less than 1 microg/mL.

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Methanococcus jannaschii genome: revisited

NASA Technical Reports Server (NTRS)

Kyrpides, N. C.; Olsen, G. J.; Klenk, H. P.; White, O.; Woese, C. R.

1996-01-01

Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).

Using Audit Information to Adjust Parameter Estimates for Data Errors in Clinical Trials

PubMed Central

Shepherd, Bryan E.; Shaw, Pamela A.; Dodd, Lori E.

2013-01-01

Background Audits are often performed to assess the quality of clinical trial data, but beyond detecting fraud or sloppiness, the audit data is generally ignored. In earlier work using data from a non-randomized study, Shepherd and Yu (2011) developed statistical methods to incorporate audit results into study estimates, and demonstrated that audit data could be used to eliminate bias. Purpose In this manuscript we examine the usefulness of audit-based error-correction methods in clinical trial settings where a continuous outcome is of primary interest. Methods We demonstrate the bias of multiple linear regression estimates in general settings with an outcome that may have errors and a set of covariates for which some may have errors and others, including treatment assignment, are recorded correctly for all subjects. We study this bias under different assumptions including independence between treatment assignment, covariates, and data errors (conceivable in a double-blinded randomized trial) and independence between treatment assignment and covariates but not data errors (possible in an unblinded randomized trial). We review moment-based estimators to incorporate the audit data and propose new multiple imputation estimators. The performance of estimators is studied in simulations. Results When treatment is randomized and unrelated to data errors, estimates of the treatment effect using the original error-prone data (i.e., ignoring the audit results) are unbiased. In this setting, both moment and multiple imputation estimators incorporating audit data are more variable than standard analyses using the original data. In contrast, in settings where treatment is randomized but correlated with data errors and in settings where treatment is not randomized, standard treatment effect estimates will be biased. And in all settings, parameter estimates for the original, error-prone covariates will be biased. Treatment and covariate effect estimates can be corrected by incorporating audit data using either the multiple imputation or moment-based approaches. Bias, precision, and coverage of confidence intervals improve as the audit size increases. Limitations The extent of bias and the performance of methods depend on the extent and nature of the error as well as the size of the audit. This work only considers methods for the linear model. Settings much different than those considered here need further study. Conclusions In randomized trials with continuous outcomes and treatment assignment independent of data errors, standard analyses of treatment effects will be unbiased and are recommended. However, if treatment assignment is correlated with data errors or other covariates, naive analyses may be biased. In these settings, and when covariate effects are of interest, approaches for incorporating audit results should be considered. PMID:22848072

Assignment of the gene locus for severe congenital neutropenia to chromosome 1q22 in the original Kostmann family from Northern Sweden.

PubMed

Melin, M; Entesarian, M; Carlsson, G; Garwicz, D; Klein, C; Fadeel, B; Nordenskjöld, M; Palmblad, J; Henter, J I; Dahl, N

2007-02-16

Autosomal recessive severe congenital neutropenia (SCN) or Kostmann syndrome is characterised by reduced neutrophil counts and subsequent recurrent bacterial infections. The disease was originally described in a large consanguineous pedigree from Northern Sweden. A genome-wide autozygosity scan was initiated on samples from four individuals in the original pedigree using high density single nucleotide polymorphism (SNP) genotyping arrays in order to map the disease locus. Thirty candidate regions were identified and the ascertainment of samples from two additional patients confirmed a single haplotype with significant association to the disorder (p<0.01) on chromosome 1q22. One affected individual from the original Kostmann pedigree was confirmed as a phenocopy. The minimal haplotype shared by affected individuals spans a candidate region of 1.2 Mb, containing several potential candidate genes.

Language use depending on news frame and immigrant origin.

PubMed

Fernández, Itziar; Igartua, Juan-José; Moral, Félix; Palacios, Elena; Acosta, Tania; Muñoz, Dolores

2013-01-01

The purpose of this study was to analyze the effect of the media on individuals' specific language use in relation to a news story on immigration: the influence of the news frame and group cue. Abstraction, complexity of language use, and negative affective language were evaluated. The 523 participants were randomly distributed to each of the four experimental conditions: news frame (crime versus economic contribution) by group cue (geographical origin of the immigrants involved: Moroccans versus Latin Americans). Through content analysis of the ideas and reflections that arose after the participants read the different news stories, using the Linguistic Category Model (LCM; Semin & Fiedler, 1991) to measure abstract language and the Linguistic Inquiry and Word Count (LIWC; Pennebaker, Booth, & Francis, 2007) to analyze complex language and negative affective language, it emerged that abstract language and negative affective language were more frequent in the participants assigned to the news frame on crime. Complex language was more commonly used when the news frame referred to the economic contribution of immigrants. Regression analyses showed the mediating role of attitude to immigration in the effects of news frame on negative affective language. The bootstrap method was used to assess the magnitude of the indirect effect. A significant mediator effect was also found through structural equation modeling. Analyses of covariance showed one interaction between news frame and group cue: Among those who read the news story in a frame linking immigration to crime and Moroccan origin, abstract language was more characteristic. The results are discussed from the theoretical perspective of framing.

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

Does Non-Compliance with Route/Destination Assignment Compromise Evacuation Efficiency?

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

Yuan, Fang; Han, Lee; Chin, Shih-Miao

2007-01-01

This paper documents studies of two real-world network evacuation cases, each with a different, but proven, simulation software package. The purpose of these studies was to examine whether the rate of evacuees' compliance with predetermined route/destination assignments would have an impact on the efficiency of evacuation operations. Results from both cases suggest that a rate of less than 100% compliance does not compromise evacuation efficiency. In fact, although this is counter-intuitive, evacuation efficiency would actually improve as a result of "sensible" non-compliance on the part of the evacuees. A closer observation of the results revealed that the somewhat unexpected improvementmore » results from a reduction in congestion along designated evacuation routes as evacuees spread out to less prominent parallel streets and other non-congested outbound routes. This suggests that by being limited by the zone-to-zone and one-to-one assignment framework, conventional evacuation plans may have fallen short of providing the most efficient guidance to evacuees. To address this issue, some systematic means, perhaps simulation-based, should be performed to assess the zone partitions, route designations, and destination assignments in existing evacuation plans. Thus, evacuation planning with route/destination assignments based on origin zones may be flawed and may deserve reconsideration. After all, once en route, where an evacuee is coming from is of far less consequence than where he or she is going.« less

(1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

PubMed

Moro, Sean L; Cocco, Melanie J

2015-10-01

The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

The role of high-level calculations in the assignment of the Q-band spectra of chlorophyll

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

Reimers, Jeffrey R.; Cai, Zheng-Li; Kobayashi, Rika

2014-10-06

We recently established a novel assignment of the visible absorption spectrum of chlorophyll-a that sees the two components Q{sub x} and Q{sub y} of the low-energy Q band as being intrinsically mixed by non-adiabatic coupling. This ended 50 years debate as to the nature of the Q bands, with prior discussion poised only in the language of the Born-Oppenheimer and Condon approximations. The new assignment presents significant ramifications for exciton transport and quantum coherence effects in photosystems. Results from state of the art electronic structure calculations have always been used to justify assignments, but quantitative inaccuracies and systematic failures havemore » historically limited usefulness. We examine the role of CAM-B3LYP time-dependent density-functional theory (TD-DFT) and Symmetry Adapted Cluster-Configuration Interaction (SAC-CI) calculations in first showing that all previous assignments were untenable, in justifying the new assignment, in making some extraordinary predictions that were vindicated by the new assignment, and in then identifying small but significant anomalies in the extensive experimental data record.« less

Quasi-Experimental Evidence of Peer Effects in First-Year Economics Courses at a Chinese University

ERIC Educational Resources Information Center

Chen, Qihui; Tian, Guoqiang; Okediji, Tade O.

2014-01-01

The authors of this article implement a quasi-experimental strategy to estimate peer effects in economic education by exploiting the institutional setting in a large public university in China, where roommates are randomly assigned conditional on a student's major and province of origin. They found significant impacts of peer academic quality,…

An Introduction to Propensity Scores: What, When, and How

ERIC Educational Resources Information Center

Beal, Sarah J.; Kupzyk, Kevin A.

2014-01-01

The use of propensity scores as a method to promote causality in studies that cannot use random assignment has increased dramatically since its original publication in 1983. While the utility of these approaches is important, the concepts underlying their use are complex. The purpose of this article is to provide a basic tutorial for conducting…

76 FR 79610 - Fisheries of the Northeastern United States; Atlantic Herring Fishery; Adjustment to 2012 Annual...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-22

... accuracy against the scanned image of the paper VTRs submitted by the owner/ operator of the vessel. VTR... review of the scanned images of the original VTR were used to assign landings to herring management area... further consideration after public comment. The National Environmental Policy Act analysis to support this...

7 CFR 1.325 - Form, filing and service of papers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 1 2010-01-01 2010-01-01 false Form, filing and service of papers. 1.325 Section 1... and service of papers. (a) Form. (1) The original and two copies of all papers in a proceeding conducted under this subpart shall be filed with the ALJ assigned to the case. (2) Every pleading and paper...

"Everybody Wants Somebody to Hear Their Story": High School Students Writing Screenplays

ERIC Educational Resources Information Center

Bedard, Carol; Fuhrken, Charles

2010-01-01

Writing a screenplay was an assignment that was part of Storytelling Through Film, a program sponsored by the Austin Film Festival, a professional film organization. In six weeks, students in creative writing and English classes first learned about the genre of screenwriting and then wrote original screenplays. The curriculum was a collaborative…