Using temporal sampling to improve attribution of source populations for invasive species.

PubMed

Goldstien, Sharyn J; Inglis, Graeme J; Schiel, David R; Gemmell, Neil J

2013-01-01

Numerous studies have applied genetic tools to the identification of source populations and transport pathways for invasive species. However, there are many gaps in the knowledge obtained from such studies because comprehensive and meaningful spatial sampling to meet these goals is difficult to achieve. Sampling populations as they arrive at the border should fill the gaps in source population identification, but such an advance has not yet been achieved with genetic data. Here we use previously acquired genetic data to assign new incursions as they invade populations within New Zealand ports and marinas. We also investigated allelelic frequency change in these recently established populations over a two-year period, and assessed the effect of temporal genetic sampling on our ability to assign new incursions to their population of source. We observed shifts in the allele frequencies among populations, as well as the complete loss of some alleles and the addition of alleles novel to New Zealand, within these recently established populations. There was no significant level of genetic differentiation observed in our samples between years, and the use of these temporal data did alter the assignment probability of new incursions. Our study further suggests that new incursions can add genetic variation to the population in a single introduction event as the founders themselves are often more genetically diverse than theory initially predicted.

A bayesian cross-validation approach to evaluate genetic baselines and forecast the necessary number of informative single nucleotide polymorphisms

USDA-ARS?s Scientific Manuscript database

Mixed stock analysis (MSA) is a powerful tool used in the management and conservation of numerous species. Its function is to estimate the sources of contributions in a mixture of populations of a species, as well as to estimate the probabilities that individuals originated at a source. Considerable...

Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

PubMed Central

BARKER, BRITTANY S.; ANDONIAN, KRIKOR; SWOPE, SARAH M.; LUSTER, DOUGLAS G.; DLUGOSCH, KATRINA M.

2017-01-01

Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species. Our analyses revealed clear population genomic structure of potential source populations in Eurasia, including deep differentiation of a lineage found in the southern Apennine and Balkan Peninsulas and divergence among populations in Asia, eastern Europe, and western Europe. We found strongest support for an evolutionary scenario in which western European populations were derived from an ancient admixture event between populations from eastern Europe and Asia, and subsequently served as the main genetic ‘bridgehead’ for introductions to the Americas. Introductions to California appear to be from a single source region, and multiple, independent introductions of divergent genotypes likely occurred into the Pacific Northwest. Plant size has evolved significantly at three points during range expansion, including a large size increase in the lineage responsible for the aggressive invasion of California’s interior. These results reveal a long history of colonization, admixture, and trait evolution in C. solstitialis, and suggest routes for improving evidence-based management decisions for one of the most ecologically and economically damaging invasive species in the western United States. PMID:28029713

Current steering to activate targeted neural pathways during deep brain stimulation of the subthalamic region

PubMed Central

Chaturvedi, Ashutosh; Foutz, Thomas J.; McIntyre, Cameron C.

2012-01-01

Deep brain stimulation (DBS) has steadily evolved into an established surgical therapy for numerous neurological disorders, most notably Parkinson’s disease (PD). Traditional DBS technology relies on voltage-controlled stimulation with a single source; however, recent engineering advances are providing current-controlled devices with multiple independent sources. These new stimulators deliver constant current to the brain tissue, irrespective of impedance changes that occur around the electrode, and enable more specific steering of current towards targeted regions of interest. In this study, we examined the impact of current steering between multiple electrode contacts to directly activate three distinct neural populations in the subthalamic region commonly stimulated for the treatment of PD: projection neurons of the subthalamic nucleus (STN), globus pallidus internus (GPi) fibers of the lenticular fasiculus, and internal capsule (IC) fibers of passage. We used three-dimensional finite element electric field models, along with detailed multi-compartment cable models of the three neural populations to determine their activations using a wide range of stimulation parameter settings. Our results indicate that selective activation of neural populations largely depends on the location of the active electrode(s). Greater activation of the GPi and STN populations (without activating any side-effect related IC fibers) was achieved by current steering with multiple independent sources, compared to a single current source. Despite this potential advantage, it remains to be seen if these theoretical predictions result in a measurable clinical effect that outweighs the added complexity of the expanded stimulation parameter search space generated by the more flexible technology. PMID:22277548

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.

PubMed

Nelson, Chase W; Moncla, Louise H; Hughes, Austin L

2015-11-15

New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population. SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie. nelsoncw@email.sc.edu or austin@biol.sc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Performance comparison of single axis tracking and 40° solar panels for sunny weather

NASA Astrophysics Data System (ADS)

Chua, Yaw Long; Yong, Yoon Kuang; Koh, Yit Yan

2017-09-01

The rapid increment in human population and economy growth had led to the rise of the energy demand globally. With the rapid diminishing fossil fuels based energy sources, renewable energy sources had been introduced due to its unlimited availability especially solar energy which is a sustainable and reliable energy. This research was conducted to study and compare the efficiency of the single axis tracking solar panel with a 40° inclined angle solar panel in sunny weather condition. The results indicated that the output generated by the solar panel was directly affected by the angle which the solar panel facing the sun. In terms of performance the single axis tracking solar panel emerged to be more efficient with greater energy generated.

V/V(max) test applied to SMM gamma-ray bursts

NASA Technical Reports Server (NTRS)

Matz, S. M.; Higdon, J. C.; Share, G. H.; Messina, D. C.; Iadicicco, A.

1992-01-01

We have applied the V/V(max) test to candidate gamma-ray bursts detected by the Gamma-Ray Spectrometer (GRS) aboard the SMM satellite to examine quantitatively the uniformity of the burst source population. For a sample of 132 candidate bursts identified in the GRS data by an automated search using a single uniform trigger criterion we find average V/V(max) = 0.40 +/- 0.025. This value is significantly different from 0.5, the average for a uniform distribution in space of the parent population of burst sources; however, the shape of the observed distribution of V/V(max) is unusual and our result conflicts with previous measurements. For these reasons we can currently draw no firm conclusion about the distribution of burst sources.

77 FR 29663 - Announcement of the Award of Single Source Expansion Supplement Grants to 11 Personal...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-18

... the minimal statistical power required to report significant outcome data that can be utilized to... competence in working in working with the target population; (d) reported gains in knowledge and intentions...

Invasive Cyprinid Fish in Europe Originate from the Single Introduction of an Admixed Source Population Followed by a Complex Pattern of Spread

PubMed Central

Simon, Andrea; Britton, Robert; Gozlan, Rodolphe; van Oosterhout, Cock; Volckaert, Filip A. M.; Hänfling, Bernd

2011-01-01

The Asian cyprinid fish, the topmouth gudgeon (Pseudorasbora parva), was introduced into Europe in the 1960s. A highly invasive freshwater fish, it is currently found in at least 32 countries outside its native range. Here we analyse a 700 base pair fragment of the mitochondrial cytochrome b gene to examine different models of colonisation and spread within the invasive range, and to investigate the factors that may have contributed to their invasion success. Haplotype and nucleotide diversity of the introduced populations from continental Europe was higher than that of the native populations, although two recently introduced populations from the British Isles showed low levels of variability. Based on coalescent theory, all introduced and some native populations showed a relative excess of nucleotide diversity compared to haplotype diversity. This suggests that these populations are not in mutation-drift equilibrium, but rather that the relative inflated level of nucleotide diversity is consistent with recent admixture. This study elucidates the colonisation patterns of P. parva in Europe and provides an evolutionary framework of their invasion. It supports the hypothesis that their European colonisation was initiated by their introduction to a single location or small geographic area with subsequent complex pattern of spread including both long distance and stepping-stone dispersal. Furthermore, it was preceded by, or associated with, the admixture of genetically diverse source populations that may have augmented its invasive-potential. PMID:21674031

THE POPULATION OF COMPACT RADIO SOURCES IN THE ORION NEBULA CLUSTER

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

Forbrich, J.; Meingast, S.; Rivilla, V. M.

We present a deep centimeter-wavelength catalog of the Orion Nebula Cluster (ONC), based on a 30 hr single-pointing observation with the Karl G. Jansky Very Large Array in its high-resolution A-configuration using two 1 GHz bands centered at 4.7 and 7.3 GHz. A total of 556 compact sources were detected in a map with a nominal rms noise of 3 μ Jy bm{sup −1}, limited by complex source structure and the primary beam response. Compared to previous catalogs, our detections increase the sample of known compact radio sources in the ONC by more than a factor of seven. The newmore » data show complex emission on a wide range of spatial scales. Following a preliminary correction for the wideband primary-beam response, we determine radio spectral indices for 170 sources whose index uncertainties are less than ±0.5. We compare the radio to the X-ray and near-infrared point-source populations, noting similarities and differences.« less

Global invasion network of the brown marmorated stink bug, Halyomorpha halys.

PubMed

Valentin, Rafael E; Nielsen, Anne L; Wiman, Nik G; Lee, Doo-Hyung; Fonseca, Dina M

2017-08-29

Human mediated transportation into novel habitats is a prerequisite for the establishment of non-native species that become invasive, so knowledge of common sources may allow prevention. The brown marmorated stink bug (BMSB, Halyomorpha halys) is an East Asian species now established across North America and Europe, that in the Eastern United States of America (US) and Italy is causing significant economic losses to agriculture. After US populations were shown to originate from Northern China, others have tried to source BMSB populations now in Canada, Switzerland, Italy, France, Greece, and Hungary. Due to selection of different molecular markers, however, integrating all the datasets to obtain a broader picture of BMSB's expansion has been difficult. To address this limitation we focused on a single locus, the barcode region in the cytochrome oxidase I mitochondrial gene, and analyzed representative BMSB samples from across its current global range using an Approximate Bayesian Computation approach. We found that China is the likely source of most non-native populations, with at least four separate introductions in North America and three in Europe. Additionally, we found evidence of one bridgehead event: a likely Eastern US source for the central Italy populations that interestingly share enhanced pest status.

Testing for multiple invasion routes and source populations for the invasive brown treesnake (Boiga irregularis) on Guam: implications for pest management

USGS Publications Warehouse

Richmond, Jonathan Q.; Wood, Dustin A.; Stanford, James W.; Fisher, Robert N.

2014-01-01

The brown treesnake (Boiga irregularis) population on the Pacific island of Guam has reached iconic status as one of the most destructive invasive species of modern times, yet no published works have used genetic data to identify a source population. We used DNA sequence data from multiple genetic markers and coalescent-based phylogenetic methods to place the Guam population within the broader phylogeographic context of B. irregularis across its native range and tested whether patterns of genetic variation on the island are consistent with one or multiple introductions from different source populations. We also modeled a series of demographic scenarios that differed in the effective size and duration of a population bottleneck immediately following the invasion on Guam, and measured the fit of these simulations to the observed data using approximate Bayesian computation. Our results exclude the possibility of serial introductions from different source populations, and instead verify a single origin from the Admiralty Archipelago off the north coast of Papua New Guinea. This finding is consistent with the hypothesis thatB. irregularis was accidentally transported to Guam during military relocation efforts at the end of World War II. Demographic model comparisons suggest that multiple snakes were transported to Guam from the source locality, but that fewer than 10 individuals could be responsible for establishing the population. Our results also provide evidence that low genetic diversity stemming from the founder event has not been a hindrance to the ecological success of B. irregularis on Guam, and at the same time offers a unique ‘genetic opening’ to manage snake density using classical biological approaches.

Sexual Reproduction in Aspergillus flavus Sclerotia: Acquisition of Novel Alleles from Soil Populations and Uniparental Mitochondrial Inheritance

PubMed Central

Horn, Bruce W.; Gell, Richard M.; Singh, Rakhi; Sorensen, Ronald B.; Carbone, Ignazio

2016-01-01

Aspergillus flavus colonizes agricultural commodities worldwide and contaminates them with carcinogenic aflatoxins. The high genetic diversity of A. flavus populations is largely due to sexual reproduction characterized by the formation of ascospore-bearing ascocarps embedded within sclerotia. A. flavus is heterothallic and laboratory crosses between strains of the opposite mating type produce progeny showing genetic recombination. Sclerotia formed in crops are dispersed onto the soil surface at harvest and are predominantly produced by single strains of one mating type. Less commonly, sclerotia may be fertilized during co-infection of crops with sexually compatible strains. In this study, laboratory and field experiments were performed to examine sexual reproduction in single-strain and fertilized sclerotia following exposure of sclerotia to natural fungal populations in soil. Female and male roles and mitochondrial inheritance in A. flavus were also examined through reciprocal crosses between sclerotia and conidia. Single-strain sclerotia produced ascospores on soil and progeny showed biparental inheritance that included novel alleles originating from fertilization by native soil strains. Sclerotia fertilized in the laboratory and applied to soil before ascocarp formation also produced ascospores with evidence of recombination in progeny, but only known parental alleles were detected. In reciprocal crosses, sclerotia and conidia from both strains functioned as female and male, respectively, indicating A. flavus is hermaphroditic, although the degree of fertility depended upon the parental sources of sclerotia and conidia. All progeny showed maternal inheritance of mitochondria from the sclerotia. Compared to A. flavus populations in crops, soil populations would provide a higher likelihood of exposure of sclerotia to sexually compatible strains and a more diverse source of genetic material for outcrossing. PMID:26731416

Clonal analysis of synovial fluid stem cells to characterize and identify stable mesenchymal stromal cell/mesenchymal progenitor cell phenotypes in a porcine model: a cell source with enhanced commitment to the chondrogenic lineage.

PubMed

Ando, Wataru; Kutcher, Josh J; Krawetz, Roman; Sen, Arindom; Nakamura, Norimasa; Frank, Cyril B; Hart, David A

2014-06-01

Previous studies have demonstrated that porcine synovial membrane stem cells can adhere to a cartilage defect in vivo through the use of a tissue-engineered construct approach. To optimize this model, we wanted to compare effectiveness of tissue sources to determine whether porcine synovial fluid, synovial membrane, bone marrow and skin sources replicate our understanding of synovial fluid mesenchymal stromal cells or mesenchymal progenitor cells from humans both at the population level and the single-cell level. Synovial fluid clones were subsequently isolated and characterized to identify cells with a highly characterized optimal phenotype. The chondrogenic, osteogenic and adipogenic potentials were assessed in vitro for skin, bone marrow, adipose, synovial fluid and synovial membrane-derived stem cells. Synovial fluid cells then underwent limiting dilution analysis to isolate single clonal populations. These clonal populations were assessed for proliferative and differentiation potential by use of standardized protocols. Porcine-derived cells demonstrated the same relationship between cell sources as that demonstrated previously for humans, suggesting that the pig may be an ideal preclinical animal model. Synovial fluid cells demonstrated the highest chondrogenic potential that was further characterized, demonstrating the existence of a unique clonal phenotype with enhanced chondrogenic potential. Porcine stem cells demonstrate characteristics similar to those in human-derived mesenchymal stromal cells from the same sources. Synovial fluid-derived stem cells contain an inherent phenotype that may be optimal for cartilage repair. This must be more fully investigated for future use in the in vivo tissue-engineered construct approach in this physiologically relevant preclinical porcine model. Copyright © 2014 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Seminal SIV in chronically-infected cynomolgus macaques is dominated by virus originating from multiple genital organs.

PubMed

Houzet, Laurent; Pérez-Losada, Marcos; Matusali, Giulia; Deleage, Claire; Dereuddre-Bosquet, Nathalie; Satie, Anne-Pascale; Aubry, Florence; Becker, Emmanuelle; Jégou, Bernard; Le Grand, Roger; Keele, Brandon F; Crandall, Keith A; Dejucq-Rainsford, Nathalie

2018-05-02

The sexual transmission of viruses is responsible for the spread of multiple infectious diseases. Although the HIV/AIDS pandemic remains fueled by sexual contacts with infected semen, the origin of virus in semen is still unknown. In a substantial number of HIV- infected men, viral strains present in semen differ from the ones in blood, suggesting that HIV is locally produced within the genital tract. Such local production may be responsible for the persistence of HIV in semen despite effective antiretroviral therapy. Here we use single genome amplification, amplicon sequencing ( env gene) and phylogenetic analyses to compare the genetic structure of SIV populations across all the male genital organs and blood in intravenously inoculated cynomolgus macaques in the chronic stage of infection. Examination of the virus populations present in the male genital tissues of the macaques revealed compartmentalized SIV populations in testis, epididymis, vas deferens, seminal vesicles and urethra. We found genetic similarities between the viral strains present in semen and those in epididymis, vas deferens and seminal vesicles. The contribution of male genital organs to virus shedding in semen varied among individuals and could not be predicted based on their infection or pro-inflammatory cytokine mRNA levels. These data indicate that, rather than a single source, multiple genital organs are involved in the release of free virus and infected cells into semen. These findings have important implications for our understanding of systemic virus shedding and persistence in semen and for the design of eradication strategies to access viral reservoirs. IMPORTANCE Semen is instrumental for the dissemination of viruses through sexual contacts. Worryingly, a number of systemic viruses such as HIV can persist in this body fluid in the absence of viremia. The local source(s) of virus in semen, however, remain unknown. To elucidate the anatomic origin(s) of the virus released in semen, we compared viral populations present in semen with those in the male genital organs and blood of the Asian macaque model, using single genome amplification, amplicon sequencing ( env gene) and phylogenetic analysis. Our results show that multiple genital tissues harbor compartmentalized strains, some of them (i.e. epididymis, vas deferens and seminal vesicle) displaying genetic similarities with the viral populations present in semen. This study is the first to uncover local genital sources of viral populations in semen, providing a new basis for innovative targeted strategies to prevent and eradicate HIV in the male genital tract. Copyright © 2018 Houzet et al.

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

NASA Astrophysics Data System (ADS)

Goldar, Arach

2011-03-01

The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

Copy Number Variation across European Populations

PubMed Central

Chen, Wanting; Hayward, Caroline; Wright, Alan F.; Hicks, Andrew A.; Vitart, Veronique; Knott, Sara; Wild, Sarah H.; Pramstaller, Peter P.; Wilson, James F.; Rudan, Igor; Porteous, David J.

2011-01-01

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations. PMID:21829696

Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.

PubMed

Jenkins, Paul A; Song, Yun S; Brem, Rachel B

2012-01-01

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

PubMed Central

Jenkins, Paul A.; Song, Yun S.; Brem, Rachel B.

2012-01-01

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance. PMID:23226196

7 CFR 1948.68 - Criteria for designation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... has historically occurred within the area; an increase (for which data or projected data is available... percent of the designated area's population; or data showing that available public facilities and services... calendar years. This data should be obtained from a single source for the entire State, if possible...

Modeling water demand when households have multiple sources of water

NASA Astrophysics Data System (ADS)

Coulibaly, Lassina; Jakus, Paul M.; Keith, John E.

2014-07-01

A significant portion of the world's population lives in areas where public water delivery systems are unreliable and/or deliver poor quality water. In response, people have developed important alternatives to publicly supplied water. To date, most water demand research has been based on single-equation models for a single source of water, with very few studies that have examined water demand from two sources of water (where all nonpublic system water sources have been aggregated into a single demand). This modeling approach leads to two outcomes. First, the demand models do not capture the full range of alternatives, so the true economic relationship among the alternatives is obscured. Second, and more seriously, economic theory predicts that demand for a good becomes more price-elastic as the number of close substitutes increases. If researchers artificially limit the number of alternatives studied to something less than the true number, the price elasticity estimate may be biased downward. This paper examines water demand in a region with near universal access to piped water, but where system reliability and quality is such that many alternative sources of water exist. In extending the demand analysis to four sources of water, we are able to (i) demonstrate why households choose the water sources they do, (ii) provide a richer description of the demand relationships among sources, and (iii) calculate own-price elasticity estimates that are more elastic than those generally found in the literature.

Open-Source Data and the Study of Homicide.

PubMed

Parkin, William S; Gruenewald, Jeff

2015-07-20

To date, no discussion has taken place in the social sciences as to the appropriateness of using open-source data to augment, or replace, official data sources in homicide research. The purpose of this article is to examine whether open-source data have the potential to be used as a valid and reliable data source in testing theory and studying homicide. Official and open-source homicide data were collected as a case study in a single jurisdiction over a 1-year period. The data sets were compared to determine whether open-sources could recreate the population of homicides and variable responses collected in official data. Open-source data were able to replicate the population of homicides identified in the official data. Also, for every variable measured, the open-sources captured as much, or more, of the information presented in the official data. Also, variables not available in official data, but potentially useful for testing theory, were identified in open-sources. The results of the case study show that open-source data are potentially as effective as official data in identifying individual- and situational-level characteristics, provide access to variables not found in official homicide data, and offer geographic data that can be used to link macro-level characteristics to homicide events. © The Author(s) 2015.

76 FR 31964 - Announcement of the Award of Nine Single-Source Expansion Supplement Grants

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-02

... period, the ORR-eligible populations will continue to have access to program services without... Grantee Location expansion supplement Church World Service/Immigration & New York, NY........ $4,694,800...,200 Immigrants. World Relief Corporation of Baltimore, MD....... 4,248,200 National Association of...

Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) – implications for future reintroductions

PubMed Central

Senn, Helen; Ogden, Rob; Frosch, Christiane; Syrůčková, Alena; Campbell-Palmer, Roisin; Munclinger, Pavel; Durka, Walter; Kraus, Robert H S; Saveljev, Alexander P; Nowak, Carsten; Stubbe, Annegret; Stubbe, Michael; Michaux, Johan; Lavrov, Vladimir; Samiya, Ravchig; Ulevicius, Alius; Rosell, Frank

2014-01-01

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487–489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction. PMID:25067948

Pollutant source identification model for water pollution incidents in small straight rivers based on genetic algorithm

NASA Astrophysics Data System (ADS)

Zhang, Shou-ping; Xin, Xiao-kang

2017-07-01

Identification of pollutant sources for river pollution incidents is an important and difficult task in the emergency rescue, and an intelligent optimization method can effectively compensate for the weakness of traditional methods. An intelligent model for pollutant source identification has been established using the basic genetic algorithm (BGA) as an optimization search tool and applying an analytic solution formula of one-dimensional unsteady water quality equation to construct the objective function. Experimental tests show that the identification model is effective and efficient: the model can accurately figure out the pollutant amounts or positions no matter single pollution source or multiple sources. Especially when the population size of BGA is set as 10, the computing results are sound agree with analytic results for a single source amount and position identification, the relative errors are no more than 5 %. For cases of multi-point sources and multi-variable, there are some errors in computing results for the reasons that there exist many possible combinations of the pollution sources. But, with the help of previous experience to narrow the search scope, the relative errors of the identification results are less than 5 %, which proves the established source identification model can be used to direct emergency responses.

Diffuse Galactic antimatter from faint thermonuclear supernovae in old stellar populations

NASA Astrophysics Data System (ADS)

Crocker, Roland M.; Ruiter, Ashley J.; Seitenzahl, Ivo R.; Panther, Fiona H.; Sim, Stuart; Baumgardt, Holger; Möller, Anais; Nataf, David M.; Ferrario, Lilia; Eldridge, J. J.; White, Martin; Tucker, Brad E.; Aharonian, Felix

2017-06-01

Our Galaxy hosts the annihilation of a few 1043 low-energy positrons every second. Radioactive isotopes capable of supplying such positrons are synthesized in stars, stellar remnants and supernovae. For decades, however, there has been no positive identification of a main stellar positron source, leading to suggestions that many positrons originate from exotic sources like the Galaxy's central supermassive black hole or dark matter annihilation. Here we show that a single type of transient source, deriving from stellar populations of age 3-6 Gyr and yielding ∼0.03 M ⊙ of the positron emitter 44Ti, can simultaneously explain the strength and morphology of the Galactic positron annihilation signal and the Solar System abundance of the 44Ti decay product 44Ca. This transient is likely the merger of two low-mass white dwarfs, observed in external galaxies as the sub-luminous, thermonuclear supernova known as SN 1991bg-like.

Utility of Capture-Recapture Methodology to Estimate Prevalence of Congenital Heart Defects Among Adolescents in 11 New York State Counties: 2008 to 2010.

PubMed

Akkaya-Hocagil, Tugba; Hsu, Wan-Hsiang; Sommerhalter, Kristin; McGarry, Claire; Van Zutphen, Alissa

2017-11-01

Congenital heart defects (CHDs) are the most common birth defects in the United States, and the population of individuals living with CHDs is growing. Though CHD prevalence in infancy has been well characterized, better prevalence estimates among children and adolescents in the United States are still needed. We used capture-recapture methods to estimate CHD prevalence among adolescents residing in 11 New York counties. The three data sources used for analysis included Statewide Planning and Research Cooperative System (SPARCS) hospital inpatient records, SPARCS outpatient records, and medical records provided by seven pediatric congenital cardiac clinics from 2008 to 2010. Bayesian log-linear models were fit using the R package Conting to account for dataset dependencies and heterogeneous catchability. A total of 2537 adolescent CHD cases were captured in our three data sources. Forty-four cases were identified in all data sources, 283 cases were identified in two of three data sources, and 2210 cases were identified in a single data source. The final model yielded an estimated total adolescent CHD population of 3845, indicating that 66% of the cases in the catchment area were identified in the case-identifying data sources. Based on 2010 Census estimates, we estimated adolescent CHD prevalence as 6.4 CHD cases per 1000 adolescents (95% confidence interval: 6.2-6.6). We used capture-recapture methodology with a population-based surveillance system in New York to estimate CHD prevalence among adolescents. Future research incorporating additional data sources may improve prevalence estimates in this population. Birth Defects Research 109:1423-1429, 2017.© 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Andean snowpack since AD 1150 inferred from rainfall, tree-ring and documentary records

USDA-ARS?s Scientific Manuscript database

The Andean snowpack is the main source of freshwater and arguably the single most important natural resource for the populated, semi-arid regions of central Chile and central-western Argentina. However, apart from recent analyses of instrumental snowpack data, very little is known about the long ter...

A comparison of energetic ions in the plasma depletion layer and the quasi-parallel magnetosheath

NASA Technical Reports Server (NTRS)

Fuselier, Stephen A.

1994-01-01

Energetic ion spectra measured by the Active Magnetospheric Particle Tracer Explorers/Charge Composition Explorer (AMPTE/CCE) downstream from the Earth's quasi-parallel bow shock (in the quasi-parallel magnetosheath) and in the plasma depletion layer are compared. In the latter region, energetic ions are from a single source, leakage of magnetospheric ions across the magnetopause and into the plasma depletion layer. In the former region, both the magnetospheric source and shock acceleration of the thermal solar wind population at the quasi-parallel shock can contribute to the energetic ion spectra. The relative strengths of these two energetic ion sources are determined through the comparison of spectra from the two regions. It is found that magnetospheric leakage can provide an upper limit of 35% of the total energetic H(+) population in the quasi-parallel magnetosheath near the magnetopause in the energy range from approximately 10 to approximately 80 keV/e and substantially less than this limit for the energetic He(2+) population. The rest of the energetic H(+) population and nearly all of the energetic He(2+) population are accelerated out of the thermal solar wind population through shock acceleration processes. By comparing the energetic and thermal He(2+) and H(+) populations in the quasi-parallel magnetosheath, it is found that the quasi-parallel bow shock is 2 to 3 times more efficient at accelerating He(2+) than H(+). This result is consistent with previous estimates from shock acceleration theory and simulati ons.

Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources?

PubMed Central

Tolo, Isaiah; Thomas, Jonathan C.; Fischer, Rebecca S. B.; Brown, Eric L.; Gray, Barry M.

2016-01-01

Staphylococcus epidermidis is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of S. epidermidis distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between fdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256, sesD [bhp], mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital. PMID:27076664

Repeatable source, site, and path effects on the standard deviation for empirical ground-motion prediction models

USGS Publications Warehouse

Lin, P.-S.; Chiou, B.; Abrahamson, N.; Walling, M.; Lee, C.-T.; Cheng, C.-T.

2011-01-01

In this study, we quantify the reduction in the standard deviation for empirical ground-motion prediction models by removing ergodic assumption.We partition the modeling error (residual) into five components, three of which represent the repeatable source-location-specific, site-specific, and path-specific deviations from the population mean. A variance estimation procedure of these error components is developed for use with a set of recordings from earthquakes not heavily clustered in space.With most source locations and propagation paths sampled only once, we opt to exploit the spatial correlation of residuals to estimate the variances associated with the path-specific and the source-location-specific deviations. The estimation procedure is applied to ground-motion amplitudes from 64 shallow earthquakes in Taiwan recorded at 285 sites with at least 10 recordings per site. The estimated variance components are used to quantify the reduction in aleatory variability that can be used in hazard analysis for a single site and for a single path. For peak ground acceleration and spectral accelerations at periods of 0.1, 0.3, 0.5, 1.0, and 3.0 s, we find that the singlesite standard deviations are 9%-14% smaller than the total standard deviation, whereas the single-path standard deviations are 39%-47% smaller.

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

PubMed Central

Bradford, T M; Adams, M; Guzik, M T; Humphreys, W F; Austin, A D; Cooper, S JB

2013-01-01

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km2 region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete. PMID:23549336

DRINKING WATER AND CANCER INCIDENCE IN IOWA. 3. ASSOCIATION OF CANCER WITH INDICES OF CONTAMINATION

EPA Science Inventory

With data from the Iowa Cancer Registry, age-adjusted sex-specific cancer incidence rates for the years 1969-1981 were determined for towns with a population of 1,000-10,000 and a public water supply from a single stable ground source. These rates were related to levels of volati...

75 FR 62841 - Award of a Single-Source Grant to Chapin Hall at the University of Chicago, Chicago, IL

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-13

... the child-only Temporary Assistance for Needy Families (TANF) client population. Chapin Hall's... and more detailed picture of the TANF child-only caseload, including the dynamics of client entry and..., to gather policy information about a vulnerable and important ACF client group. OPRE will administer...

High-energy neutrinos from FR0 radio galaxies?

NASA Astrophysics Data System (ADS)

Tavecchio, F.; Righi, C.; Capetti, A.; Grandi, P.; Ghisellini, G.

2018-04-01

The sources responsible for the emission of high-energy (≳100 TeV) neutrinos detected by IceCube are still unknown. Among the possible candidates, active galactic nuclei with relativistic jets are often examined, since the outflowing plasma seems to offer the ideal environment to accelerate the required parent high-energy cosmic rays. The non-detection of single-point sources or - almost equivalently - the absence, in the IceCube events, of multiplets originating from the same sky position - constrains the cosmic density and the neutrino output of these sources, pointing to a numerous population of faint sources. Here we explore the possibility that FR0 radio galaxies, the population of compact sources recently identified in large radio and optical surveys and representing the bulk of radio-loud AGN population, can represent suitable candidates for neutrino emission. Modelling the spectral energy distribution of an FR0 radio galaxy recently associated with a γ-ray source detected by the Large Area Telescope onboard Fermi, we derive the physical parameters of its jet, in particular the power carried by it. We consider the possible mechanisms of neutrino production, concluding that pγ reactions in the jet between protons and ambient radiation is too inefficient to sustain the required output. We propose an alternative scenario, in which protons, accelerated in the jet, escape from it and diffuse in the host galaxy, producing neutrinos as a result of pp scattering with the interstellar gas, in strict analogy with the processes taking place in star-forming galaxies.

Demographic changes following mechanical removal of exotic brown trout in an Intermountain West (USA), high-elevation stream

USGS Publications Warehouse

Saunders, W. Carl; Budy, Phaedra E.; Thiede, Gary P.

2015-01-01

Exotic species present a great threat to native fish conservation; however, eradicating exotics is expensive and often impractical. Mechanical removal can be ineffective for eradication, but nonetheless may increase management effectiveness by identifying portions of a watershed that are strong sources of exotics. We used mechanical removal to understand processes driving exotic brown trout (Salmo trutta) populations in the Logan River, Utah. Our goals were to: (i) evaluate the demographic response of brown trout to mechanical removal, (ii) identify sources of brown trout recruitment at a watershed scale and (iii) evaluate whether mechanical removal can reduce brown trout densities. We removed brown trout from 2 km of the Logan River (4174 fish), and 5.6 km of Right Hand Fork (RHF, 15,245 fish), a low-elevation tributary, using single-pass electrofishing. We compared fish abundance and size distributions prior to, and after 2 years of mechanical removal. In the Logan River, immigration to the removal reach and high natural variability in fish abundances limited the response to mechanical removal. In contrast, mechanical removal in RHF resulted in a strong recruitment pulse, shifting the size distribution towards smaller fish. These results suggest that, before removal, density-dependent mortality or emigration of juvenile fish stabilised adult populations and may have provided a source of juveniles to the main stem. Overall, in sites demonstrating strong density-dependent population regulation, or near sources of exotics, short-term mechanical removal has limited effects on brown trout populations but may help identify factors governing populations and inform large-scale management of exotic species.

Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands

PubMed Central

Kamst, Miranda; van Hunen, Rianne; de Zwaan, Carolina Catherina; Mulder, Arnout; Supply, Philip; Anthony, Richard; van der Hoek, Wim; van Soolingen, Dick

2017-01-01

ABSTRACT Since 2004, variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084; P = 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386; P = 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants. PMID:29142049

The Y-STR genetic diversity of an Idaho Basque population, with comparison to European Basques and US Caucasians.

PubMed

Zubizarreta, Josu; Davis, Michael C; Hampikian, Greg

2011-12-01

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA H4.1 and DYS385a/b). In total, 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a United States Caucasian population. The haplotype diversity for the immigrant Basque sample is within 0.4% of the haplotype diversity of the European Basques (0.9903); thus the power of discrimination is similar for each population. The Idaho Basque population has less diversity in 9 out of 16 loci (considering DYS385a/b together) and 3% less diversity across all loci, compared to the European Basque population. A multidimensional scaling analysis (MDS) was created using pairwise R(ST) values to compare the Idaho Basques to other populations. Based upon R(ST) and F(ST) measures, no significant differentiation was found between the Idaho and source European Basque population.

Two-photon interference and coherent control of single InAs quantum dot emissions in an Ag-embedded structure

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

Liu, X., E-mail: iu.xiangming@nims.go.jp; National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044; Kumano, H.

2014-07-28

We have recently reported the successful fabrication of bright single-photon sources based on Ag-embedded nanocone structures that incorporate InAs quantum dots. The source had a photon collection efficiency as high as 24.6%. Here, we show the results of various types of photonic characterizations of the Ag-embedded nanocone structures that confirm their versatility as regards a broad range of quantum optical applications. We measure the first-order autocorrelation function to evaluate the coherence time of emitted photons, and the second-order correlation function, which reveals the strong suppression of multiple photon generation. The high indistinguishability of emitted photons is shown by the Hong-Ou-Mandel-typemore » two-photon interference. With quasi-resonant excitation, coherent population flopping is demonstrated through Rabi oscillations. Extremely high single-photon purity with a g{sup (2)}(0) value of 0.008 is achieved with π-pulse quasi-resonant excitation.« less

The Miracle Baby Grows Up: Hypoplastic Left Heart Syndrome in the Adult.

PubMed

Lewis, Matthew; Rosenbaum, Marlon

2017-08-01

Hypoplastic left heart syndrome (HLHS) is characterized by underdevelopment of the mitral valve, left ventricle, and aorta and is ultimately palliated with a single-ventricle repair. Universally fatal in infancy prior to the advent of modern surgical techniques, the majority of HLHS patients will now reach adulthood. However, despite improvements in early survival, the HLHS population continues to face significant morbidity and early mortality. This review delineates common sources of patient morbidity and highlights areas in need of additional research for this growing segment of the adult congenital heart disease population. It has become increasingly clear that palliated adult single ventricle patients, like those with HLHS, face significant life-long morbidity from elevated systemic venous pressures as a consequence of the Fontan procedure. Downstream organ dysfunction secondary to elevated Fontan pressures has the potential to significantly impact long-term management decisions, including strategies of organ allocation. Because of the presence of a morphologic systemic right ventricle, HLHS patients may be at even higher risk than other adult patients with a Fontan. Because the adult HLHS population continues to grow, recognition of common sources of patient morbidity and mortality is becoming increasingly important. A coordinated effort between patients and providers is necessary to address the many remaining areas of clinical uncertainty to help ensure continued improvement in patient prognosis and quality of life.

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

PubMed Central

Becraft, Eric D.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.; Ohlsson, J. Ingemar; Briggs, Brandon R.; Kanbar, Jad; De Vlaminck, Iwijn; Quake, Stephen R.; Dong, Hailiang; Hedlund, Brian P.

2015-01-01

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “Calescamantes” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs. PMID:26637598

Multiplicity among Solar-type Stars

NASA Astrophysics Data System (ADS)

Fuhrmann, K.; Chini, R.; Kaderhandt, L.; Chen, Z.

2017-02-01

We present a multiplicity census for a volume-complete all-sky survey of 422 stars with distances less than 25 pc and primary main-sequence effective temperatures T eff ≥ 5300 K. Very similar to previous results that have been presented for various subsets of this survey, we confirm the positive correlation of the stellar multiplicities with primary mass. We find for the F- and G-type Population I stars that 58% are non-single and 21% are in triple or higher level systems. For the old intermediate-disk and Population II stars—virtually all of G type and less massive—even two out of three sources prove to be non-single. These numbers being lower limits because of the continuous flow of new discoveries, the unbiased survey clearly demonstrates that the standard case for solar-type field stars is a hydrogen-burning source with at least one ordinary or degenerate stellar companion, and a surprisingly large number of stars are organized in multiple systems. A principal consequence is that orbital evolution, including the formation of blue straggler stars, is a potentially important issue on all spatial scales and timescales for a significant percentage of the stellar systems, in particular among Population II stars. We discuss a number of recent observations of known or suspected companions in the local survey, including a new detection of a double-lined Ba-Bb subsystem to the visual binary HR 8635.

Feeding ducks, bacterial chemotaxis, and the Gini index

NASA Astrophysics Data System (ADS)

Peaudecerf, François J.; Goldstein, Raymond E.

2015-08-01

Classic experiments on the distribution of ducks around separated food sources found consistency with the "ideal free" distribution in which the local population is proportional to the local supply rate. Motivated by this experiment and others, we examine the analogous problem in the microbial world: the distribution of chemotactic bacteria around multiple nearby food sources. In contrast to the optimization of uptake rate that may hold at the level of a single cell in a spatially varying nutrient field, nutrient consumption by a population of chemotactic cells will modify the nutrient field, and the uptake rate will generally vary throughout the population. Through a simple model we study the distribution of resource uptake in the presence of chemotaxis, consumption, and diffusion of both bacteria and nutrients. Borrowing from the field of theoretical economics, we explore how the Gini index can be used as a means to quantify the inequalities of uptake. The redistributive effect of chemotaxis can lead to a phenomenon we term "chemotactic levelling," and the influence of these results on population fitness are briefly considered.

Deep 20-GHz survey of the Chandra Deep Field South and SDSS Stripe 82: source catalogue and spectral properties

NASA Astrophysics Data System (ADS)

Franzen, Thomas M. O.; Sadler, Elaine M.; Chhetri, Rajan; Ekers, Ronald D.; Mahony, Elizabeth K.; Murphy, Tara; Norris, Ray P.; Waldram, Elizabeth M.; Whittam, Imogen H.

2014-04-01

We present a source catalogue and first results from a deep, blind radio survey carried out at 20 GHz with the Australia Telescope Compact Array, with follow-up observations at 5.5, 9 and 18 GHz. The Australia Telescope 20 GHz (AT20G) deep pilot survey covers a total area of 5 deg2 in the Chandra Deep Field South and in Stripe 82 of the Sloan Digital Sky Survey. We estimate the survey to be 90 per cent complete above 2.5 mJy. Of the 85 sources detected, 55 per cent have steep spectra (α _{1.4}^{20} < -0.5) and 45 per cent have flat or inverted spectra (α _{1.4}^{20} ≥ -0.5). The steep-spectrum sources tend to have single power-law spectra between 1.4 and 18 GHz, while the spectral indices of the flat- or inverted-spectrum sources tend to steepen with frequency. Among the 18 inverted-spectrum (α _{1.4}^{20} ≥ 0.0) sources, 10 have clearly defined peaks in their spectra with α _{1.4}^{5.5} > 0.15 and α 9^{18} < -0.15. On a 3-yr time-scale, at least 10 sources varied by more than 15 per cent at 20 GHz, showing that variability is still common at the low flux densities probed by the AT20G-deep pilot survey. We find a strong and puzzling shift in the typical spectral index of the 15-20-GHz source population when combining data from the AT20G, Ninth Cambridge and Tenth Cambridge surveys: there is a shift towards a steeper-spectrum population when going from ˜1 Jy to ˜5 mJy, which is followed by a shift back towards a flatter-spectrum population below ˜5 mJy. The 5-GHz source-count model by Jackson & Wall, which only includes contributions from FRI and FRII sources, and star-forming galaxies, does not reproduce the observed flattening of the flat-spectrum counts below ˜5 mJy. It is therefore possible that another population of sources is contributing to this effect.

Evidence for a Population of High-Redshift Submillimeter Galaxies from Interferometric Imaging

NASA Astrophysics Data System (ADS)

Younger, Joshua D.; Fazio, Giovanni G.; Huang, Jia-Sheng; Yun, Min S.; Wilson, Grant W.; Ashby, Matthew L. N.; Gurwell, Mark A.; Lai, Kamson; Peck, Alison B.; Petitpas, Glen R.; Wilner, David J.; Iono, Daisuke; Kohno, Kotaro; Kawabe, Ryohei; Hughes, David H.; Aretxaga, Itziar; Webb, Tracy; Martínez-Sansigre, Alejo; Kim, Sungeun; Scott, Kimberly S.; Austermann, Jason; Perera, Thushara; Lowenthal, James D.; Schinnerer, Eva; Smolčić, Vernesa

2007-12-01

We have used the Submillimeter Array to image a flux-limited sample of seven submillimeter galaxies, selected by the AzTEC camera on the JCMT at 1.1 mm, in the COSMOS field at 890 μm with ~2" resolution. All of the sources-two radio-bright and five radio-dim-are detected as single point sources at high significance (>6 σ), with positions accurate to ~0.2" that enable counterpart identification at other wavelengths observed with similarly high angular resolution. All seven have IRAC counterparts, but only two have secure counterparts in deep HST ACS imaging. As compared to the two radio-bright sources in the sample, and those in previous studies, the five radio-dim sources in the sample (1) have systematically higher submillimeter-to-radio flux ratios, (2) have lower IRAC 3.6-8.0 μm fluxes, and (3) are not detected at 24 μm. These properties, combined with size constraints at 890 μm (θ<~1.2''), suggest that the radio-dim submillimeter galaxies represent a population of very dusty starbursts, with physical scales similar to local ultraluminous infrared galaxies, with an average redshift higher than radio-bright sources.

[Efficiency of 27-plex single nucleotide polymorphism multiplex system for ancestry inference in different populations].

PubMed

Feng, Xing-Ling; Sun, Qi-Fan; Liu, Hong; Wei, Yi-Liang; DU, Wei-An; Li, Cai-Xia; Chen, Ling; Liu, Chao

2016-04-20

To validate the efficiency of 27-plex single nucleotide polymorphism (SNP) multiplex system for ancestry inference. The 27-plex SNP system was validated for its sensitivity and species specificity. A total of 533 samples were collected from African, Southern Chinese Han, China's ethic minorities (Yi, Hui, Miao, Tibet, and Uygur), European, Central Asian, Western Asian, Southern Asian, Southeast Asian and South American populations for clustering analysis of the genotypes by citing 3 representative continental ancestral groups [East Asia (CHB), Europe (CEU), and Africa (YRI)] from HapMap database. The system sensitivity is 0.125 ng. Twenty and six genotypes were detected in chimpanzee and monkeys, respectively. Except in rs10496971, no more products were found in other animals. The system was capable of differentiating intercontinental populations but not of distinguishing between East Asian and Southeast Asian population or between Southern Chinese Han population and Chinese Ethnic populations (Hui, Miao, Yi and Tibet). This system achieved a 100% accuracy for intercontinental population source inference for 46 blind test samples. 27-plex SNPs multiplex system has a high sensitivity and species specificity and can correctly differentiate the ancestry origins of individuals from African, European and East Asian for criminal case investigation. But this system is not capable of distinguishing subpopulation groups and more specific ancestry-informative markers are needed to improve its recognition of Southeast Asian and Chinese ethnic populations.

Eccentric Black Hole Gravitational-wave Capture Sources in Galactic Nuclei: Distribution of Binary Parameters

NASA Astrophysics Data System (ADS)

Gondán, László; Kocsis, Bence; Raffai, Péter; Frei, Zsolt

2018-06-01

Mergers of binary black holes on eccentric orbits are among the targets for second-generation ground-based gravitational-wave detectors. These sources may commonly form in galactic nuclei due to gravitational-wave emission during close flyby events of single objects. We determine the distributions of initial orbital parameters for a population of these gravitational-wave sources. Our results show that the initial dimensionless pericenter distance systematically decreases with the binary component masses and the mass of the central supermassive black hole, and its distribution depends sensitively on the highest possible black hole mass in the nuclear star cluster. For a multi-mass black hole population with masses between 5 {M}ȯ and 80 {M}ȯ , we find that between ∼43–69% (68–94%) of 30 {M}ȯ –30 {M}ȯ (10 M ⊙–10 M ⊙) sources have an eccentricity greater than 0.1 when the gravitational-wave signal reaches 10 Hz, but less than ∼10% of the sources with binary component masses less than 30 {M}ȯ remain eccentric at this level near the last stable orbit (LSO). The eccentricity at LSO is typically between 0.005–0.05 for the lower-mass BHs, and 0.1–0.2 for the highest-mass BHs. Thus, due to the limited low-frequency sensitivity, the six currently known quasicircular LIGO/Virgo sources could still be compatible with this originally highly eccentric source population. However, at the design sensitivity of these instruments, the measurement of the eccentricity and mass distribution of merger events may be a useful diagnostic to identify the fraction of GW sources formed in this channel.

An avoidance behavior model for migrating whale populations

NASA Astrophysics Data System (ADS)

Buck, John R.; Tyack, Peter L.

2003-04-01

A new model is presented for the avoidance behavior of migrating marine mammals in the presence of a noise stimulus. This model assumes that each whale will adjust its movement pattern near a sound source to maintain its exposure below its own individually specific maximum received sound-pressure level, called its avoidance threshold. The probability distribution function (PDF) of this avoidance threshold across individuals characterizes the migrating population. The avoidance threshold PDF may be estimated by comparing the distribution of migrating whales during playback and control conditions at their closest point of approach to the sound source. The proposed model was applied to the January 1998 experiment which placed a single acoustic source from the U.S. Navy SURTASS-LFA system in the migration corridor of grey whales off the California coast. This analysis found that the median avoidance threshold for this migrating grey whale population was 135 dB, with 90% confidence that the median threshold was within +/-3 dB of this value. This value is less than the 141 dB value for 50% avoidance obtained when the 1984 ``Probability of Avoidance'' model of Malme et al.'s was applied to the same data. [Work supported by ONR.

Humpback whale-generated ambient noise levels provide insight into singers' spatial densities.

PubMed

Seger, Kerri D; Thode, Aaron M; Urbán-R, Jorge; Martínez-Loustalot, Pamela; Jiménez-López, M Esther; López-Arzate, Diana

2016-09-01

Baleen whale vocal activity can be the dominant underwater ambient noise source for certain locations and seasons. Previous wind-driven ambient-noise formulations have been adjusted to model ambient noise levels generated by random distributions of singing humpback whales in ocean waveguides and have been combined to a single model. This theoretical model predicts that changes in ambient noise levels with respect to fractional changes in singer population (defined as the noise "sensitivity") are relatively unaffected by the source level distributions and song spectra of individual humpback whales (Megaptera novaeangliae). However, the noise "sensitivity" does depend on frequency and on how the singers' spatial density changes with population size. The theoretical model was tested by comparing visual line transect surveys with bottom-mounted passive acoustic data collected during the 2013 and 2014 humpback whale breeding seasons off Los Cabos, Mexico. A generalized linear model (GLM) estimated the noise "sensitivity" across multiple frequency bands. Comparing the GLM estimates with the theoretical predictions suggests that humpback whales tend to maintain relatively constant spacing between one another while singing, but that individual singers either slightly increase their source levels or song duration, or cluster more tightly as the singing population increases.

Fast radio burst event rate counts - I. Interpreting the observations

NASA Astrophysics Data System (ADS)

Macquart, J.-P.; Ekers, R. D.

2018-02-01

The fluence distribution of the fast radio burst (FRB) population (the `source count' distribution, N (>F) ∝Fα), is a crucial diagnostic of its distance distribution, and hence the progenitor evolutionary history. We critically reanalyse current estimates of the FRB source count distribution. We demonstrate that the Lorimer burst (FRB 010724) is subject to discovery bias, and should be excluded from all statistical studies of the population. We re-examine the evidence for flat, α > -1, source count estimates based on the ratio of single-beam to multiple-beam detections with the Parkes multibeam receiver, and show that current data imply only a very weak constraint of α ≲ -1.3. A maximum-likelihood analysis applied to the portion of the Parkes FRB population detected above the observational completeness fluence of 2 Jy ms yields α = -2.6_{-1.3}^{+0.7 }. Uncertainties in the location of each FRB within the Parkes beam render estimates of the Parkes event rate uncertain in both normalizing survey area and the estimated post-beam-corrected completeness fluence; this uncertainty needs to be accounted for when comparing the event rate against event rates measured at other telescopes.

'Between one and three million': towards the demographic reconstruction of a decade of Cambodian history (1970-79).

PubMed

Heuveline, P

1998-03-01

Estimates of mortality in Camabodia during the Khmer Rouge regime (1975-79) range from 20,000 deaths according to former Khmer Rouge sources, to over three million victims according to Vietnamese government sources. This paper uses an unusual data source - the 1992 electoral lists registered by the United Nations - to estimate the population size after the Khmer Rouge regime and the extent of "excess" mortality in the 1970s. These data also provide the first breakdown of population by single year of age, which allows analysis of the age structure of "excess" mortality and inference of the relative importance of violence as a cause of death in that period. The estimates derived here are more comparable with the higher estimates made in the past. In addition, the analysis of likely causes of death that could have generated the age pattern of "excess" mortality clearly shows a larger contribution of direct or violent mortality than has been previously recognized.

Broadband Spectral Modeling of the Extreme Gigahertz-peaked Spectrum Radio Source PKS B0008-421

NASA Astrophysics Data System (ADS)

Callingham, J. R.; Gaensler, B. M.; Ekers, R. D.; Tingay, S. J.; Wayth, R. B.; Morgan, J.; Bernardi, G.; Bell, M. E.; Bhat, R.; Bowman, J. D.; Briggs, F.; Cappallo, R. J.; Deshpande, A. A.; Ewall-Wice, A.; Feng, L.; Greenhill, L. J.; Hazelton, B. J.; Hindson, L.; Hurley-Walker, N.; Jacobs, D. C.; Johnston-Hollitt, M.; Kaplan, D. L.; Kudrayvtseva, N.; Lenc, E.; Lonsdale, C. J.; McKinley, B.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Oberoi, D.; Offringa, A. R.; Ord, S. M.; Pindor, B.; Prabu, T.; Procopio, P.; Riding, J.; Srivani, K. S.; Subrahmanyan, R.; Udaya Shankar, N.; Webster, R. L.; Williams, A.; Williams, C. L.

2015-08-01

We present broadband observations and spectral modeling of PKS B0008-421 and identify it as an extreme gigahertz-peaked spectrum (GPS) source. PKS B0008-421 is characterized by the steepest known spectral slope below the turnover, close to the theoretical limit of synchrotron self-absorption, and the smallest known spectral width of any GPS source. Spectral coverage of the source spans from 0.118 to 22 GHz, which includes data from the Murchison Widefield Array and the wide bandpass receivers on the Australia Telescope Compact Array. We have implemented a Bayesian inference model fitting routine to fit the data with internal free-free absorption (FFA), single- and double-component FFA in an external homogeneous medium, FFA in an external inhomogeneous medium, or single- and double-component synchrotron self-absorption models, all with and without a high-frequency exponential break. We find that without the inclusion of a high-frequency break these models cannot accurately fit the data, with significant deviations above and below the peak in the radio spectrum. The addition of a high-frequency break provides acceptable spectral fits for the inhomogeneous FFA and double-component synchrotron self-absorption models, with the inhomogeneous FFA model statistically favored. The requirement of a high-frequency spectral break implies that the source has ceased injecting fresh particles. Additional support for the inhomogeneous FFA model as being responsible for the turnover in the spectrum is given by the consistency between the physical parameters derived from the model fit and the implications of the exponential spectral break, such as the necessity of the source being surrounded by a dense ambient medium to maintain the peak frequency near the gigahertz region. This implies that PKS B0008-421 should display an internal H i column density greater than 1020 cm-2. The discovery of PKS B0008-421 suggests that the next generation of low radio frequency surveys could reveal a large population of GPS sources that have ceased activity, and that a portion of the ultra-steep-spectrum source population could be composed of these GPS sources in a relic phase.

Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers.

PubMed

Gonçalves, Rita; Rosa, Alexandra; Freitas, Ana; Fernandes, Ana; Kivisild, Toomas; Villems, Richard; Brehm, António

2003-11-01

The Y-chromosome haplogroup composition of the population of the Cabo Verde Archipelago was profiled by using 32 single-nucleotide polymorphism markers and compared with potential source populations from Iberia, west Africa, and the Middle East. According to the traditional view, the major proportion of the founding population of Cabo Verde was of west African ancestry with the addition of a minor fraction of male colonizers from Europe. Unexpectedly, more than half of the paternal lineages (53.5%) of Cabo Verdeans clustered in haplogroups I, J, K, and R1, which are characteristic of populations of Europe and the Middle East, while being absent in the probable west African source population of Guiné-Bissau. Moreover, a high frequency of J* lineages in Cabo Verdeans relates them more closely to populations of the Middle East and probably provides the first genetic evidence of the legacy of the Jews. In addition, the considerable proportion (20.5%) of E3b(xM81) lineages indicates a possible gene flow from the Middle East or northeast Africa, which, at least partly, could be ascribed to the Sephardic Jews. In contrast to the predominance of west African mitochondrial DNA haplotypes in their maternal gene pool, the major west African Y-chromosome lineage E3a was observed only at a frequency of 15.9%. Overall, these results indicate that gene flow from multiple sources and various sex-specific patterns have been important in the formation of the genomic diversity in the Cabo Verde islands.

Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers

USDA-ARS?s Scientific Manuscript database

Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the...

Geographic proximity not a prerequisite for invasion: Hawaii not the source of California invasion by light brown apple moth (Epiphyas postvittana).

PubMed

Rubinoff, Daniel; Holland, Brenden S; San Jose, Michael; Powell, Jerry A

2011-01-27

The light brown apple moth (LBAM), Epiphyas postvittana (Walker), is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific. We sequenced mitochondrial DNA (mtDNA) from 1293 LBAM individuals from California (695), Hawaii (448), New Zealand (147), and Australia (3) to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity. LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for quarantine, and suggests that probability of invasion is not directly related to geographic distance. Surprisingly, Hawaiian LBAM populations have much lower genetic diversity than California, despite being older.

Geographic Proximity Not a Prerequisite for Invasion: Hawaii Not the Source of California Invasion by Light Brown Apple Moth (Epiphyas postvittana)

PubMed Central

Rubinoff, Daniel; Holland, Brenden S.; San Jose, Michael; Powell, Jerry A.

2011-01-01

Background The light brown apple moth (LBAM), Epiphyas postvittana (Walker), is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific. Methodology/Principal Findings We sequenced mitochondrial DNA (mtDNA) from 1293 LBAM individuals from California (695), Hawaii (448), New Zealand (147), and Australia (3) to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity. Conclusions/Significance LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for quarantine, and suggests that probability of invasion is not directly related to geographic distance. Surprisingly, Hawaiian LBAM populations have much lower genetic diversity than California, despite being older. PMID:21298019

Effect of phonon-bath dimensionality on the spectral tuning of single-photon emitters in the Purcell regime

NASA Astrophysics Data System (ADS)

Chassagneux, Yannick; Jeantet, Adrien; Claude, Théo; Voisin, Christophe

2018-05-01

We develop a theoretical frame to investigate the spectral dependence of the brightness of a single-photon source made of a solid-state nanoemitter embedded in a high-quality factor microcavity. This study encompasses the cases of localized excitons embedded in a one-, two-, or three-dimensional matrix. The population evolution is calculated based on a spin-boson model, using the noninteracting blip approximation. We find that the spectral dependence of the single-photon source brightness (hereafter called spectral efficiency) can be expressed analytically through the free-space emission and absorption spectra of the emitter, the vacuum Rabi splitting, and the loss rates of the system. In other words, the free-space spectrum of the emitter encodes all the relevant information on the interaction between the exciton and the phonon bath to obtain the dynamics of the cavity-coupled system. We compute numerically the spectral efficiency for several types of localized emitters differing by the phonon bath dimensionality. In particular, in low-dimensional systems where this interaction is enhanced, a pronounced asymmetric energy exchange between the emitter and the cavity on the phonon sidebands yields a considerable extension of the tuning range of the source through phonon-assisted cavity feeding, possibly surpassing that of a purely resonant system.

Recording human cortical population spikes non-invasively--An EEG tutorial.

PubMed

Waterstraat, Gunnar; Fedele, Tommaso; Burghoff, Martin; Scheer, Hans-Jürgen; Curio, Gabriel

2015-07-30

Non-invasively recorded somatosensory high-frequency oscillations (sHFOs) evoked by electric nerve stimulation are markers of human cortical population spikes. Previously, their analysis was based on massive averaging of EEG responses. Advanced neurotechnology and optimized off-line analysis can enhance the signal-to-noise ratio of sHFOs, eventually enabling single-trial analysis. The rationale for developing dedicated low-noise EEG technology for sHFOs is unfolded. Detailed recording procedures and tailored analysis principles are explained step-by-step. Source codes in Matlab and Python are provided as supplementary material online. Combining synergistic hardware and analysis improvements, evoked sHFOs at around 600 Hz ('σ-bursts') can be studied in single-trials. Additionally, optimized spatial filters increase the signal-to-noise ratio of components at about 1 kHz ('κ-bursts') enabling their detection in non-invasive surface EEG. sHFOs offer a unique possibility to record evoked human cortical population spikes non-invasively. The experimental approaches and algorithms presented here enable also non-specialized EEG laboratories to combine measurements of conventional low-frequency EEG with the analysis of concomitant cortical population spike responses. Copyright © 2014 Elsevier B.V. All rights reserved.

Laser Induced Fluorescence of Helium Ions in a Helicon Plasma

NASA Astrophysics Data System (ADS)

Compton, C. S.; Biloui, C.; Hardin, R. A.; Keesee, A. M.; Scime, E. E.; Boivin, R.

2003-10-01

The lack of a suitable Laser Induced Fluorescence (LIF) scheme for helium ions at visible wavelengths has prevented LIF from being employed in helium plasmas for measurements of ion temperature and bulk ion flow speeds. In this work, we will discuss our attempts to perform LIF of helium ions in a helicon source plasma using an infrared, tunable diode laser operating at 1012.36 nm. The infrared transition corresponds to excitation from the n = 4 level (4f ^2F) to the n = 5 (5g ^2G) level of singly ionized helium and therefore requires substantial electron temperatures (> 10 eV) to maintain an adequate ion population in the n = 4 state. Calculations using a steady state coronal model predict that the n = 4 state population will be 25% larger than the n = 5 population for our experimental conditions. The fluorescence decay from the n = 5 (5f ^2F) level of singly ionized helium level to the n = 3 (3d ^2D) level at 320.31 nm is monitored as the diode laser is swept through 10 GHz around the 1012.36 nm line. Note that the fluorescence emission requires a collisionally coupled transition between two different n = 5 quantum states. We will also present measurements of the emission intensities of both the 1012.36 nm and the 320.31 nm lines as a function of source neutral pressure, rf power, and plasma density. This work supported by the U.S. DoE EPSCoR Lab Partnership Program.

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.

PubMed

Becraft, Eric D; Dodsworth, Jeremy A; Murugapiran, Senthil K; Ohlsson, J Ingemar; Briggs, Brandon R; Kanbar, Jad; De Vlaminck, Iwijn; Quake, Stephen R; Dong, Hailiang; Hedlund, Brian P; Swingley, Wesley D

2016-02-15

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow

PubMed Central

Levin, Alex; Reich, David; Patterson, Nick; Berger, Bonnie

2013-01-01

The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here, we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for Human Genome Diversity Cell Line Panel individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20–40% ancient northern Eurasian ancestry. PMID:23709261

The use of the virtual source technique in computing scattering from periodic ocean surfaces.

PubMed

Abawi, Ahmad T

2011-08-01

In this paper the virtual source technique is used to compute scattering of a plane wave from a periodic ocean surface. The virtual source technique is a method of imposing boundary conditions using virtual sources, with initially unknown complex amplitudes. These amplitudes are then determined by applying the boundary conditions. The fields due to these virtual sources are given by the environment Green's function. In principle, satisfying boundary conditions on an infinite surface requires an infinite number of sources. In this paper, the periodic nature of the surface is employed to populate a single period of the surface with virtual sources and m surface periods are added to obtain scattering from the entire surface. The use of an accelerated sum formula makes it possible to obtain a convergent sum with relatively small number of terms (∼40). The accuracy of the technique is verified by comparing its results with those obtained using the integral equation technique.

NuSTAR Hard X-Ray Survey of the Galactic Center Region. II. X-Ray Point Sources

NASA Technical Reports Server (NTRS)

Hong, Jaesub; Mori, Kaya; Hailey, Charles J.; Nynka, Melania; Zhang, Shou; Gotthelf, Eric; Fornasini, Francesca M.; Krivonos, Roman; Bauer, Franz; Perez, Kerstin;

Einstein Observatory survey of X-ray emission from solar-type stars - The late F and G dwarf stars

NASA Technical Reports Server (NTRS)

Maggio, A.; Sciortino, S.; Vaiana, G. S.; Majer, P.; Bookbinder, J.

1987-01-01

Results of a volume-limited X-ray survey of stars of luminosity classes IV and V in the spectral range F7-G9 observed with the Einstein Observatory are presented. Using survival analysis techniques, the stellar X-ray luminosity function in the 0.15-4.0 keV energy band for both single and multiple sources. It is shown that the difference in X-ray luminosity between these two classes of sources is consistent with the superposition of individual components in multiple-component systems, whose X-ray properties are similar to those of the single-component sources. The X-ray emission of the stars in our sample is well correlated with their chromospheric CA II H-K line emission and with their projected equatorial rotational velocity. Comparison of the X-ray luminosity function constructed for the sample of the dG stars of the local population with the corresponding functions derived elsewhere for the Hyades, the Pleiades, and the Orion Ic open cluster confirms that the level of X-ray emission decreases with stellar age.

Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine

PubMed Central

Holmes, E.C.; Stephenson, A.G.

2014-01-01

Determining the extent and structure of intra-host genetic diversity and the magnitude and impact of population bottlenecks is central to understanding the mechanisms of viral evolution. To determine the nature of viral evolution following systemic movement through a plant, we performed deep sequencing of 23 leaves that grew sequentially along a single Cucurbita pepo vine that was infected with zucchini yellow mosaic virus (ZYMV), and on a leaf that grew in on a side branch. Strikingly, of 112 genetic (i.e. sub-consensus) variants observed in the data set as a whole, only 22 were found in multiple leaves. Similarly, only three of the 13 variants present in the inoculating population were found in the subsequent leaves on the vine. Hence, it appears that systemic movement is characterized by sequential population bottlenecks, although not sufficient to reduce the population to a single virion as multiple variants were consistently transmitted between leaves. In addition, the number of variants within a leaf increases as a function of distance from the inoculated (source) leaf, suggesting that the circulating sap may serve as a continual source of virus. Notably, multiple mutational variants were observed in the cylindrical Inclusion (CI) protein (known to be involved in both cell-to-cell and systemic movement of the virus) that were present in multiple (19/24) leaf samples. These mutations resulted in a conformational change, suggesting that they might confer a selective advantage in systemic movement within the vine. Overall, these data reveal that bottlenecks occur during systemic movement, that variants circulate in the phloem sap throughout the infection process, and that important conformational changes in CI protein may arise during individual infections. PMID:25107623

Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants.

PubMed

Montes-Borrego, Miguel; Lopes, Joao R S; Jiménez-Díaz, Rafael M; Landa, Blanca B

2015-03-01

Two haplotypes of Xylella fastidiosa subsp. pauca (Xfp) that correlated with their host of origin were identified in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the gyrB sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of Xfp according to the host source. The protocol proved to be robust for the prediction of the Xfp host source in blind tests using DNA from cultures of the bacterium, infected plants, and insect vectors allowed to feed on Xfp-infected citrus plants. AMOVA and STRUCTURE analyses of microsatellite data separated most Xfp populations on the basis of their host source, indicating that they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR markers showed that two haplotypes and distinct isolates of Xfp infect citrus and coffee in Brazil and that multiple, genetically different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies of the epidemiology of Xfp-induced diseases, host specificity of bacterial genotypes, the occurrence of Xfp host jumping, vector feeding habits, etc., in economically important cultivated plants or weed host reservoirs of Xfp in Brazil and elsewhere. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Analysis of the NMI01 marker for a population database of cannabis seeds.

PubMed

Shirley, Nicholas; Allgeier, Lindsay; Lanier, Tommy; Coyle, Heather Miller

2013-01-01

We have analyzed the distribution of genotypes at a single hexanucleotide short tandem repeat (STR) locus in a Cannabis sativa seed database along with seed-packaging information. This STR locus is defined by the polymerase chain reaction amplification primers CS1F and CS1R and is referred to as NMI01 (for National Marijuana Initiative) in our study. The population database consists of seed seizures of two categories: seed samples from labeled and unlabeled packages regarding seed bank source. Of a population database of 93 processed seeds including 12 labeled Cannabis varieties, the observed genotypes generated from single seeds exhibited between one and three peaks (potentially six alleles if in homozygous state). The total number of observed genotypes was 54 making this marker highly specific and highly individualizing even among seeds of common lineage. Cluster analysis associated many but not all of the handwritten labeled seed varieties tested to date as well as the National Park seizure to our known reference database containing Mr. Nice Seedbank and Sensi Seeds commercially packaged reference samples. © 2012 American Academy of Forensic Sciences.

Dissociation between sustained single-neuron spiking and transient β-LFP oscillations in primate motor cortex

PubMed Central

Rule, Michael E.; Vargas-Irwin, Carlos E.; Donoghue, John P.

2017-01-01

Determining the relationship between single-neuron spiking and transient (20 Hz) β-local field potential (β-LFP) oscillations is an important step for understanding the role of these oscillations in motor cortex. We show that whereas motor cortex firing rates and beta spiking rhythmicity remain sustained during steady-state movement preparation periods, β-LFP oscillations emerge, in contrast, as short transient events. Single-neuron mean firing rates within and outside transient β-LFP events showed no differences, and no consistent correlation was found between the beta oscillation amplitude and firing rates, as was the case for movement- and visual cue-related β-LFP suppression. Importantly, well-isolated single units featuring beta-rhythmic spiking (43%, 125/292) showed no apparent or only weak phase coupling with the transient β-LFP oscillations. Similar results were obtained for the population spiking. These findings were common in triple microelectrode array recordings from primary motor (M1), ventral (PMv), and dorsal premotor (PMd) cortices in nonhuman primates during movement preparation. Although beta spiking rhythmicity indicates strong membrane potential fluctuations in the beta band, it does not imply strong phase coupling with β-LFP oscillations. The observed dissociation points to two different sources of variation in motor cortex β-LFPs: one that impacts single-neuron spiking dynamics and another related to the generation of mesoscopic β-LFP signals. Furthermore, our findings indicate that rhythmic spiking and diverse neuronal firing rates, which encode planned actions during movement preparation, may naturally limit the ability of different neuronal populations to strongly phase-couple to a single dominant oscillation frequency, leading to the observed spiking and β-LFP dissociation. NEW & NOTEWORTHY We show that whereas motor cortex spiking rates and beta (~20 Hz) spiking rhythmicity remain sustained during steady-state movement preparation periods, β-local field potential (β-LFP) oscillations emerge, in contrast, as transient events. Furthermore, the β-LFP phase at which neurons spike drifts: phase coupling is typically weak or absent. This dissociation points to two sources of variation in the level of motor cortex beta: one that impacts single-neuron spiking and another related to the generation of measured mesoscopic β-LFPs. PMID:28100654

Sources and Characteristics of Medium Scale Traveling Ionospheric Disturbances Observed by a Longitudinally Distributed Chain of SuperDARN Radars Across the United States

NASA Astrophysics Data System (ADS)

Frissell, N. A.; Baker, J. B. H.; Ruohoniemi, J. M.; Gerrard, A. J.; Miller, E. S.; West, M. L.; Bristow, W.

2014-12-01

Medium Scale Traveling Ionospheric Disturbances (MSTIDs) are wave-like perturbations of the F-region ionosphere with horizontal wavelengths on the order of 100-250 km and periods between ~15 - 60 min. In SuperDARN data, MSTID signatures are manifested as quasi-periodic enhancements of ground scatter power moving through the radar FOV. High latitude SuperDARN MSTIDs have been studied for many years and are generally attributed to atmospheric gravity waves (AGWs) launched by auroral sources. Recent extension of the SuperDARN network to midlatitudes has revealed that MSTIDs are routinely observed at midlatitudes as well. Our previous research using the single radar in Blackstone, Virginia found a primary MSTID propagation direction which suggests that high latitude activity is also the primary source of midlatitude MSTIDs. However, there is also a population of MSTIDs that could be generated by tropospheric sources. This study extends this research by surveying multiple midlatitude radars in Oregon (CVW and CVE), Kansas (FHW and FHW) and Virginia (BKS and WAL) from 1 November 2012 through 1 January 2013 for MSTID signatures in order understand the longitudinal distribution of midlatitude MSTID characteristics and understand possible influences of varied terrain on MSTID observations. MSTIDs observed by all radars had typical wavelengths between 250 to 500 km and horizontal velocities between 100 and 250 m/s. In all radars, the dominant population of MSTIDs propagated in a southward direction, ranging from 135˚ to 250˚ geographic azimuth. The dominant southward propagation direction suggests auroral sources are the dominant source of MSTIDs observed by SuperDARN radars at midlatitudes, which reinforces findings regarding the primary population in previous work.

The [O III] Profiles of Infrared-selected Active Galactic Nuclei: More Powerful Outflows in the Obscured Population

NASA Astrophysics Data System (ADS)

DiPompeo, M. A.; Hickox, R. C.; Carroll, C. M.; Runnoe, J. C.; Mullaney, J. R.; Fischer, T. C.

2018-03-01

We explore the kinematics of ionized gas via the [O III] λ5007 emission lines in active galactic nuclei (AGNs) selected on the basis of their mid-infrared (IR) emission, and split into obscured and unobscured populations based on their optical‑IR colors. After correcting for differences in redshift distributions, we provide composite spectra of spectroscopically and photometrically defined obscured/Type 2 and unobscured/Type 1 AGNs from 3500 to 7000 Å. The IR-selected obscured sources contain a mixture of narrow-lined Type 2 AGNs and intermediate sources that have broad Hα emission and significantly narrower Hβ. Using both [O III] luminosities and AGN luminosities derived from optical‑IR spectral energy distribution fitting, we find evidence for enhanced large-scale obscuration in the obscured sources. In matched bins of luminosity we find that the obscured population typically has broader, more blueshifted [O III] emission than in the unobscured sample, suggestive of more powerful AGN-driven outflows. This trend is not seen in spectroscopically classified samples, and is unlikely to be entirely explained by orientation effects. In addition, outflow velocities increase from small to moderate AGN E(B ‑ V) values, before flattening out (as traced by FWHM) and even decreasing (as traced by blueshift). While difficult to fully interpret in a single physical model, due to both the averaging over populations and the spatially averaged spectra, these results agree with previous findings that simple geometric unification models are insufficient for the IR-selected AGN population, and may fit into an evolutionary model for obscured and unobscured AGNs.

Bolide Airbursts as a Seismic Source for the 2018 Mars InSight Mission

NASA Astrophysics Data System (ADS)

Stevanović, J.; Teanby, N. A.; Wookey, J.; Selby, N.; Daubar, I. J.; Vaubaillon, J.; Garcia, R.

2017-10-01

In 2018, NASA will launch InSight, a single-station suite of geophysical instruments, designed to characterise the martian interior. We investigate the seismo-acoustic signal generated by a bolide entering the martian atmosphere and exploding in a terminal airburst, and assess this phenomenon as a potential observable for the SEIS seismic payload. Terrestrial analogue data from four recent events are used to identify diagnostic airburst characteristics in both the time and frequency domain. In order to estimate a potential number of detectable events for InSight, we first model the impactor source population from observations made on the Earth, scaled for planetary radius, entry velocity and source density. We go on to calculate a range of potential airbursts from the larger incident impactor population. We estimate there to be {˜} 1000 events of this nature per year on Mars. To then derive a detectable number of airbursts for InSight, we scale this number according to atmospheric attenuation, air-to-ground coupling inefficiencies and by instrument capability for SEIS. We predict between 10-200 detectable events per year for InSight.

Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance

PubMed Central

Taboada, Eduardo; Grant, Christopher C. R.; Blakeston, Connie; Pollari, Frank; Marshall, Barbara; Rahn, Kris; MacKinnon, Joanne; Daignault, Danielle; Pillai, Dylan; Ng, Lai-King

2012-01-01

Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population. PMID:22162562

Addressing potential local adaptation in species distribution models: implications for conservation under climate change

USGS Publications Warehouse

Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

2016-01-01

Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

THE HIGHEST-ENERGY COSMIC RAYS CANNOT BE DOMINANTLY PROTONS FROM STEADY SOURCES

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

Fang, Ke; Kotera, Kumiko

The bulk of observed ultrahigh-energy cosmic rays could be light or heavier elements and originate from an either steady or transient population of sources. This leaves us with four general categories of sources. Energetic requirements set a lower limit on single-source luminosities, while the distribution of particle arrival directions in the sky sets a lower limit on the source number density. The latter constraint depends on the angular smearing in the skymap due to the magnetic deflections of the charged particles during their propagation from the source to the Earth. We contrast these limits with the luminosity functions from surveysmore » of existing luminous steady objects in the nearby universe and strongly constrain one of the four categories of source models, namely, steady proton sources. The possibility that cosmic rays with energy >8 × 10{sup 19} eV are dominantly pure protons coming from steady sources is excluded at 95% confidence level, under the safe assumption that protons experience less than 30° magnetic deflection on flight.« less

Integrating clinical research with the Healthcare Enterprise: from the RE-USE project to the EHR4CR platform.

PubMed

El Fadly, AbdenNaji; Rance, Bastien; Lucas, Noël; Mead, Charles; Chatellier, Gilles; Lastic, Pierre-Yves; Jaulent, Marie-Christine; Daniel, Christel

2011-12-01

There are different approaches for repurposing clinical data collected in the Electronic Healthcare Record (EHR) for use in clinical research. Semantic integration of "siloed" applications across domain boundaries is the raison d'être of the standards-based profiles developed by the Integrating the Healthcare Enterprise (IHE) initiative - an initiative by healthcare professionals and industry promoting the coordinated use of established standards such as DICOM and HL7 to address specific clinical needs in support of optimal patient care. In particular, the combination of two IHE profiles - the integration profile "Retrieve Form for Data Capture" (RFD), and the IHE content profile "Clinical Research Document" (CRD) - offers a straightforward approach to repurposing EHR data by enabling the pre-population of the case report forms (eCRF) used for clinical research data capture by Clinical Data Management Systems (CDMS) with previously collected EHR data. Implement an alternative solution of the RFD-CRD integration profile centered around two approaches: (i) Use of the EHR as the single-source data-entry and persistence point in order to ensure that all the clinical data for a given patient could be found in a single source irrespective of the data collection context, i.e. patient care or clinical research; and (ii) Maximize the automatic pre-population process through the use of a semantic interoperability services that identify duplicate or semantically-equivalent eCRF/EHR data elements as they were collected in the EHR context. The RE-USE architecture and associated profiles are focused on defining a set of scalable, standards-based, IHE-compliant profiles that can enable single-source data collection/entry and cross-system data reuse through semantic integration. Specifically, data reuse is realized through the semantic mapping of data collection fields in electronic Case Report Forms (eCRFs) to data elements previously defined as part of patient care-centric templates in the EHR context. The approach was evaluated in the context of a multi-center clinical trial conducted in a large, multi-disciplinary hospital with an installed EHR. Data elements of seven eCRFs used in a multi-center clinical trial were mapped to data elements of patient care-centric templates in use in the EHR at the George Pompidou hospital. 13.4% of the data elements of the eCRFs were found to be represented in EHR templates and were therefore candidate for pre-population. During the execution phase of the clinical study, the semantic mapping architecture enabled data persisted in the EHR context as part of clinical care to be used to pre-populate eCRFS for use without secondary data entry. To ensure that the pre-populated data is viable for use in the clinical research context, all pre-populated eCRF data needs to be first approved by a trial investigator prior to being persisted in a research data store within a CDMS. Single-source data entry in the clinical care context for use in the clinical research context - a process enabled through the use of the EHR as single point of data entry, can - if demonstrated to be a viable strategy - not only significantly reduce data collection efforts while simultaneously increasing data collection accuracy secondary to elimination of transcription or double-entry errors between the two contexts but also ensure that all the clinical data for a given patient, irrespective of the data collection context, are available in the EHR for decision support and treatment planning. The RE-USE approach used mapping algorithms to identify semantic coherence between clinical care and clinical research data elements and pre-populate eCRFs. The RE-USE project utilized SNOMED International v.3.5 as its "pivot reference terminology" to support EHR-to-eCRF mapping, a decision that likely enhanced the "recall" of the mapping algorithms. The RE-USE results demonstrate the difficult challenges involved in semantic integration between the clinical care and clinical research contexts. Copyright © 2011 Elsevier Inc. All rights reserved.

Calibration of a time-resolved hard-x-ray detector using radioactive sources

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

Stoeckl, C., E-mail: csto@lle.rochester.edu; Theobald, W.; Regan, S. P.

A four-channel, time-resolved, hard x-ray detector (HXRD) has been operating at the Laboratory for Laser Energetics for more than a decade. The slope temperature of the hot-electron population in direct-drive inertial confinement fusion experiments is inferred by recording the hard x-ray radiation generated in the interaction of the electrons with the target. Measuring the energy deposited by hot electrons requires an absolute calibration of the hard x-ray detector. A novel method to obtain an absolute calibration of the HXRD using single photons from radioactive sources was developed, which uses a thermoelectrically cooled, low-noise, charge-sensitive amplifier.

Predictive thresholds for plague in Kazakhstan.

PubMed

Davis, Stephen; Begon, Mike; De Bruyn, Luc; Ageyev, Vladimir S; Klassovskiy, Nikolay L; Pole, Sergey B; Viljugrein, Hildegunn; Stenseth, Nils Chr; Leirs, Herwig

2004-04-30

In Kazakhstan and elsewhere in central Asia, the bacterium Yersinia pestis circulates in natural populations of gerbils, which are the source of human cases of bubonic plague. Our analysis of field data collected between 1955 and 1996 shows that plague invades, fades out, and reinvades in response to fluctuations in the abundance of its main reservoir host, the great gerbil (Rhombomys opimus). This is a rare empirical example of the two types of abundance thresholds for infectious disease-invasion and persistence- operating in a single wildlife population. We parameterized predictive models that should reduce the costs of plague surveillance in central Asia and thereby encourage its continuance.

High-performance semiconductor quantum-dot single-photon sources

NASA Astrophysics Data System (ADS)

Senellart, Pascale; Solomon, Glenn; White, Andrew

2017-11-01

Single photons are a fundamental element of most quantum optical technologies. The ideal single-photon source is an on-demand, deterministic, single-photon source delivering light pulses in a well-defined polarization and spatiotemporal mode, and containing exactly one photon. In addition, for many applications, there is a quantum advantage if the single photons are indistinguishable in all their degrees of freedom. Single-photon sources based on parametric down-conversion are currently used, and while excellent in many ways, scaling to large quantum optical systems remains challenging. In 2000, semiconductor quantum dots were shown to emit single photons, opening a path towards integrated single-photon sources. Here, we review the progress achieved in the past few years, and discuss remaining challenges. The latest quantum dot-based single-photon sources are edging closer to the ideal single-photon source, and have opened new possibilities for quantum technologies.

Dipole anisotropy in cosmic electrons and positrons: inspection on local sources

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

Manconi, S.; Donato, F.; Mauro, M. Di, E-mail: manconi@to.infn.it, E-mail: mdimauro@slac.stanford.edu, E-mail: donato@to.infn.it

The cosmic electrons and positrons have been measured with unprecedented statistics up to several hundreds GeV, thus permitting to explore the role that close single sources can have in shaping the flux at different energies. In the present analysis, we consider electrons and positrons in cosmic rays to be produced by spallations of hadron fluxes with the interstellar medium, by a smooth Supernova Remnant (SNR) population, by all the ATNF catalog pulsars, and by few discrete, local SNRs. We test several source models on the e {sup ++} e {sup −} and e {sup +} AMS-02 flux data. For themore » configurations compatible with the data, we compute the dipole anisotropy in e {sup ++} e {sup −}, e {sup +}, e {sup +}/ e {sup −} from single sources. Our study includes a dedicated analysis to the Vela SNR. We show that Fermi -LAT present data on dipole anisotropy of e {sup ++} e {sup −} start to explore some of the models for the Vela SNR selected by AMS-02 flux data. We also investigate how the observed anisotropy could result from a combination of local sources. Our analysis shows that the search of anisotropy in the lepton fluxes up to TeV energies can be an interesting tool for the inspection of properties of close SNRs, complementary to the high precision flux data.« less

Epidemiological Outbreaks of Pneumocystis jirovecii Pneumonia Are Not Limited to Kidney Transplant Recipients: Genotyping Confirms Common Source of Transmission in a Liver Transplantation Unit

PubMed Central

Dominique, Manon; Morio, Florent; Thepault, Rose-Anne; Franck-Martel, Claire; Tellier, Anne-Charlotte; Ferrandière, Martine; Hennequin, Christophe; Bernard, Louis; Salamé, Ephrem; Bailly, Éric; Chandenier, Jacques

2016-01-01

Over a 5-month period, four liver transplant patients at a single hospital were diagnosed with Pneumocystis jirovecii pneumonia (PCP). This unusually high incidence was investigated using molecular genotyping. Bronchoalveolar lavage fluids (BALF) obtained from the four liver recipients diagnosed with PCP were processed for multilocus sequence typing (MLST) at three loci (SOD, mt26s, and CYB). Twenty-four other BALF samples, which were positive for P. jirovecii and collected from 24 epidemiologically unrelated patients with clinical signs of PCP, were studied in parallel by use of the same method. Pneumocystis jirovecii isolates from the four liver recipients all had the same genotype, which was different from those of the isolates from all the epidemiologically unrelated individuals studied. These findings supported the hypothesis of a common source of contamination or even cross-transmission of a single P. jirovecii clone between the four liver recipients. Hospitalization mapping showed several possible encounters between these four patients, including outpatient consultations on one particular date when they all possibly met. This study demonstrates the value of molecular genotyping of P. jirovecii isolated from clinical samples for epidemiological investigation of PCP outbreaks. It is also the first description of a common source of exposure to a single P. jirovecii clone between liver transplant recipients and highlights the importance of prophylaxis in such a population. PMID:26935726

Enhanced biological phosphorus removal with different carbon sources.

PubMed

Shen, Nan; Zhou, Yan

2016-06-01

Enhanced biological phosphorus removal (EBPR) process is one of the most economical and sustainable methods for phosphorus removal from wastewater. However, the performance of EBPR can be affected by available carbon sources types in the wastewater that may induce different functional microbial communities in the process. Glycogen accumulating organisms (GAOs) and polyphosphate accumulating organisms (PAOs) are commonly found by coexisting in the EBPR process. Predominance of GAO population may lead to EBPR failure due to the competition on carbon source with PAO without contributing phosphorus removal. Carbon sources indeed play an important role in alteration of PAOs and GAOs in EBPR processes. Various types of carbon sources have been investigated for EBPR performance. Certain carbon sources tend to enrich specific groups of GAOs and/or PAOs. This review summarizes the types of carbon sources applied in EBPR systems and highlights the roles of these carbon sources in PAO and GAO competition. Both single (e.g., acetate, propionate, glucose, ethanol, and amino acid) and complex carbon sources (e.g., yeast extract, peptone, and mixed carbon sources) are discussed in this review. Meanwhile, the environmental friendly and economical carbon sources that are derived from waste materials, such as crude glycerol and wasted sludge, are also discussed and compared.

High-throughput label-free screening of euglena gracilis with optofluidic time-stretch quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Guo, Baoshan; Lei, Cheng; Ito, Takuro; Yaxiaer, Yalikun; Kobayashi, Hirofumi; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke

2017-02-01

The development of reliable, sustainable, and economical sources of alternative fuels is an important, but challenging goal for the world. As an alternative to liquid fossil fuels, microalgal biofuel is expected to play a key role in reducing the detrimental effects of global warming since microalgae absorb atmospheric CO2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid contents and fail to characterize a diverse population of microalgal cells with single-cell resolution in a noninvasive and interference-free manner. Here we demonstrate high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy. In particular, we use Euglena gracilis - an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement) within lipid droplets. Our optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch phase-contrast microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase contents of every single cell at a high throughput of 10,000 cells/s. We characterize heterogeneous populations of E. gracilis cells under two different culture conditions to evaluate their lipid production efficiency. Our method holds promise as an effective analytical tool for microalgaebased biofuel production.

X-Ray source populations in old open clusters: Collinder 261

NASA Astrophysics Data System (ADS)

Vats, Smriti; van den Berg, Maureen; Wijnands, Rudy

2014-09-01

We are carrying out an X-ray survey of old open clusters with the Chandra X-ray Observatory. Single old stars, being slow rotators, are very faint in X-rays (L_X < 1×10^27 erg/s). Hence, X-rays produced by mass transfer in cataclysmic variables (CVs) or by rapid rotation of the stars in tidally locked, detached binaries (active binaries; ABs) can be detected, without contamination from single stars. By comparing the properties of various types of interacting binaries in different environments (the Galactic field, old open clusters, globular clusters), we aim to study binary evolution and how it may be affected by dynamical encounters with other cluster stars. Stellar clusters are good targets to study binaries, as age, distance, chemical composition, are well constrained. Collinder (Cr) 261 is an old open cluster (age ~ 7 Gyr), with one of the richest populations inferred of close binaries and blue stragglers of all open clusters and is therefore an obvious target to study the products of close encounters in open clusters. We will present the first results of this study, detailing the low-luminosity X-ray population of Cr 261, in conjunction with other open clusters in our survey (NGC 188, Berkeley 17, NGC 6253, M67, NGC 6791) and in comparison with populations in globular clusters.

Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation.

PubMed

Stervander, Martin; Illera, Juan Carlos; Kvist, Laura; Barbosa, Pedro; Keehnen, Naomi P; Pruisscher, Peter; Bensch, Staffan; Hansson, Bengt

2015-05-01

Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences. © 2015 John Wiley & Sons Ltd.

Bridgehead Effect in the Worldwide Invasion of the Biocontrol Harlequin Ladybird

PubMed Central

Lombaert, Eric; Guillemaud, Thomas; Cornuet, Jean-Marie; Malausa, Thibaut; Facon, Benoît; Estoup, Arnaud

2010-01-01

Recent studies of the routes of worldwide introductions of alien organisms suggest that many widespread invasions could have stemmed not from the native range, but from a particularly successful invasive population, which serves as the source of colonists for remote new territories. We call here this phenomenon the invasive bridgehead effect. Evaluating the likelihood of such a scenario is heuristically challenging. We solved this problem by using approximate Bayesian computation methods to quantitatively compare complex invasion scenarios based on the analysis of population genetics (microsatellite variation) and historical (first observation dates) data. We applied this approach to the Harlequin ladybird Harmonia axyridis (HA), a coccinellid native to Asia that was repeatedly introduced as a biocontrol agent without becoming established for decades. We show that the recent burst of worldwide invasions of HA followed a bridgehead scenario, in which an invasive population in eastern North America acted as the source of the colonists that invaded the European, South American and African continents, with some admixture with a biocontrol strain in Europe. This demonstration of a mechanism of invasion via a bridgehead has important implications both for invasion theory (i.e., a single evolutionary shift in the bridgehead population versus multiple changes in case of introduced populations becoming invasive independently) and for ongoing efforts to manage invasions by alien organisms (i.e., heightened vigilance against invasive bridgeheads). PMID:20305822

Phenotype heterogeneity in cancer cell populations

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

Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean

2016-06-08

Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a fewmore » results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as “bet hedging” of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to represent evolution towards heterogeneity, possibly polyclonal, in cancer cell populations and propose innovative directions for therapeutic strategies based on such frameworks.« less

Phenotype heterogeneity in cancer cell populations

NASA Astrophysics Data System (ADS)

Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean; Escargueil, Alexandre; Lorenzi, Tommaso; Lorz, Alexander; Trélat, Emmanuel

2016-06-01

Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as "bet hedging" of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to represent evolution towards heterogeneity, possibly polyclonal, in cancer cell populations and propose innovative directions for therapeutic strategies based on such frameworks.

Population activity statistics dissect subthreshold and spiking variability in V1.

PubMed

Bányai, Mihály; Koman, Zsombor; Orbán, Gergő

2017-07-01

Response variability, as measured by fluctuating responses upon repeated performance of trials, is a major component of neural responses, and its characterization is key to interpret high dimensional population recordings. Response variability and covariability display predictable changes upon changes in stimulus and cognitive or behavioral state, providing an opportunity to test the predictive power of models of neural variability. Still, there is little agreement on which model to use as a building block for population-level analyses, and models of variability are often treated as a subject of choice. We investigate two competing models, the doubly stochastic Poisson (DSP) model assuming stochasticity at spike generation, and the rectified Gaussian (RG) model tracing variability back to membrane potential variance, to analyze stimulus-dependent modulation of both single-neuron and pairwise response statistics. Using a pair of model neurons, we demonstrate that the two models predict similar single-cell statistics. However, DSP and RG models have contradicting predictions on the joint statistics of spiking responses. To test the models against data, we build a population model to simulate stimulus change-related modulations in pairwise response statistics. We use single-unit data from the primary visual cortex (V1) of monkeys to show that while model predictions for variance are qualitatively similar to experimental data, only the RG model's predictions are compatible with joint statistics. These results suggest that models using Poisson-like variability might fail to capture important properties of response statistics. We argue that membrane potential-level modeling of stochasticity provides an efficient strategy to model correlations. NEW & NOTEWORTHY Neural variability and covariability are puzzling aspects of cortical computations. For efficient decoding and prediction, models of information encoding in neural populations hinge on an appropriate model of variability. Our work shows that stimulus-dependent changes in pairwise but not in single-cell statistics can differentiate between two widely used models of neuronal variability. Contrasting model predictions with neuronal data provides hints on the noise sources in spiking and provides constraints on statistical models of population activity. Copyright © 2017 the American Physiological Society.

A Neighboring Dwarf Irregular Galaxy Hidden by the Milky Way

NASA Astrophysics Data System (ADS)

Massey, Philip; Henning, P. A.; Kraan-Korteweg, R. C.

2003-11-01

We have obtained VLA and optical follow-up observations of the low-velocity H I source HIZSS 3 discovered by Henning et al. and Rivers in a survey for nearby galaxies hidden by the disk of the Milky Way. Its radio characteristics are consistent with this being a nearby (~1.8 Mpc) low-mass dwarf irregular galaxy (dIm). Our optical imaging failed to reveal a resolved stellar population but did detect an extended Hα emission region. The location of the Hα source is coincident with a partially resolved H I cloud in the 21 cm map. Spectroscopy confirms that the Hα source has a similar radial velocity to that of the H I emission at this location, and thus we have identified an optical counterpart. The Hα emission (100 pc in diameter and with a luminosity of 1.4×1038 ergs s-1) is characteristic of a single H II region containing a modest population of OB stars. The galaxy's radial velocity and distance from the solar apex suggests that it is not a Local Group member, although a more accurate distance is needed to be certain. The properties of HIZSS 3 are comparable to those of GR 8, a nearby dIm with a modest amount of current star formation. Further observations are needed to characterize its stellar population, determine the chemical abundances, and obtain a more reliable distance estimate.

Sources of drinking water in a pediatric population.

PubMed

Jadav, Urvi G; Acharya, Bhavini S; Velasquez, Gisela M; Vance, Bradley J; Tate, Robert H; Quock, Ryan L

2014-01-01

The purpose of this study was to determine the primary sources of water used for consumption and cooking by the patients of a university-based pediatric dental practice. A simple, prewritten questionnaire-consisting of seven questions and available in English and Spanish-was conducted verbally with the caregivers of 123 pediatric patients during a designated timeframe. Analysis of responses included descriptive statistics and a chi-square test for a single proportion. Nonfiltered tap water accounted for the primary drinking water source in only 10 percent of the respondents. Firty-two percent of the respondents selected bottled water as the primary source of drinking water, and 24 percent selected vended water stations as a primary drinking water source. Nonfiltered tap water was much more likely to be utilized in cooking (58 percent). The majority of the patients in this study's pediatric dental practice do not consume fluoridated tap water. With the vast majority of the patients primarily consuming bottled or vended water, these patients are likely missing out on the caries-protective effects of water fluoridation.

Cetacean population density estimation from single fixed sensors using passive acoustics.

PubMed

Küsel, Elizabeth T; Mellinger, David K; Thomas, Len; Marques, Tiago A; Moretti, David; Ward, Jessica

2011-06-01

Passive acoustic methods are increasingly being used to estimate animal population density. Most density estimation methods are based on estimates of the probability of detecting calls as functions of distance. Typically these are obtained using receivers capable of localizing calls or from studies of tagged animals. However, both approaches are expensive to implement. The approach described here uses a MonteCarlo model to estimate the probability of detecting calls from single sensors. The passive sonar equation is used to predict signal-to-noise ratios (SNRs) of received clicks, which are then combined with a detector characterization that predicts probability of detection as a function of SNR. Input distributions for source level, beam pattern, and whale depth are obtained from the literature. Acoustic propagation modeling is used to estimate transmission loss. Other inputs for density estimation are call rate, obtained from the literature, and false positive rate, obtained from manual analysis of a data sample. The method is applied to estimate density of Blainville's beaked whales over a 6-day period around a single hydrophone located in the Tongue of the Ocean, Bahamas. Results are consistent with those from previous analyses, which use additional tag data. © 2011 Acoustical Society of America

A comprehensive assessment of mercury exposure in penguin populations throughout the Southern Hemisphere: Using trophic calculations to identify sources of population-level variation.

PubMed

Brasso, Rebecka L; Chiaradia, André; Polito, Michael J; Raya Rey, Andrea; Emslie, Steven D

2015-08-15

The wide geographic distribution of penguins (Order Sphenisciformes) throughout the Southern Hemisphere provided a unique opportunity to use a single taxonomic group as biomonitors of mercury among geographically distinct marine ecosystems. Mercury concentrations were compared among ten species of penguins representing 26 geographically distinct breeding populations. Mercury concentrations were relatively low (⩽2.00ppm) in feathers from 18/26 populations considered. Population-level differences in trophic level explained variation in mercury concentrations among Little, King, and Gentoo penguin populations. However, Southern Rockhopper and Magellanic penguins breeding on Staten Island, Tierra del Fuego, had the highest mercury concentrations relative to their conspecifics despite foraging at a lower trophic level. The concurrent use of stable isotope and mercury data allowed us to document penguin populations at the greatest risk of exposure to harmful concentrations of mercury as a result of foraging at a high trophic level or in geographic 'hot spots' of mercury availability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Developing population models with data from marked individuals

USGS Publications Warehouse

Hae Yeong Ryu,; Kevin T. Shoemaker,; Eva Kneip,; Anna Pidgeon,; Patricia Heglund,; Brooke Bateman,; Thogmartin, Wayne E.; Reşit Akçakaya,

2016-01-01

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern.

Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

PubMed Central

Mastretta-Yanes, Alicia; Zamudio, Sergio; Jorgensen, Tove H.; Arrigo, Nils; Alvarez, Nadir; Piñero, Daniel; Emerson, Brent C.

2014-01-01

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species. PMID:25223767

Polyandrous females found fitter populations.

PubMed

Power, D J; Holman, L

2014-09-01

Multiple mating by females (polyandry) requires an evolutionary explanation, because it carries fitness costs in many species. When mated females disperse alone to a new habitat, their offspring may have no option but to mate with their siblings and incur inbreeding depression. However, some of the offspring of polyandrous females may only be half siblings, reducing inbreeding depression when isolated groups of siblings only have each other as mates. We investigated this putative benefit of polyandry over monandry by initiating multiple genetically isolated populations of Callosobruchus maculatus beetles, each founded by a single female, who received a complete ejaculate from either one or two males. The early generations had comparable fitness, but the F4 and F5 descendants of doubly inseminated females were more numerous and had higher egg-to-adult survival than the descendants of singly inseminated females. This fitness benefit was of similar magnitude whether beetles were reared on their standard food plant, or on a less favourable food source. Our results suggest that polyandrous females produce fitter descendants in inbred founder populations and therefore that polyandry may affect movement ecology and invasion biology. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

NASA Astrophysics Data System (ADS)

Maier, E.; Buckenmaier, A.; Tollrian, R.; Nürnberger, B.

2012-06-01

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.

Single photon source with individualized single photon certifications

NASA Astrophysics Data System (ADS)

Migdall, Alan L.; Branning, David A.; Castelletto, Stefania; Ware, M.

2002-12-01

As currently implemented, single-photon sources cannot be made to produce single photons with high probability, while simultaneously suppressing the probability of yielding two or more photons. Because of this, single photon sources cannot really produce single photons on demand. We describe a multiplexed system that allows the probabilities of producing one and more photons to be adjusted independently, enabling a much better approximation of a source of single photons on demand. The scheme uses a heralded photon source based on parametric downconversion, but by effectively breaking the trigger detector area into multiple regions, we are able to extract more information about a heralded photon than is possible with a conventional arrangement. This scheme allows photons to be produced along with a quantitative 'certification' that they are single photons. Some of the single-photon certifications can be significantly better than what is possible with conventional downconversion sources, as well as being better than faint laser sources. With such a source of more tightly certified single photons, it should be possible to improve the maximum secure bit rate possible over a quantum cryptographic link. We present an analysis of the relative merits of this method over the conventional arrangement.

Single-source precursors for ternary chalcopyrite materials, and methods of making and using the same

NASA Technical Reports Server (NTRS)

Banger, Kulbinder K. (Inventor); Hepp, Aloysius F. (Inventor); Harris, Jerry D. (Inventor); Jin, Michael Hyun-Chul (Inventor); Castro, Stephanie L. (Inventor)

2006-01-01

A single source precursor for depositing ternary I-III-VI.sub.2 chalcopyrite materials useful as semiconductors. The single source precursor has the I-III-VI.sub.2 stoichiometry built into a single precursor molecular structure which degrades on heating or pyrolysis to yield the desired I-III-VI.sub.2 ternary chalcopyrite. The single source precursors effectively degrade to yield the ternary chalcopyrite at low temperature, e.g. below 500.degree. C., and are useful to deposit thin film ternary chalcopyrite layers via a spray CVD technique. The ternary single source precursors according to the invention can be used to provide nanocrystallite structures useful as quantum dots. A method of making the ternary single source precursors is also provided.

Adult Human Gingival Epithelial Cells as a Source for Whole-tooth Bioengineering

PubMed Central

Angelova Volponi, A.; Kawasaki, M.; Sharpe, P.T.

2013-01-01

Teeth develop from interactions between embryonic oral epithelium and neural-crest-derived mesenchyme. These cells can be separated into single-cell populations and recombined to form normal teeth, providing a basis for bioengineering new teeth if suitable, non-embryonic cell sources can be identified. We show here that cells can be isolated from adult human gingival tissue that can be expanded in vitro and, when combined with mouse embryonic tooth mesenchyme cells, form teeth. Teeth with developing roots can be produced from this cell combination following transplantation into renal capsules. These bioengineered teeth contain dentin and enamel with ameloblast-like cells and rests of Malassez of human origin. PMID:23458883

Phylogenetic comparison of rabies viruses from disease outbreaks on the Svalbard Islands.

PubMed

Johnson, N; Dicker, A; Mork, T; Marston, D A; Fooks, A R; Tryland, M; Fuglei, E; Müller, T

2007-01-01

Periodic wildlife rabies epizootics occur in Arctic regions. The original sources of these outbreaks are rarely identified. In 1980, a wildlife epizootic of rabies occurred on the previously rabies-free Svalbard Islands, Norway. After this outbreak of rabies in the arctic fox population (Alopex lagopus), only single cases have been reported from the Islands over the following two decades. Phylogenetic characterization of four viruses isolated from infected arctic foxes from Svalbard from three different time periods suggest that the source of these epizootics could have been migration of this species from the Russian mainland. Arctic fox migration has likely contributed to the establishment of another zoonotic disease, Echinococcus multilocularis, on Svalbard in recent years.

A FOURTH H I 21 cm ABSORPTION SYSTEM IN THE SIGHT LINE OF MG J0414+0534: A RECORD FOR INTERVENING ABSORBERS

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

Tanna, A.; Webb, J. K.; Curran, S. J.

2013-08-01

We report the detection of a strong H I 21 cm absorption system at z = 0.5344, as well as a candidate system at z = 0.3389, in the sight line toward the z = 2.64 quasar MG J0414+0534. This, in addition to the absorption at the host redshift and the other two intervening absorbers, takes the total to four (possibly five). The previous maximum number of 21 cm absorbers detected along a single sight line is two and so we suspect that this number of gas-rich absorbers is in some way related to the very red color of themore » background source. Despite this, no molecular gas (through OH absorption) has yet been detected at any of the 21 cm redshifts, although, from the population of 21 cm absorbers as a whole, there is evidence for a weak correlation between the atomic line strength and the optical-near-infrared color. In either case, the fact that so many gas-rich galaxies (likely to be damped Ly{alpha} absorption systems) have been found along a single sight line toward a highly obscured source may have far-reaching implications for the population of faint galaxies not detected in optical surveys, a possibility which could be addressed through future wide-field absorption line surveys with the Square Kilometer Array.« less

Demographic variation, reintroduction, and persistence of an island duck (Anas laysanensis)

USGS Publications Warehouse

Reynolds, Michelle H.; Weiser, Emily; Jamieson, Ian; Hatfield, Jeffrey S.

2013-01-01

Population variation in life history can be important for predicting successful establishment and persistence of reintroduced populations of endangered species. The Laysan duck (Anas laysanensis) is an endangered bird native to the Hawaiian Archipelago that was extirpated from most islands after the introduction of mammalian predators. Laysan ducks were restricted to a single remote island, Laysan Island (4.1 km2), for nearly 150 years. Since the species is not known to disperse between distant Hawaiian Islands today, 42 wild birds from Laysan Island were translocated to another mammalian predator-free low-lying atoll (Midway Atoll; 6.0 km2) to reduce extinction risk. We explored how variation in demography influences establishment and longer-term retention of genetic diversity (rare alleles) for reintroductions of this species. We observed dramatic differences in population growth between the source (λ = 1.18) and reintroduced (λ = 3.28) population. The number of eggs hatched at Midway Atoll was greater than at Laysan Island, however, we found no difference in hatching success (proportion of clutch hatched) between populations. Adult females produced 3 times as many fledglings per breeding year on Midway Atoll compared to Laysan Island. We estimated population abundance of both populations until 2010 and applied a Gompertz model with a Bayesian approach to infer density dependence, process variation, observation error, and carrying capacity for the Laysan Island and Midway Atoll populations. The carrying capacity from the Gompertz model for Midway Atoll (K = 883 ± 210 SD) was estimated to be greater than that of Laysan Island (K = 598 ± 76 SD). Translocations with small numbers of founders and no immigration can create population bottlenecks, leading to loss of genetic variation over time, and potentially reducing the reintroduced population's viability or its potential to serve as a source for future translocations. Therefore, we also assessed the probability of retaining rare alleles in an isolated reintroduced Laysan duck population using life history parameters observed from the Laysan Island and Midway Atoll populations; we concluded that additional founders are needed under scenarios using demographic estimates from both Laysan Island and Midway Atoll to retain either 90% or 95% of source population genetic diversity.

Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama

PubMed Central

Obaldia, Nicanor; Baro, Nicholas K.; Calzada, Jose E.; Santamaria, Ana M.; Daniels, Rachel; Wong, Wesley; Chang, Hsiao-Han; Hamilton, Elizabeth J.; Arevalo-Herrera, Myriam; Herrera, Socrates; Wirth, Dyann F.; Hartl, Daniel L.; Marti, Matthias; Volkman, Sarah K.

2015-01-01

Identifying the source of resurgent parasites is paramount to a strategic, successful intervention for malaria elimination. Although the malaria incidence in Panama is low, a recent outbreak resulted in a 6-fold increase in reported cases. We hypothesized that parasites sampled from this epidemic might be related and exhibit a clonal population structure. We tested the genetic relatedness of parasites, using informative single-nucleotide polymorphisms and drug resistance loci. We found that parasites were clustered into 3 clonal subpopulations and were related to parasites from Colombia. Two clusters of Panamanian parasites shared identical drug resistance haplotypes, and all clusters shared a chloroquine-resistance genotype matching the pfcrt haplotype of Colombian origin. Our findings suggest these resurgent parasite populations are highly clonal and that the high clonality likely resulted from epidemic expansion of imported or vestigial cases. Malaria outbreak investigations that use genetic tools can illuminate potential sources of epidemic malaria and guide strategies to prevent further resurgence in areas where malaria has been eliminated. PMID:25336725

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

PubMed

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

2010-06-17

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

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel

2008-10-10

In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.

Evidence of low genetic variation and rare alleles in a bottlenecked endangered island endemic, the Lasan Teal (Anas laysanensis)

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Peters Jeffrey L,; Courtot, Karen; Seixas, Pedro P.

2015-01-01

Genetic diversity is assumed to reflect the evolutionary potential and adaptability of populations, and thus quantifying the genetic diversity of endangered species is useful for recovery programs. In particular, if conservation strategies include reintroductions, periodic genetic assessments are useful to evaluate whether management efforts have resulted in the maximization or loss of genetic variation within populations over generations. In this study, we collected blood, feather, and tissue samples during 1999–2009 and quantified genetic diversity for a critically endangered waterfowl species endemic to the Hawaiian archipelago, the Laysan teal or duck (Anas laysanensis; n = 239 individual birds sampled). The last extant population of this species at Laysan Island was sourced in 2004–2005 for a ‘wild to wild’ translocation of 42 individuals for an experimental reintroduction to Midway Atoll. To inform future management strategies, we compared genetic diversity sampled from the source population (n = 133 Laysan birds) including 23 of Midway’s founders and offspring of the translocated population 2–5 years post release (n = 96 Midway birds). We attempted to identify polymorphic markers by screening nuclear microsatellite (N = 83) and intronic loci (N = 19), as well as the mitochondrial control region (mtDNA) for a subset of samples. Among 83 microsatellite loci screened, six were variable. We found low nuclear variation consistent with the species’ historical population bottlenecks and sequence variation was observed at a single intron locus. We detected no variation within the mtDNA. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within islands. Two rare alleles found in the Laysan Island source population were not present in the Midway translocated group, and a rare allele was discovered in an individual on Midway in 2008. We found similar genetic diversity and low, but statistically significant, levels of differentiation (0.6%) between island populations suggesting that genetic drift (as a result of translocation-induced population bottlenecking) has had a limited effect within five years post-release. Our results have utility for informing translocation and genetic management decisions.

Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana)

NASA Astrophysics Data System (ADS)

von Beeren, Christoph; Stoeckle, Mark Y.; Xia, Joyce; Burke, Griffin; Kronauer, Daniel J. C.

2015-02-01

DNA barcoding promises to be a useful tool to identify pest species assuming adequate representation of genetic variants in a reference library. Here we examined mitochondrial DNA barcodes in a global urban pest, the American cockroach (Periplaneta americana). Our sampling effort generated 284 cockroach specimens, most from New York City, plus 15 additional U.S. states and six other countries, enabling the first large-scale survey of P. americana barcode variation. Periplaneta americana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate from other Periplaneta species. We found three distinct P. americana haplogroups with relatively small differences within (<=0.6%) and larger differences among groups (2.4%-4.7%). This could be interpreted as indicative of multiple cryptic species. However, nuclear DNA sequences (n = 77 specimens) revealed extensive gene flow among mitochondrial haplogroups, confirming a single species. This unusual genetic pattern likely reflects multiple introductions from genetically divergent source populations, followed by interbreeding in the invasive range. Our findings highlight the need for comprehensive reference databases in DNA barcoding studies, especially when dealing with invasive populations that might be derived from multiple genetically distinct source populations.

Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting.

PubMed

Becht, Etienne; Simoni, Yannick; Coustan-Smith, Elaine; Maximilien, Evrard; Cheng, Yang; Ng, Lai Guan; Campana, Dario; Newell, Evan

2018-06-21

Recent flow and mass cytometers generate datasets of dimensions 20 to 40 and a million single cells. From these, many tools facilitate the discovery of new cell populations associated with diseases or physiology. These new cell populations require the identification of new gating strategies, but gating strategies become exponentially more difficult to optimize when dimensionality increases. To facilitate this step, we developed Hypergate, an algorithm which given a cell population of interest identifies a gating strategy optimized for high yield and purity. Hypergate achieves higher yield and purity than human experts, Support Vector Machines and Random-Forests on public datasets. We use it to revisit some established gating strategies for the identification of innate lymphoid cells, which identifies concise and efficient strategies that allow gating these cells with fewer parameters but higher yield and purity than the current standards. For phenotypic description, Hypergate's outputs are consistent with fields' knowledge and sparser than those from a competing method. Hypergate is implemented in R and available on CRAN. The source code is published at http://github.com/ebecht/hypergate under an Open Source Initiative-compliant licence. Supplementary data are available at Bioinformatics online.

Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

PubMed Central

Ananda, Guruprasad; Hile, Suzanne E.; Breski, Amanda; Wang, Yanli; Kelkar, Yogeshwar; Makova, Kateryna D.; Eckert, Kristin A.

2014-01-01

Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation. However, human polymorphism levels at interrupted microsatellites (iMSs) are not known at a genome-wide scale, and the pathways for gaining interruptions are poorly understood. Using the 1000 Genomes Phase-1 variant call set, we interrogated mono-, di-, tri-, and tetranucleotide repeats up to 10 units in length. We detected ∼26,000–40,000 iMSs within each of four human population groups (African, European, East Asian, and American). We identified population-specific iMSs within exonic regions, and discovered that known disease-associated iMSs contain alleles present at differing frequencies among the populations. By analyzing longer microsatellites in primate genomes, we demonstrate that single interruptions result in a genome-wide average two- to six-fold reduction in microsatellite mutability, as compared with perfect microsatellites. Centrally located interruptions lowered mutability dramatically, by two to three orders of magnitude. Using a biochemical approach, we tested directly whether the mutability of a specific iMS is lower because of decreased DNA polymerase strand slippage errors. Modeling the adenomatous polyposis coli tumor suppressor gene sequence, we observed that a single base substitution interruption reduced strand slippage error rates five- to 50-fold, relative to a perfect repeat, during synthesis by DNA polymerases α, β, or η. Computationally, we demonstrate that iMSs arise primarily by base substitution mutations within individual human genomes. Our biochemical survey of human DNA polymerase α, β, δ, κ, and η error rates within certain microsatellites suggests that interruptions are created most frequently by low fidelity polymerases. Our combined computational and biochemical results demonstrate that iMSs are abundant in human genomes and are sources of population-specific genetic variation that may affect genome stability. The genome-wide identification of iMSs in human populations presented here has important implications for current models describing the impact of microsatellite polymorphisms on gene expression. PMID:25033203

The effects of parasite age and intensity on variability in acanthocephalan-induced behavioural manipulation.

PubMed

Franceschi, Nathalie; Bauer, Alexandre; Bollache, Loïc; Rigaud, Thierry

2008-08-01

Numerous parasites with complex life cycles are able to manipulate the behaviour of their intermediate host in a way that increases their trophic transmission to the definitive host. Pomphorhynchus laevis, an acanthocephalan parasite, is known to reverse the phototactic behaviour of its amphipod intermediate host, Gammarus pulex, leading to an increased predation by fish hosts. However, levels of behavioural manipulation exhibited by naturally-infected gammarids are extremely variable, with some individuals being strongly manipulated whilst others are almost not affected by infection. To investigate parasite age and parasite intensity as potential sources of this variation, we carried out controlled experimental infections on gammarids using parasites from two different populations. We first determined that parasite intensity increased with exposure dose, but found no relationship between infection and host mortality. Repeated measures confirmed that the parasite alters host behaviour only when it reaches the cystacanth stage which is infective for the definitive host. They also revealed, we believe for the first time, that the older the cystacanth, the more it manipulates its host. The age of the parasite is therefore a major source of variation in parasite manipulation. The number of parasites within a host was also a source of variation. Manipulation was higher in hosts infected by two parasites than in singly infected ones, but above this intensity, manipulation did not increase. Since the development time of the parasite was also different according to parasite intensity (it was longer in doubly infected hosts than in singly infected ones, but did not increase more in multi-infected hosts), individual parasite fitness could depend on the compromise between development time and manipulation efficiency. Finally, the two parasite populations tested induced slightly different degrees of behavioural manipulation.

Evaluating the Use of Existing Data Sources, Probabilistic Linkage, and Multiple Imputation to Build Population-based Injury Databases Across Phases of Trauma Care

PubMed Central

Newgard, Craig; Malveau, Susan; Staudenmayer, Kristan; Wang, N. Ewen; Hsia, Renee Y.; Mann, N. Clay; Holmes, James F.; Kuppermann, Nathan; Haukoos, Jason S.; Bulger, Eileen M.; Dai, Mengtao; Cook, Lawrence J.

2012-01-01

Objectives The objective was to evaluate the process of using existing data sources, probabilistic linkage, and multiple imputation to create large population-based injury databases matched to outcomes. Methods This was a retrospective cohort study of injured children and adults transported by 94 emergency medical systems (EMS) agencies to 122 hospitals in seven regions of the western United States over a 36-month period (2006 to 2008). All injured patients evaluated by EMS personnel within specific geographic catchment areas were included, regardless of field disposition or outcome. The authors performed probabilistic linkage of EMS records to four hospital and postdischarge data sources (emergency department [ED] data, patient discharge data, trauma registries, and vital statistics files) and then handled missing values using multiple imputation. The authors compare and evaluate matched records, match rates (proportion of matches among eligible patients), and injury outcomes within and across sites. Results There were 381,719 injured patients evaluated by EMS personnel in the seven regions. Among transported patients, match rates ranged from 14.9% to 87.5% and were directly affected by the availability of hospital data sources and proportion of missing values for key linkage variables. For vital statistics records (1-year mortality), estimated match rates ranged from 88.0% to 98.7%. Use of multiple imputation (compared to complete case analysis) reduced bias for injury outcomes, although sample size, percentage missing, type of variable, and combined-site versus single-site imputation models all affected the resulting estimates and variance. Conclusions This project demonstrates the feasibility and describes the process of constructing population-based injury databases across multiple phases of care using existing data sources and commonly available analytic methods. Attention to key linkage variables and decisions for handling missing values can be used to increase match rates between data sources, minimize bias, and preserve sampling design. PMID:22506952

Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys.

PubMed

Dupuis, Julian R; Guerrero, Felix D; Skoda, Steven R; Phillips, Pamela L; Welch, John B; Schlater, Jack L; Azeredo-Espin, Ana Maria L; Pérez de León, Adalberto A; Geib, Scott M

2018-05-19

New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.

A genomic view of the peopling of the Americas

PubMed Central

Skoglund, Pontus; Reich, David

2016-01-01

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ~4,500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research. PMID:27507099

A genomic view of the peopling of the Americas.

PubMed

Skoglund, Pontus; Reich, David

2016-12-01

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

PubMed Central

2017-01-01

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. PMID:29181279

Epidemiological Outbreaks of Pneumocystis jirovecii Pneumonia Are Not Limited to Kidney Transplant Recipients: Genotyping Confirms Common Source of Transmission in a Liver Transplantation Unit.

PubMed

Desoubeaux, Guillaume; Dominique, Manon; Morio, Florent; Thepault, Rose-Anne; Franck-Martel, Claire; Tellier, Anne-Charlotte; Ferrandière, Martine; Hennequin, Christophe; Bernard, Louis; Salamé, Ephrem; Bailly, Éric; Chandenier, Jacques

2016-05-01

Over a 5-month period, four liver transplant patients at a single hospital were diagnosed with Pneumocystis jirovecii pneumonia (PCP). This unusually high incidence was investigated using molecular genotyping. Bronchoalveolar lavage fluids (BALF) obtained from the four liver recipients diagnosed with PCP were processed for multilocus sequence typing (MLST) at three loci (SOD, mt26s, and CYB). Twenty-four other BALF samples, which were positive for P. jirovecii and collected from 24 epidemiologically unrelated patients with clinical signs of PCP, were studied in parallel by use of the same method. Pneumocystis jirovecii isolates from the four liver recipients all had the same genotype, which was different from those of the isolates from all the epidemiologically unrelated individuals studied. These findings supported the hypothesis of a common source of contamination or even cross-transmission of a single P. jirovecii clone between the four liver recipients. Hospitalization mapping showed several possible encounters between these four patients, including outpatient consultations on one particular date when they all possibly met. This study demonstrates the value of molecular genotyping of P. jirovecii isolated from clinical samples for epidemiological investigation of PCP outbreaks. It is also the first description of a common source of exposure to a single P. jirovecii clone between liver transplant recipients and highlights the importance of prophylaxis in such a population. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Screening for coronary artery disease in respiratory patients: comparison of single- and dual-source CT in patients with a heart rate above 70 bpm.

PubMed

Pansini, Vittorio; Remy-Jardin, Martine; Tacelli, Nunzia; Faivre, Jean-Baptiste; Flohr, Thomas; Deken, Valérie; Duhamel, Alain; Remy, Jacques

2008-10-01

To evaluate the assessibility of coronary arteries in respiratory patients with high heart rates. This study was based on the comparative analysis of two paired populations of 54 patients with a heart rate >70 bpm evaluated with dual-source (group 1) and single-source (group 2) CT. The mean heart rate was 89.1 bpm in group 1 and 86.7 bpm in group 2 (P=0.26). The mean number of assessable segments per patient was significantly higher in group 1 compared to group 2 (P

Worldwide F(ST) estimates relative to five continental-scale populations.

PubMed

Steele, Christopher D; Court, Denise Syndercombe; Balding, David J

2014-11-01

We estimate the population genetics parameter FST (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. FST is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate FST comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which FST is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low FST values, with posterior 97.5 percentiles < 3% when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find FST < 5%. These are much smaller than single nucleotide polymorphism-based inter-continental FST estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of FST up to 3% in forensic calculations, which corresponds to some current practice.

Genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay

USGS Publications Warehouse

Duda, T. F.

1994-01-01

The genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay was described using starch gel electrophoresis at eight presumptive loci. Specimens were taken from five environmentally distinct sites located throughout the bay. The population maintains a high degree of genetic variation, with a mean heterozygosity of 0.295, a mean polymorphism of 0.75, and an average of 3.70 alleles per locus. The population is genetically homogeneous, as evidenced from genetic distance values and F-statistics. However, heterogeneity of populations was indicated from a contingency chi-square test. Significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found at the Lap-1 locus for all populations and at the Lap-2 locus for a single population. High levels of variability could represent a universal characteristic of invading species, the levels of variability in the source population(s), and/or the dynamics of the introduction. Lack of differentiation between subpopulations may be due to the immaturity of the San Francisco Bay population, the “general purpose” phenotype genetic strategy of the species, high rates of gene flow in the population, and/or the selective neutrality of the loci investigated.

High-throughput, label-free, single-cell, microalgal lipid screening by machine-learning-equipped optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke

2017-05-01

The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO 2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

THE CONTRIBUTION OF FERMI -2LAC BLAZARS TO DIFFUSE TEV–PEV NEUTRINO FLUX

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

Aartsen, M. G.; Abraham, K.; Ackermann, M.

2017-01-20

The recent discovery of a diffuse cosmic neutrino flux extending up to PeV energies raises the question of which astrophysical sources generate this signal. Blazars are one class of extragalactic sources which may produce such high-energy neutrinos. We present a likelihood analysis searching for cumulative neutrino emission from blazars in the 2nd Fermi -LAT AGN catalog (2LAC) using IceCube neutrino data set 2009-12, which was optimized for the detection of individual sources. In contrast to those in previous searches with IceCube, the populations investigated contain up to hundreds of sources, the largest one being the entire blazar sample in themore » 2LAC catalog. No significant excess is observed, and upper limits for the cumulative flux from these populations are obtained. These constrain the maximum contribution of 2LAC blazars to the observed astrophysical neutrino flux to 27% or less between around 10 TeV and 2 PeV, assuming the equipartition of flavors on Earth and a single power-law spectrum with a spectral index of −2.5. We can still exclude the fact that 2LAC blazars (and their subpopulations) emit more than 50% of the observed neutrinos up to a spectral index as hard as −2.2 in the same energy range. Our result takes into account the fact that the neutrino source count distribution is unknown, and it does not assume strict proportionality of the neutrino flux to the measured 2LAC γ -ray signal for each source. Additionally, we constrain recent models for neutrino emission by blazars.« less

Remote Sensing of Marine Life and Submerged Target Motions with Ocean Waveguide Acoustics

NASA Astrophysics Data System (ADS)

Gong, Zheng

Many species of fish that inhabit the continental shelf waters can cause significant acoustic scattering at low- to mid-frequencies due to the large impedance contrast between their air-filled swimbladders and the surrounding water. In this thesis, we investigate the acoustic resonance scattering response from distributed fish groups both experimentally and theoretically including the effects of multiple scattering, attenuation, and dispersion in a random range-dependent ocean waveguide using an instantaneous wide-area imaging system. In navy sonar operations, the biological organisms can cause high false alarm rates or missed target detections since the biological scattering can be confused with or camouflage the returns from other discrete and distributed objects, such as underwater vehicles and geologic features. From an ecological perspective, the ability to instantaneously survey fish populations distributed over wide areas is important for fisheries management. The low-frequency target strength of shoaling Atlantic herring ( Clupea harengus) in the Gulf of Maine during their Autumn 2006 spawning season is estimated from experimental data acquired simultaneously at multiple frequencies in the 300 to 1200 Hz range using (1) a low-frequency ocean acoustic waveguide remote sensing (OAWRS) system, (2) areal population density calibration with several conventional fish finding sonar (CFFS) systems, and (3) low-frequency transmission loss measurements. The OAWRS system's instantaneous imaging diameter of 100 km and regular updating enabled unaliased monitoring of fish populations over ecosystem scales including shoals of Atlantic herring containing as many as 200 million individuals, as estimated based on single scattering assumption and confirmed by concurrent trawl and CFFS sampling. The mean scattering cross-section of an individual shoaling herring is found to consistently exhibit a strong, roughly 20 dB/octave roll-off with decreasing frequency over all days of the roughly 2-week experiment, consistent with the steep roll-offs expected for sub-resonance scattering from fish with air-filled swimbladders. A numerical Monte-Carlo model is developed to determine the statistical moments of the broadband matched filtered scattered returns from fish groups spanning over multiple range and cross-range resolution cells of a waveguide remote sensing system. It uses the parabolic equation to simulate acoustic field propagation in a random range-dependent ocean waveguide. The effects of (1) multiple scattering, (2) attenuation due to scattering, and (3) fish group 3D spatial configuration on fish population density imaging are examined. The model is applied to investigate (a) population density imaging of shoaling Atlantic herring during the 2006 Gulf of Maine Experiment (GOME06) and (b) examine the wide-area imaging of sparse aggregation of ground fish species, such as Atlantic Cod, in Ipswich Bay continental shelf environment using the waveguide remote sensing system. Incoherent intensities are shown to dominate the total scattered returns from distributed fish groups making single scattering assumption valid for inferring fish areal population densities from their matched filtered scattered intensities. Multiple scattering, attenuation, fish group 3D spatial configuration, and coherent effects, such as resonance shift, sub- and super-local-maxima are found to be negligible at the imaging frequencies employed and for the herring densities observed. Similar results are obtained for the sparsely aggregated cod, but coherent effects such as the double-peak in school resonance can be prominent at much lower fish densities. Attenuation due to scattering can be significant when the fish flesh viscosity is high, especially true for cod. We also investigate approaches for instantaneous long-range passive source localization and tracking with a towed horizontal line-array in a random range-dependent ocean waveguide using passive waveguide acoustics. This is very important for many sonar applications, such as localizing and tracking underwater vehicles and vocalizing marine mammal populations. Instantaneous passive source localization applying the (1) synthetic aperture tracking, (2) array invariant, (3) bearings-only target motion analysis in modified polar coordinates via the extended Kalman filter, and (4) bearings-migration minimum mean-square error methods using measurements made on a single towed horizontal receiver array in a random range-dependent ocean waveguide are examined. These methods are employed to localize and track a vertical source array deployed in the far-field of a towed horizontal receiver array during the Gulf of Maine 2006 Experiment. The source transmitted intermittent broadband pulses in the 300--1200 Hz frequency range. All four methods are found to be comparable with average errors of between 9% to 13% in estimating the mean source positions in a wide variety of source-receiver geometries and range separations up to 20 km. In the case of a relatively stationary source, the synthetic aperture tracking outperformed the other three methods by a factor of two with only 4% error. For a moving source, the Kalman filter method yielded the best performance with 8% error. The array invariant was the best approach for localizing sources within the endfire beam of the receiver array with less than 10% error.

A singly charged ion source for radioactive {sup 11}C ion acceleration

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

Katagiri, K.; Noda, A.; Nagatsu, K.

2016-02-15

A new singly charged ion source using electron impact ionization has been developed to realize an isotope separation on-line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive {sup 11}C ion beams. Low-energy electron beams are used in the electron impact ion source to produce singly charged ions. Ionization efficiency was calculated in order to decide the geometric parameters of the ion source and to determine the required electron emission current for obtaining high ionization efficiency. Based on these considerations, the singly charged ion source was designed and fabricated. In testing, the fabricated ion source wasmore » found to have favorable performance as a singly charged ion source.« less

Multiple estimates of transmissibility for the 2009 influenza pandemic based on influenza-like-illness data from small US military populations.

PubMed

Riley, Pete; Ben-Nun, Michal; Armenta, Richard; Linker, Jon A; Eick, Angela A; Sanchez, Jose L; George, Dylan; Bacon, David P; Riley, Steven

2013-01-01

Rapidly characterizing the amplitude and variability in transmissibility of novel human influenza strains as they emerge is a key public health priority. However, comparison of early estimates of the basic reproduction number during the 2009 pandemic were challenging because of inconsistent data sources and methods. Here, we define and analyze influenza-like-illness (ILI) case data from 2009-2010 for the 50 largest spatially distinct US military installations (military population defined by zip code, MPZ). We used publicly available data from non-military sources to show that patterns of ILI incidence in many of these MPZs closely followed the pattern of their enclosing civilian population. After characterizing the broad patterns of incidence (e.g. single-peak, double-peak), we defined a parsimonious SIR-like model with two possible values for intrinsic transmissibility across three epochs. We fitted the parameters of this model to data from all 50 MPZs, finding them to be reasonably well clustered with a median (mean) value of 1.39 (1.57) and standard deviation of 0.41. An increasing temporal trend in transmissibility ([Formula: see text], p-value: 0.013) during the period of our study was robust to the removal of high transmissibility outliers and to the removal of the smaller 20 MPZs. Our results demonstrate the utility of rapidly available - and consistent - data from multiple populations.

Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations

PubMed Central

Riley, Pete; Ben-Nun, Michal; Armenta, Richard; Linker, Jon A.; Eick, Angela A.; Sanchez, Jose L.; George, Dylan; Bacon, David P.; Riley, Steven

2013-01-01

Rapidly characterizing the amplitude and variability in transmissibility of novel human influenza strains as they emerge is a key public health priority. However, comparison of early estimates of the basic reproduction number during the 2009 pandemic were challenging because of inconsistent data sources and methods. Here, we define and analyze influenza-like-illness (ILI) case data from 2009–2010 for the 50 largest spatially distinct US military installations (military population defined by zip code, MPZ). We used publicly available data from non-military sources to show that patterns of ILI incidence in many of these MPZs closely followed the pattern of their enclosing civilian population. After characterizing the broad patterns of incidence (e.g. single-peak, double-peak), we defined a parsimonious SIR-like model with two possible values for intrinsic transmissibility across three epochs. We fitted the parameters of this model to data from all 50 MPZs, finding them to be reasonably well clustered with a median (mean) value of 1.39 (1.57) and standard deviation of 0.41. An increasing temporal trend in transmissibility (, p-value: 0.013) during the period of our study was robust to the removal of high transmissibility outliers and to the removal of the smaller 20 MPZs. Our results demonstrate the utility of rapidly available – and consistent – data from multiple populations. PMID:23696723

Bait distribution among multiple colonies of Pharaoh ants (hymenoptera: Formicidae).

PubMed

Oi, D H; Vail, K M; Williams, D F

2000-08-01

Pharaoh ant, Monomorium pharaonis (L.), infestations often consist of several colonies located at different nest sites. To achieve control, it is desirable to suppress or eliminate the populations of a majority of these colonies. We compared the trophallactic distribution and efficacy of two ant baits, with different modes of action, among groups of four colonies of Pharaoh ants. Baits contained either the metabolic-inhibiting active ingredient hydramethylnon or the insect growth regulator (IGR) pyriproxyfen. Within 3 wk, the hydramethylnon bait reduced worker and brood populations by at least 80%, and queen reductions ranged between 73 and 100%, when nests were in proximity (within 132 cm) to the bait source. However, these nest sites were reoccupied by ants from other colonies located further from the bait source. The pyriproxyfen bait was distributed more thoroughly to all nest locations with worker populations gradually declining by 73% at all nest sites after 8 wk. Average queen reductions ranged from 31 to 49% for all nest sites throughout the study. Even though some queens survived, brood reductions were rapid in the pyriproxyfen treatment, with reductions of 95% at all locations by week 3. Unlike the metabolic inhibitor, the IGR did not kill adult worker ants quickly, thus, more surviving worker ants were available to distribute the bait to all colonies located at different nest sites. Thus, from a single bait source, the slow-acting bait toxicant provided gradual, but long-term control, whereas the fast-acting bait toxicant provided rapid, localized control for a shorter duration.

Genetic Diversity of Bactrocera dorsalis (Diptera: Tephritidae) on the Hawaiian Islands: Implications for an Introduction Pathway Into California.

PubMed

Barr, Norman B; Ledezma, Lisa A; Leblanc, Luc; San Jose, Michael; Rubinoff, Daniel; Geib, Scott M; Fujita, Brian; Bartels, David W; Garza, Daniel; Kerr, Peter; Hauser, Martin; Gaimari, Stephen

2014-10-01

Population genetic diversity of the oriental fruit fly, Bactrocera dorsalis (Hendel), on the Hawaiian islands of Oahu, Maui, Kauai, and Hawaii (the Big Island) was estimated using DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene. In total, 932 flies representing 36 sampled sites across the four islands were sequenced for a 1,500-bp fragment of the gene named the C1500 marker. Genetic variation was low on the Hawaiian Islands with >96% of flies having just two haplotypes: C1500-Haplotype 1 (63.2%) or C1500-Haplotype 2 (33.3%). The other 33 flies (3.5%) had haplotypes similar to the two dominant haplotypes. No population structure was detected among the islands or within islands. The two haplotypes were present at similar frequencies at each sample site, suggesting that flies on the various islands can be considered one population. Comparison of the Hawaiian data set to DNA sequences of 165 flies from outbreaks in California between 2006 and 2012 indicates that a single-source introduction pathway of Hawaiian origin cannot explain many of the flies in California. Hawaii, however, could not be excluded as a maternal source for 69 flies. There was no clear geographic association for Hawaiian or non-Hawaiian haplotypes in the Bay Area or Los Angeles Basin over time. This suggests that California experienced multiple, independent introductions from different sources. © 2014 Entomological Society of America.

Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

PubMed Central

McCann, Honour C.; Rikkerink, Erik H. A.; Bertels, Frederic; Fiers, Mark; Lu, Ashley; Rees-George, Jonathan; Andersen, Mark T.; Gleave, Andrew P.; Haubold, Bernhard; Wohlers, Mark W.; Guttman, David S.; Wang, Pauline W.; Straub, Christina; Vanneste, Joel; Rainey, Paul B.; Templeton, Matthew D.

2013-01-01

The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease. PMID:23935484

Indirect Potable Reuse: A Sustainable Water Supply Alternative

PubMed Central

Rodriguez, Clemencia; Van Buynder, Paul; Lugg, Richard; Blair, Palenque; Devine, Brian; Cook, Angus; Weinstein, Philip

2009-01-01

The growing scarcity of potable water supplies is among the most important issues facing many cities, in particular those using single sources of water that are climate dependent. Consequently, urban centers are looking to alternative sources of water supply that can supplement variable rainfall and meet the demands of population growth. A diversified portfolio of water sources is required to ensure public health, as well as social, economical and environmental sustainability. One of the options considered is the augmentation of drinking water supplies with advanced treated recycled water. This paper aims to provide a state of the art review of water recycling for drinking purposes with emphasis on membrane treatment processes. An overview of significant indirect potable reuse projects is presented followed by a description of the epidemiological and toxicological studies evaluating any potential human health impacts. Finally, a summary of key operational measures to protect human health and the areas that require further research are discussed. PMID:19440440

Indirect potable reuse: a sustainable water supply alternative.

PubMed

Rodriguez, Clemencia; Van Buynder, Paul; Lugg, Richard; Blair, Palenque; Devine, Brian; Cook, Angus; Weinstein, Philip

2009-03-01

The growing scarcity of potable water supplies is among the most important issues facing many cities, in particular those using single sources of water that are climate dependent. Consequently, urban centers are looking to alternative sources of water supply that can supplement variable rainfall and meet the demands of population growth. A diversified portfolio of water sources is required to ensure public health, as well as social, economical and environmental sustainability. One of the options considered is the augmentation of drinking water supplies with advanced treated recycled water. This paper aims to provide a state of the art review of water recycling for drinking purposes with emphasis on membrane treatment processes. An overview of significant indirect potable reuse projects is presented followed by a description of the epidemiological and toxicological studies evaluating any potential human health impacts. Finally, a summary of key operational measures to protect human health and the areas that require further research are discussed.

Fatty acid profile of unconventional oilseeds.

PubMed

Sabikhi, Latha; Sathish Kumar, M H

2012-01-01

The continued increase in human population has resulted in the rise in the demand as well as the price of edible oils, leading to the search for alternative unconventional sources of oils, particularly in the developing countries. There are hundreds of un- or underexplored plant seeds rich in oil suitable for edible or industrial purposes. Many of them are rich in polyunsaturated essential fatty acids, which establish their utility as "healthy oils." Some agrowaste products such as rice bran have gained importance as a potential source of edible oil. Genetic modification has paved the way for increasing the oil yields and improving the fatty acid profiles of traditional as well as unconventional oilseeds. Single cell oils are also novel sources of edible oil. Some of these unconventional oils may have excellent potential for medicinal and therapeutic uses, even if their low oil contents do not promote commercial production as edible oils. Copyright © 2012 Elsevier Inc. All rights reserved.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

PubMed Central

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F; Abbazia, Patrick; Ababio, Amma; Adam, Naazneen

2015-01-01

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001 PMID:25919952

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

PubMed

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

2015-04-28

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

Biodiversity losses: The downward spiral

USGS Publications Warehouse

Tomback, Diana F.; Kendall, Katherine C.; Tomback, Diana F.; Arno, Stephen F.; Keane, Robert E.

2001-01-01

The dramatic decline of whitebark pine (Pinus albicaulis) populations in the northwestern United States and southwestern Canada from the combined effects of fire exclusion, mountain pine beetles (Dendroctonus ponderosae), and white pine blister rust (Cronartium ribicola), and the projected decline of whitebark pine populations rangewide (Chapters 10 and 11) do not simply add up to local extirpations of a single tree species. Instead, the loss of whitebark pine has broad ecosystem-level consequences, eroding local plant and animal biodiversity, changing the time frame of succession, and altering the distribution of subalpine vegetation (Chapter 1). One potential casualty of this decline may be the midcontinental populations of the grizzly bear (Ursus arctos horribilis), which use whitebark pine seeds as a major food source (Chapter 7). Furthermore, whitebark pine is linked to other white pine ecosystems in the West through its seed-disperser, Clark's nutcracker (Nucifraga columbiana) (Chapter 5). Major declines in nutcracker populations ultimately seal the fate of several white pine ecosystems, and raise the question of whether restoration is possible once a certain threshold of decline is reached.

Indigenous obesity in the news: a media analysis of news representation of obesity in Australia's Indigenous population.

PubMed

Islam, Salwa; Fitzgerald, Lisa

2016-01-01

High rates of obesity are a significant issue amongst Indigenous populations in many countries around the world. Media framing of issues can play a critical role in shaping public opinion and government policy. A broad range of media analyses have been conducted on various aspects of obesity, however media representation of Indigenous obesity remains unexplored. In this study we investigate how obesity in Australia's Indigenous population is represented in newsprint media coverage. Media articles published between 2007 and 2014 were analysed for the distribution and extent of coverage over time and across Indigenous and mainstream media sources using quantitative content analysis. Representation of the causes and solutions of Indigenous obesity and framing in text and image content was examined using qualitative framing analysis. Media coverage of Indigenous obesity was very limited with no clear trends in reporting over time or across sources. The single Indigenous media source was the second largest contributor to the media discourse of this issue. Structural causes/origins were most often cited and individual solutions were comparatively overrepresented. A range of frames were employed across the media sources. All images reinforced textual framing except for one article where the image depicted individual factors whereas the text referred to structural determinants. This study provides a starting point for an important area of research that needs further investigation. The findings highlight the importance of alternative news media outlets, such as The Koori Mail, and that these should be developed to enhance the quality and diversity of media coverage. Media organisations can actively contribute to improving Indigenous health through raising awareness, evidence-based balanced reporting, and development of closer ties with Indigenous health workers.

Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency

PubMed Central

Pedrini, Paolo; Bragalanti, Natalia; Groff, Claudio

2017-01-01

Recently-developed methods that integrate multiple data sources arising from the same ecological processes have typically utilized structured data from well-defined sampling protocols (e.g., capture-recapture and telemetry). Despite this new methodological focus, the value of opportunistic data for improving inference about spatial ecological processes is unclear and, perhaps more importantly, no procedures are available to formally test whether parameter estimates are consistent across data sources and whether they are suitable for integration. Using data collected on the reintroduced brown bear population in the Italian Alps, a population of conservation importance, we combined data from three sources: traditional spatial capture-recapture data, telemetry data, and opportunistic data. We developed a fully integrated spatial capture-recapture (SCR) model that included a model-based test for data consistency to first compare model estimates using different combinations of data, and then, by acknowledging data-type differences, evaluate parameter consistency. We demonstrate that opportunistic data lend itself naturally to integration within the SCR framework and highlight the value of opportunistic data for improving inference about space use and population size. This is particularly relevant in studies of rare or elusive species, where the number of spatial encounters is usually small and where additional observations are of high value. In addition, our results highlight the importance of testing and accounting for inconsistencies in spatial information from structured and unstructured data so as to avoid the risk of spurious or averaged estimates of space use and consequently, of population size. Our work supports the use of a single modeling framework to combine spatially-referenced data while also accounting for parameter consistency. PMID:28973034

Local extinction of dragonfly and damselfly populations in low- and high-quality habitat patches.

PubMed

Suhonen, Jukka; Hilli-Lukkarinen, Milla; Korkeamäki, Esa; Kuitunen, Markku; Kullas, Johanna; Penttinen, Jouni; Salmela, Jukka

2010-08-01

Understanding the risk of extinction of a single population is an important problem in both theoretical and applied ecology. Local extinction risk depends on several factors, including population size, demographic or environmental stochasticity, natural catastrophe, or the loss of genetic diversity. The probability of local extinction may also be higher in low-quality sink habitats than in high-quality source habitats. We tested this hypothesis by comparing local extinction rates of 15 species of Odonata (dragonflies and damselflies) between 1930-1975 and 1995-2003 in central Finland. Local extinction rates were higher in low-quality than in high-quality habitats. Nevertheless, for the three most common species there were no differences in extinction rates between low- and high-quality habitats. Our results suggest that a good understanding of habitat quality is crucial for the conservation of species in heterogeneous landscapes.

Emergence of Persistent Infection due to Heterogeneity

NASA Astrophysics Data System (ADS)

Agrawal, Vidit; Moitra, Promit; Sinha, Sudeshna

2017-02-01

We explore the emergence of persistent infection in a closed region where the disease progression of the individuals is given by the SIRS model, with an individual becoming infected on contact with another infected individual. We investigate the persistence of contagion qualitatively and quantitatively, under increasing heterogeneity in the partitioning of the population into different disease compartments, as well as increasing heterogeneity in the phases of the disease among individuals within a compartment. We observe that when the initial population is uniform, consisting of individuals at the same stage of disease progression, infection arising from a contagious seed does not persist. However when the initial population consists of randomly distributed refractory and susceptible individuals, a single source of infection can lead to sustained infection in the population, as heterogeneity facilitates the de-synchronization of the phases in the disease cycle of the individuals. We also show how the average size of the window of persistence of infection depends on the degree of heterogeneity in the initial composition of the population. In particular, we show that the infection eventually dies out when the entire initial population is susceptible, while even a few susceptibles among an heterogeneous refractory population gives rise to a large persistent infected set.

Herschel Key Program Heritage: a Far-Infrared Source Catalog for the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Seale, Jonathan P.; Meixner, Margaret; Sewiło, Marta; Babler, Brian; Engelbracht, Charles W.; Gordon, Karl; Hony, Sacha; Misselt, Karl; Montiel, Edward; Okumura, Koryo; Panuzzo, Pasquale; Roman-Duval, Julia; Sauvage, Marc; Boyer, Martha L.; Chen, C.-H. Rosie; Indebetouw, Remy; Matsuura, Mikako; Oliveira, Joana M.; Srinivasan, Sundar; van Loon, Jacco Th.; Whitney, Barbara; Woods, Paul M.

2014-12-01

Observations from the HERschel Inventory of the Agents of Galaxy Evolution (HERITAGE) have been used to identify dusty populations of sources in the Large and Small Magellanic Clouds (LMC and SMC). We conducted the study using the HERITAGE catalogs of point sources available from the Herschel Science Center from both the Photodetector Array Camera and Spectrometer (PACS; 100 and 160 μm) and Spectral and Photometric Imaging Receiver (SPIRE; 250, 350, and 500 μm) cameras. These catalogs are matched to each other to create a Herschel band-merged catalog and then further matched to archival Spitzer IRAC and MIPS catalogs from the Spitzer Surveying the Agents of Galaxy Evolution (SAGE) and SAGE-SMC surveys to create single mid- to far-infrared (far-IR) point source catalogs that span the wavelength range from 3.6 to 500 μm. There are 35,322 unique sources in the LMC and 7503 in the SMC. To be bright in the FIR, a source must be very dusty, and so the sources in the HERITAGE catalogs represent the dustiest populations of sources. The brightest HERITAGE sources are dominated by young stellar objects (YSOs), and the dimmest by background galaxies. We identify the sources most likely to be background galaxies by first considering their morphology (distant galaxies are point-like at the resolution of Herschel) and then comparing the flux distribution to that of the Herschel Astrophysical Terahertz Large Area Survey (ATLAS) survey of galaxies. We find a total of 9745 background galaxy candidates in the LMC HERITAGE images and 5111 in the SMC images, in agreement with the number predicted by extrapolating from the ATLAS flux distribution. The majority of the Magellanic Cloud-residing sources are either very young, embedded forming stars or dusty clumps of the interstellar medium. Using the presence of 24 μm emission as a tracer of star formation, we identify 3518 YSO candidates in the LMC and 663 in the SMC. There are far fewer far-IR bright YSOs in the SMC than the LMC due to both the SMC's smaller size and its lower dust content. The YSO candidate lists may be contaminated at low flux levels by background galaxies, and so we differentiate between sources with a high (“probable”) and moderate (“possible”) likelihood of being a YSO. There are 2493/425 probable YSO candidates in the LMC/SMC. Approximately 73% of the Herschel YSO candidates are newly identified in the LMC, and 35% in the SMC. We further identify a small population of dusty objects in the late stages of stellar evolution including extreme and post-asymptotic giant branch, planetary nebulae, and supernova remnants. These populations are identified by matching the HERITAGE catalogs to lists of previously identified objects in the literature. Approximately half of the LMC sources and one quarter of the SMC sources are too faint to obtain accurate ample FIR photometry and are unclassified.

Resident and parental perceptions of adolescent problems and family communications in a low socioeconomic population.

PubMed

Hawley, L E; Shear, C L; Stark, A M; Goodman, P R

1984-11-01

This cross-sectional survey of a low socioeconomic patient group was designed to determine the prevalence and severity of parentally perceived behavioral problems in adolescents as well as to investigate the correlation between such problems and single parenting, family communications, and medical care delivered. The sample population consisted of 79 parents and 121 teenagers selected from a family practice center. The medical record and telephone interview were the sources of information. Results include a parental perception of a high prevalence of problems with school grades (48 percent), school attendance (38 percent), and household problems (chores and sibling rivalry). Of low prevalence but high severity were perceived problems related to suicidal ideation, running away, sexual activity, and gang membership. Single-parent homes had a threefold higher incidence of behavioral problems, a greater degree of communication, and a lower use of community resources than two-parent families. None of the approximately 400 perceived behavioral problems listed by parents was found in the family physicians' master problem list. The results indicate the need for physician education of low socioeconomic and single-parent patients with regard to communication and coping style. In addition, it appears that training programs should provide more education in the care of adolescents.

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

PubMed Central

Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

2011-01-01

Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

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.

Genetic Heterogeneity in Algerian Human Populations

PubMed Central

Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

2015-01-01

The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region. PMID:26402429

Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus.

PubMed

Hoarau, G; Coyer, J A; Veldsink, J H; Stam, W T; Olsen, J L

2007-09-01

The last glacial maximum (20,000-18,000 years ago) dramatically affected extant distributions of virtually all northern European biota. Locations of refugia and postglacial recolonization pathways were examined in Fucus serratus (Heterokontophyta; Fucaceae) using a highly variable intergenic spacer developed from the complete mitochondrial genome of Fucus vesiculosus. Over 1,500 samples from the entire range of F. serratus were analysed using fluorescent single strand conformation polymorphism. A total of 28 mtDNA haplotypes was identified and sequenced. Three refugia were recognized based on high haplotype diversities and the presence of endemic haplotypes: southwest Ireland, the northern Brittany-Hurd Deep area of the English Channel, and the northwest Iberian Peninsula. The Irish refugium was the source for a recolonization sweep involving a single haplotype via northern Scotland and throughout Scandinavia, whereas recolonization from the Brittany-Hurd Deep refugium was more limited, probably because of unsuitable soft-bottom habitat in the Bay of Biscay and along the Belgian and Dutch coasts. The Iberian populations reflect a remnant refugium at the present-day southern boundary of the species range. A generalized skyline plot suggested exponential population expansion beginning in the mid-Pleistocene with maximal growth during the Eems interglacial 128,000-67,000 years ago, implying that the last glacial maximum mainly shaped population distributions rather than demography.

Single Pulse Searches for Pulsars in the Galactic Center

NASA Astrophysics Data System (ADS)

Cushey, Daniel Joseph; Majid, Walid A.; Prince, Thomas Allen

2017-01-01

The discovery of the magnetar J1745-2900 within 3'' of Sgr A* by Mori et al. (2013) has renewed strong interest in Galactic Center (GC) pulsars and motivated expanded searches for their pulses due to their extensive applications to gravitational and plasma physics. There are currently 5 known pulsars within 15' of the Sgr A*; however, gamma ray excesses from the GC suggest a source population of 102-103 millisecond pulsars within the same region. Although this discrepancy is readily explained by the hyper-strong scattering environment of the GC which obscures pulses, the discovery of J1745-2900 challenges this attribution and further observations and analysis are needed to reconcile the observed GC pulsar population with theory. We present a pipeline developed to search for these "missing" GC pulsars using a single pulse search algorithm. Observations of the GC using the Deep Space Network 70m antenna were taken in the high frequency regime in order to minimize scattering, and search parameters were calibrated using pulses from RRAT J1819-1458. Any detected pulses that are distinct from those of J1745-2900 warrant extensive follow-up observations and analysis, and confirmed new members of the elusive GC pulsar population would be incredibly valuable as probes of the GC's magnetic and potential fields.

Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.

PubMed

Mastretta-Yanes, Alicia; Zamudio, Sergio; Jorgensen, Tove H; Arrigo, Nils; Alvarez, Nadir; Piñero, Daniel; Emerson, Brent C

2014-09-14

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Magnetic-Activated Cell Sorting for the Fast and Efficient Separation of Human and Rodent Schwann Cells from Mixed Cell Populations.

PubMed

Ravelo, Kristine M; Andersen, Natalia D; Monje, Paula V

2018-01-01

To date, magnetic-activated cell sorting (MACS) remains a powerful method to isolate distinct cell populations based on differential cell surface labeling. Optimized direct and indirect MACS protocols for cell immunolabeling are presented here as methods to divest Schwann cell (SC) cultures of contaminating cells (specifically, fibroblast cells) and isolate SC populations at different stages of differentiation. This chapter describes (1) the preparation of single-cell suspensions from established human and rat SC cultures, (2) the design and application of cell selection strategies using SC-specific (p75 NGFR , O4, and O1) and fibroblast-specific (Thy-1) markers, and (3) the characterization of both the pre- and post-sorting cell populations. A simple protocol for the growth of hybridoma cell cultures as a source of monoclonal antibodies for cell surface immunolabeling of SCs and fibroblasts is provided as a cost-effective alternative for commercially available products. These steps allow for the timely and efficient recovery of purified SC populations without compromising the viability and biological activity of the cells.

Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

PubMed

George-Nascimento, Mario; Oliva, Marcelo

2015-01-01

Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

Photochemical properties and source of pollutants during continuous pollution episodes in Beijing, October, 2011.

PubMed

Gao, Jian; Zhang, Yuechong; Zhang, Meng; Zhang, Jingqiao; Wang, Shulan; Tao, Jun; Wang, Han; Luo, Datong; Chai, Fahe; Ren, Chun

2014-01-01

Beijing suffered from serious air pollution in October, 2011 with the occurrence of three continuous episodes. Here we analyze the pollution status of particulate matter, the relationship between the gaseous pollutants, physical and chemical properties of single particles, and the profile of water-soluble ions in PM2.5 during the three episodes. Regional and photochemically aged air masses, which were characterized as having high values of O3 and SO2, were hypothesized to have played a dominant role in the first episode. After mixing local air masses with freshly-emitted primary pollutants, the concentration of NO(x) continued to increase and the size of SO4(2-), NO3(-) and NH4(+) in the particle population continued to become smaller. The amount of elemental carbon-rich and organic carbon-rich particles in the scaled single particles (0.2-2 microm) and water-soluble K(+) in PM2.5 also increased in the episodes. All the available information suggests that the biomass or fuel burning sources in or around Beijing may have had a huge impact on the last two episodes.

Development and validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: a multiplex assay for the direct amplification of single-source samples.

PubMed

Wang, Dennis Y; Chang, Chien-Wei; Lagacé, Robert E; Oldroyd, Nicola J; Hennessy, Lori K

2011-07-01

The AmpFℓSTR(®) Identifiler(®) Direct PCR Amplification Kit is a new short tandem repeat multiplex assay optimized to allow the direct amplification of single-source blood and buccal samples on FTA(®) card without the need for sample purification and quantification. This multiplex assay has been validated according to the FBI/National Standards and SWGDAM guidelines. Validation results revealed that slight variations in primer concentration, master mix component concentration, and thermal cycling parameters did not affect the performance of the chemistry. The assay's sensitivity was demonstrated by amplifying known amounts of white blood cells spotted onto FTA(®) cards, and the assay's specificity was verified by establishing minimal cross-reactivity with nonhuman DNA. No effect on the age of the sample stored on the FTA(®) substrate was observed and full concordance was established in the population study. These findings of the validation study support the use of the Identifiler(®) Direct Kit for forensic standards and database samples genotyping. © 2011 American Academy of Forensic Sciences.

Life away from the coverslip. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Shepherd, Douglas

2015-06-01

Understanding how a population acts based on the collective actions of individuals is a long-standing challenge across all scientific fields. Over the last twenty years, a revolution in the detection of individual fluorescent molecules has brought together scientists from multiple fields, particularly with respect to imaging applications in cellular and microbiology [1-3]. Recently, new techniques have paved the way for sub-diffraction limit imaging of biological regulation in fixed and live cells, generating a wealth of new data [4-9]. However, this explosion in our ability to generate information on biology at the single-molecule level has so far outpaced our ability to robustly analyze, test, and understand what these experiments are actually reporting [10-12]. Because there are many sources of noise in these experiments, ranging from instrumental to stochastic chemical reactions, it is important to understand each source of noise and how to utilize it. In this sense, there is information in all the fluctuations that occur in these experiments.

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

Seale, Jonathan P.; Meixner, Margaret; Sewiło, Marta

Observations from the HERschel Inventory of the Agents of Galaxy Evolution (HERITAGE) have been used to identify dusty populations of sources in the Large and Small Magellanic Clouds (LMC and SMC). We conducted the study using the HERITAGE catalogs of point sources available from the Herschel Science Center from both the Photodetector Array Camera and Spectrometer (PACS; 100 and 160 μm) and Spectral and Photometric Imaging Receiver (SPIRE; 250, 350, and 500 μm) cameras. These catalogs are matched to each other to create a Herschel band-merged catalog and then further matched to archival Spitzer IRAC and MIPS catalogs from themore » Spitzer Surveying the Agents of Galaxy Evolution (SAGE) and SAGE-SMC surveys to create single mid- to far-infrared (far-IR) point source catalogs that span the wavelength range from 3.6 to 500 μm. There are 35,322 unique sources in the LMC and 7503 in the SMC. To be bright in the FIR, a source must be very dusty, and so the sources in the HERITAGE catalogs represent the dustiest populations of sources. The brightest HERITAGE sources are dominated by young stellar objects (YSOs), and the dimmest by background galaxies. We identify the sources most likely to be background galaxies by first considering their morphology (distant galaxies are point-like at the resolution of Herschel) and then comparing the flux distribution to that of the Herschel Astrophysical Terahertz Large Area Survey (ATLAS) survey of galaxies. We find a total of 9745 background galaxy candidates in the LMC HERITAGE images and 5111 in the SMC images, in agreement with the number predicted by extrapolating from the ATLAS flux distribution. The majority of the Magellanic Cloud-residing sources are either very young, embedded forming stars or dusty clumps of the interstellar medium. Using the presence of 24 μm emission as a tracer of star formation, we identify 3518 YSO candidates in the LMC and 663 in the SMC. There are far fewer far-IR bright YSOs in the SMC than the LMC due to both the SMC's smaller size and its lower dust content. The YSO candidate lists may be contaminated at low flux levels by background galaxies, and so we differentiate between sources with a high (“probable”) and moderate (“possible”) likelihood of being a YSO. There are 2493/425 probable YSO candidates in the LMC/SMC. Approximately 73% of the Herschel YSO candidates are newly identified in the LMC, and 35% in the SMC. We further identify a small population of dusty objects in the late stages of stellar evolution including extreme and post-asymptotic giant branch, planetary nebulae, and supernova remnants. These populations are identified by matching the HERITAGE catalogs to lists of previously identified objects in the literature. Approximately half of the LMC sources and one quarter of the SMC sources are too faint to obtain accurate ample FIR photometry and are unclassified.« less

DEEP WIDEBAND SINGLE POINTINGS AND MOSAICS IN RADIO INTERFEROMETRY: HOW ACCURATELY DO WE RECONSTRUCT INTENSITIES AND SPECTRAL INDICES OF FAINT SOURCES?

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

Rau, U.; Bhatnagar, S.; Owen, F. N., E-mail: rurvashi@nrao.edu

Many deep wideband wide-field radio interferometric surveys are being designed to accurately measure intensities, spectral indices, and polarization properties of faint source populations. In this paper, we compare various wideband imaging methods to evaluate the accuracy to which intensities and spectral indices of sources close to the confusion limit can be reconstructed. We simulated a wideband single-pointing (C-array, L-Band (1–2 GHz)) and 46-pointing mosaic (D-array, C-Band (4–8 GHz)) JVLA observation using a realistic brightness distribution ranging from 1 μ Jy to 100 mJy and time-, frequency-, polarization-, and direction-dependent instrumental effects. The main results from these comparisons are (a) errors in themore » reconstructed intensities and spectral indices are larger for weaker sources even in the absence of simulated noise, (b) errors are systematically lower for joint reconstruction methods (such as Multi-Term Multi-Frequency-Synthesis (MT-MFS)) along with A-Projection for accurate primary beam correction, and (c) use of MT-MFS for image reconstruction eliminates Clean-bias (which is present otherwise). Auxiliary tests include solutions for deficiencies of data partitioning methods (e.g., the use of masks to remove clean bias and hybrid methods to remove sidelobes from sources left un-deconvolved), the effect of sources not at pixel centers, and the consequences of various other numerical approximations within software implementations. This paper also demonstrates the level of detail at which such simulations must be done in order to reflect reality, enable one to systematically identify specific reasons for every trend that is observed, and to estimate scientifically defensible imaging performance metrics and the associated computational complexity of the algorithms/analysis procedures.« less

Impact of methodological "shortcuts" in conducting public health surveys: Results from a vaccination coverage survey

PubMed Central

Luman, Elizabeth T; Sablan, Mariana; Stokley, Shannon; McCauley, Mary M; Shaw, Kate M

2008-01-01

Background Lack of methodological rigor can cause survey error, leading to biased results and suboptimal public health response. This study focused on the potential impact of 3 methodological "shortcuts" pertaining to field surveys: relying on a single source for critical data, failing to repeatedly visit households to improve response rates, and excluding remote areas. Methods In a vaccination coverage survey of young children conducted in the Commonwealth of the Northern Mariana Islands in July 2005, 3 sources of vaccination information were used, multiple follow-up visits were made, and all inhabited areas were included in the sampling frame. Results are calculated with and without these strategies. Results Most children had at least 2 sources of data; vaccination coverage estimated from any single source was substantially lower than from all sources combined. Eligibility was ascertained for 79% of households after the initial visit and for 94% of households after follow-up visits; vaccination coverage rates were similar with and without follow-up. Coverage among children on remote islands differed substantially from that of their counterparts on the main island indicating a programmatic need for locality-specific information; excluding remote islands from the survey would have had little effect on overall estimates due to small populations and divergent results. Conclusion Strategies to reduce sources of survey error should be maximized in public health surveys. The impact of the 3 strategies illustrated here will vary depending on the primary outcomes of interest and local situations. Survey limitations such as potential for error should be well-documented, and the likely direction and magnitude of bias should be considered. PMID:18371195

Star Formation and Young Population of the H II Complex Sh2-294

NASA Astrophysics Data System (ADS)

Samal, M. R.; Pandey, A. K.; Ojha, D. K.; Chauhan, N.; Jose, J.; Pandey, B.

2012-08-01

The Sh2-294 H II region ionized by a single B0V star features several infrared excess sources, a photodissociation region, and also a group of reddened stars at its border. The star formation scenario in this region seems to be quite complex. In this paper, we present follow-up results of Sh2-294 H II region at 3.6, 4.5, 5.8, and 8.0 μm observed with the Spitzer Space Telescope Infrared Array Camera (IRAC), coupled with H2 (2.12 μm) observation, to characterize the young population of the region and to understand its star formation history. We identified 36 young stellar object (YSO, Class I, Class II, and Class I/II) candidates using IRAC color-color diagrams. It is found that Class I sources are preferentially located at the outskirts of the H II region and associated with enhanced H2 emission; none of them are located near the central cluster. Combining the optical to mid-infrared (MIR) photometry of the YSO candidates and using the spectral energy distribution fitting models, we constrained stellar parameters and the evolutionary status of 33 YSO candidates. Most of them are interpreted by the model as low-mass (<4 M ⊙) YSOs; however, we also detected a massive YSO (~9 M ⊙) of Class I nature, embedded in a cloud of visual extinction of ~24 mag. Present analysis suggests that the Class I sources are indeed a younger population of the region relative to Class II sources (age ~ 4.5 × 106 yr). We suggest that the majority of the Class I sources, including the massive YSOs, are second-generation stars of the region whose formation is possibly induced by the expansion of the H II region powered by a ~4 × 106 yr B0 main-sequence star.

STAR FORMATION AND YOUNG POPULATION OF THE H II COMPLEX Sh2-294

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

Samal, M. R.; Pandey, A. K.; Chauhan, N.

The Sh2-294 H II region ionized by a single B0V star features several infrared excess sources, a photodissociation region, and also a group of reddened stars at its border. The star formation scenario in this region seems to be quite complex. In this paper, we present follow-up results of Sh2-294 H II region at 3.6, 4.5, 5.8, and 8.0 {mu}m observed with the Spitzer Space Telescope Infrared Array Camera (IRAC), coupled with H{sub 2} (2.12 {mu}m) observation, to characterize the young population of the region and to understand its star formation history. We identified 36 young stellar object (YSO, Classmore » I, Class II, and Class I/II) candidates using IRAC color-color diagrams. It is found that Class I sources are preferentially located at the outskirts of the H II region and associated with enhanced H{sub 2} emission; none of them are located near the central cluster. Combining the optical to mid-infrared (MIR) photometry of the YSO candidates and using the spectral energy distribution fitting models, we constrained stellar parameters and the evolutionary status of 33 YSO candidates. Most of them are interpreted by the model as low-mass (<4 M{sub Sun }) YSOs; however, we also detected a massive YSO ({approx}9 M{sub Sun }) of Class I nature, embedded in a cloud of visual extinction of {approx}24 mag. Present analysis suggests that the Class I sources are indeed a younger population of the region relative to Class II sources (age {approx} 4.5 Multiplication-Sign 10{sup 6} yr). We suggest that the majority of the Class I sources, including the massive YSOs, are second-generation stars of the region whose formation is possibly induced by the expansion of the H II region powered by a {approx}4 Multiplication-Sign 10{sup 6} yr B0 main-sequence star.« less

Sources of population and family planning assistance.

PubMed

1983-01-01

This document assesses the current status of population and family planning assistance throughout the world and provides brief sketches of the available sources including national governments, intergovernmental agencies such as the UNFPA and other UN entities, and nongovernmental funding, technical assistance, or funding and technical assistance organizations. The descriptions of aid-granting organizations describe their purposes, sources of funding, and activities, and give addresses where further information may be sought. At present about $100 million of the US $1 billion spent for family planning in developing countries each year comes from individuals paying for their own supplies and services, over $400 million is spent by national governments on their own programs, and about $450 million comes from developed country governments and private agencies. Over half of external assistance appears to be channeled through international agencies, and only a few countries provide a substantial proportion of aid bilaterally. In the past decade several governments, particularly in Asia, significantly increased the share of program costs they assumed themselves, and the most populous developing countries, China, India, and Indonesia, now contribute most of the funding for their own programs. Although at least 130 countries have provided population aid at some time, most is given by 12 industrialized countries. The US Agency for International Development (USAID) is the largest single donor, but the US share of population assistance has declined to 50% of all assistance in 1981 from 60% in the early 1970s. Governments of Communist bloc countries have made only small contributions to international population assistance. Most governmental asistance is in cash grant form, but loans, grants in kind, and technical assistance are also provided. Private organizations give assistance primarily to other private organizations in developing countries, and have been major innovators in research, training and service delivery. Loan assistance is provided by the World Bank for combined health, nutrition, and population projects as well as poupulation education. Although international population assistance from donor governments and private organizations increased from about $165 million in 1971 to about $445 million in 1980, the increase in constant value was only about 10% after inflation. About 2/3 of international assistance goes to family planning services and contraceptives; other activities receiving support are basic data collection, research, and IEC. Greatly increased expenditures will be needed if population stability is to be achieved.

Deterministic and storable single-photon source based on a quantum memory.

PubMed

Chen, Shuai; Chen, Yu-Ao; Strassel, Thorsten; Yuan, Zhen-Sheng; Zhao, Bo; Schmiedmayer, Jörg; Pan, Jian-Wei

2006-10-27

A single-photon source is realized with a cold atomic ensemble (87Rb atoms). A single excitation, written in an atomic quantum memory by Raman scattering of a laser pulse, is retrieved deterministically as a single photon at a predetermined time. It is shown that the production rate of single photons can be enhanced considerably by a feedback circuit while the single-photon quality is conserved. Such a single-photon source is well suited for future large-scale realization of quantum communication and linear optical quantum computation.

Feasibility study of earthquake early warning (EEW) in Hawaii

USGS Publications Warehouse

Thelen, Weston A.; Hotovec-Ellis, Alicia J.; Bodin, Paul

2016-09-30

The effects of earthquake shaking on the population and infrastructure across the State of Hawaii could be catastrophic, and the high seismic hazard in the region emphasizes the likelihood of such an event. Earthquake early warning (EEW) has the potential to give several seconds of warning before strong shaking starts, and thus reduce loss of life and damage to property. The two approaches to EEW are (1) a network approach (such as ShakeAlert or ElarmS) where the regional seismic network is used to detect the earthquake and distribute the alarm and (2) a local approach where a critical facility has a single seismometer (or small array) and a warning system on the premises.The network approach, also referred to here as ShakeAlert or ElarmS, uses the closest stations within a regional seismic network to detect and characterize an earthquake. Most parameters used for a network approach require observations on multiple stations (typically 3 or 4), which slows down the alarm time slightly, but the alarms are generally more reliable than with single-station EEW approaches. The network approach also benefits from having stations closer to the source of any potentially damaging earthquake, so that alarms can be sent ahead to anyone who subscribes to receive the notification. Thus, a fully implemented ShakeAlert system can provide seconds of warning for both critical facilities and general populations ahead of damaging earthquake shaking.The cost to implement and maintain a fully operational ShakeAlert system is high compared to a local approach or single-station solution, but the benefits of a ShakeAlert system would be felt statewide—the warning times for strong shaking are potentially longer for most sources at most locations.The local approach, referred to herein as “single station,” uses measurements from a single seismometer to assess whether strong earthquake shaking can be expected. Because of the reliance on a single station, false alarms are more common than when using a regional network of seismometers. Given the current network, a single-station approach provides more warning for damaging earthquakes that occur close to the station, but it would have limited benefit compared to a fully implemented ShakeAlert system. For Honolulu, for example, the single-station approach provides an advantage over ShakeAlert only for earthquakes that occur in a narrow zone extending northeast and southwest of O‘ahu. Instrumentation and alarms associated with the single-station approach are typically maintained and assessed within the target facility, and thus no outside connectivity is required. A single-station approach, then, is unlikely to help broader populations beyond the individuals at the target facility, but they have the benefit of being commercially available for relatively little cost. The USGS Hawaiian Volcano Observatory (HVO) is the Advanced National Seismic System (ANSS) regional seismic network responsible for locating and characterizing earthquakes across the State of Hawaii. During 2014 and 2015, HVO tested a network-based EEW algorithm within the current seismic network in order to assess the suitability for building a full EEW system. Using the current seismic instrumentation and processing setup at HVO, it is possible for a network approach to release an alarm a little more than 3 seconds after the earthquake is recorded on the fourth seismometer. Presently, earthquakes having M≥3 detected with the ElarmS algorithm have an average location error of approximately 4.5 km and an average magnitude error of -0.3 compared to the reviewed catalog locations from the HVO. Additional stations and upgrades to existing seismic stations would serve to improve solution precision and warning times and additional staffing would be required to provide support for a robust, network-based EEW system. For a critical facility on the Island of Hawaiʻi, such as the telescopes atop Mauna Kea, one phased approach to mitigate losses could be to immediately install a single station system to establish some level of warning. Subsequently, supporting the implementation of a full network-based EEW system on the Island of Hawaiʻi would provide additional benefit in the form of improved warning times once the system is fully installed and operational, which may take several years. Distributed populations across the Hawaiian Islands, including those outside the major cities and far from the likely earthquake source areas, would likely only benefit from a network approach such as ShakeAlert to provide warnings of strong shaking.

Spatial, seasonal, and source variability in the stable oxygen and hydrogen isotopic composition of tap waters throughout the USA

USGS Publications Warehouse

Landwehr, Jurate M.; Coplen, Tyler B.; Stewart, David W.

2013-01-01

To assess spatial, seasonal, and source variability in stable isotopic composition of human drinking waters throughout the entire USA, we have constructed a database of δ18O and δ2H of US tap waters. An additional purpose was to create a publicly available dataset useful for evaluating the forensic applicability of these isotopes for human tissue source geolocation. Samples were obtained at 349 sites, from diverse population centres, grouped by surface hydrologic units for regional comparisons. Samples were taken concurrently during two contrasting seasons, summer and winter. Source supply (surface, groundwater, mixed, and cistern) and system (public and private) types were noted. The isotopic composition of tap waters exhibits large spatial and regional variation within each season as well as significant at-site differences between seasons at many locations, consistent with patterns found in environmental (river and precipitation) waters deriving from hydrologic processes influenced by geographic factors. However, anthropogenic factors, such as the population of a tap’s surrounding community and local availability from diverse sources, also influence the isotopic composition of tap waters. Even within a locale as small as a single metropolitan area, tap waters with greatly differing isotopic compositions can be found, so that tap water within a region may not exhibit the spatial or temporal coherence predicted for environmental water. Such heterogeneities can be confounding factors when attempting forensic inference of source water location, and they underscore the necessity of measurements, not just predictions, with which to characterize the isotopic composition of regional tap waters. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

Single-shot ultrabroadband two-dimensional electronic spectroscopy of the light-harvesting complex LH2.

PubMed

Harel, Elad; Long, Phillip D; Engel, Gregory S

2011-05-01

Here we present two-dimensional (2D) electronic spectra of the light-harvesting complex LH2 from purple bacteria using coherent pulses with bandwidth of over 100 nm FWHM. This broadband excitation and detection has allowed the simultaneous capture of both the B800 and B850 bands using a single light source. We demonstrate that one laser pulse is sufficient to capture the entire 2D electronic spectrum with a high signal-to-noise ratio. At a waiting time of 800 fs, we observe population transfer from the B800 to B850 band as manifested by a prominent cross peak. These results will enable observation of the dynamics of biological systems across both ultrafast (<1 ps) and slower (>1 ms) timescales simultaneously.

Understanding the contribution of habitats and regional variation to long-term population trends in tricolored blackbirds

PubMed Central

Graves, Emily E; Holyoak, Marcel; Rodd Kelsey, T; Meese, Robert J

2013-01-01

Population trends represent a minimum amount of information required to assess the conservation status of a species. However, understanding and detecting trends can be complicated by variation among habitats and regions, and by dispersal connecting habitats through source-sink dynamics. We analyzed trends in breeding populations between habitats and regions to better understand the overall dynamics of a species' decline. Specifically, we analyzed historical trends in breeding populations of tricolored blackbirds (Agelaius tricolor) using breeding records from 1907 to 2009. The species breeds itinerantly and ephemerally uses multiple habitat types and breeding areas, which make interpretation of trends complex. We found overall abundance declines of 63% between 1935 and 1975. Since 1980 overall declines became nonsignificant and obscure despite large amounts of data from 1980 to 2009. Temporal trends differed between breeding habitat types and were associated with regional differences in population declines. A new habitat, triticale crops (a wheat-rye hybrid grain) produced colonies 40× larger, on average, than other breeding habitats, and contributed to a change in regional distribution since it primarily occurred in a single region. The mechanism for such an effect is not clear, but could represent the local availability of foodstuffs in the landscape rather than something specific to triticale crops. While variation in trends among habitats clearly occurred, they could not easily be ascribed to source-sink dynamics, ecological traps, habitat selection or other detailed ecological mechanisms. Nonetheless, such exchanges provide valuable information to guide management of dynamic systems. PMID:24101977

Cultural interaction and biological distance in postclassic period Mexico.

PubMed

Ragsdale, Corey S; Edgar, Heather J H

2015-05-01

Economic, political, and cultural relationships connected virtually every population throughout Mexico during Postclassic period (AD 900-1520). Much of what is known about population interaction in prehistoric Mexico is based on archaeological or ethnohistoric data. What is unclear, especially for the Postclassic period, is how these data correlate with biological population structure. We address this by assessing biological (phenotypic) distances among 28 samples based upon a comparison of dental morphology trait frequencies, which serve as a proxy for genetic variation, from 810 individuals. These distances were compared with models representing geographic and cultural relationships among the same groups. Results of Mantel and partial Mantel matrix correlation tests show that shared migration and trade are correlated with biological distances, but geographic distance is not. Trade and political interaction are also correlated with biological distance when combined in a single matrix. These results indicate that trade and political relationships affected population structure among Postclassic Mexican populations. We suggest that trade likely played a major role in shaping patterns of interaction between populations. This study also shows that the biological distance data support the migration histories described in ethnohistoric sources. © 2015 Wiley Periodicals, Inc.

Dutch population specific sex estimation formulae using the proximal femur.

PubMed

Colman, K L; Janssen, M C L; Stull, K E; van Rijn, R R; Oostra, R J; de Boer, H H; van der Merwe, A E

2018-05-01

Sex estimation techniques are frequently applied in forensic anthropological analyses of unidentified human skeletal remains. While morphological sex estimation methods are able to endure population differences, the classification accuracy of metric sex estimation methods are population-specific. No metric sex estimation method currently exists for the Dutch population. The purpose of this study is to create Dutch population specific sex estimation formulae by means of osteometric analyses of the proximal femur. Since the Netherlands lacks a representative contemporary skeletal reference population, 2D plane reconstructions, derived from clinical computed tomography (CT) data, were used as an alternative source for a representative reference sample. The first part of this study assesses the intra- and inter-observer error, or reliability, of twelve measurements of the proximal femur. The technical error of measurement (TEM) and relative TEM (%TEM) were calculated using 26 dry adult femora. In addition, the agreement, or accuracy, between the dry bone and CT-based measurements was determined by percent agreement. Only reliable and accurate measurements were retained for the logistic regression sex estimation formulae; a training set (n=86) was used to create the models while an independent testing set (n=28) was used to validate the models. Due to high levels of multicollinearity, only single variable models were created. Cross-validated classification accuracies ranged from 86% to 92%. The high cross-validated classification accuracies indicate that the developed formulae can contribute to the biological profile and specifically in sex estimation of unidentified human skeletal remains in the Netherlands. Furthermore, the results indicate that clinical CT data can be a valuable alternative source of data when representative skeletal collections are unavailable. Copyright © 2017 Elsevier B.V. All rights reserved.

Consolidating Data of Global Urban Populations: a Comparative Approach

NASA Astrophysics Data System (ADS)

Blankespoor, B.; Khan, A.; Selod, H.

2017-12-01

Global data on city populations are essential for the study of urbanization, city growth and the spatial distribution of human settlements. Such data are either gathered by combining official estimates of urban populations from across countries or extracted from gridded population models that combine these estimates with geospatial data. These data sources provide varying estimates of urban populations and each approach has its advantages and limitations. In particular, official figures suffer from a lack of consistency in defining urban units (across both space and time) and often provide data for jurisdictions rather than the functionally meaningful urban area. On the other hand, gridded population models require a user-imposed definition to identify urban areas and are constrained by the modelling techniques and input data employed. To address these drawbacks, we combine these approaches by consolidating information from three established sources: (i) the Citypopulation.de (Brinkhoff, 2016); (ii) the World Urban Prospects data (United Nations, 2014); and (iii) the Global Human Settlements population grid (GHS-POP) (EC - JRC, 2015). We create urban footprints with GHS-POP and spatially merge georeferenced city points from both UN WUP and Citypopulation.de with these urban footprints to identify city points that belong to a single agglomeration. We create a consolidated dataset by combining population data from the UN WUP and Citypopulation.de. The flexible framework outlined can incorporate information from alternative inputs to identify urban clusters e.g. by using night-time lights, built-up area or alternative gridded population models (e.g WorldPop or Landscan) and the parameters employed (e.g. density thresholds for urban footprints) may also be adjusted, e.g., as a function of city-specific characteristics. Our consolidated dataset provides a wider and more accurate coverage of city populations to support studies of urbanization. We apply the data to re-examine Zipf's Law. Brinkhoff, Thomas. 2016. City Population.EC - JRC; Columbia University, CIESIN. 2015. GHS population grid, derived from GPW4, multi-temporal (1975, 1990, 2000, 2015).United Nations, Department of Economic and Social Affairs, Population Division. 2014. World Urbanization Prospects: 2014 Revision.

Accounting for multiple sources of uncertainty in impact assessments: The example of the BRACE study

NASA Astrophysics Data System (ADS)

O'Neill, B. C.

2015-12-01

Assessing climate change impacts often requires the use of multiple scenarios, types of models, and data sources, leading to a large number of potential sources of uncertainty. For example, a single study might require a choice of a forcing scenario, climate model, bias correction and/or downscaling method, societal development scenario, model (typically several) for quantifying elements of societal development such as economic and population growth, biophysical model (such as for crop yields or hydrology), and societal impact model (e.g. economic or health model). Some sources of uncertainty are reduced or eliminated by the framing of the question. For example, it may be useful to ask what an impact outcome would be conditional on a given societal development pathway, forcing scenario, or policy. However many sources of uncertainty remain, and it is rare for all or even most of these sources to be accounted for. I use the example of a recent integrated project on the Benefits of Reduced Anthropogenic Climate changE (BRACE) to explore useful approaches to uncertainty across multiple components of an impact assessment. BRACE comprises 23 papers that assess the differences in impacts between two alternative climate futures: those associated with Representative Concentration Pathways (RCPs) 4.5 and 8.5. It quantifies difference in impacts in terms of extreme events, health, agriculture, tropical cyclones, and sea level rise. Methodologically, it includes climate modeling, statistical analysis, integrated assessment modeling, and sector-specific impact modeling. It employs alternative scenarios of both radiative forcing and societal development, but generally uses a single climate model (CESM), partially accounting for climate uncertainty by drawing heavily on large initial condition ensembles. Strengths and weaknesses of the approach to uncertainty in BRACE are assessed. Options under consideration for improving the approach include the use of perturbed physics ensembles of CESM, employing results from multiple climate models, and combining the results from single impact models with statistical representations of uncertainty across multiple models. A key consideration is the relationship between the question being addressed and the uncertainty approach.

SU-E-T-667: Radiosensitization Due to Gold Nanoparticles: A Monte Carlo Cellular Dosimetry Investigation of An Expansive Parameter Space

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

Martinov, M; Thomson, R

2015-06-15

Purpose: To investigate dose enhancement to cellular compartments following gold nanoparticle (GNP) uptake in tissue, varying cell and tissue morphology, intra and extracellular GNP distribution, and source energy using Monte Carlo (MC) simulations. Methods: Models of single and multiple cells are developed for normal and cancerous tissues; cells (outer radii 5–10 µm) are modeled as concentric spheres comprising the nucleus (radii 2.5–7.5 µm) and cytoplasm. GNP distributions modeled include homogeneous distributions throughout the cytoplasm, variable numbers of GNP-containing endosomes within the cytoplasm, or distributed in a spherical shell about the nucleus. Gold concentrations range from 1 to 30 mg/g. Dosemore » to nucleus and to cytoplasm for simulations including GNPs are compared to simulations without GNPs to compute Nuclear and Cytoplasm Dose Enhancement Factors (NDEF, CDEF). Photon source energies are between 20 keV and 1.25 MeV. Results: DEFs are highly sensitive to GNP intracellular distribution; for a 2.5 µm radius nucleus irradiated by a 30 keV source, NDEF varies from 1.2 for a single endosome containing all GNPs to 8.2 for GNPs distributed about the nucleus (7 mg/g). DEFs vary with cell dimensions and source energy: NDEFs vary from 2.5 (90 keV) to 8.2 (30 keV) for a 2.5 µm radius nucleus and from 1.1 (90 keV) to 1.3 (30 keV) for a 7.5 µm radius nucleus, both with GNPs in a spherical shell about the nucleus (7 mg/g). NDEF and CDEF are generally different within a single cell. For multicell models, the presence of gold within intervening tissues between source and target perturbs the fluence reaching cellular targets, resulting in DEF inhomogeneities within a population of irradiated cells. Conclusion: DEFs vary by an order of magnitude for different cell models, GNP distributions, and source energies, demonstrating the importance of detailed modelling for advancing GNP development for radiotherapy. Funding provided by the Natural Sciences and Engineering Council of Canada (NSERC), and the Canada Research Chairs Program (CRC)« less

Development of a novel cell sorting method that samples population diversity in flow cytometry.

PubMed

Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L

2015-11-01

Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance. © 2015 International Society for Advancement of Cytometry.

[Brazilian medical literature about the white plague: 1870-1940].

PubMed

Sheppard, D S

2001-01-01

The Darwinian theories compound the paradigm adopted by the physicians in Southern United States, when they turned to the subject of the differences in morbidity and mortality among the races after abolition. These physicians engaged in thoughts about the health crisis that assaulted the African-American population on that region. The Brazilian physicians, on the other hand, would not try to understand or explain the health crisis that overtook the population descended from Africans on their country. Actually, not a single Brazilian medical journal, since the end of abolition to the 1930s, published an article where a physician indicated the morbidity and mortality of his negro patients, or of negroes in general, as caused by any source related to the racial paradigm. The psychiatrists and eugenicist doctors were exceptions.

Procedure for Separating Noise Sources in Measurements of Turbofan Engine Core Noise

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2006-01-01

The study of core noise from turbofan engines has become more important as noise from other sources like the fan and jet have been reduced. A multiple microphone and acoustic source modeling method to separate correlated and uncorrelated sources has been developed. The auto and cross spectrum in the frequency range below 1000 Hz is fitted with a noise propagation model based on a source couplet consisting of a single incoherent source with a single coherent source or a source triplet consisting of a single incoherent source with two coherent point sources. Examples are presented using data from a Pratt & Whitney PW4098 turbofan engine. The method works well.

A source number estimation method for single optical fiber sensor

NASA Astrophysics Data System (ADS)

Hu, Junpeng; Huang, Zhiping; Su, Shaojing; Zhang, Yimeng; Liu, Chunwu

2015-10-01

The single-channel blind source separation (SCBSS) technique makes great significance in many fields, such as optical fiber communication, sensor detection, image processing and so on. It is a wide range application to realize blind source separation (BSS) from a single optical fiber sensor received data. The performance of many BSS algorithms and signal process methods will be worsened with inaccurate source number estimation. Many excellent algorithms have been proposed to deal with the source number estimation in array signal process which consists of multiple sensors, but they can not be applied directly to the single sensor condition. This paper presents a source number estimation method dealing with the single optical fiber sensor received data. By delay process, this paper converts the single sensor received data to multi-dimension form. And the data covariance matrix is constructed. Then the estimation algorithms used in array signal processing can be utilized. The information theoretic criteria (ITC) based methods, presented by AIC and MDL, Gerschgorin's disk estimation (GDE) are introduced to estimate the source number of the single optical fiber sensor's received signal. To improve the performance of these estimation methods at low signal noise ratio (SNR), this paper make a smooth process to the data covariance matrix. By the smooth process, the fluctuation and uncertainty of the eigenvalues of the covariance matrix are reduced. Simulation results prove that ITC base methods can not estimate the source number effectively under colored noise. The GDE method, although gets a poor performance at low SNR, but it is able to accurately estimate the number of sources with colored noise. The experiments also show that the proposed method can be applied to estimate the source number of single sensor received data.

Augmenting superpopulation capture-recapture models with population assignment data

USGS Publications Warehouse

Wen, Zhi; Pollock, Kenneth; Nichols, James; Waser, Peter

2011-01-01

Ecologists applying capture-recapture models to animal populations sometimes have access to additional information about individuals' populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual's genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture-recapture model with such information. We consider a single superpopulation model without age structure, and split each entry probability into separate components due to births in situ and immigration. We show that it is possible to estimate these two probabilities separately. We first consider the case of perfect information about population of origin, where we can distinguish individuals born in situ from immigrants with certainty. Then we consider the more realistic case of imperfect information, where we use genetic or other information to assign probabilities to each individual's origin as in situ or outside the population. We use a resampling approach to impute the true population of origin from imperfect assignment information. The integration of data on population of origin with capture-recapture data allows us to determine the contributions of immigration and in situ reproduction to the growth of the population, an issue of importance to ecologists. We illustrate our new models with capture-recapture and genetic assignment data from a population of banner-tailed kangaroo rats Dipodomys spectabilis in Arizona.

Optimizing single irrigation scheme to improve water use efficiency by manipulating winter wheat sink-source relationships in Northern China Plain.

PubMed

Xu, Xuexin; Zhang, Yinghua; Li, Jinpeng; Zhang, Meng; Zhou, Xiaonan; Zhou, Shunli; Wang, Zhimin

2018-01-01

Improving winter wheat grain yield and water use efficiency (WUE) with minimum irrigation is very important for ensuring agricultural and ecological sustainability in the Northern China Plain (NCP). A three-year field experiment was conducted to determine how single irrigation can improve grain yield and WUE by manipulating the "sink-source" relationships. To achieve this, no-irrigation after sowing (W0) as a control, and five single irrigation treatments after sowing (75 mm of each irrigation) were established. They included irrigation at upstanding (WU), irrigation at jointing (WJ), irrigation at booting (WB), irrigation at anthesis (WA) and irrigation at medium milk (WM). Results showed that compared with no-irrigation after sowing (W0), WU, WJ, WB, WA and WM significantly improved mean grain yield by 14.1%, 19.9%, 17.9%, 11.6%, and 7.5%, respectively. WJ achieved the highest grain yield (8653.1 kg ha-1) and WUE (20.3 kg ha-1 mm-1), and WB observed the same level of grain yield and WUE as WJ. In comparison to WU, WJ and WB coordinated pre- and post-anthesis water use while reducing pre-anthesis and total evapotranspiration (ET). They also retained higher soil water content above 180 cm soil layers at anthesis, increased post-anthesis water use, and ultimately increased WUE. WJ and WB optimized population quantity and individual leaf size, delayed leaf senescence, extended grain-filling duration, improved post-anthesis biomass and biomass remobilization (source supply capacity) as well as post-anthesis biomass per unit anthesis leaf area (PostBA-leaf ratio). WJ also optimized the allocation of assimilation, increased the spike partitioning index (SPI, spike biomass/biomass at anthesis) and grain production efficiency (GPE, the ratio of grain number to biomass at anthesis), thus improved mean sink capacity by 28.1%, 5.7%, 21.9%, and 26.7% in comparison to W0, WU, WA and WM, respectively. Compared with WA and WM, WJ and WB also increased sink capacity, post-anthesis biomass and biomass remobilization. These results demonstrated that single irrigation at jointing or booting could improve grain yield and WUE via coordinating the "source-sink" relationships with the high sink capacity and source supply capacity. Therefore, we propose that under adequate soil moisture conditions before sowing, single irrigation scheme from jointing to booting with 75 mm irrigation amount is the optimal minimum irrigation practice for wheat production in this region.

Fundamental properties of Fanaroff-Riley type II radio galaxies investigated via Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Kapińska, A. D.; Uttley, P.; Kaiser, C. R.

2012-08-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large-scale structure. We explore the intrinsic and extrinsic properties of the population of Fanaroff-Riley type II (FR II) objects, i.e. their kinetic luminosities, lifetimes and the central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux-limited radio catalogues of the Third Cambridge Revised Revised Catalogue (3CRR) and Best et al. We construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, we compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The new Monte Carlo method we present here allows us to (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, as has not been done before, we allow the source physical properties (kinetic luminosities, lifetimes and central densities) to co-evolve with redshift, and we find that all the investigated parameters most likely undergo cosmological evolution. Strikingly, we find that the break in the kinetic luminosity function must undergo redshift evolution of at least (1 + z)3. The fundamental parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. We use the estimated kinetic luminosity functions to set constraints on the duty cycles of these powerful radio sources. A comparison of the duty cycles of powerful FR IIs with those determined from radiative luminosities of active galactic nuclei of comparable black hole mass suggests a transition in behaviour from high to low redshifts, corresponding to either a drop in the typical black hole mass of powerful FR IIs at low redshifts, or a transition to a kinetically dominated, radiatively inefficient FR II population.

The choice of the source space and the Laplacian matrix in LORETA and the spatio-temporal Kalman filter EEG inverse methods.

PubMed

Habboush, Nawar; Hamid, Laith; Japaridze, Natia; Wiegand, Gert; Heute, Ulrich; Stephani, Ulrich; Galka, Andreas; Siniatchkin, Michael

2015-08-01

The discretization of the brain and the definition of the Laplacian matrix influence the results of methods based on spatial and spatio-temporal smoothness, since the Laplacian operator is used to define the smoothness based on the neighborhood of each grid point. In this paper, the results of low resolution electromagnetic tomography (LORETA) and the spatiotemporal Kalman filter (STKF) are computed using, first, a greymatter source space with the standard definition of the Laplacian matrix and, second, using a whole-brain source space and a modified definition of the Laplacian matrix. Electroencephalographic (EEG) source imaging results of five inter-ictal spikes from a pre-surgical patient with epilepsy are used to validate the two aforementioned approaches. The results using the whole-brain source space and the modified definition of the Laplacian matrix were concentrated in a single source activation, stable, and concordant with the location of the focal cortical dysplasia (FCD) in the patient's brain compared with the results which use a grey-matter grid and the classical definition of the Laplacian matrix. This proof-of-concept study demonstrates a substantial improvement of source localization with both LORETA and STKF and constitutes a basis for further research in a large population of patients with epilepsy.

Nonpoint and Point Sources of Nitrogen in Major Watersheds of the United States

USGS Publications Warehouse

Puckett, Larry J.

1994-01-01

Estimates of nonpoint and point sources of nitrogen were made for 107 watersheds located in the U.S. Geological Survey's National Water-Quality Assessment Program study units throughout the conterminous United States. The proportions of nitrogen originating from fertilizer, manure, atmospheric deposition, sewage, and industrial sources were found to vary with climate, hydrologic conditions, land use, population, and physiography. Fertilizer sources of nitrogen are proportionally greater in agricultural areas of the West and the Midwest than in other parts of the Nation. Animal manure contributes large proportions of nitrogen in the South and parts of the Northeast. Atmospheric deposition of nitrogen is generally greatest in areas of greatest precipitation, such as the Northeast. Point sources (sewage and industrial) generally are predominant in watersheds near cities, where they may account for large proportions of the nitrogen in streams. The transport of nitrogen in streams increases as amounts of precipitation and runoff increase and is greatest in the Northeastern United States. Because no single nonpoint nitrogen source is dominant everywhere, approaches to control nitrogen must vary throughout the Nation. Watershed-based approaches to understanding nonpoint and point sources of contamination, as used by the National Water-Quality Assessment Program, will aid water-quality and environmental managers to devise methods to reduce nitrogen pollution.

Improved Single-Source Precursors for Solar-Cell Absorbers

NASA Technical Reports Server (NTRS)

Banger, Kulbinder K.; Harris, Jerry; Hepp, Aloysius

2007-01-01

Improved single-source precursor compounds have been invented for use in spray chemical vapor deposition (spray CVD) of chalcopyrite semiconductor absorber layers of thin-film cells. A "single-source precursor compound" is a single molecular compound that contains all the required elements, which when used under the spray CVD conditions, thermally decomposes to form CuIn(x)Ga(1-x)S(y)Se(2-y).

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy.

PubMed

Kearney, Mary F; Anderson, Elizabeth M; Coomer, Charles; Smith, Luke; Shao, Wei; Johnson, Nicholas; Kline, Christopher; Spindler, Jonathan; Mellors, John W; Coffin, John M; Ambrose, Zandrea

2015-11-11

Determining the anatomic compartments that contribute to plasma HIV-1 is critical to understanding the sources of residual viremia during combination antiretroviral therapy (ART). We analyzed viral DNA and RNA populations in the plasma and tissues from macaques infected with SIV containing HIV-1 RT (RT-SHIV) to identify possible sources of persistent viremia and to investigate the effect of ART on viral replication in tissues. Tissues were collected at necropsy from four pigtailed macaques infected for 30 weeks with a diverse population of RT-SHIV. Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks. A total of 1800 single-genome RT-SHIV pol and env DNA and RNA sequences were analyzed from the plasma, PBMCs, axillary and mesenteric lymph nodes, spleen, thymus, small intestine, bone marrow, lung, and brain. Analyses of intracellular DNA and RNA populations revealed that the majority of proviruses in tissues from untreated animal 8232 were not expressed, whereas a greater proportion of proviruses in tissues were expressed from 6760. Few intracellular RNA sequences were detected in treated animals and most contained inactivating mutations, such as frame shifts or large deletions. Phylogenetics showed that RT-SHIV DNA populations in tissues were not different from virus in contemporary plasma samples in the treated or untreated animals, demonstrating a lack of anatomic compartmentalization and suggesting that plasma viremia is derived from multiple tissue sources. No sequence divergence was detected in the plasma or between tissues in the treated animals after 20 weeks of ART indicating a lack of ongoing replication in tissues during treatment. Virus populations in plasma and tissues did not differ significantly in either treated or untreated macaques, suggesting frequent exchange of virus or infected cells between tissues and plasma, consistent with non-compartmentalized and widely disseminated infection. There was no genetic evidence of ongoing replication in tissues during suppressive ART.

DETECTORS AND EXPERIMENTAL METHODS: Equivalent properties of single event burnout induced by different sources

NASA Astrophysics Data System (ADS)

Yang, Shi-Yu; Cao, Zhou; Da, Dao-An; Xue, Yu-Xiong

2009-05-01

The experimental results of single event burnout induced by heavy ions and 252Cf fission fragments in power MOSFET devices have been investigated. It is concluded that the characteristics of single event burnout induced by 252Cf fission fragments is consistent to that in heavy ions. The power MOSFET in the “turn-off" state is more susceptible to single event burnout than it is in the “turn-on" state. The thresholds of the drain-source voltage for single event burnout induced by 173 MeV bromine ions and 252Cf fission fragments are close to each other, and the burnout cross section is sensitive to variation of the drain-source voltage above the threshold of single event burnout. In addition, the current waveforms of single event burnouts induced by different sources are similar. Different power MOSFET devices may have different probabilities for the occurrence of single event burnout.

Gene Expression in Single Cells Isolated from the CWR-R1 Prostate Cancer Cell Line and Human Prostate Tissue Based on the Side Population Phenotype.

PubMed

Gangavarapu, Kalyan J; Miller, Austin; Huss, Wendy J

2016-09-01

Defining biological signals at the single cell level can identify cancer initiating driver mutations. Techniques to isolate single cells such as microfluidics sorting and magnetic capturing systems have limitations such as: high cost, labor intense, and the requirement of a large number of cells. Therefore, the goal of our current study is to identify a cost and labor effective, reliable, and reproducible technique that allows single cell isolation for analysis to promote regular laboratory use, including standard reverse transcription PCR (RT-PCR). In the current study, we utilized single prostate cells isolated from the CWR-R1 prostate cancer cell line and human prostate clinical specimens, based on the ATP binding cassette (ABC) transporter efflux of dye cycle violet (DCV), side population assay. Expression of four genes: ABCG2; Aldehyde dehydrogenase1A1 (ALDH1A1); androgen receptor (AR); and embryonic stem cell marker, Oct-4, were determined. Results from the current study in the CWR-R1 cell line showed ABCG2 and ALDH1A1 gene expression in 67% of single side population cells and in 17% or 100% of non-side population cells respectively. Studies using single cells isolated from clinical specimens showed that the Oct-4 gene is detected in only 22% of single side population cells and in 78% of single non-side population cells. Whereas, AR gene expression is in 100% single side population and non-side population cells isolated from the same human prostate clinical specimen. These studies show that performing RT-PCR on single cells isolated by FACS can be successfully conducted to determine gene expression in single cells from cell lines and enzymatically digested tissue. While these studies provide a simple yes/no expression readout, the more sensitive quantitative RT-PCR would be able to provide even more information if necessary.

Gene Expression in Single Cells Isolated from the CWR-R1 Prostate Cancer Cell Line and Human Prostate Tissue Based on the Side Population Phenotype

PubMed Central

Gangavarapu, Kalyan J; Miller, Austin; Huss, Wendy J

2016-01-01

Defining biological signals at the single cell level can identify cancer initiating driver mutations. Techniques to isolate single cells such as microfluidics sorting and magnetic capturing systems have limitations such as: high cost, labor intense, and the requirement of a large number of cells. Therefore, the goal of our current study is to identify a cost and labor effective, reliable, and reproducible technique that allows single cell isolation for analysis to promote regular laboratory use, including standard reverse transcription PCR (RT-PCR). In the current study, we utilized single prostate cells isolated from the CWR-R1 prostate cancer cell line and human prostate clinical specimens, based on the ATP binding cassette (ABC) transporter efflux of dye cycle violet (DCV), side population assay. Expression of four genes: ABCG2; Aldehyde dehydrogenase1A1 (ALDH1A1); androgen receptor (AR); and embryonic stem cell marker, Oct-4, were determined. Results from the current study in the CWR-R1 cell line showed ABCG2 and ALDH1A1 gene expression in 67% of single side population cells and in 17% or 100% of non-side population cells respectively. Studies using single cells isolated from clinical specimens showed that the Oct-4 gene is detected in only 22% of single side population cells and in 78% of single non-side population cells. Whereas, AR gene expression is in 100% single side population and non-side population cells isolated from the same human prostate clinical specimen. These studies show that performing RT-PCR on single cells isolated by FACS can be successfully conducted to determine gene expression in single cells from cell lines and enzymatically digested tissue. While these studies provide a simple yes/no expression readout, the more sensitive quantitative RT-PCR would be able to provide even more information if necessary. PMID:27785389

Entangling quantum-logic gate operated with an ultrabright semiconductor single-photon source.

PubMed

Gazzano, O; Almeida, M P; Nowak, A K; Portalupi, S L; Lemaître, A; Sagnes, I; White, A G; Senellart, P

2013-06-21

We demonstrate the unambiguous entangling operation of a photonic quantum-logic gate driven by an ultrabright solid-state single-photon source. Indistinguishable single photons emitted by a single semiconductor quantum dot in a micropillar optical cavity are used as target and control qubits. For a source brightness of 0.56 photons per pulse, the measured truth table has an overlap with the ideal case of 68.4±0.5%, increasing to 73.0±1.6% for a source brightness of 0.17 photons per pulse. The gate is entangling: At a source brightness of 0.48, the Bell-state fidelity is above the entangling threshold of 50% and reaches 71.0±3.6% for a source brightness of 0.15.

Adding bevacizumab to single agent chemotherapy for the treatment of platinum-resistant recurrent ovarian cancer: A cost effectiveness analysis of the AURELIA trial.

PubMed

Wysham, Weiya Z; Schaffer, Elisabeth M; Coles, Theresa; Roque, Dario R; Wheeler, Stephanie B; Kim, Kenneth H

2017-05-01

AURELIA, a randomized phase III trial of adding bevacizumab (B) to single agent chemotherapy (CT) for the treatment of platinum-resistant recurrent ovarian cancer, demonstrated improved progression free survival (PFS) in the B+CT arm compared to CT alone. We aimed to evaluate the cost effectiveness of adding B to CT in the treatment of platinum-resistant recurrent ovarian cancer. A decision tree model was constructed to evaluate the cost effectiveness of adding bevacizumab (B) to single agent chemotherapy (CT) based on the arms of the AURELIA trial. Costs, quality-adjusted life years (QALYs), and progression free survival (PFS) were modeled over fifteen months. Model inputs were extracted from published literature and public sources. Incremental cost effectiveness ratios (ICERs) per QALY gained and ICERs per progression free life year saved (PF-LYS) were calculated. One-way sensitivity analyses were performed to evaluate the robustness of results. The ICER associated with B+CT is $410,455 per QALY gained and $217,080 per PF-LYS. At a willingness to pay (WTP) threshold of $50,000/QALY, adding B to single agent CT is not cost effective for this patient population. Even at a WTP threshold of $100,000/QALY, B+CT is not cost effective. These findings are robust to sensitivity analyses. Despite gains in QALY and PFS, the addition of B to single agent CT for treatment of platinum-resistant recurrent ovarian cancer is not cost effective. Benefits, risks, and costs associated with treatment should be taken into consideration when prescribing chemotherapy for this patient population. Copyright © 2017 Elsevier Inc. All rights reserved.

Near-infrared-to-near-infrared down-shifting and upconversion luminescence of KY{sub 3}F{sub 10} with single dopant of Nd{sup 3+} ion

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

Lin, Huihong; State Key Laboratory of Luminescence Materials and Devices and Institute of Optical Communication Materials, South China University of Technology, Guangzhou 510641; Yu, Ting

2016-01-25

We have studied the structural and near-infrared (NIR) luminescent properties of KY{sub 3}F{sub 10} phosphors, singly doped with Nd{sup 3+} serving as both sensitizer and activator. With a single laser diode at the wavelength of 808 nm as a pump source, simultaneous NIR-to-NIR upconversion (UC) and down-shifting (DS) emissions are effectively achieved, due to the specific energy levels of Nd{sup 3+} dopant and the low phonon energy of the host. The luminescence mechanism related to energy transfer is discussed. The luminescence can be modulated through controlling the population of Nd{sup 3+}:{sup 4}F{sub 3/2} state in our experiment. Interestingly, both UC andmore » DS emissions of the material fall within the dual biological window, suggesting that the prepared phosphors have potential applications in the bioimaging field.« less

Integrating single-cell transcriptomic data across different conditions, technologies, and species.

PubMed

Butler, Andrew; Hoffman, Paul; Smibert, Peter; Papalexi, Efthymia; Satija, Rahul

2018-06-01

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

Does source population size affect performance in new environments?

PubMed Central

Yates, Matthew C; Fraser, Dylan J

2014-01-01

Small populations are predicted to perform poorly relative to large populations when experiencing environmental change. To explore this prediction in nature, data from reciprocal transplant, common garden, and translocation studies were compared meta-analytically. We contrasted changes in performance resulting from transplantation to new environments among individuals originating from different sized source populations from plants and salmonids. We then evaluated the effect of source population size on performance in natural common garden environments and the relationship between population size and habitat quality. In ‘home-away’ contrasts, large populations exhibited reduced performance in new environments. In common gardens, the effect of source population size on performance was inconsistent across life-history stages (LHS) and environments. When transplanted to the same set of new environments, small populations either performed equally well or better than large populations, depending on life stage. Conversely, large populations outperformed small populations within native environments, but only at later life stages. Population size was not associated with habitat quality. Several factors might explain the negative association between source population size and performance in new environments: (i) stronger local adaptation in large populations and antagonistic pleiotropy, (ii) the maintenance of genetic variation in small populations, and (iii) potential environmental differences between large and small populations. PMID:25469166

Milky Way demographics with the VVV survey. I. The 84-million star colour-magnitude diagram of the Galactic bulge

NASA Astrophysics Data System (ADS)

Saito, R. K.; Minniti, D.; Dias, B.; Hempel, M.; Rejkuba, M.; Alonso-García, J.; Barbuy, B.; Catelan, M.; Emerson, J. P.; Gonzalez, O. A.; Lucas, P. W.; Zoccali, M.

2012-08-01

Context. The Milky Way (MW) bulge is a fundamental Galactic component for understanding the formation and evolution of galaxies, in particular our own. The ESO Public Survey VISTA Variables in the Vía Láctea is a deep near-IR survey mapping the Galactic bulge and southern plane. Particularly for the bulge area, VVV is covering ~315 deg2. Data taken during 2010 and 2011 covered the entire bulge area in the JHKs bands. Aims: We used VVV data for the whole bulge area as a single and homogeneous data set to build for the first time a single colour - magnitude diagram (CMD) for the entire Galactic bulge. Methods: Photometric data in the JHKs bands were combined to produce a single and huge data set containing 173 150 467 sources in the three bands, for the ~315 deg2 covered by VVV in the bulge. Selecting only the data points flagged as stellar, the total number of sources is 84 095 284. Results: We built the largest colour-magnitude diagrams published up to date, containing 173.1+ million sources for all data points, and more than 84.0 million sources accounting for the stellar sources only. The CMD has a complex shape, mostly owing to the complexity of the stellar population and the effects of extinction and reddening towards the Galactic centre. The red clump (RC) giants are seen double in magnitude at b ~ -8° -10°, while in the inner part (b ~ -3°) they appear to be spreading in colour, or even splitting into a secondary peak. Stellar population models show the predominance of main-sequence and giant stars. The analysis of the outermost bulge area reveals a well-defined sequence of late K and M dwarfs, seen at (J - Ks) ~ 0.7-0.9 mag and Ks ≳ 14 mag. Conclusions: The interpretation of the CMD yields important information about the MW bulge, showing the fingerprint of its structure and content. We report a well-defined red dwarf sequence in the outermost bulge, which is important for the planetary transit searches of VVV. The double RC in magnitude seen in the outer bulge is the signature of the X-shaped MW bulge, while the spreading of the RC in colour, and even its splitting into a secondary peak, are caused by reddening effects. The region around the Galactic centre is harder to interpret because it is strongly affected by reddening and extinction. Based on observations taken within the ESO VISTA Public Survey VVV, Programme ID 179.B-2002.The VVV survey data are available through the ESO archive http://www.eso.org/sci/archive.html

Functional modeling of the human auditory brainstem response to broadband stimulationa)

PubMed Central

Verhulst, Sarah; Bharadwaj, Hari M.; Mehraei, Golbarg; Shera, Christopher A.; Shinn-Cunningham, Barbara G.

2015-01-01

Population responses such as the auditory brainstem response (ABR) are commonly used for hearing screening, but the relationship between single-unit physiology and scalp-recorded population responses are not well understood. Computational models that integrate physiologically realistic models of single-unit auditory-nerve (AN), cochlear nucleus (CN) and inferior colliculus (IC) cells with models of broadband peripheral excitation can be used to simulate ABRs and thereby link detailed knowledge of animal physiology to human applications. Existing functional ABR models fail to capture the empirically observed 1.2–2 ms ABR wave-V latency-vs-intensity decrease that is thought to arise from level-dependent changes in cochlear excitation and firing synchrony across different tonotopic sections. This paper proposes an approach where level-dependent cochlear excitation patterns, which reflect human cochlear filter tuning parameters, drive AN fibers to yield realistic level-dependent properties of the ABR wave-V. The number of free model parameters is minimal, producing a model in which various sources of hearing-impairment can easily be simulated on an individualized and frequency-dependent basis. The model fits latency-vs-intensity functions observed in human ABRs and otoacoustic emissions while maintaining rate-level and threshold characteristics of single-unit AN fibers. The simulations help to reveal which tonotopic regions dominate ABR waveform peaks at different stimulus intensities. PMID:26428802

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing.

PubMed

Cooper, James; Ding, Yi; Song, Jiuzhou; Zhao, Keji

2017-11-01

Increased chromatin accessibility is a feature of cell-type-specific cis-regulatory elements; therefore, mapping of DNase I hypersensitive sites (DHSs) enables the detection of active regulatory elements of transcription, including promoters, enhancers, insulators and locus-control regions. Single-cell DNase sequencing (scDNase-seq) is a method of detecting genome-wide DHSs when starting with either single cells or <1,000 cells from primary cell sources. This technique enables genome-wide mapping of hypersensitive sites in a wide range of cell populations that cannot be analyzed using conventional DNase I sequencing because of the requirement for millions of starting cells. Fresh cells, formaldehyde-cross-linked cells or cells recovered from formalin-fixed paraffin-embedded (FFPE) tissue slides are suitable for scDNase-seq assays. To generate scDNase-seq libraries, cells are lysed and then digested with DNase I. Circular carrier plasmid DNA is included during subsequent DNA purification and library preparation steps to prevent loss of the small quantity of DHS DNA. Libraries are generated for high-throughput sequencing on the Illumina platform using standard methods. Preparation of scDNase-seq libraries requires only 2 d. The materials and molecular biology techniques described in this protocol should be accessible to any general molecular biology laboratory. Processing of high-throughput sequencing data requires basic bioinformatics skills and uses publicly available bioinformatics software.

Incidence and characteristics of acute referred orofacial pain caused by a posterior single tooth pulpitis in an Iranian population.

PubMed

Hashemipour, Maryam Alsadat; Borna, Roya

2014-02-01

This study was designed to evaluate incidence and characteristics of acute referred orofacial pain caused by a posterior single tooth pulpitis in an Iranian population. In this cross-sectional study, 3,150 patients (1,400 males and 1,750 females) with pain in the orofacial region were evaluated via clinical and radiographic examination to determine their pain source. Patients completed a standardized clinical questionnaire consisting of a numerical rating scale for pain intensity and chose verbal descriptors from short form McGill questionnaire to describe the quality of their pain. Visual analog scale (VAS) was used to score pain intensity. In addition, patients indicated sites to which pain referred by drawing on an illustration of the head and neck. Data were analyzed using chi-square, fisher exact, and Mann-Whitney tests. Two thousand and hundred twenty patients (67/3%) reported pain in sites that diagnostically differed from the pain source. According to statistical analysis, sex (P = 0.02), intensity of pain (0.04), and quality (P = 0.001) of pain influenced its referral nature, while age of patients and kind of stimulus had no considerable effect on pain referral (P > 0.05). The results of the present study show the prevalence of referred pain in the head, face, and neck region is moderately high. Therefore, in patients with orofacial pain, it is essential to carefully examination before carrying out treatment that could be inappropriate. © 2013 The Authors Pain Practice © 2013 World Institute of Pain.

Single-channel mixed signal blind source separation algorithm based on multiple ICA processing

NASA Astrophysics Data System (ADS)

Cheng, Xiefeng; Li, Ji

2017-01-01

Take separating the fetal heart sound signal from the mixed signal that get from the electronic stethoscope as the research background, the paper puts forward a single-channel mixed signal blind source separation algorithm based on multiple ICA processing. Firstly, according to the empirical mode decomposition (EMD), the single-channel mixed signal get multiple orthogonal signal components which are processed by ICA. The multiple independent signal components are called independent sub component of the mixed signal. Then by combining with the multiple independent sub component into single-channel mixed signal, the single-channel signal is expanded to multipath signals, which turns the under-determined blind source separation problem into a well-posed blind source separation problem. Further, the estimate signal of source signal is get by doing the ICA processing. Finally, if the separation effect is not very ideal, combined with the last time's separation effect to the single-channel mixed signal, and keep doing the ICA processing for more times until the desired estimated signal of source signal is get. The simulation results show that the algorithm has good separation effect for the single-channel mixed physiological signals.

A taxonomic study of crested caracaras (Falconidae)

USGS Publications Warehouse

Dove, C.J.; Banks, R.C.

1999-01-01

The taxonomic status of the crested caracaras (Caracara spp., Falconidae) has been unsettled for many years. Current sources such as the AOU Check-list recognize a single species that includes three taxa formerly considered distinct, citing observations by Hellmayr and Conover (1949) on two specimens considered to be intermediate. We studied plumage characters and measurements of over 392 museum specimens and found no evidence of clinal change between the northern and southern continental populations. Sixteen specimens from localities near the Amazon River where these two populations sporadically meet exhibit a mosaic of plumage elements from both forms. Measurements of wing chord, bill length, and bill depth indicate that size is positively correlated with latitude north and south of the equator and that females are larger than males in the northern population. These populations do not meet in western South America. We conclude that three biological species can be identified in the crested caracaras: the insular Guadalupe Caracara (Caracara lutosus); and two continental species, Northern (C. cheriway) and Southern caracara (C. plancus), neither of which shows subspecific variation.

Genetic structure of faucet snail, Bithynia tentaculata populations in North Americal based on microsattelite markers

USGS Publications Warehouse

Perez, Kathryn E.; Werren, Rebecca L.; Lynum, Christopher A.; Hartman, Levi A.; Majoros, Gabor; Cole, Rebecca A.

2016-01-01

Bithynia tentaculata is believed to have been extirpated from North America during the last glacial maximum. It was reintroduced into North America via the Great Lakes basin in the 1800’s and has recently been expanding its geographic range. This snail serves as intermediate host for three trematodes that cause extensive recurring morbidity and mortality events in migratory water birds along the Mississippi River. Using twelve microsatellite loci for ~200 individual snails from 11 populations in North America and Europe, we examined one of the three major geographic regions from which founding populations into the Great Lakes typically originate. Our data supports a single recolonization of North America into the Great Lakes Basin followed by subsequent introduction events from the Great Lakes to other large watersheds in North America. However, additional watersheds in Europe require sampling to confirm this result. No populations with genetic signatures indicative of North American glacial relics were found. The initial invasion of North America was likely not from the Ponto-Caspian basin, the usual source of freshwater invasive species to the Laurentian Great Lakes.

Statistical tools for analysis and modeling of cosmic populations and astronomical time series: CUDAHM and TSE

NASA Astrophysics Data System (ADS)

Loredo, Thomas; Budavari, Tamas; Scargle, Jeffrey D.

2018-01-01

This presentation provides an overview of open-source software packages addressing two challenging classes of astrostatistics problems. (1) CUDAHM is a C++ framework for hierarchical Bayesian modeling of cosmic populations, leveraging graphics processing units (GPUs) to enable applying this computationally challenging paradigm to large datasets. CUDAHM is motivated by measurement error problems in astronomy, where density estimation and linear and nonlinear regression must be addressed for populations of thousands to millions of objects whose features are measured with possibly complex uncertainties, potentially including selection effects. An example calculation demonstrates accurate GPU-accelerated luminosity function estimation for simulated populations of $10^6$ objects in about two hours using a single NVIDIA Tesla K40c GPU. (2) Time Series Explorer (TSE) is a collection of software in Python and MATLAB for exploratory analysis and statistical modeling of astronomical time series. It comprises a library of stand-alone functions and classes, as well as an application environment for interactive exploration of times series data. The presentation will summarize key capabilities of this emerging project, including new algorithms for analysis of irregularly-sampled time series.

Multi-voxel pattern analysis reveals increased memory targeting and reduced use of retrieved details during single-agenda source monitoring

PubMed Central

McDuff, Susan G. R.; Frankel, Hillary C.; Norman, Kenneth A.

2009-01-01

We used multi-voxel pattern analysis (MVPA) of fMRI data to gain insight into how subjects’ retrieval agendas influence source memory judgments (was item X studied using source Y?). In Experiment 1, we used a single-agenda test where subjects judged whether items were studied with the targeted source or not. In Experiment 2, we used a multi-agenda test where subjects judged whether items were studied using the targeted source, studied using a different source, or nonstudied. To evaluate the differences between single- and multi-agenda source monitoring, we trained a classifier to detect source-specific fMRI activity at study, and then we applied the classifier to data from the test phase. We focused on trials where the targeted source and the actual source differed, so we could use MVPA to track neural activity associated with both the targeted source and the actual source. Our results indicate that single-agenda monitoring was associated with increased focus on the targeted source (as evidenced by increased targeted-source activity, relative to baseline) and reduced use of information relating to the actual, non-target source. In the multi-agenda experiment, high-levels of actual-source activity were associated with increased correct rejections, suggesting that subjects were using recollection of actual-source information to avoid source memory errors. In the single-agenda experiment, there were comparable levels of actual-source activity (suggesting that recollection was taking place), but the relationship between actual-source activity and behavior was absent (suggesting that subjects were failing to make proper use of this information). PMID:19144851

Assessing the Financial Benefits of Faster Development Times: The Case of Single-source Versus Multi-vendor Outsourced Biopharmaceutical Manufacturing.

PubMed

DiMasi, Joseph A; Smith, Zachary; Getz, Kenneth A

2018-05-10

The extent to which new drug developers can benefit financially from shorter development times has implications for development efficiency and innovation incentives. We provided a real-world example of such gains by using recent estimates of drug development costs and returns. Time and fee data were obtained on 5 single-source manufacturing projects. Time and fees were modeled for these projects as if the drug substance and drug product processes had been contracted separately from 2 vendors. The multi-vendor model was taken as the base case, and financial impacts from single-source contracting were determined relative to the base case. The mean and median after-tax financial benefits of shorter development times from single-source contracting were $44.7 million and $34.9 million, respectively (2016 dollars). The after-tax increases in sponsor fees from single-source contracting were small in comparison (mean and median of $0.65 million and $0.25 million). For the data we examined, single-source contracting yielded substantial financial benefits over multi-source contracting, even after accounting for somewhat higher sponsor fees. Copyright © 2018 Elsevier HS Journals, Inc. All rights reserved.

Variation in general practitioners' information-seeking behaviour - a cross-sectional study on the influence of gender, age and practice form.

PubMed

Le, Jette V; Pedersen, Line B; Riisgaard, Helle; Lykkegaard, Jesper; Nexøe, Jørgen; Lemmergaard, Jeanette; Søndergaard, Jens

2016-12-01

To assess general practitioners' (GPs') information-seeking behaviour and perceived importance of sources of scientific medical information and to investigate associations with GP characteristics. A national cross-sectional survey was distributed electronically in December 2013. Danish general practice. A population of 3440 GPs (corresponding to approximately 96% of all Danish GPs). GPs' use and perceived importance of information sources. Multilevel mixed-effects logit models were used to investigate associations with GP characteristics after adjusting for relevant covariates. A total of 1580 GPs (46.4%) responded to the questionnaire. GPs' information-seeking behaviour is associated with gender, age and practice form. Single-handed GPs use their colleagues as an information source significantly less than GPs working in partnership practices and they do not use other sources more frequently. Compared with their younger colleagues, GPs aged above 44 years are less likely to seek information from colleagues, guidelines and websites, but more likely to seek information from medical journals. Male and female GPs seek information equally frequently. However, whereas male GPs are more likely than female GPs to find that pharmaceutical sales representative and non-refundable CME meetings are important, they are less likely to find that colleagues, refundable CME meetings, guidelines and websites are important. Results from this study indicate that GP characteristics should be taken into consideration when disseminating scientific medical information, to ensure that patients receive medically updated, high-quality care. KEY POINTS Research indicates that information-seeking behaviour is associated with GP characteristics. Further insights could provide opportunities for targeting information dissemination strategies. Single-handed GPs seek information from colleagues less frequently than GPs in partnerships and do not use other sources more frequently. GPs aged above 44 years do not seek information as frequently as their younger colleagues and prefer other information sources. Male and female GPs seek information equally frequently, but do not consider information sources equally important in keeping medically updated.

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

PubMed Central

Roman, Theodore; Xie, Lu

2017-01-01

With increasing appreciation for the extent and importance of intratumor heterogeneity, much attention in cancer research has focused on profiling heterogeneity on a single patient level. Although true single-cell genomic technologies are rapidly improving, they remain too noisy and costly at present for population-level studies. Bulk sequencing remains the standard for population-scale tumor genomics, creating a need for computational tools to separate contributions of multiple tumor clones and assorted stromal and infiltrating cell populations to pooled genomic data. All such methods are limited to coarse approximations of only a few cell subpopulations, however. In prior work, we demonstrated the feasibility of improving cell type deconvolution by taking advantage of substructure in genomic mixtures via a strategy called simplicial complex unmixing. We improve on past work by introducing enhancements to automate learning of substructured genomic mixtures, with specific emphasis on genome-wide copy number variation (CNV) data, as well as the ability to process quantitative RNA expression data, and heterogeneous combinations of RNA and CNV data. We introduce methods for dimensionality estimation to better decompose mixture model substructure; fuzzy clustering to better identify substructure in sparse, noisy data; and automated model inference methods for other key model parameters. We further demonstrate their effectiveness in identifying mixture substructure in true breast cancer CNV data from the Cancer Genome Atlas (TCGA). Source code is available at https://github.com/tedroman/WSCUnmix PMID:29059177

Biodynamic modelling of the accumulation of Ag, Cd and Zn by the deposit-feeding polychaete Nereis diversicolor: inter-population variability and a generalised predictive model.

PubMed

Kalman, J; Smith, B D; Riba, I; Blasco, J; Rainbow, P S

2010-06-01

Biodynamic parameters of the ragworm Nereis diversicolor from southern Spain and south England were experimentally derived to assess the inter-population variability of physiological parameters of the bioaccumulation of Ag, Cd and Zn from water and sediment. Although there were some limited variations, these were not consistent with the local metal bioavailability nor with temperature changes. Incorporating the biodynamic parameters into a defined biodynamic model, confirmed that sediment is the predominant source of Cd and Zn accumulated by the worms, accounting in each case for 99% of the overall accumulated metals, whereas the contribution of dissolved Ag to the total accumulated by the worm increased from about 27 to about 53% with increasing dissolved Ag concentration. Standardised values of metal-specific parameters were chosen to generate a generalised model to be extended to N. diversicolor populations across a wide geographical range from western Europe to North Africa. According to the assumptions of this model, predicted steady state concentrations of Cd and Zn in N. diversicolor were overestimated, those of Ag underestimated, but still comparable to independent field measurements. We conclude that species-specific physiological metal bioaccumulation parameters are relatively constant over large geographical distances, and a single generalised biodynamic model does have potential to predict accumulated Ag, Cd and Zn concentrations in this polychaete from a single sediment metal concentration.

Public Health Surveillance of Fatal Child Maltreatment: Analysis of 3 State Programs

PubMed Central

Schnitzer, Patricia G.; Covington, Theresa M.; Wirtz, Stephen J.; Verhoek-Oftedahl, Wendy; Palusci, Vincent J.

2008-01-01

Objectives. We sought to describe approaches to surveillance of fatal child maltreatment and to identify options for improving case ascertainment. Methods. Three states—California, Michigan, and Rhode Island—used multiple data sources for surveillance. Potential cases were identified, operational definitions were applied, and the number of maltreatment deaths was determined. Results. These programs identified 258 maltreatment deaths in California, 192 in Michigan, and 60 in Rhode Island. Corresponding maltreatment fatality rates ranged from 2.5 per 100000 population in Michigan to 8.8 in Rhode Island. Most deaths were identified by child death review teams in Rhode Island (98%), Uniform Crime Reports in California (56%), and child welfare agency data in Michigan (44%). Compared with the total number of cases identified, child welfare agency (the official source for maltreatment reports) and death certificate data underascertain child maltreatment deaths by 55% to 76% and 80% to 90%, respectively. In all 3 states, more than 90% of cases ascertained could be identified by combining 2 data sources. Conclusions. No single data source was adequate for thorough surveillance of fatal child maltreatment, but combining just 2 sources substantially increased case ascertainment. The child death review team process may be the most promising surveillance approach. PMID:17538060

Public health surveillance of fatal child maltreatment: analysis of 3 state programs.

PubMed

Schnitzer, Patricia G; Covington, Theresa M; Wirtz, Stephen J; Verhoek-Oftedahl, Wendy; Palusci, Vincent J

2008-02-01

We sought to describe approaches to surveillance of fatal child maltreatment and to identify options for improving case ascertainment. Three states--California, Michigan, and Rhode Island--used multiple data sources for surveillance. Potential cases were identified, operational definitions were applied, and the number of maltreatment deaths was determined. These programs identified 258 maltreatment deaths in California, 192 in Michigan, and 60 in Rhode Island. Corresponding maltreatment fatality rates ranged from 2.5 per 100,000 population in Michigan to 8.8 in Rhode Island. Most deaths were identified by child death review teams in Rhode Island (98%), Uniform Crime Reports in California (56%), and child welfare agency data in Michigan (44%). Compared with the total number of cases identified, child welfare agency (the official source for maltreatment reports) and death certificate data underascertain child maltreatment deaths by 55% to 76% and 80% to 90%, respectively. In all 3 states, more than 90% of cases ascertained could be identified by combining 2 data sources. No single data source was adequate for thorough surveillance of fatal child maltreatment, but combining just 2 sources substantially increased case ascertainment. The child death review team process may be the most promising surveillance approach.

Psychological effect on single-species population models in a polluted environment.

PubMed

Wei, Fengying; Chen, Lihong

2017-08-01

We formulate and investigate the psychological effect of single-species population models in a polluted environment in this paper. For the deterministic single-species population model, the conditions that guarantee the local extinction and persistence in the mean are derived firstly. We then show that, around the pollution-free equilibrium, the stochastic single-species population is weakly persistent in the mean, and is stochastically permanent under some conditions. As a consequence, some numerical simulations demonstrate the efficiency of the main results. Copyright © 2017 Elsevier Inc. All rights reserved.

Generation of Single Photons and Entangled Photon Pairs from a Quantum Dot

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Pelton, M.; Santori, C.; Solomon, G. S.

2002-10-01

Current quantum cryptography systems are limited by the Poissonian photon statistics of a standard light source: a security loophole is opened up by the possibility of multiple-photon pulses. By replacing the source with a single-photon emitter, transmission rates of secure information can be improved. A single photon source is also essential to implement a linear optics quantum computer. We have investigated the use of single self-assembled InAs/GaAs quantum dots as such single-photon sources, and have seen a hundred-fold reduction in the multi-photon probability as compared to Poissonian pulses. An extension of our experiment should also allow for the generation of triggered, polarizationentangled photon pairs.

77 FR 58404 - Announcing the Award of Two Urgent Single-Source Grants To Support Unaccompanied Alien Children...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-20

...] Announcing the Award of Two Urgent Single-Source Grants To Support Unaccompanied Alien Children Program...) announces the award of two urgent single-source grants from the Unaccompanied Alien Children's Program to... providing services under the Unaccompanied Alien Children's program. Award Grantee organization Location...

75 FR 48691 - Single Source Cooperative Agreement Award for the World Health Organization (WHO) To Continue...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-11

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Single Source Cooperative Agreement Award for the World... Agreement Award for the World Health Organization (WHO) To Continue Development of Sustainable Influenza... September 29, 2013. In FY 2010, BARDA plans to provide a Single Source Continuation Award to the World...

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates.

PubMed

Cox, Murray P; Karafet, Tatiana M; Lansing, J Stephen; Sudoyo, Herawati; Hammer, Michael F

2010-05-22

The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian-Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations-one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates.

Probing the X-Ray Binary Populations of the Ring Galaxy NGC 1291

NASA Technical Reports Server (NTRS)

Luo, B.; Fabbiano, G.; Fragos, T.; Kim, D. W.; Belczynski, K.; Brassington, N. J.; Pellegrini, S.; Tzanavaris, P.; Wang, J.; Zezas, A.

2012-01-01

We present Chandra studies of the X-ray binary (XRB) populations in the bulge and ring regions of the ring galaxy NGC 1291. We detect 169 X-ray point sources in the galaxy, 75 in the bulge and 71 in the ring, utilizing the four available Chandra observations totaling an effective exposure of 179 ks. We report photometric properties of these sources in a point-source catalog. There are approx. 40% of the bulge sources and approx. 25% of the ring sources showing > 3(sigma) long-term variability in their X-ray count rate. The X-ray colors suggest that a significant fraction of the bulge (approx. 75%) and ring (approx. 65%) sources are likely low-mass X-ray binaries (LMXBs). The spectra of the nuclear source indicate that it is a low-luminosity AGN with moderate obscuration; spectral variability is observed between individual observations. We construct 0.3-8.0 keV X-ray luminosity functions (XLFs) for the bulge and ring XRB populations, taking into account the detection incompleteness and background AGN contamination. We reach 90% completeness limits of approx.1.5 x 10(exp 37) and approx. 2.2 x 10(exp 37) erg/s for the bulge and ring populations, respectively. Both XLFs can be fit with a broken power-law model, and the shapes are consistent with those expected for populations dominated by LMXBs. We perform detailed population synthesis modeling of the XRB populations in NGC 1291 , which suggests that the observed combined XLF is dominated by aD old LMXB population. We compare the bulge and ring XRB populations, and argue that the ring XRBs are associated with a younger stellar population than the bulge sources, based on the relative over-density of X-ray sources in the ring, the generally harder X-ray color of the ring sources, the overabundance of luminous sources in the combined XLF, and the flatter shape of the ring XLF.

Heterogeneity in multiple transmission pathways: modelling the spread of cholera and other waterborne disease in networks with a common water source.

PubMed

Robertson, Suzanne L; Eisenberg, Marisa C; Tien, Joseph H

2013-01-01

Many factors influencing disease transmission vary throughout and across populations. For diseases spread through multiple transmission pathways, sources of variation may affect each transmission pathway differently. In this paper we consider a disease that can be spread via direct and indirect transmission, such as the waterborne disease cholera. Specifically, we consider a system of multiple patches with direct transmission occurring entirely within patch and indirect transmission via a single shared water source. We investigate the effect of heterogeneity in dual transmission pathways on the spread of the disease. We first present a 2-patch model for which we examine the effect of variation in each pathway separately and propose a measure of heterogeneity that incorporates both transmission mechanisms and is predictive of R(0). We also explore how heterogeneity affects the final outbreak size and the efficacy of intervention measures. We conclude by extending several results to a more general n-patch setting.

Single cell versus large population analysis: cell variability in elemental intracellular concentration and distribution.

PubMed

Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano

2018-01-01

The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!

A community outbreak of Legionnaires' disease: evidence of a cooling tower as the source.

PubMed

Sabria, M; Alvarez, J; Dominguez, A; Pedrol, A; Sauca, G; Salleras, L; Lopez, A; Garcia-Nuñez, M A; Parron, I; Barrufet, M P

2006-07-01

A community outbreak of Legionella pneumonia in the district of Cerdanyola, Mataró (Catalonia, Spain) was investigated in an epidemiological, environmental and molecular study. Each patient was interviewed to ascertain personal risk-factors and the clinical and epidemiological data. Isolates of Legionella from patients and water samples were subtyped by pulsed-field gel electrophoresis. Between 7 August and 25 August 2002, 113 cases of Legionella pneumonia fulfilling the outbreak case definition criteria were reported, with 84 (74%) cases being located within a 500-m radius of the suspected cooling tower source. In this area, the relative risk of being infected was 54.6 (95% CI 25.3-118.1) compared with individuals living far from the cooling tower. Considering the population residing in the Cerdanyola district (28,256 inhabitants) as a reference population, the attack rate for the outbreak was 399.9 cases/100,000 inhabitants, and the case fatality rate was 1.8%. A single DNA subtype was observed among the ten clinical isolates, and one of the subtypes from the cooling tower matched exactly with the clinical subtype. Nine days after closing the cooling tower, new cases of pneumonia caused by Legionella ceased to appear. The epidemiological features of the outbreak, and the microbiological and molecular investigations, implicated the cooling tower as the source of infection.

The Artisanal Production of Pulque, a Traditional Beverage of the Mexican Highlands.

PubMed

Valadez-Blanco, Rogelio; Bravo-Villa, Griselda; Santos-Sánchez, Norma F; Velasco-Almendarez, Sandra I; Montville, Thomas J

2012-06-01

Pulque is a traditional fermented alcoholic, acidic, viscous drink of the Mexican central highlands. Its production from the "aguamiel" (sap) of agave plants dates back ~1,500 years and continues to be made by artisanal methods. However, the variability of pulque's quality and its instability hamper its widespread distribution and consumption. Microbiological surveys of pulque from three ranches revealed tremendous variability in the types and quantity of the indigenous microbiota. The population of lactic acid bacteria ranged from 6 × 10(7) to 2 × 10(11) CFU/mL. This variability might be attributed to the conditions on the ranches where the pulque was made. In an attempt to identify these sources of variability, the microbial populations of aguamiel and pulque from a single agave plant were determined. Surprisingly, the population size of the "unfermented" aguamiel and the pulque converged by the end of 3 weeks. The potential use of bacteriocinogenic LAB and known starter cultures to improve pulque properties are discussed.

Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources.

PubMed

Winton, Clare L; Plante, Yves; Hind, Pamela; McMahon, Robert; Hegarty, Matthew J; McEwan, Neil R; Davies-Morel, Mina C G; Morgan, Charly M; Powell, Wayne; Nash, Deborah M

2015-08-01

Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.

American pikas (Ochotona princeps) in northwestern Nevada: A newly discovered population at a low-elevation site

USGS Publications Warehouse

Beever, E.A.; Wilkening, J.L.; McIvor, D.E.; Weber, S.S.; Brussard, P.F.

2008-01-01

The central tenet of island biogeography theory - that species assemblages on islands are functions of island area, isolation from mainlands, and vicariance - has been altered by the demonstrable effects that rapid climate change is imposing on insular faunas, at least in isolated mountaintops. Although populations of American pikas (Ochotona princeps) continue to suffer extirpations, and although the lower bounds of the pika's elevational distribution are shifting upslope across the Great Basin, we report here on the new discovery of a low-elevation population of pikas in a mountain range from which they had not been reported previously. This discovery, particularly in the context of relatively rapid ecological change, highlights the importance of seeking out original sources of information and performing spatially extensive fieldwork. Results presented here further illustrate that although thermal influences appear to be the single strongest determinant of pika distribution currently, such influences interact with a number of other factors to determine persistence.

HIITE: HIV-1 incidence and infection time estimator.

PubMed

Park, Sung Yong; Love, Tanzy M T; Kapoor, Shivankur; Lee, Ha Youn

2018-06-15

Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting. We created a web-based platform, HIV-1 incidence and infection time estimator (HIITE), which processes envelope gene sequences using hierarchical clustering algorithms and informs the stage of infection, along with time since infection for incident cases. HIITE's performance was evaluated using 585 incident and 305 chronic specimens' envelope gene sequences collected from global cohorts including HIV-1 vaccine trial participants. HIITE precisely identified chronically infected individuals as being chronic with an error less than 1% and correctly classified 94% of recently infected individuals as being incident. Using a mixed-effect model, an incident specimen's time since infection was estimated from its single lineage diversity, showing 14% prediction error for time since infection. HIITE is the first algorithm to inform two key metrics from a single time point sequence sample. HIITE has the capacity for assessing not only population-level epidemic spread but also individual-level transmission events from a single survey, advancing HIV prevention and intervention programs. Web-based HIITE and source code of HIITE are available at http://www.hayounlee.org/software.html. Supplementary data are available at Bioinformatics online.

Comparison of Various Databases for Estimation of Dietary Polyphenol Intake in the Population of Polish Adults.

PubMed

Witkowska, Anna M; Zujko, Małgorzata E; Waśkiewicz, Anna; Terlikowska, Katarzyna M; Piotrowski, Walerian

2015-11-11

The primary aim of the study was to estimate the consumption of polyphenols in a population of 6661 subjects aged between 20 and 74 years representing a cross-section of the Polish society, and the second objective was to compare the intakes of flavonoids calculated on the basis of the two commonly used databases. Daily food consumption data were collected in 2003-2005 using a single 24-hour dietary recall. Intake of total polyphenols was estimated using an online Phenol-Explorer database, and flavonoid intake was determined using following data sources: the United States Department of Agriculture (USDA) database combined of flavonoid and isoflavone databases, and the Phenol-Explorer database. Total polyphenol intake, which was calculated with the Phenol-Explorer database, was 989 mg/day with the major contributions of phenolic acids 556 mg/day and flavonoids 403.5 mg/day. The flavonoid intake calculated on the basis of the USDA databases was 525 mg/day. This study found that tea is the primary source of polyphenols and flavonoids for the studied population, including mainly flavanols, while coffee is the most important contributor of phenolic acids, mostly hydroxycinnamic acids. Our study also demonstrated that flavonoid intakes estimated according to various databases may substantially differ. Further work should be undertaken to expand polyphenol databases to better reflect their food contents.

Development of Theoretical and Computational Methods for Single-Source Bathymetric Data

DTIC Science & Technology

2016-09-15

Methods for Single-Source N00014-16-1-2035 Bathymetric Data Sb. GRANT NUMBER 11893686 Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Sd. PROJECT NUMBER...A method is outlined for fusing the information inherent in such source documents, at different scales, into a single picture for the marine...algorithm reliability, which reflects the degree of inconsistency of the source documents, is also provided. A conceptual outline of the method , and a

Biomass burning in the Amazon region: Aerosol source apportionment and associated health risk assessment

NASA Astrophysics Data System (ADS)

de Oliveira Alves, Nilmara; Brito, Joel; Caumo, Sofia; Arana, Andrea; de Souza Hacon, Sandra; Artaxo, Paulo; Hillamo, Risto; Teinilä, Kimmo; Batistuzzo de Medeiros, Silvia Regina; de Castro Vasconcellos, Pérola

2015-11-01

The Brazilian Amazon represents about 40% of the world's remaining tropical rainforest. However, human activities have become important drivers of disturbance in that region. The majority of forest fire hotspots in the Amazon arc due to deforestation are impacting the health of the local population of over 10 million inhabitants. In this study we characterize western Amazonia biomass burning emissions through the quantification of 14 Polycyclic Aromatic Hydrocarbons (PAHs), Organic Carbon, Elemental Carbon and unique tracers of biomass burning such as levoglucosan. From the PAHs dataset a toxic equivalence factor is calculated estimating the carcinogenic and mutagenic potential of biomass burning emissions during the studied period. Peak concentration of PM10 during the dry seasons was observed to reach 60 μg m-3 on the 24 h average. Conversely, PM10 was relatively constant throughout the wet season indicating an overall stable balance between aerosol sources and sinks within the filter sampling resolution. Similar behavior is identified for OC and EC components. Levoglucosan was found in significant concentrations (up to 4 μg m-3) during the dry season. Correspondingly, the estimated lung cancer risk calculated during the dry seasons largely exceeded the WHO health-based guideline. A source apportionment study was carried out through the use of Absolute Principal Factor Analysis (APFA), identifying a three-factor solution. The biomass burning factor is found to be the dominating aerosol source, having 75.4% of PM10 loading. The second factor depicts an important contribution of several PAHs without a single source class and therefore was considered as mixed sources factor, contributing to 6.3% of PM10. The third factor was mainly associated with fossil fuel combustion emissions, contributing to 18.4% of PM10. This work enhances the knowledge of aerosol sources and its impact on climate variability and local population, on a site representative of the deforestation which occupies a significant fraction of the Amazon basin.

Fabry disease: Evidence for a regional founder effect of the GLA gene mutation 30delG in Brazilian patients.

PubMed

de Alencar, Dayse Oliveira; Netto, Cristina; Ashton-Prolla, Patricia; Giugliani, Roberto; Ribeiro-Dos-Santos, Ândrea; Pereira, Fernanda; Matte, Ursula; Santos, Ney; Santos, Sidney

2014-01-01

The Fabry disease is caused by mutations in the gene ( GLA ) that encodes the enzyme α-galactosidase A (α-Gal A). More than 500 pathologic variants of GLA have already been described, most of them are family-specific. In southern Brazil, a frequent single-base deletion ( GLA 30delG) was identified among four families that do not recognize any common ancestral. In order to investigate the history of this mutation (investigate the founder effect, estimate the mutation age and the most likely source), six gene-flanking microsatellite markers of the X chromosome on the mutation carriers and their parents, 150 individuals from the same population and 300 individuals that compose the Brazilian parental populations (Europeans, Africans and Native Americans) were genotyped. A common haplotype to the four families was identified and characterized as founder. The age was estimated with two statistics software (DMLE 2.2 and ESTIAGE) that agreed with 11 to 12 generations old. This result indicates that the mutation GLA 30delG was originated from a single event on the X chromosome of a European immigrant, during the southern Brazil colonization between 1710 and 1740.

Evaluating outcomes of management targeting the recovery of a migratory songbird of conservation concern

USGS Publications Warehouse

Streby, Henry M.; Kramer, Gunnar R.; Peterson, Sean M.; Andersen, David

2018-01-01

Assessing outcomes of habitat management is critical for informing and adapting conservation plans. From 2013 – 2019, a multi-stage management initiative aims to create >25,000 ha of shrubland and early-successional vegetation to benefit Golden-winged Warblers (Vermivora chrysoptera) in managed forested landscapes of the western Great Lakes region. We studied a dense breeding population of Golden-winged Warblers at Rice Lake National Wildlife Refuge (NWR) in Minnesota, USA, where shrubs and young trees were sheared during the winter of 2014-2015 in a single treatment supported in part by the American Bird Conservancy (ABC) and in part by other funding source(s) to benefit Golden-winged Warblers and other species associated with young forest [e.g., American Woodcock (Scalopax minor)] and as part of maintenance of early successional forest cover on the refuge.

Boson Sampling with Single-Photon Fock States from a Bright Solid-State Source.

PubMed

Loredo, J C; Broome, M A; Hilaire, P; Gazzano, O; Sagnes, I; Lemaitre, A; Almeida, M P; Senellart, P; White, A G

2017-03-31

A boson-sampling device is a quantum machine expected to perform tasks intractable for a classical computer, yet requiring minimal nonclassical resources as compared to full-scale quantum computers. Photonic implementations to date employed sources based on inefficient processes that only simulate heralded single-photon statistics when strongly reducing emission probabilities. Boson sampling with only single-photon input has thus never been realized. Here, we report on a boson-sampling device operated with a bright solid-state source of single-photon Fock states with high photon-number purity: the emission from an efficient and deterministic quantum dot-micropillar system is demultiplexed into three partially indistinguishable single photons, with a single-photon purity 1-g^{(2)}(0) of 0.990±0.001, interfering in a linear optics network. Our demultiplexed source is between 1 and 2 orders of magnitude more efficient than current heralded multiphoton sources based on spontaneous parametric down-conversion, allowing us to complete the boson-sampling experiment faster than previous equivalent implementations.

Room temperature single photon source using fiber-integrated hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Vogl, Tobias; Lu, Yuerui; Lam, Ping Koy

2017-07-01

Single photons are a key resource for quantum optics and optical quantum information processing. The integration of scalable room temperature quantum emitters into photonic circuits remains to be a technical challenge. Here we utilize a defect center in hexagonal boron nitride (hBN) attached by Van der Waals force onto a multimode fiber as a single photon source. We perform an optical characterization of the source in terms of spectrum, state lifetime, power saturation and photostability. A special feature of our source is that it allows for easy switching between fiber-coupled and free space single photon generation modes. In order to prove the quantum nature of the emission we measure the second-order correlation function {{g}(2)}≤ft(τ \\right) . For both fiber-coupled and free space emission, the {{g}(2)}≤ft(τ \\right) dips below 0.5 indicating operation in the single photon regime. The results so far demonstrate the feasibility of 2D material single photon sources for scalable photonic quantum information processing.

Coordinated single-phase control scheme for voltage unbalance reduction in low voltage network.

PubMed

Pullaguram, Deepak; Mishra, Sukumar; Senroy, Nilanjan

2017-08-13

Low voltage (LV) distribution systems are typically unbalanced in nature due to unbalanced loading and unsymmetrical line configuration. This situation is further aggravated by single-phase power injections. A coordinated control scheme is proposed for single-phase sources, to reduce voltage unbalance. A consensus-based coordination is achieved using a multi-agent system, where each agent estimates the averaged global voltage and current magnitudes of individual phases in the LV network. These estimated values are used to modify the reference power of individual single-phase sources, to ensure system-wide balanced voltages and proper power sharing among sources connected to the same phase. Further, the high X / R ratio of the filter, used in the inverter of the single-phase source, enables control of reactive power, to minimize voltage unbalance locally. The proposed scheme is validated by simulating a LV distribution network with multiple single-phase sources subjected to various perturbations.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).

On-Chip Waveguide Coupling of a Layered Semiconductor Single-Photon Source.

PubMed

Tonndorf, Philipp; Del Pozo-Zamudio, Osvaldo; Gruhler, Nico; Kern, Johannes; Schmidt, Robert; Dmitriev, Alexander I; Bakhtinov, Anatoly P; Tartakovskii, Alexander I; Pernice, Wolfram; Michaelis de Vasconcellos, Steffen; Bratschitsch, Rudolf

2017-09-13

Fully integrated quantum technology based on photons is in the focus of current research, because of its immense potential concerning performance and scalability. Ideally, the single-photon sources, the processing units, and the photon detectors are all combined on a single chip. Impressive progress has been made for on-chip quantum circuits and on-chip single-photon detection. In contrast, nonclassical light is commonly coupled onto the photonic chip from the outside, because presently only few integrated single-photon sources exist. Here, we present waveguide-coupled single-photon emitters in the layered semiconductor gallium selenide as promising on-chip sources. GaSe crystals with a thickness below 100 nm are placed on Si 3 N 4 rib or slot waveguides, resulting in a modified mode structure efficient for light coupling. Using optical excitation from within the Si 3 N 4 waveguide, we find nonclassicality of generated photons routed on the photonic chip. Thus, our work provides an easy-to-implement and robust light source for integrated quantum technology.

Propagation characteristics of audible noise generated by single corona source under positive DC voltage

NASA Astrophysics Data System (ADS)

Li, Xuebao; Cui, Xiang; Lu, Tiebing; Wang, Donglai

2017-10-01

The directivity and lateral profile of corona-generated audible noise (AN) from a single corona source are measured through experiments carried out in the semi-anechoic laboratory. The experimental results show that the waveform of corona-generated AN consists of a series of random sound pressure pulses whose pulse amplitudes decrease with the increase of measurement distance. A single corona source can be regarded as a non-directional AN source, and the A-weighted SPL (sound pressure level) decreases 6 dB(A) as doubling the measurement distance. Then, qualitative explanations for the rationality of treating the single corona source as a point source are given on the basis of the Ingard's theory for sound generation in corona discharge. Furthermore, we take into consideration of the ground reflection and the air attenuation to reconstruct the propagation features of AN from the single corona source. The calculated results agree with the measurement well, which validates the propagation model. Finally, the influence of the ground reflection on the SPL is presented in the paper.

Estimating Effects of Species Interactions on Populations of Endangered Species.

PubMed

Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

2016-04-01

Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

Holographic imaging and photostimulation of neural activity.

PubMed

Yang, Weijian; Yuste, Rafael

2018-06-01

Optical imaging methods are powerful tools in neuroscience as they can systematically monitor the activity of neuronal populations with high spatiotemporal resolution using calcium or voltage indicators. Moreover, caged compounds and optogenetic actuators enable to optically manipulate neural activity. Among optical methods, computer-generated holography offers an enormous flexibility to sculpt the excitation light in three-dimensions (3D), particularly when combined with two-photon light sources. By projecting holographic light patterns on the sample, the activity of multiple neurons across a 3D brain volume can be simultaneously imaged or optically manipulated with single-cell precision. This flexibility makes two-photon holographic microscopy an ideal all-optical platform to simultaneously read and write activity in neuronal populations in vivo in 3D, a critical ability to dissect the function of neural circuits. Copyright © 2018 Elsevier Ltd. All rights reserved.

The effect of spatial distribution on the annoyance caused by simultaneous sounds

NASA Astrophysics Data System (ADS)

Vos, Joos; Bronkhorst, Adelbert W.; Fedtke, Thomas

2004-05-01

A considerable part of the population is exposed to simultaneous and/or successive environmental sounds from different sources. In many cases, these sources are different with respect to their locations also. In a laboratory study, it was investigated whether the annoyance caused by the multiple sounds is affected by the spatial distribution of the sources. There were four independent variables: (1) sound category (stationary or moving), (2) sound type (stationary: lawn-mower, leaf-blower, and chain saw; moving: road traffic, railway, and motorbike), (3) spatial location (left, right, and combinations), and (4) A-weighted sound exposure level (ASEL of single sources equal to 50, 60, or 70 dB). In addition to the individual sounds in isolation, various combinations of two or three different sources within each sound category and sound level were presented for rating. The annoyance was mainly determined by sound level and sound source type. In most cases there were neither significant main effects of spatial distribution nor significant interaction effects between spatial distribution and the other variables. It was concluded that for rating the spatially distrib- uted sounds investigated, the noise dose can simply be determined by a summation of the levels for the left and right channels. [Work supported by CEU.

76 FR 78015 - Announcing the Award of a Single-Source Grant to Support Services for Haitian Medical Evacuees to...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-15

... Single-Source Grant to Support Services for Haitian Medical Evacuees to the Florida Department of...: Notice to award a single-source grant to support medical evacuees from the Haiti earthquake of 2010. CFDA... supportive social services to Haitian medical evacuees affected by the earthquake in 2010. The Haitian...

77 FR 65896 - Award of a Single-Source Replacement Grant to SOS Children's Villages Illinois in Chicago, IL

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-31

....623] Award of a Single-Source Replacement Grant to SOS Children's Villages Illinois in Chicago, IL... (FYSB) announces the award of a single-source replacement grant to SOS Children's Villages Illinois in... grant. ACYF/FYSB has designated SOS Children's Villages Illinois, a 501(c)(3) non-profit organization...

Electrically driven polarized single-photon emission from an InGaN quantum dot in a GaN nanowire.

PubMed

Deshpande, Saniya; Heo, Junseok; Das, Ayan; Bhattacharya, Pallab

2013-01-01

In a classical light source, such as a laser, the photon number follows a Poissonian distribution. For quantum information processing and metrology applications, a non-classical emitter of single photons is required. A single quantum dot is an ideal source of single photons and such single-photon sources in the visible spectral range have been demonstrated with III-nitride and II-VI-based single quantum dots. It has been suggested that short-wavelength blue single-photon emitters would be useful for free-space quantum cryptography, with the availability of high-speed single-photon detectors in this spectral region. Here we demonstrate blue single-photon emission with electrical injection from an In0.25Ga0.75N quantum dot in a single nanowire. The emitted single photons are linearly polarized along the c axis of the nanowire with a degree of linear polarization of ~70%.

Source spectral variation and yield estimation for small, near-source explosions

NASA Astrophysics Data System (ADS)

Yoo, S.; Mayeda, K. M.

2012-12-01

Significant S-wave generation is always observed from explosion sources which can lead to difficulty in discriminating explosions from natural earthquakes. While there are numerous S-wave generation mechanisms that are currently the topic of significant research, the mechanisms all remain controversial and appear to be dependent upon the near-source emplacement conditions of that particular explosion. To better understand the generation and partitioning of the P and S waves from explosion sources and to enhance the identification and discrimination capability of explosions, we investigate near-source explosion data sets from the 2008 New England Damage Experiment (NEDE), the Humble-Redwood (HR) series of explosions, and a Massachusetts quarry explosion experiment. We estimate source spectra and characteristic source parameters using moment tensor inversions, direct P and S waves multi-taper analysis, and improved coda spectral analysis using high quality waveform records from explosions from a variety of emplacement conditions (e.g., slow/fast burning explosive, fully tamped, partially tamped, single/ripple-fired, and below/above ground explosions). The results from direct and coda waves are compared to theoretical explosion source model predictions. These well-instrumented experiments provide us with excellent data from which to document the characteristic spectral shape, relative partitioning between P and S-waves, and amplitude/yield dependence as a function of HOB/DOB. The final goal of this study is to populate a comprehensive seismic source reference database for small yield explosions based on the results and to improve nuclear explosion monitoring capability.

Genetic diversity and structure of Megabalanus azoricus in the Azores: Implications for aquaculture management

NASA Astrophysics Data System (ADS)

De Girolamo, Mirko; Torboli, Valentina; Pallavicini, Alberto; Isidro, Eduardo

2017-11-01

Megabalanus azoricus giant barnacles are the most traditional seafood of the Azores archipelago (NE Atlantic). This valuable commercial species has been highly exploited in the past and it is considered one of the key species for the development of aquaculture in the region. Despite the importance for conservation and aquaculture there is still a lack of basic information about M. azoricus genetic diversity and population structure. Here we used seven microsatellites markers to analyse 300 samples collected at six out of nine islands of the Azores archipelago, including also different locations from a single island, to provide information on the scale of genetic diversity and population structure of this species. Parameters like heterozygosity, allelic richness and effective number of alleles indicated a high genetic diversity and variability among islands. Pairwise comparisons and PCoA analysis on FST and Jost's DEST showed significant and evident differentiation among sampling locations. Additionally, AMOVA allocates a small (6.02%) but statistically significant portion of the variance to the among Island level revealing also a weak resolution (1.87%) at finer scale. Additionally Monte Carlo resampling methods indicated the most likely sources of the recruits were the local or adjacent populations. Genetic risks associated with the giant barnacle potential production scheme should be taken into account in a future management plan delimiting, as precautionary measure, this culture at a single island or at groups of islands here identified. Moreover a monitoring strategy should be implemented with the aim to evaluate possible changes in genetic parameters of native populations.

EHDViz: clinical dashboard development using open-source technologies

PubMed Central

Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

2016-01-01

Objective To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. Materials and methods We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Results Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14 221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Conclusions Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. PMID:27013597

Salt intakes around the world: implications for public health.

PubMed

Brown, Ian J; Tzoulaki, Ioanna; Candeias, Vanessa; Elliott, Paul

2009-06-01

High levels of dietary sodium (consumed as common salt, sodium chloride) are associated with raised blood pressure and adverse cardiovascular health. Despite this, public health efforts to reduce sodium consumption remain limited to a few countries. Comprehensive, contemporaneous sodium intake data from around the world are needed to inform national/international public health initiatives to reduce sodium consumption. Use of standardized 24-h sodium excretion estimates for adults from the international INTERSALT (1985-87) and INTERMAP (1996-99) studies, and recent dietary and urinary sodium data from observational or interventional studies--identified by a comprehensive search of peer-reviewed and 'grey' literature--presented separately for adults and children. Review of methods for the estimation of sodium intake/excretion. Main food sources of sodium are presented for several Asian, European and Northern American countries, including previously unpublished INTERMAP data. Sodium intakes around the world are well in excess of physiological need (i.e. 10-20 mmol/day). Most adult populations have mean sodium intakes >100 mmol/day, and for many (particularly the Asian countries) mean intakes are >200 mmol/day. Possible exceptions include estimates from Cameroon, Ghana, Samoa, Spain, Taiwan, Tanzania, Uganda and Venezuela, though methodologies were sub-optimal and samples were not nationally representative. Sodium intakes were commonly >100 mmol/day in children over 5 years old, and increased with age. In European and Northern American countries, sodium intake is dominated by sodium added in manufactured foods ( approximately 75% of intake). Cereals and baked goods were the single largest contributor to dietary sodium intake in UK and US adults. In Japan and China, salt added at home (in cooking and at the table) and soy sauce were the largest sources. Unfavourably high sodium intakes remain prevalent around the world. Sources of dietary sodium vary largely worldwide. If policies for salt reduction at the population level are to be effective, policy development and implementation needs to target the main source of dietary sodium in the various populations.

AN ESTIMATION OF THE EXPOSURE OF THE POPULATION OF ISRAEL TO NATURAL SOURCES OF IONIZING RADIATION.

PubMed

Epstein, L; Koch, J; Riemer, T; Haquin, G; Orion, I

2017-11-01

The radiation dose to the population of Israel due to exposure to natural sources of ionizing radiation was assessed. The main contributor to the dose is radon that accounts for 60% of the exposure to natural sources. The dose due to radon inhalation was assessed by combining the results of a radon survey in single-family houses with the results of a survey in apartments in multi-storey buildings. The average annual dose due to radon inhalation was found to be 1.2 mSv. The dose rate due to exposure to cosmic radiation was assessed using a code that calculates the dose rate at different heights above sea level, taking into account the solar cycle. The annual dose was calculated based on the fraction of time spent indoors and the attenuation provided by buildings and was found to be 0.2 mSv. The annual dose due to external exposure to the terrestrial radionuclides was similarly assessed. The indoor dose rate was calculated using a model that takes into account the concentrations of the natural radionuclides in building materials, the density and the thickness of the walls. The dose rate outdoors was calculated based on the concentrations of the natural radionuclides in different geological units in Israel as measured in an aerial survey and measurements above ground. The annual dose was found to be 0.2 mSv. Doses due to internal exposure other than exposure to radon were also calculated and were found to be 0.4 mSv. The overall annual exposure of the population of Israel to natural sources of ionizing radiation is therefore 2 mSv and ranges between 1.7 and 2.7 mSv. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

On-chip low loss heralded source of pure single photons.

PubMed

Spring, Justin B; Salter, Patrick S; Metcalf, Benjamin J; Humphreys, Peter C; Moore, Merritt; Thomas-Peter, Nicholas; Barbieri, Marco; Jin, Xian-Min; Langford, Nathan K; Kolthammer, W Steven; Booth, Martin J; Walmsley, Ian A

2013-06-03

A key obstacle to the experimental realization of many photonic quantum-enhanced technologies is the lack of low-loss sources of single photons in pure quantum states. We demonstrate a promising solution: generation of heralded single photons in a silica photonic chip by spontaneous four-wave mixing. A heralding efficiency of 40%, corresponding to a preparation efficiency of 80% accounting for detector performance, is achieved due to efficient coupling of the low-loss source to optical fibers. A single photon purity of 0.86 is measured from the source number statistics without narrow spectral filtering, and confirmed by direct measurement of the joint spectral intensity. We calculate that similar high-heralded-purity output can be obtained from visible to telecom spectral regions using this approach. On-chip silica sources can have immediate application in a wide range of single-photon quantum optics applications which employ silica photonics.

Accumulation of microplastic on shorelines woldwide: sources and sinks.

PubMed

Browne, Mark Anthony; Crump, Phillip; Niven, Stewart J; Teuten, Emma; Tonkin, Andrew; Galloway, Tamara; Thompson, Richard

2011-11-01

Plastic debris <1 mm (defined here as microplastic) is accumulating in marine habitats. Ingestion of microplastic provides a potential pathway for the transfer of pollutants, monomers, and plastic-additives to organisms with uncertain consequences for their health. Here, we show that microplastic contaminates the shorelines at 18 sites worldwide representing six continents from the poles to the equator, with more material in densely populated areas, but no clear relationship between the abundance of miocroplastics and the mean size-distribution of natural particulates. An important source of microplastic appears to be through sewage contaminated by fibers from washing clothes. Forensic evaluation of microplastic from sediments showed that the proportions of polyester and acrylic fibers used in clothing resembled those found in habitats that receive sewage-discharges and sewage-effluent itself. Experiments sampling wastewater from domestic washing machines demonstrated that a single garment can produce >1900 fibers per wash. This suggests that a large proportion of microplastic fibers found in the marine environment may be derived from sewage as a consequence of washing of clothes. As the human population grows and people use more synthetic textiles, contamination of habitats and animals by microplastic is likely to increase.

Characterization of the near-source population around five ...

EPA Pesticide Factsheets

Many ports are currently preparing for increased freight traffic, which may result in elevated local air pollution in areas near the port and freight transportation corridors. In this study, a geographical information system (GIS) analysis of areas surrounding five ports – Port of New York and New Jersey, Port of Virginia, Port of Savannah, Port of Miami, and Port of Houston – was conducted to characterize the population that might be affected by air emissions from the freight transportation network and to determine which sources had the potential to affect the most people. Defining “near-source” populations as living within 300 m of the freight transportation network, namely the port and associated truck routes, railroads, and intermodal facilities (e. g. rail yards and warehouses); near-source populations ranged from 37,000 to over a million within 10 km of a port. At the ports considered, the population living within 300 m of the port boundary constituted <10 % of the total near-source population. Sensitive population exposure was also indicated, such as the 81 day care centers and K-12 schools in near-source environments within 2 km of the Port of New York and New Jersey. Minority groups constituted 55 % to 85 % of the near-source populations in the five port areas. For four of the five ports, the mean and median income of the near-source population was lower and the minority percentage was higher than the population living adjacent to the near-sou

Experimental test of genetic rescue in isolated populations of brook trout

USGS Publications Warehouse

Robinson, Zachary L.; Coombs, Jason A.; Hudy, Mark; Nislow, Keith H.; Letcher, Benjamin H.; Whiteley, Andrew R.

2017-01-01

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.

Experimental test of genetic rescue in isolated populations of brook trout.

PubMed

Robinson, Zachary L; Coombs, Jason A; Hudy, Mark; Nislow, Keith H; Letcher, Benjamin H; Whiteley, Andrew R

2017-09-01

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations. © 2017 John Wiley & Sons Ltd.

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.

Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean.

PubMed

Selwyn, Jason D; Johnson, John E; Downey-Wall, Alan M; Bynum, Adam M; Hamner, Rebecca M; Hogan, J Derek; Bird, Christopher E

2017-01-01

The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish ( Pterois volitans ) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54-514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22-328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48-216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106-950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists, such as the lionfish being introduced in a single event. While we conservatively modelled the introduction pathway as a single release of lionfish in one location, it is more likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida, which could have led to even larger numbers of colonists than simulated here. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.

Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean

PubMed Central

Selwyn, Jason D.; Johnson, John E.; Downey-Wall, Alan M.; Bynum, Adam M.; Hamner, Rebecca M.; Hogan, J. Derek

2017-01-01

The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54–514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22–328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48–216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106–950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists, such as the lionfish being introduced in a single event. While we conservatively modelled the introduction pathway as a single release of lionfish in one location, it is more likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida, which could have led to even larger numbers of colonists than simulated here. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations. PMID:29302383

Effect of feeding on the pharmacokinetics of oral minocycline in healthy research dogs.

PubMed

Hnot, Melanie L; Cole, Lynette K; Lorch, Gwendolen; Rajala-Schultz, Paivi J; Papich, Mark G

2015-12-01

The effect of food on minocycline oral absorption in dogs is unknown. The objective was to determine the pharmacokinetics of minocycline after administration of a single oral dose in fed and fasted dogs. Ten research hounds were administered oral minocycline (approximately 5 mg/kg) with and without food, in a crossover study, with a one-week wash-out between treatments. Blood samples were collected immediately prior to minocycline administration and over 24 h. Minocycline plasma drug concentrations were measured using high-performance liquid chromatography using ultraviolet detection and were analysed with compartmental modelling to determine primary pharmacokinetic parameters. Each dog was analysed independently, followed by calculation of means and variation of the dogs. The Wilcoxon signed-rank test [analysing secondary pharmacokinetic parameters - peak concentration (CMAX ), area under the concentration versus time curve (AUC)] was used to compare the two groups. A population pharmacokinetic modelling approach was performed using nonlinear mixed effects modelling of primary parameters for the population as fixed effects and the difference between subjects as a random effect. Covariate analysis was used to identify the source of variability in the population. No significant difference was found between treatments for AUC (P = 0.0645), although AUC was higher in fasted dogs. A significant difference was found for CMAX (P = 0.0059), with fasted dogs attaining a higher CMAX . The covariate of fed versus fasted accounted for a significant variation in the pharmacokinetics. Because feeding was a significant source of variation for the population's primary pharmacokinetic parameters and fasted dogs had higher minocycline concentrations, we recommend administering minocycline without food. © 2015 ESVD and ACVD.

Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift

PubMed Central

Slatkin, Montgomery; Excoffier, Laurent

2012-01-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1 – 1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population. PMID:22367031

Serial founder effects during range expansion: a spatial analog of genetic drift.

PubMed

Slatkin, Montgomery; Excoffier, Laurent

2012-05-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.

78 FR 27240 - Announcing the Award of a New Single-Source Award to the National Council on Family Violence in...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-09

....095] Announcing the Award of a New Single-Source Award to the National Council on Family Violence in... single-source cooperative agreement to the National Council on Family Violence to support the National...), Administration on Children, Youth and Families (ACYF), Family and Youth Services Bureau (FYSB), Division of...

High-Performance Single-Photon Sources via Spatial Multiplexing

DTIC Science & Technology

2014-01-01

ingredient for tasks such as quantum cryptography , quantum repeater, quantum teleportation, quantum computing, and truly-random number generation. Recently...SECURITY CLASSIFICATION OF: Single photons sources are desired for many potential quantum information applications. One common method to produce...photons sources are desired for many potential quantum information applications. One common method to produce single photons is based on a “heralding

Methods for forming particles from single source precursors

DOEpatents

Fox, Robert V [Idaho Falls, ID; Rodriguez, Rene G [Pocatello, ID; Pak, Joshua [Pocatello, ID

2011-08-23

Single source precursors are subjected to carbon dioxide to form particles of material. The carbon dioxide may be in a supercritical state. Single source precursors also may be subjected to supercritical fluids other than supercritical carbon dioxide to form particles of material. The methods may be used to form nanoparticles. In some embodiments, the methods are used to form chalcopyrite materials. Devices such as, for example, semiconductor devices may be fabricated that include such particles. Methods of forming semiconductor devices include subjecting single source precursors to carbon dioxide to form particles of semiconductor material, and establishing electrical contact between the particles and an electrode.

Single photon sources with single semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Shan, Guang-Cun; Yin, Zhang-Qi; Shek, Chan Hung; Huang, Wei

2014-04-01

In this contribution, we briefly recall the basic concepts of quantum optics and properties of semiconductor quantum dot (QD) which are necessary to the understanding of the physics of single-photon generation with single QDs. Firstly, we address the theory of quantum emitter-cavity system, the fluorescence and optical properties of semiconductor QDs, and the photon statistics as well as optical properties of the QDs. We then review the localization of single semiconductor QDs in quantum confined optical microcavity systems to achieve their overall optical properties and performances in terms of strong coupling regime, efficiency, directionality, and polarization control. Furthermore, we will discuss the recent progress on the fabrication of single photon sources, and various approaches for embedding single QDs into microcavities or photonic crystal nanocavities and show how to extend the wavelength range. We focus in particular on new generations of electrically driven QD single photon source leading to high repetition rates, strong coupling regime, and high collection efficiencies at elevated temperature operation. Besides, new developments of room temperature single photon emission in the strong coupling regime are reviewed. The generation of indistinguishable photons and remaining challenges for practical single-photon sources are also discussed.

Assessing Model Characterization of Single Source ...

EPA Pesticide Factsheets

Aircraft measurements made downwind from specific coal fired power plants during the 2013 Southeast Nexus field campaign provide a unique opportunity to evaluate single source photochemical model predictions of both O3 and secondary PM2.5 species. The model did well at predicting downwind plume placement. The model shows similar patterns of an increasing fraction of PM2.5 sulfate ion to the sum of SO2 and PM2.5 sulfate ion by distance from the source compared with ambient based estimates. The model was less consistent in capturing downwind ambient based trends in conversion of NOX to NOY from these sources. Source sensitivity approaches capture near-source O3 titration by fresh NO emissions, in particular subgrid plume treatment. However, capturing this near-source chemical feature did not translate into better downwind peak estimates of single source O3 impacts. The model estimated O3 production from these sources but often was lower than ambient based source production. The downwind transect ambient measurements, in particular secondary PM2.5 and O3, have some level of contribution from other sources which makes direct comparison with model source contribution challenging. Model source attribution results suggest contribution to secondary pollutants from multiple sources even where primary pollutants indicate the presence of a single source. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, deci

Deep Wideband Single Pointings and Mosaics in Radio Interferometry: How Accurately Do We Reconstruct Intensities and Spectral Indices of Faint Sources?

NASA Astrophysics Data System (ADS)

Rau, U.; Bhatnagar, S.; Owen, F. N.

2016-11-01

Many deep wideband wide-field radio interferometric surveys are being designed to accurately measure intensities, spectral indices, and polarization properties of faint source populations. In this paper, we compare various wideband imaging methods to evaluate the accuracy to which intensities and spectral indices of sources close to the confusion limit can be reconstructed. We simulated a wideband single-pointing (C-array, L-Band (1-2 GHz)) and 46-pointing mosaic (D-array, C-Band (4-8 GHz)) JVLA observation using a realistic brightness distribution ranging from 1 μJy to 100 mJy and time-, frequency-, polarization-, and direction-dependent instrumental effects. The main results from these comparisons are (a) errors in the reconstructed intensities and spectral indices are larger for weaker sources even in the absence of simulated noise, (b) errors are systematically lower for joint reconstruction methods (such as Multi-Term Multi-Frequency-Synthesis (MT-MFS)) along with A-Projection for accurate primary beam correction, and (c) use of MT-MFS for image reconstruction eliminates Clean-bias (which is present otherwise). Auxiliary tests include solutions for deficiencies of data partitioning methods (e.g., the use of masks to remove clean bias and hybrid methods to remove sidelobes from sources left un-deconvolved), the effect of sources not at pixel centers, and the consequences of various other numerical approximations within software implementations. This paper also demonstrates the level of detail at which such simulations must be done in order to reflect reality, enable one to systematically identify specific reasons for every trend that is observed, and to estimate scientifically defensible imaging performance metrics and the associated computational complexity of the algorithms/analysis procedures. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.

Accuracy of Dual-Energy Virtual Monochromatic CT Numbers: Comparison between the Single-Source Projection-Based and Dual-Source Image-Based Methods.

PubMed

Ueguchi, Takashi; Ogihara, Ryota; Yamada, Sachiko

2018-03-21

To investigate the accuracy of dual-energy virtual monochromatic computed tomography (CT) numbers obtained by two typical hardware and software implementations: the single-source projection-based method and the dual-source image-based method. A phantom with different tissue equivalent inserts was scanned with both single-source and dual-source scanners. A fast kVp-switching feature was used on the single-source scanner, whereas a tin filter was used on the dual-source scanner. Virtual monochromatic CT images of the phantom at energy levels of 60, 100, and 140 keV were obtained by both projection-based (on the single-source scanner) and image-based (on the dual-source scanner) methods. The accuracy of virtual monochromatic CT numbers for all inserts was assessed by comparing measured values to their corresponding true values. Linear regression analysis was performed to evaluate the dependency of measured CT numbers on tissue attenuation, method, and their interaction. Root mean square values of systematic error over all inserts at 60, 100, and 140 keV were approximately 53, 21, and 29 Hounsfield unit (HU) with the single-source projection-based method, and 46, 7, and 6 HU with the dual-source image-based method, respectively. Linear regression analysis revealed that the interaction between the attenuation and the method had a statistically significant effect on the measured CT numbers at 100 and 140 keV. There were attenuation-, method-, and energy level-dependent systematic errors in the measured virtual monochromatic CT numbers. CT number reproducibility was comparable between the two scanners, and CT numbers had better accuracy with the dual-source image-based method at 100 and 140 keV. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Assessment of Population and Microenvironmental Exposure to Fine Particulate Matter (PM2.5)

NASA Astrophysics Data System (ADS)

Jiao, Wan

A positive relationship exists between fine particulate matter (PM 2.5) exposure and adverse health effects. PM2.5 concentration-response functions used in the quantitative risk assessment were based on findings from human epidemiological studies that relied on areawide ambient concentrations as surrogate for actual ambient exposure, which cannot capture the spatial and temporal variability in human exposures. The goal of the study is to assess inter-individual, geographic and seasonal variability in population exposures to inform the interpretation of available epidemiological studies, and to improve the understanding of how exposure-related factors in important exposure microenvironments contribute to the variability in individual PM2.5 exposure. Typically, the largest percentage of time in which an individual is exposed to PM2.5 of ambient origin occurs in indoor residence, and the highest ambient PM2.5 concentrations occur in transportation microenvironments because of the proximity to on-road traffic emissions. Therefore, indoor residence and traffic-related transportation microenvironments were selected for further assessment in the study. Population distributions of individual daily PM2.5 exposures were estimated for the selected regions and seasons using the Stochastic Human Exposure and Dose Simulation Model for Particulate Matter (SHEDS-PM). For the indoor residence, the current practice by assuming the entire residence to be one large single zone for calculating the indoor residential PM 2.5 concentration was evaluated by applying an indoor air quality model, RISK, to compare indoor PM2.5 concentrations between single-zone and multi-zone scenarios. For the transportation microenvironments, one field data collection focused on in-vehicle microenvironment and was conducted to quantify the variability in the in-vehicle PM2.5 concentration with respect to the outside vehicle concentration for a wide range of conditions that affect intra-vehicle variability in exposure concentration, including ventilation air source, window status, fan setting, AC utilization, vehicle speed, road type, travel direction, and time of day. Another field data collection measured PM2.5 exposure concentrations on pre-selected routes across transportation modes of pedestrian, bus, and car to quantify the variability in the transportation mode concentration ratios, and identify factors affecting variability in traffic-related concentrations. In general, population daily average exposure to ambient PM2.5 is less than the ambient concentration by approximately half. The ratio of PM2.5 ambient exposure to ambient concentration (Ea/C) varies by individual, geographic area and season, as a result of regional differences in housing stock and seasonal differences in air exchange rates (ACH). For the indoor residence, the single-zone assumption is biased when any non-ambient source is presented. Bias correction factors are developed for cooking and smoking scenarios, separately, to improve the concentration estimates. Correction factors are most sensitive to changes in ACH but relatively insensitive to variations in source emission rate and duration. In a SHEDS-PM case study, the population daily average total exposure increased by 17% after applying correction factors. Transportation mode exposure concentrations are sensitive to mode, and are affected by factors such as vehicle ventilation and proximity to on-road emission sources. The in-vehicle to outside vehicle concentration (I/O) ratio is highly sensitive to whether windows are open or, for closed windows, to whether fresh air or recirculating air is used. Both model simulations and field studies are needed to inform better understanding of human exposure. Exposure, and not just concentration, should be considered in developing risk management strategies to reduce uncertainty in health effect estimates, and to identify highly exposed groups and possible exposure reduction strategies.

The cumulative MeHg and PCBs exposure and risk of tribal ...

EPA Pesticide Factsheets

Studies have shown that the U.S. population continues to be exposed to methyl mercury (MeHg) and polychlorinated biphenyls (PCBs) due to the long half-life of those environmental contaminants. Fish intake of Tribal populations is much higher than the U.S. general population due to dietary habits and unique cultural practices. Large fish tissue concentration data sets from the Environmental Protections Agency’s (EPA’s) Office of Water, USGS’s EMMMA program, and other data sources, were integrated, analyzed, and combined with recent tribal fish intake data for exposure analyses using the dietary module within EPA’s SHEDS-Multimedia model. SHEDS-Multimedia is a physically-based, probabilistic model, which can simulate cumulative (multiple chemicals) or aggregate (single chemical) exposures over time for a population via various pathways of exposure for a variety of multimedia, multipathway environmental chemicals. Our results show that MeHg and total PCBs exposure of tribal populations from fish are about 3 to 10 and 5 to 15 times higher than the US general population, respectively, and that the estimated exposures pose potential health risks. The cumulative exposures of MeHg and total PCBs will be assessed to generate the joint exposure profiles for Tribal and US general populations. Model sensitivity analyses will identify the important contributions of the cumulative exposures of MeHg and total PCBs such as fish types, locations, and size, and key expos

Anomalous single-electron transfer in common-gate quadruple-dot single-electron devices with asymmetric junction capacitances

NASA Astrophysics Data System (ADS)

Imai, Shigeru; Ito, Masato

2018-06-01

In this paper, anomalous single-electron transfer in common-gate quadruple-dot turnstile devices with asymmetric junction capacitances is revealed. That is, the islands have the same total number of excess electrons at high and low gate voltages of the swing that transfers a single electron. In another situation, two electrons enter the islands from the source and two electrons leave the islands for the source and drain during a gate voltage swing cycle. First, stability diagrams of the turnstile devices are presented. Then, sequences of single-electron tunneling events by gate voltage swings are investigated, which demonstrate the above-mentioned anomalous single-electron transfer between the source and the drain. The anomalous single-electron transfer can be understood by regarding the four islands as “three virtual islands and a virtual source or drain electrode of a virtual triple-dot device”. The anomalous behaviors of the four islands are explained by the normal behavior of the virtual islands transferring a single electron and the behavior of the virtual electrode.

Diversity-oriented synthesis yields novel multistage antimalarial inhibitors.

PubMed

Kato, Nobutaka; Comer, Eamon; Sakata-Kato, Tomoyo; Sharma, Arvind; Sharma, Manmohan; Maetani, Micah; Bastien, Jessica; Brancucci, Nicolas M; Bittker, Joshua A; Corey, Victoria; Clarke, David; Derbyshire, Emily R; Dornan, Gillian L; Duffy, Sandra; Eckley, Sean; Itoe, Maurice A; Koolen, Karin M J; Lewis, Timothy A; Lui, Ping S; Lukens, Amanda K; Lund, Emily; March, Sandra; Meibalan, Elamaran; Meier, Bennett C; McPhail, Jacob A; Mitasev, Branko; Moss, Eli L; Sayes, Morgane; Van Gessel, Yvonne; Wawer, Mathias J; Yoshinaga, Takashi; Zeeman, Anne-Marie; Avery, Vicky M; Bhatia, Sangeeta N; Burke, John E; Catteruccia, Flaminia; Clardy, Jon C; Clemons, Paul A; Dechering, Koen J; Duvall, Jeremy R; Foley, Michael A; Gusovsky, Fabian; Kocken, Clemens H M; Marti, Matthias; Morningstar, Marshall L; Munoz, Benito; Neafsey, Daniel E; Sharma, Amit; Winzeler, Elizabeth A; Wirth, Dyann F; Scherer, Christina A; Schreiber, Stuart L

2016-10-20

Antimalarial drugs have thus far been chiefly derived from two sources-natural products and synthetic drug-like compounds. Here we investigate whether antimalarial agents with novel mechanisms of action could be discovered using a diverse collection of synthetic compounds that have three-dimensional features reminiscent of natural products and are underrepresented in typical screening collections. We report the identification of such compounds with both previously reported and undescribed mechanisms of action, including a series of bicyclic azetidines that inhibit a new antimalarial target, phenylalanyl-tRNA synthetase. These molecules are curative in mice at a single, low dose and show activity against all parasite life stages in multiple in vivo efficacy models. Our findings identify bicyclic azetidines with the potential to both cure and prevent transmission of the disease as well as protect at-risk populations with a single oral dose, highlighting the strength of diversity-oriented synthesis in revealing promising therapeutic targets.

Repeatability and reproducibility of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy

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

Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A.; Malucelli, E., E-mail: emil.malucelli@unibo.it

2016-01-28

Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, reproducibility and repeatability of these measurements is one of the majormore » obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.« less

Transitions theory: a trajectory of theoretical development in nursing.

PubMed

Im, Eun-Ok

2011-01-01

There have been very few investigations into how any single nursing theory has actually evolved historically. In this paper, a trajectory of theoretical development in nursing is explored through reviewing the theoretical development of a single nursing theory-transitions theory. The literature related to transitions theory was searched and retrieved using multiple databases. Ninety-nine papers were analyzed according to type of theory, populations of interest, sources of theorizing, and theoretical methods. Transitions theory originated in research but was initially borrowed. It also arose in research with immigrants and from national and international collaborative research efforts. A product of mentoring, transitions theory is used widely in nursing education, research, and practice. Diverse thoughts related to transitions theory coexist. For future theoretical development in nursing, we need to remain open to new ideas and continue to engage in multiple collaborative efforts. Copyright © 2011 Elsevier Inc. All rights reserved.

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf.

PubMed

Magella, Bliss; Adam, Mike; Potter, Andrew S; Venkatasubramanian, Meenakshi; Chetal, Kashish; Hay, Stuart B; Salomonis, Nathan; Potter, S Steven

2018-02-01

The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages. Copyright © 2017 Elsevier Inc. All rights reserved.

Generating single microwave photons in a circuit.

PubMed

Houck, A A; Schuster, D I; Gambetta, J M; Schreier, J A; Johnson, B R; Chow, J M; Frunzio, L; Majer, J; Devoret, M H; Girvin, S M; Schoelkopf, R J

2007-09-20

Microwaves have widespread use in classical communication technologies, from long-distance broadcasts to short-distance signals within a computer chip. Like all forms of light, microwaves, even those guided by the wires of an integrated circuit, consist of discrete photons. To enable quantum communication between distant parts of a quantum computer, the signals must also be quantum, consisting of single photons, for example. However, conventional sources can generate only classical light, not single photons. One way to realize a single-photon source is to collect the fluorescence of a single atom. Early experiments measured the quantum nature of continuous radiation, and further advances allowed triggered sources of photons on demand. To allow efficient photon collection, emitters are typically placed inside optical or microwave cavities, but these sources are difficult to employ for quantum communication on wires within an integrated circuit. Here we demonstrate an on-chip, on-demand single-photon source, where the microwave photons are injected into a wire with high efficiency and spectral purity. This is accomplished in a circuit quantum electrodynamics architecture, with a microwave transmission line cavity that enhances the spontaneous emission of a single superconducting qubit. When the qubit spontaneously emits, the generated photon acts as a flying qubit, transmitting the quantum information across a chip. We perform tomography of both the qubit and the emitted photons, clearly showing that both the quantum phase and amplitude are transferred during the emission. Both the average power and voltage of the photon source are characterized to verify performance of the system. This single-photon source is an important addition to a rapidly growing toolbox for quantum optics on a chip.

Quantifying intrinsic and extrinsic control of single-cell fates in cancer and stem/progenitor cell pedigrees with competing risks analysis

PubMed Central

Cornwell, J. A.; Hallett, R. M.; der Mauer, S. Auf; Motazedian, A.; Schroeder, T.; Draper, J. S.; Harvey, R. P.; Nordon, R. E.

2016-01-01

The molecular control of cell fate and behaviour is a central theme in biology. Inherent heterogeneity within cell populations requires that control of cell fate is studied at the single-cell level. Time-lapse imaging and single-cell tracking are powerful technologies for acquiring cell lifetime data, allowing quantification of how cell-intrinsic and extrinsic factors control single-cell fates over time. However, cell lifetime data contain complex features. Competing cell fates, censoring, and the possible inter-dependence of competing fates, currently present challenges to modelling cell lifetime data. Thus far such features are largely ignored, resulting in loss of data and introducing a source of bias. Here we show that competing risks and concordance statistics, previously applied to clinical data and the study of genetic influences on life events in twins, respectively, can be used to quantify intrinsic and extrinsic control of single-cell fates. Using these statistics we demonstrate that 1) breast cancer cell fate after chemotherapy is dependent on p53 genotype; 2) granulocyte macrophage progenitors and their differentiated progeny have concordant fates; and 3) cytokines promote self-renewal of cardiac mesenchymal stem cells by symmetric divisions. Therefore, competing risks and concordance statistics provide a robust and unbiased approach for evaluating hypotheses at the single-cell level. PMID:27250534

Survival of mountain quail translocated from two distinct source populations

USGS Publications Warehouse

Troy, Ronald J.; Coates, Peter S.; Connelly, John W.; Gillette, Gifford; Delehanty, David J.

2013-01-01

Translocation of mountain quail (Oreortyx pictus) to restore viable populations to their former range has become a common practice. Because differences in post-release vital rates between animals from multiple source populations has not been well studied, wildlife and land managers may arbitrarily choose the source population or base the source population on immediate availability when planning translocation projects. Similarly, an understanding of the optimal proportion of individuals from different age and sex classes for translocation would benefit translocation planning. During 2006 and 2007, we captured and translocated 125 mountain quail from 2 ecologically distinct areas: 38 from southern California and 87 from southwestern Oregon. We released mountain quail in the Bennett Hills of south-central Idaho. We radio-marked and monitored a subsample of 58 quail and used them for a 2-part survival analysis. Cumulative survival probability was 0.23 ± 0.05 (SE) at 150 days post-release. We first examined an a priori hypothesis (model) that survival varied between the 2 distinct source populations. We found that source population did not explain variation in survival. This result suggests that wildlife managers have flexibility in selecting source populations for mountain quail translocation efforts. In a post hoc examination, we pooled the quail across source populations and evaluated differences in survival probabilities between sex and age classes. The most parsimonious model indicated that adult male survival was substantially less than survival rates of other mountain quail age and sex classes (i.e., interaction between sex and age). This result suggests that translocation success could benefit by translocating yearling males rather than adult males, perhaps because adult male breeding behavior results in vulnerability to predators

The voyage of an invasive species across continents: genetic diversity of North American and European Colorado potato beetle populations.

PubMed

Grapputo, Alessandro; Boman, Sanna; Lindström, Leena; Lyytinen, Anne; Mappes, Johanna

2005-12-01

The paradox of successful invading species is that they are likely to be genetically depauperate compared to their source population. This study on Colorado potato beetles is one of the few studies of the genetic consequences of continent-scale invasion in an insect pest. Understanding gene flow, population structure and the potential for rapid evolution in native and invasive populations offers insights both into the dynamics of small populations that become successful invaders and for their management as pests. We used this approach to investigate the invasion of the Colorado potato beetle (Leptinotarsa decemlineata) from North America to Europe. The beetles invaded Europe at the beginning of the 20th century and expanded almost throughout the continent in about 30 years. From the analysis of mitochondrial DNA (mtDNA) and amplified fragment length polymorphism (AFLP) markers, we found the highest genetic diversity in beetle populations from the central United States. The European populations clearly contained only a fraction of the genetic variability observed in North American populations. European populations show a significant reduction at nuclear markers (AFLPs) and are fixed for one mitochondrial haplotype, suggesting a single successful founder event. Despite the high vagility of the species and the reduction of genetic diversity in Europe, we found a similar, high level of population structure and low gene flow among populations on both continents. Founder events during range expansion, agricultural management with crop rotation, and selection due to insecticide applications are most likely the causes partitioning genetic diversity in this species.

Dispersal of Mycobacterium tuberculosis via the Canadian fur trade

PubMed Central

Pepperell, Caitlin S.; Granka, Julie M.; Alexander, David C.; Behr, Marcel A.; Chui, Linda; Gordon, Janet; Guthrie, Jennifer L.; Jamieson, Frances B.; Langlois-Klassen, Deanne; Long, Richard; Nguyen, Dao; Wobeser, Wendy; Feldman, Marcus W.

2011-01-01

Patterns of gene flow can have marked effects on the evolution of populations. To better understand the migration dynamics of Mycobacterium tuberculosis, we studied genetic data from European M. tuberculosis lineages currently circulating in Aboriginal and French Canadian communities. A single M. tuberculosis lineage, characterized by the DS6Quebec genomic deletion, is at highest frequency among Aboriginal populations in Ontario, Saskatchewan, and Alberta; this bacterial lineage is also dominant among tuberculosis (TB) cases in French Canadians resident in Quebec. Substantial contact between these human populations is limited to a specific historical era (1710–1870), during which individuals from these populations met to barter furs. Statistical analyses of extant M. tuberculosis minisatellite data are consistent with Quebec as a source population for M. tuberculosis gene flow into Aboriginal populations during the fur trade era. Historical and genetic analyses suggest that tiny M. tuberculosis populations persisted for ∼100 y among indigenous populations and subsequently expanded in the late 19th century after environmental changes favoring the pathogen. Our study suggests that spread of TB can occur by two asynchronous processes: (i) dispersal of M. tuberculosis by minimal numbers of human migrants, during which small pathogen populations are sustained by ongoing migration and slow disease dynamics, and (ii) expansion of the M. tuberculosis population facilitated by shifts in host ecology. If generalizable, these migration dynamics can help explain the low DNA sequence diversity observed among isolates of M. tuberculosis and the difficulties in global elimination of tuberculosis, as small, widely dispersed pathogen populations are difficult both to detect and to eradicate. PMID:21464295

Cosmological evolution of supermassive black holes in the centres of galaxies

NASA Astrophysics Data System (ADS)

Kapinska, Anna D.

2012-06-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large scale structure. Their jets inject a significant amount of energy into the surrounding medium, hence they can provide useful information in the study of the density and evolution of the intergalactic and intracluster medium. The jet activity is also believed to regulate the growth of massive galaxies via the AGN feedback. In this thesis I explore the intrinsic and extrinsic physical properties of the population of Fanaroff-Riley II (FR II) objects, i.e. their kinetic luminosities, lifetimes, and central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux limited radio catalogues of 3CRR and BRL. I construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, I compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The Monte Carlo method presented here allows one to: (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented, and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, I allow the source physical properties to co-evolve with redshift, and I find that all the investigated parameters most likely undergo cosmological evolution; however these parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. Furthermore, since it has been suggested that low luminosity FR IIs may be distinct from their powerful equivalents, I attempt to investigate fundamental properties of a sample of low redshift, low radio luminosity density radio galaxies. Based on SDSS-FIRST-NVSS radio sample I construct a low frequency (325 MHz) sample of radio galaxies and attempt to explore the fundamental properties of these low luminosity radio sources. The results are discussed through comparison with the results from the powerful radio sources of the 3CRR and BRL samples. Finally, I investigate the total power injected by populations of these powerful radio sources at various cosmological epochs and discuss the significance of the impact of these sources on the evolving Universe. Remarkably, sets of two degenerate fundamental parameters, the kinetic luminosity and maximum lifetimes of radio sources, despite the degeneracy provide particularly robust estimates of the total power produced by FR IIs during their lifetimes. This can be also used for robust estimations of the quenching of the cooling flows in cluster of galaxies.

Study of the atmospheric aerosol composition in equatorial Africa using PIXE as analytical technique

NASA Astrophysics Data System (ADS)

Maenhaut, W.; Akilimali, K.

1987-03-01

Small Nuclepore total filter holders and a single orifice 8-stage cascade impactor were used to collect atmospheric aerosol samples in Kinshasa, Zaire, and Butare, Rwanda. The samples were analyzed for about 20 elements by means of the PIXE technique. The results obtained for parallel samples, taken with two total filter holders and one cascade impactor, were generally in excellent agreement, suggesting that the different samplers collected very similar aerosol particle populations. Most elements were associated with a crustal dust dispersion source, which may include road dust dispersal. The Butare samples, particularly those collected during the night, were significantly influenced by biomass burning, as was deduced from enhanced filter blackness and noncrustal K levels. The pyrogenic component also contained P, S, Mn and Rb. Br and Pb were highly enriched at both locations, indicating that automotive sources had a strong influence on the aerosol composition.

Systematic analysis of the contributions of stochastic voltage gated channels to neuronal noise

PubMed Central

O'Donnell, Cian; van Rossum, Mark C. W.

2014-01-01

Electrical signaling in neurons is mediated by the opening and closing of large numbers of individual ion channels. The ion channels' state transitions are stochastic and introduce fluctuations in the macroscopic current through ion channel populations. This creates an unavoidable source of intrinsic electrical noise for the neuron, leading to fluctuations in the membrane potential and spontaneous spikes. While this effect is well known, the impact of channel noise on single neuron dynamics remains poorly understood. Most results are based on numerical simulations. There is no agreement, even in theoretical studies, on which ion channel type is the dominant noise source, nor how inclusion of additional ion channel types affects voltage noise. Here we describe a framework to calculate voltage noise directly from an arbitrary set of ion channel models, and discuss how this can be use to estimate spontaneous spike rates. PMID:25360105

Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

PubMed

Szappanos, Balázs; Fritzemeier, Jonathan; Csörgő, Bálint; Lázár, Viktória; Lu, Xiaowen; Fekete, Gergely; Bálint, Balázs; Herczeg, Róbert; Nagy, István; Notebaart, Richard A; Lercher, Martin J; Pál, Csaba; Papp, Balázs

2016-05-20

A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes.

Adaptive evolution of complex innovations through stepwise metabolic niche expansion

PubMed Central

Szappanos, Balázs; Fritzemeier, Jonathan; Csörgő, Bálint; Lázár, Viktória; Lu, Xiaowen; Fekete, Gergely; Bálint, Balázs; Herczeg, Róbert; Nagy, István; Notebaart, Richard A.; Lercher, Martin J.; Pál, Csaba; Papp, Balázs

2016-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes. PMID:27197754

The economic legacy of divorce and separation for women in old age.

PubMed

McDonald, Lynn; Robb, A Leslie

2004-01-01

Although progress has been made over the last 20 years, the burden of a low income in old age is still carried by unattached women. Few researchers, however, have examined exactly where the burden of poverty falls within the category of unattached older women or what the nature of this poverty is. Like any other group of older Canadians, unattached women are not a homogeneous population. The category of unattached includes the separated, divorced, widowed, and ever single, all of whom face different circumstances in old age because of differences over the life course. Using Survey of Labour and Income Dynamics (SLID) data, we examine income and sources of income from 1993 to 1999 to identify differences among these groups. The findings indicate that the separated and divorced are the poorest of all older unattached women in Canada. A key source of the difference is the differential growth in private pension incomes.

Investigating the widespread introduction of a tropical marine fouling species.

PubMed

Sheets, Elizabeth A; Cohen, C Sarah; Ruiz, Gregory M; da Rocha, Rosana M

2016-04-01

Little is known about the number and rate of introductions into terrestrial and marine tropical regions, and if introduction patterns and processes differ from temperate latitudes. Botryllid ascidians (marine invertebrate chordates) are an interesting group to study such introduction differences because several congeners have established populations across latitudes. While temperate botryllid invasions have been repeatedly highlighted, the global spread of tropical Botrylloides nigrum (Herdman, 1886) has been largely ignored. We sampled B. nigrum from 16 worldwide warm water locations, including around the Panama Canal, one of the largest shipping hubs in the world and a possible introduction corridor. Using mitochondrial (COI) and nuclear (ANT) markers, we discovered a single species with low genetic divergence and diversity that has established in the Atlantic, Pacific, Indo-Pacific, and Mediterranean Oceans. The Atlantic Ocean contained the highest diversity and multilocus theta estimates and may be a source for introductions to other regions. A high frequency of one mitochondrial haplotype was detected in Pacific populations that may represent a recent introduction in this region. In comparison to temperate relatives, B. nigrum displayed lower (but similar to temperate Botrylloides violaceus) genetic divergence and diversity at both loci that may represent a more recent global spread or differences in introduction pressures in tropical regions. Additionally, chimeras (genetically distinct individuals sharing a single body) were detected in three populations by the mitochondrial locus and validated using cloning, and these individuals contained new haplotype diversity not detected in any other colonies.

Standing Genetic Variation and the Evolution of Drug Resistance in HIV

PubMed Central

Pennings, Pleuni Simone

2012-01-01

Drug resistance remains a major problem for the treatment of HIV. Resistance can occur due to mutations that were present before treatment starts or due to mutations that occur during treatment. The relative importance of these two sources is unknown. Resistance can also be transmitted between patients, but this process is not considered in the current study. We study three different situations in which HIV drug resistance may evolve: starting triple-drug therapy, treatment with a single dose of nevirapine and interruption of treatment. For each of these three cases good data are available from literature, which allows us to estimate the probability that resistance evolves from standing genetic variation. Depending on the treatment we find probabilities of the evolution of drug resistance due to standing genetic variation between and . For patients who start triple-drug combination therapy, we find that drug resistance evolves from standing genetic variation in approximately 6% of the patients. We use a population-dynamic and population-genetic model to understand the observations and to estimate important evolutionary parameters under the assumption that treatment failure is caused by the fixation of a single drug resistance mutation. We find that both the effective population size of the virus before treatment, and the fitness of the resistant mutant during treatment, are key-parameters which determine the probability that resistance evolves from standing genetic variation. Importantly, clinical data indicate that both of these parameters can be manipulated by the kind of treatment that is used. PMID:22685388

What are single photons good for?

NASA Astrophysics Data System (ADS)

Sangouard, Nicolas; Zbinden, Hugo

2012-10-01

In a long-held preconception, photons play a central role in present-day quantum technologies. But what are sources producing photons one by one good for precisely? Well, in opposition to what many suggest, we show that single-photon sources are not helpful for point to point quantum key distribution because faint laser pulses do the job comfortably. However, there is no doubt about the usefulness of sources producing single photons for future quantum technologies. In particular, we show how single-photon sources could become the seed of a revolution in the framework of quantum communication, making the security of quantum key distribution device-independent or extending quantum communication over many hundreds of kilometers. Hopefully, these promising applications will provide a guideline for researchers to develop more and more efficient sources, producing narrowband, pure and indistinguishable photons at appropriate wavelengths.

A Method for Simulation of Rotorcraft Fly-In Noise for Human Response Studies

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Christian, Andrew

2015-01-01

The low frequency content of rotorcraft noise allows it to be heard over great distances. This factor contributes to the disruption of natural quiet in national parks and wilderness areas, and can lead to annoyance in populated areas. Further, it can result in detection at greater distances compared to higher altitude fixed wing aircraft operations. Human response studies conducted in the field are made difficult since test conditions are difficult to control. Specifically, compared to fixed wing aircraft, the source noise itself may significantly vary over time even for nominally steady flight conditions, and the propagation of that noise is more variable due to low altitude meteorological conditions. However, it is possible to create the salient features of rotorcraft fly-in noise in a more controlled laboratory setting through recent advancements made in source noise synthesis, propagation modeling and reproduction. This paper concentrates on the first two of these. In particular, the rotorcraft source noise pressure time history is generated using single blade passage signatures from the main and tail rotors. These may be obtained from either acoustic source noise predictions or back-propagation of ground-based measurements. Propagation effects include atmospheric absorption, spreading loss, Doppler shift, and ground plane reflections.

Procedural justice and layoff survivors' commitment: a quantitative review.

PubMed

Grubb, W Lee

2006-10-01

Layoffs are common in today's organizations. Most studies that have examined the correlation between procedural justice and the organizational commitment of layoff survivors have yielded positive correlations, but the magnitude of the correlations varies widely. This study is the first to estimate the population correlation and to identify the primary sources that cause variation in the correlation across studies. The results indicated that justice and commitment correlations can always be expected to be positive. Based on a total sample size of 9080 individuals, the estimated mean population correlation was .34. Variation was primarily explained by attributes of the justice measure where multiple items scales and scales composed of both interactional and procedural justice items yielded higher correlations than single item measures. Therefore, it is important that employers recognize the substantial assuaging affect that procedural and interactional justice can have on survivors' organizational commitment.

The metrological assurance of quality petroleum products. Methods for determining octane and sulfur numbers in the petroleum products

NASA Astrophysics Data System (ADS)

Shalkov, A. V.; Fadeev, Y. A.

2018-01-01

At present, solving environmental problems in industrially developed regions with a large concentration of mining and machine building enterprises is one of the main socially important tasks. Taking into account the increase in the volume of mining, there is an increase in the environmental burden, which affects the internal migration of the population. This is particularly evident in the examples of single-industry towns, in which a gradual decrease in the young workable population occurs. The article presents an analysis of the sources of maximum pollution of the environment by coal mining enterprises. Modern methods of controlling automobile fuel were analyzed. The analysis of fuel quality and the environmental assessment of combustion products was carried out. The equipment used in the article makes it possible to exclude substandard fuel and to reduce harmful emissions of vehicles to the atmosphere.

[How has social status been measured in health research? A review of the international literature].

PubMed

Cabieses, Báltica; Zitko, Pedro; Pinedo, Rafael; Espinoza, Manuel; Albor, Christo

2011-06-01

Social status (SS) is a multidimensional variable that is used widely in health research. There is no single optimal method for estimating social status. Rather, in each case the measurement may vary depending on the research subject, the base theory considered, the population of interest, the event of interest and, in some cases, the available information. This literature review develops the following topics related to SS measurement, based on the international scientific sources available electronically: i) identification of the role of SS in the context of social epidemiology research, ii) description of the principal indicators and methodological approaches used to measure SS in health research, and iii) analysis of the distinct difficulties of SS measurement in specific populations such as ethnic groups, women, children, the elderly, and in rural vs. urban contexts. The review finally makes it possible to describe some of the implications of SS measurement in Latin American countries.

Computer simulations of sympatric speciation in a simple food web

NASA Astrophysics Data System (ADS)

Luz-Burgoa, K.; Dell, Tony; de Oliveira, S. Moss

2005-07-01

Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with the formation of the species. Inspired by them, in this paper we investigate the process of sympatric speciation in a simple food web model. For that we modify the individual-based Penna model that has been widely used to study aging as well as other evolutionary processes. Initially, our web consists of a primary food source and a single herbivore species that feeds on this resource. Subsequently we introduce a predator that feeds on the herbivore. In both instances we manipulate directly a basal resource distribution and monitor the changes in the populations. Sympatric speciation is obtained for the top species in both cases, and our results suggest that the speciation velocity depends on how far up, in the food chain, the focus population is feeding. Simulations are done with three different sexual imprintinglike mechanisms, in order to discuss adaptation by natural selection.

Comparison of temporal properties of auditory single units in response to cochlear infrared laser stimulation recorded with multi-channel and single tungsten electrodes

NASA Astrophysics Data System (ADS)

Tan, Xiaodong; Xia, Nan; Young, Hunter; Richter, Claus-Peter

2015-02-01

Auditory prostheses may benefit from Infrared Neural Stimulation (INS) because optical stimulation allows for spatially selective activation of neuron populations. Selective activation of neurons in the cochlear spiral ganglion can be determined in the central nucleus of the inferior colliculus (ICC) because the tonotopic organization of frequencies in the cochlea is maintained throughout the auditory pathway. The activation profile of INS is well represented in the ICC by multichannel electrodes (MCEs). To characterize single unit properties in response to INS, however, single tungsten electrodes (STEs) should be used because of its better signal-to-noise ratio. In this study, we compared the temporal properties of ICC single units recorded with MCEs and STEs in order to characterize the response properties of single auditory neurons in response to INS in guinea pigs. The length along the cochlea stimulated with infrared radiation corresponded to a frequency range of about 0.6 octaves, similar to that recorded with STEs. The temporal properties of single units recorded with MCEs showed higher maximum rates, shorter latencies, and higher firing efficiencies compared to those recorded with STEs. When the preset amplitude threshold for triggering MCE recordings was raised to twice over the noise level, the temporal properties of the single units became similar to those obtained with STEs. Undistinguishable neural activities from multiple sources in MCE recordings could be responsible for the response property difference between MCEs and STEs. Thus, caution should be taken in single unit recordings with MCEs.

Microwave Assisted Helicon Plasmas

NASA Astrophysics Data System (ADS)

McKee, John; Caron, David; Jemiolo, Andrew; Scime, Earl

2017-10-01

The use of two (or more) rf sources at different frequencies is a common technique in the plasma processing industry to control ion energy characteristics separately from plasma generation. A similar approach is presented here with the focus on modifying the electron population in argon and helium plasmas. The plasma is generated by a helicon source at a frequency f0 = 13.56 MHz. Microwaves of frequency f1 = 2.45 GHz are then injected into the helicon source chamber perpendicular to the background magnetic field. The microwaves damp on the electrons via X-mode Electron Cyclotron Heating (ECH) at the upper hybrid resonance, providing additional energy input into the electrons. The effects of this secondary-source heating on electron density, temperature, and energy distribution function are examined and compared to helicon-only single source plasmas as well as numeric models suggesting that the heating is not evenly distributed. Optical Emission Spectroscopy (OES) is used to examine the impact of the energetic tail of the electron distribution on ion and neutral species via collisional excitation. Large enhancements of neutral spectral lines are observed in both Ar and He. While small enhancement of ion lines is seen in Ar, ion lines not normally present in He are observed during microwave injection. U.S. National Science Foundation Grant No. PHY-1360278.

A European model and case studies for aggregate exposure assessment of pesticides.

PubMed

Kennedy, Marc C; Glass, C Richard; Bokkers, Bas; Hart, Andy D M; Hamey, Paul Y; Kruisselbrink, Johannes W; de Boer, Waldo J; van der Voet, Hilko; Garthwaite, David G; van Klaveren, Jacob D

2015-05-01

Exposures to plant protection products (PPPs) are assessed using risk analysis methods to protect public health. Traditionally, single sources, such as food or individual occupational sources, have been addressed. In reality, individuals can be exposed simultaneously to multiple sources. Improved regulation therefore requires the development of new tools for estimating the population distribution of exposures aggregated within an individual. A new aggregate model is described, which allows individual users to include as much, or as little, information as is available or relevant for their particular scenario. Depending on the inputs provided by the user, the outputs can range from simple deterministic values through to probabilistic analyses including characterisations of variability and uncertainty. Exposures can be calculated for multiple compounds, routes and sources of exposure. The aggregate model links to the cumulative dietary exposure model developed in parallel and is implemented in the web-based software tool MCRA. Case studies are presented to illustrate the potential of this model, with inputs drawn from existing European data sources and models. These cover exposures to UK arable spray operators, Italian vineyard spray operators, Netherlands users of a consumer spray and UK bystanders/residents. The model could also be adapted to handle non-PPP compounds. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Source apportionment of PM10 and PM2.5 air pollution, and possible impacts of study characteristics in South Korea.

PubMed

Ryou, Hyoung Gon; Heo, Jongbae; Kim, Sun-Young

2018-09-01

Studies of source apportionment (SA) for particulate matter (PM) air pollution have enhanced understanding of dominant pollution sources and quantification of their contribution. Although there have been many SA studies in South Korea over the last two decades, few studies provided an integrated understanding of PM sources nationwide. The aim of this study was to summarize findings of PM SA studies of South Korea and to explore study characteristics. We selected studies that estimated sources of PM 10 and PM 2.5 performed for 2000-2017 in South Korea using Positive Matrix Factorization and Chemical Mass Balance. We reclassified the original PM sources identified in each study into seven categories: motor vehicle, secondary aerosol, soil dust, biomass/field burning, combustion/industry, natural source, and others. These seven source categories were summarized by using frequency and contribution across four regions, defined by northwest, west, southeast, and southwest regions, by PM 10 and PM 2.5 . We also computed the population-weighted mean contribution of each source category. In addition, we compared study features including sampling design, sampling and lab analysis methods, chemical components, and the inclusion of Asian dust days. In the 21 selected studies, all six PM 10 studies identified motor vehicle, soil dust, and combustion/industry, while all 15 PM 2.5 studies identified motor vehicle and soil dust. Different from the frequency, secondary aerosol produced a large contribution to both PM 10 and PM 2.5 . Motor vehicle contributed highly to both, whereas the contribution of combustion/industry was high for PM 10 . The population-weighted mean contribution was the highest for the motor vehicle and secondary aerosol sources for both PM10 and PM2.5. However, these results were based on different subsets of chemical speciation data collected at a single sampling site, commonly in metropolitan areas, with short overlap and measured by different lab analysis methods. We found that motor vehicle and secondary aerosol were the most common and influential sources for PM in South Korea. Our study, however, suggested a caution to understand SA findings from heterogeneous study features for study designs and input data. Copyright © 2018. Published by Elsevier Ltd.

Source Detection with Bayesian Inference on ROSAT All-Sky Survey Data Sample

NASA Astrophysics Data System (ADS)

Guglielmetti, F.; Voges, W.; Fischer, R.; Boese, G.; Dose, V.

2004-07-01

We employ Bayesian inference for the joint estimation of sources and background on ROSAT All-Sky Survey (RASS) data. The probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS). Background maps were estimated in a single step together with the detection of sources without pixel censoring. Consistent uncertainties of background and sources are provided. The source probability is evaluated for single pixels as well as for pixel domains to enhance source detection of weak and extended sources.

Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters

NASA Astrophysics Data System (ADS)

Munsky, Brian; Trinh, Brooke; Khammash, Mustafa

2010-03-01

The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations exhibit cell-to-cell variability that can manifest significant prototypical differences. Noise induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified using flow cytometry, single molecule fluorescence in situ hybridization, time lapse fluorescence microscopy and other single cell and single molecule measurement techniques. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. We use theoretical investigations to establish experimental guidelines for the identification of gene regulatory networks, and we apply these guideline to experimentally identify predictive models for different regulatory mechanisms in bacteria and yeast.

Prevalence of traumatic brain injury in intimate partner violence offenders compared to the general population: a meta-analysis.

PubMed

Farrer, Thomas J; Frost, R Brock; Hedges, Dawson W

2012-04-01

Intimate partner violence (IPV) is widespread. Several risk factors are associated with IPV perpetuation, including alcohol use and educational level. The aggression and violence associated with traumatic brain injury (TBI) suggest that brain trauma may also be a risk factor for IPV. To examine the association between TBI and IPV, the authors conducted a meta-analysis of peer-reviewed published studies reporting the prevalence of TBI in IPV perpetrators. The authors compared the frequency of TBI among IPV perpetuators to estimates of TBI in the general population using a single-sample test of proportions. Six studies containing a total of 222 subjects met inclusion criteria. Fifty-three percent (119) of the IPV perpetuators had a history of TBI, a prevalence significantly higher (p < .0001) than estimates of TBI in the general population. The prevalence of TBI among perpetuators of IPV appears significantly higher than the prevalence of TBI in the general population. To the extent that this association is causal, TBI may be a risk factor for interpersonal violence, although comparatively few source studies, lack of standardized information about TBI severity, and the inability to investigate potential confounding variables necessarily limit this conclusion.

Single Neurons in the Avian Auditory Cortex Encode Individual Identity and Propagation Distance in Naturally Degraded Communication Calls.

PubMed

Mouterde, Solveig C; Elie, Julie E; Mathevon, Nicolas; Theunissen, Frédéric E

2017-03-29

One of the most complex tasks performed by sensory systems is "scene analysis": the interpretation of complex signals as behaviorally relevant objects. The study of this problem, universal to species and sensory modalities, is particularly challenging in audition, where sounds from various sources and localizations, degraded by propagation through the environment, sum to form a single acoustical signal. Here we investigated in a songbird model, the zebra finch, the neural substrate for ranging and identifying a single source. We relied on ecologically and behaviorally relevant stimuli, contact calls, to investigate the neural discrimination of individual vocal signature as well as sound source distance when calls have been degraded through propagation in a natural environment. Performing electrophysiological recordings in anesthetized birds, we found neurons in the auditory forebrain that discriminate individual vocal signatures despite long-range degradation, as well as neurons discriminating propagation distance, with varying degrees of multiplexing between both information types. Moreover, the neural discrimination performance of individual identity was not affected by propagation-induced degradation beyond what was induced by the decreased intensity. For the first time, neurons with distance-invariant identity discrimination properties as well as distance-discriminant neurons are revealed in the avian auditory cortex. Because these neurons were recorded in animals that had prior experience neither with the vocalizers of the stimuli nor with long-range propagation of calls, we suggest that this neural population is part of a general-purpose system for vocalizer discrimination and ranging. SIGNIFICANCE STATEMENT Understanding how the brain makes sense of the multitude of stimuli that it continually receives in natural conditions is a challenge for scientists. Here we provide a new understanding of how the auditory system extracts behaviorally relevant information, the vocalizer identity and its distance to the listener, from acoustic signals that have been degraded by long-range propagation in natural conditions. We show, for the first time, that single neurons, in the auditory cortex of zebra finches, are capable of discriminating the individual identity and sound source distance in conspecific communication calls. The discrimination of identity in propagated calls relies on a neural coding that is robust to intensity changes, signals' quality, and decreases in the signal-to-noise ratio. Copyright © 2017 Mouterde et al.

A hierarchical modeling approach to estimate regional acute health effects of particulate matter sources

PubMed Central

Krall, J. R.; Hackstadt, A. J.; Peng, R. D.

2017-01-01

Exposure to particulate matter (PM) air pollution has been associated with a range of adverse health outcomes, including cardiovascular disease (CVD) hospitalizations and other clinical parameters. Determining which sources of PM, such as traffic or industry, are most associated with adverse health outcomes could help guide future recommendations aimed at reducing harmful pollution exposure for susceptible individuals. Information obtained from multisite studies, which is generally more precise than information from a single location, is critical to understanding how PM impacts health and to informing local strategies for reducing individual-level PM exposure. However, few methods exist to perform multisite studies of PM sources, which are not generally directly observed, and adverse health outcomes. We developed SHARE, a hierarchical modeling approach that facilitates reproducible, multisite epidemiologic studies of PM sources. SHARE is a two-stage approach that first summarizes information about PM sources across multiple sites. Then, this information is used to determine how community-level (i.e. county- or city-level) health effects of PM sources should be pooled to estimate regional-level health effects. SHARE is a type of population value decomposition that aims to separate out regional-level features from site-level data. Unlike previous approaches for multisite epidemiologic studies of PM sources, the SHARE approach allows the specific PM sources identified to vary by site. Using data from 2000–2010 for 63 northeastern US counties, we estimated regional-level health effects associated with short-term exposure to major types of PM sources. We found PM from secondary sulfate, traffic, and metals sources was most associated with CVD hospitalizations. PMID:28098412

Skeletal muscle-derived interstitial progenitor cells (PICs) display stem cell properties, being clonogenic, self-renewing, and multi-potent in vitro and in vivo.

PubMed

Cottle, Beverley J; Lewis, Fiona C; Shone, Victoria; Ellison-Hughes, Georgina M

2017-07-04

The development of cellular therapies to treat muscle wastage with disease or age is paramount. Resident muscle satellite cells are not currently regarded as a viable cell source due to their limited migration and growth capability ex vivo. This study investigated the potential of muscle-derived PW1 + /Pax7 - interstitial progenitor cells (PICs) as a source of tissue-specific stem/progenitor cells with stem cell properties and multipotency. Sca-1 + /PW1 + PICs were identified on tissue sections from hind limb muscle of 21-day-old mice, isolated by magnetic-activated cell sorting (MACS) technology and their phenotype and characteristics assessed over time in culture. Green fluorescent protein (GFP)-labelled PICs were used to determine multipotency in vivo in a tumour formation assay. Isolated PICs expressed markers of pluripotency (Oct3/4, Sox2, and Nanog), were clonogenic, and self-renewing with >60 population doublings, and a population doubling time of 15.8 ± 2.9 h. PICs demonstrated an ability to generate both striated and smooth muscle, whilst also displaying the potential to differentiate into cell types of the three germ layers both in vitro and in vivo. Moreover, PICs did not form tumours in vivo. These findings open new avenues for a variety of solid tissue engineering and regeneration approaches, utilising a single multipotent stem cell type isolated from an easily accessible source such as skeletal muscle.

Reducing health risks from indoor exposures in rapidly developing urban China.

PubMed

Zhang, Yinping; Mo, Jinhan; Weschler, Charles J

2013-07-01

Over the past two decades there has been a large migration of China's population from rural to urban regions. At the same time, residences in cities have changed in character from single-story or low-rise buildings to high-rise structures constructed and furnished with many synthetic materials. As a consequence, indoor exposures (to pollutants with outdoor and indoor sources) have changed significantly. We briefly discuss the inferred impact that urbanization and modernization have had on indoor exposures and public health in China. We argue that growing adverse health costs associated with these changes are not inevitable, and we present steps that could be taken to reduce indoor exposures to harmful pollutants. As documented by China's Ministry of Health, there have been significant increases in morbidity and mortality among urban residents over the past 20 years. Evidence suggests that the population's exposure to air pollutants has contributed to increases in lung cancer, cardiovascular disease, pulmonary disease, and birth defects. Whether a pollutant has an outdoor or an indoor source, most exposure to the pollutant occurs indoors. Going forward, indoor exposures can be reduced by limiting the ingress of outdoor pollutants (while providing adequate ventilation with clean air), minimizing indoor sources of pollutants, updating government policies related to indoor pollution, and addressing indoor air quality during a building's initial design. Taking the suggested steps could lead to significant reductions in morbidity and mortality, greatly reducing the societal costs associated with pollutant derived ill health.

Effects of pollution on land snail abundance, size and diversity as resources for pied flycatcher, Ficedula hypoleuca.

PubMed

Eeva, Tapio; Rainio, Kalle; Suominen, Otso

2010-09-01

Passerine birds need extra calcium during their breeding for developing egg shells and proper growth of nestling skeleton. Land snails are an important calcium source for many passerines and human-induced changes in snail populations may pose a severe problem for breeding birds. We studied from the bird's viewpoint how air pollution affects the shell mass, abundance and diversity of land snail communities along a pollution gradient of a copper smelter. We sampled remnant snail shells from the nests of an insectivorous passerine, the pied flycatcher, Ficedula hypoleuca, to find out how the availability of land snails varies along the pollution gradient. The total snail shell mass increased towards the pollution source but declined abruptly in the vicinity of the smelter. This spatial variation in shell mass was evident also within a single snail species and could not be wholly explained by spatially varying snail numbers or species composition. Instead, the total shell mass was related to their shell size, individuals being largest at the moderately polluted areas. Smaller shell size suggests inferior growth of snails in the most heavily polluted area. Our study shows that pollution affects the diversity, abundance (available shell mass) and individual quality of land snails, posing reproductive problems for birds that rely on snails as calcium sources during breeding. There are probably both direct pollution-related (heavy metal and calcium levels) and indirect (habitat change) effects behind the observed changes in snail populations. Copyright 2010 Elsevier B.V. All rights reserved.

Subtle Change in the Charge Distribution of Surface Residues May Affect the Secondary Functions of Cytochrome c*

PubMed Central

Paul, Simanta Sarani; Sil, Pallabi; Haldar, Shubhasis; Mitra, Samaresh; Chattopadhyay, Krishnananda

2015-01-01

Although the primary function of cytochrome c (cyt c) is electron transfer, the protein caries out an additional secondary function involving its interaction with membrane cardiolipin (CDL), its peroxidase activity, and the initiation of apoptosis. Whereas the primary function of cyt c is essentially conserved, its secondary function varies depending on the source of the protein. We report here a detailed experimental and computational study, which aims to understand, at the molecular level, the difference in the secondary functions of cyt c obtained from horse heart (mammalian) and Saccharomyces cerevisiae (yeast). The conformational landscape of cyt c has been found to be heterogeneous, consisting of an equilibrium between the compact and extended conformers as well as the oligomeric species. Because the determination of relative populations of these conformers is difficult to obtain by ensemble measurements, we used fluorescence correlation spectroscopy (FCS), a method that offers single-molecule resolution. The population of different species is found to depend on multiple factors, including the protein source, the presence of CDL and urea, and their concentrations. The complex interplay between the conformational distribution and oligomerization plays a crucial role in the variation of the pre-apoptotic regulation of cyt c observed from different sources. Finally, computational studies reveal that the variation in the charge distribution at the surface and the charge reversal sites may be the key determinant of the conformational stability of cyt c. PMID:25873393

Rethinking sources of representative controls for the conduct of case-control studies in minority populations.

PubMed

Bandera, Elisa V; Chandran, Urmila; Zirpoli, Gary; McCann, Susan E; Ciupak, Gregory; Ambrosone, Christine B

2013-05-31

Recruitment of controls remains a challenge in case-control studies and particularly in studies involving minority populations. We compared characteristics of controls recruited through random digit dialing (RDD) to those of community controls enrolled through churches, health events and other outreach sources among women of African ancestry (AA) participating in the Women's Circle of Health Study, a case-control study of breast cancer. Odds ratios and 95% confidence intervals were also computed using unconditional logistic regression to evaluate the impact of including the community controls for selected variables relevant to breast cancer and for which there were significant differences in distribution between the two control groups. Compared to community controls (n=347), RDD controls (n=207) had more years of education and higher income, lower body mass index, were more likely to have private insurance, and less likely to be single. While the percentage of nulliparous women in the two groups was similar, community controls tended to have more children, have their first child at a younger age, and were less likely to breastfeed their children. Dietary intake was similar in the two groups. Compared to census data, the combination of RDD and community controls seems to be more representative of the general population than RDD controls alone. Furthermore, the inclusion of the community group had little impact on the magnitude of risk estimates for most variables, while enhancing statistical power. Community-based recruitment was found to be an efficient and feasible method to recruit AA controls.

Depth Discrimination Using Rg-to-Sg Spectral Amplitude Ratios for Seismic Events in Utah Recorded at Local Distances

DOE PAGES

Tibi, Rigobert; Koper, Keith D.; Pankow, Kristine L.; ...

2018-03-20

Most of the commonly used seismic discrimination approaches are designed for regional data. Relatively little attention has focused on discriminants for local distances (< 200 km), the range at which the smallest events are recorded. We take advantage of the variety of seismic sources and the existence of a dense regional seismic network in the Utah region to evaluate amplitude ratio seismic discrimination at local distances. First, we explored phase-amplitude Pg-to-Sg ratios for multiple frequency bands to classify events in a dataset that comprises populations of single-shot surface explosions, shallow and deep ripple-fired mining blasts, mining-induced events, and tectonic earthquakes.more » We achieved a limited success. Then, for the same dataset, we combined the Pg-to-Sg phase-amplitude ratios with Sg-to-Rg spectral amplitude ratios in a multivariate quadratic discriminant function (QDF) approach. For two-category, pairwise classification, seven out of ten population pairs show misclassification rates of about 20% or less, with five pairs showing rates of about 10% or less. The approach performs best for the pair involving the populations of single-shot explosions and mining-induced events. By combining both Pg-to-Sg and Rg-to-Sg ratios in the multivariate QDFs, we are able to achieve an average improvement of about 4–14% in misclassification rates compared to Pg-to-Sg ratios alone. When all five event populations are considered simultaneously, as expected, the potential for misclassification increases and our QDF approach using both Pg-to-Sg and Rg-to-Sg ratios achieves an average success rate of about 74%, compared to the rate of about 86% for two-category, pairwise classification.« less

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates

PubMed Central

Cox, Murray P.; Karafet, Tatiana M.; Lansing, J. Stephen; Sudoyo, Herawati; Hammer, Michael F.

2010-01-01

The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian–Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations—one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates. PMID:20106848

Depth Discrimination Using Rg-to-Sg Spectral Amplitude Ratios for Seismic Events in Utah Recorded at Local Distances

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

Tibi, Rigobert; Koper, Keith D.; Pankow, Kristine L.

Most of the commonly used seismic discrimination approaches are designed for regional data. Relatively little attention has focused on discriminants for local distances (< 200 km), the range at which the smallest events are recorded. We take advantage of the variety of seismic sources and the existence of a dense regional seismic network in the Utah region to evaluate amplitude ratio seismic discrimination at local distances. First, we explored phase-amplitude Pg-to-Sg ratios for multiple frequency bands to classify events in a dataset that comprises populations of single-shot surface explosions, shallow and deep ripple-fired mining blasts, mining-induced events, and tectonic earthquakes.more » We achieved a limited success. Then, for the same dataset, we combined the Pg-to-Sg phase-amplitude ratios with Sg-to-Rg spectral amplitude ratios in a multivariate quadratic discriminant function (QDF) approach. For two-category, pairwise classification, seven out of ten population pairs show misclassification rates of about 20% or less, with five pairs showing rates of about 10% or less. The approach performs best for the pair involving the populations of single-shot explosions and mining-induced events. By combining both Pg-to-Sg and Rg-to-Sg ratios in the multivariate QDFs, we are able to achieve an average improvement of about 4–14% in misclassification rates compared to Pg-to-Sg ratios alone. When all five event populations are considered simultaneously, as expected, the potential for misclassification increases and our QDF approach using both Pg-to-Sg and Rg-to-Sg ratios achieves an average success rate of about 74%, compared to the rate of about 86% for two-category, pairwise classification.« less

Consolidated Bio-Processing of Cellulosic Biomass for Efficient Biofuel Production Using Yeast Consortium

NASA Astrophysics Data System (ADS)

Goyal, Garima

Fossil fuels have been the major source for liquid transportation fuels for ages. However, decline in oil reserves and environmental concerns have raised a lot of interest in alternative and renewable energy sources. One promising alternative is the conversion of plant biomass into ethanol. The primary biomass feed stocks currently being used for the ethanol industry have been food based biomass (corn and sugar cane). However, interest has recently shifted to replace these traditional feed-stocks with more abundant, non-food based cellulosic biomass such as agriculture wastes (corn stover) or crops (switch grass). The use of cellulosic biomass as feed stock for the production of ethanol via bio-chemical routes presents many technical challenges not faced with the use of corn or sugar-cane as feed-stock. Recently, a new process called consolidated Bio-processing (CBP) has been proposed. This process combines simultaneous saccharification of lignocellulose with fermentation of the resulting sugars into a single process step mediated by a single microorganism or microbial consortium. Although there is no natural microorganism that possesses all properties of lignocellulose utilization and ethanol production desired for CBP, some bacteria and fungi exhibit some of the essential traits. The yeast Saccharomyces cerevisiae is the most attractive host organism for the usage of this strategy due to its high ethanol productivity at close to theoretical yields (0.51g ethanol/g glucose consumed), high osmo- and ethanol- tolerance, natural robustness in industrial processes, and ease of genetic manipulation. Introduction of the cellulosome, found naturally in microorganisms, has shown new directions to deal with recalcitrant biomass. In this case enzymes work in synergy in order to hydrolyze biomass more effectively than in case of free enzymes. A microbial consortium has been successfully developed, which ensures the functional assembly of minicellulosome on the yeast surface composed of four yeast populations. These yeast populations include: one displaying scaffoldin on its surface and three populations secreting three different cellulases in the medium to hydrolyze the cellulose. The modular nature of the consortium system allows for the fine-tuning of each population by changing their initial inoculum ratio, thereby optimizing the cellulose hydrolysis and hence ethanol production. When comparing the optimized consortium with equal ratio consortium, the optimized one produced almost double the amount of ethanol (1.87 g/l) with a yield of 0.475 g ethanol/g cellulose. To further evaluate the feasibility of using consortium for CBP, it was grown at very low optical density (OD) under anaerobic conditions. Under stressful conditions like low OD and no oxygen, the consortium system was proficient in assembling the cellulosome on its surface and growing on the PAS-avicel as sole carbon source and concomitantly producing ethanol with a yield of 87% of the theoretical value. For the dynamic study of yeast consortium system, quantitative real time PCR was used to enumerate the individual yeast population in the mixed culture. At the end of the cultivation, ratios of each population in this consortium maintained similar number as the initial inoculums ratios, which further confirms the consortium system is suitable for the application of CBP.

A stable wavelength-tunable triggered source of single photons and cascaded photon pairs at the telecom C-band

NASA Astrophysics Data System (ADS)

Zeuner, Katharina D.; Paul, Matthias; Lettner, Thomas; Reuterskiöld Hedlund, Carl; Schweickert, Lucas; Steinhauer, Stephan; Yang, Lily; Zichi, Julien; Hammar, Mattias; Jöns, Klaus D.; Zwiller, Val

2018-04-01

The implementation of fiber-based long-range quantum communication requires tunable sources of single photons at the telecom C-band. Stable and easy-to-implement wavelength-tunability of individual sources is crucial to (i) bring remote sources into resonance, (ii) define a wavelength standard, and (iii) ensure scalability to operate a quantum repeater. So far, the most promising sources for true, telecom single photons are semiconductor quantum dots, due to their ability to deterministically and reliably emit single and entangled photons. However, the required wavelength-tunability is hard to attain. Here, we show a stable wavelength-tunable quantum light source by integrating strain-released InAs quantum dots on piezoelectric substrates. We present triggered single-photon emission at 1.55 μm with a multi-photon emission probability as low as 0.097, as well as photon pair emission from the radiative biexciton-exciton cascade. We achieve a tuning range of 0.25 nm which will allow us to spectrally overlap remote quantum dots or tuning distant quantum dots into resonance with quantum memories. This opens up realistic avenues for the implementation of photonic quantum information processing applications at telecom wavelengths.

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.

PubMed

Brynildsrud, Ola; Bohlin, Jon; Scheffer, Lonneke; Eldholm, Vegard

2016-11-25

Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .

Typologi of Island City in Indonesia

NASA Astrophysics Data System (ADS)

Maulana, Alvaryan; Benita, Tania

2017-07-01

As an archipelagic country, Indonesia consist of thousands of island. Some of them are big enough to contain growth and become the center of settlement and activity in Indonesia. However, growth and habitation are not only mushrooming in main island. Several small island also experience growth and become densely population places and simply become a city within island. This study aims to identify island city in Indonesia and creating the typology of the island city. This study is using exploratory approach and heavily rely on statistical figure of every single autonomous region as data sources. Eventually, this study found twelve (12) island cities in Indonesia, and three distinctive typology of island cities.

New York City social workers after 9/11: their attachment, resiliency, and compassion fatigue.

PubMed

Tosone, Carol; Bettmann, Joanna E; Minami, Takuya; Jasperson, Rachael A

2010-01-01

This study examines the relationship between attachment classification, resiliency, and compassion fatigue in New York social workers following 9/11. We used single occasion, quasi-random sampling, surveying 481 social workers living in Manhattan. Hierarchical regression analyses revealed that secure attachment is predictive of the ability to cope with secondary traumatic stress as well as capacity for resilience, explaining approximately 7% of the variance in both compassion fatigue and resiliency. These findings suggest that secure attachment may serve as a source of resilience for social workers, immunizing them from significant compassion fatigue. Such findings have significant implications for clinicians working with traumatized populations.

Integrated spatial multiplexing of heralded single-photon sources

PubMed Central

Collins, M.J.; Xiong, C.; Rey, I.H.; Vo, T.D.; He, J.; Shahnia, S.; Reardon, C.; Krauss, T.F.; Steel, M.J.; Clark, A.S.; Eggleton, B.J.

2013-01-01

The non-deterministic nature of photon sources is a key limitation for single-photon quantum processors. Spatial multiplexing overcomes this by enhancing the heralded single-photon yield without enhancing the output noise. Here the intrinsic statistical limit of an individual source is surpassed by spatially multiplexing two monolithic silicon-based correlated photon pair sources in the telecommunications band, demonstrating a 62.4% increase in the heralded single-photon output without an increase in unwanted multipair generation. We further demonstrate the scalability of this scheme by multiplexing photons generated in two waveguides pumped via an integrated coupler with a 63.1% increase in the heralded photon rate. This demonstration paves the way for a scalable architecture for multiplexing many photon sources in a compact integrated platform and achieving efficient two-photon interference, required at the core of optical quantum computing and quantum communication protocols. PMID:24107840

Multi-photon absorption limits to heralded single photon sources

PubMed Central

Husko, Chad A.; Clark, Alex S.; Collins, Matthew J.; De Rossi, Alfredo; Combrié, Sylvain; Lehoucq, Gaëlle; Rey, Isabella H.; Krauss, Thomas F.; Xiong, Chunle; Eggleton, Benjamin J.

2013-01-01

Single photons are of paramount importance to future quantum technologies, including quantum communication and computation. Nonlinear photonic devices using parametric processes offer a straightforward route to generating photons, however additional nonlinear processes may come into play and interfere with these sources. Here we analyse spontaneous four-wave mixing (SFWM) sources in the presence of multi-photon processes. We conduct experiments in silicon and gallium indium phosphide photonic crystal waveguides which display inherently different nonlinear absorption processes, namely two-photon (TPA) and three-photon absorption (ThPA), respectively. We develop a novel model capturing these diverse effects which is in excellent quantitative agreement with measurements of brightness, coincidence-to-accidental ratio (CAR) and second-order correlation function g(2)(0), showing that TPA imposes an intrinsic limit on heralded single photon sources. We build on these observations to devise a new metric, the quantum utility (QMU), enabling further optimisation of single photon sources. PMID:24186400

Benefits of dietary fiber in clinical nutrition.

PubMed

Klosterbuer, Abby; Roughead, Zamzam Fariba; Slavin, Joanne

2011-10-01

Dietary fiber is widely recognized as an important part of a healthy diet and is a common addition to enteral nutrition (EN) formulas. Fiber sources differ in characteristics such as solubility, fermentability, and viscosity, and it is now well known that different types of fiber exert varying physiological effects in the body. Clinical studies suggest fiber can exert a wide range of benefits in areas such as bowel function, gut health, immunity, blood glucose control, and serum lipid levels. Although early clinical nutrition products contained fiber from a single source, it is now thought that blends of fiber from multiple sources more closely resemble a regular diet and may provide a greater range of benefits for the patient. Current recommendations support the use of dietary fiber in clinical nutrition when no contraindications exist, but little information exists about which types and combinations of fibers provide the relevant benefit in certain patient populations. This article summarizes the different types of fiber commonly added to EN products and reviews the current literature on the use of fiber blends in clinical nutrition.

Synthesis and Characterization of the First Liquid Single Source Precursors for the Deposition of Ternary Chalcopyrite (CuInS2) Thin Film Materials

NASA Technical Reports Server (NTRS)

Banger, Kulbinder K.; Cowen, Jonathan; Hepp, Aloysius

2002-01-01

Molecular engineering of ternary single source precursors based on the [{PBu3}2Cu(SR')2In(SR')2] architecture have afforded the first liquid CIS ternary single source precursors (when R = Et, n-Pr), which are suitable for low temperature deposition (< 350 C). Thermogravimetric analyses (TGA) and modulated-differential scanning calorimetry (DSC) confirm their liquid phase and reduced stability. X-ray diffraction studies, energy dispersive analyzer (EDS), and scanning electron microscopy (SEM) support the formation of the single-phase chalcopyrite CuInS2 at low temperatures.

Polyommatus ripartii : The Biological Basis for the Conservation and the Morphology of the Developmental Stages of a Critically Endangered, Relict Population in Central Europe

PubMed Central

Przybyłowicz, Łukasz

2014-01-01

Abstract Ripart’s Anomalous Blue Polyommatus ripartii (Freyer, 1830) is one of the most seriously endangered butterfly species in central Europe, a small, relict population of which has survived in two localities in Poland. This isolated population is undoubtedly the last and northernmost remnant of a once much wider range in central Europe. P. ripartii is associated with highly xerophilous vegetation on gypsum and calcareous soils. Only active conservation measures can ensure its survival. For these to be successful, however, precise information on the butterfly’s biology, behavior and also its morphology is crucial. The first to do so, this article describes the butterfly’s egg-laying preferences, and specifies the numbers of eggs on a single shoot and their placement on it. A unique behavioral trait of the female—the secretion of oviposition-deterring pheromones—is reported. The preferred plant associations and nectar sources have been investigated, and information on overnight roosts is given. In addition, an exhaustive description of the morphologies of the egg, final instar and pupa, as well as new details of adult behavior are provided. The main conclusion of the this study is that the existence of a stable population in the Nida Region is determined by the presence of large patches of sainfoin, which is both the larval host plant and a source of nectar for the imago. Moreover, stress is laid on the importance of Inula ensifolia L. as the secondary nectaring plant, which may facilitate dispersion among patches of suitable habitat. Finally, the study shows that searching for the easily detected eggs may be the best method for proving the existence of the species in a given locality. PMID:25525109

Comparison of Marker-Based Genomic Estimated Breeding Values and Phenotypic Evaluation for Selection of Bacterial Spot Resistance in Tomato.

PubMed

Liabeuf, Debora; Sim, Sung-Chur; Francis, David M

2018-03-01

Bacterial spot affects tomato crops (Solanum lycopersicum) grown under humid conditions. Major genes and quantitative trait loci (QTL) for resistance have been described, and multiple loci from diverse sources need to be combined to improve disease control. We investigated genomic selection (GS) prediction models for resistance to Xanthomonas euvesicatoria and experimentally evaluated the accuracy of these models. The training population consisted of 109 families combining resistance from four sources and directionally selected from a population of 1,100 individuals. The families were evaluated on a plot basis in replicated inoculated trials and genotyped with single nucleotide polymorphisms (SNP). We compared the prediction ability of models developed with 14 to 387 SNP. Genomic estimated breeding values (GEBV) were derived using Bayesian least absolute shrinkage and selection operator regression (BL) and ridge regression (RR). Evaluations were based on leave-one-out cross validation and on empirical observations in replicated field trials using the next generation of inbred progeny and a hybrid population resulting from selections in the training population. Prediction ability was evaluated based on correlations between GEBV and phenotypes (r g ), percentage of coselection between genomic and phenotypic selection, and relative efficiency of selection (r g /r p ). Results were similar with BL and RR models. Models using only markers previously identified as significantly associated with resistance but weighted based on GEBV and mixed models with markers associated with resistance treated as fixed effects and markers distributed in the genome treated as random effects offered greater accuracy and a high percentage of coselection. The accuracy of these models to predict the performance of progeny and hybrids exceeded the accuracy of phenotypic selection.

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

PubMed

Grad, Yonatan H; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M; Cerqueira, Gustavo C; Fitzgerald, Michael; Godfrey, Paul; Haas, Brian J; Murphy, Cheryl I; Russ, Carsten; Sykes, Sean; Walker, Bruce J; Wortman, Jennifer R; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; Desmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas M; Struve, Carsten; Krogfelt, Karen A; Bingen, Edouard; Weill, François-Xavier; Lander, Eric S; Nusbaum, Chad; Birren, Bruce W; Hung, Deborah T; Hanage, William P

2012-02-21

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

PubMed Central

Grad, Yonatan H.; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M.; Cerqueira, Gustavo C.; FitzGerald, Michael; Godfrey, Paul; Haas, Brian J.; Murphy, Cheryl I.; Russ, Carsten; Sykes, Sean; Walker, Bruce J.; Wortman, Jennifer R.; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; DeSmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas M.; Struve, Carsten; Krogfelt, Karen A.; Bingen, Edouard; Weill, François-Xavier; Lander, Eric S.; Nusbaum, Chad; Birren, Bruce W.; Hung, Deborah T.; Hanage, William P.

2012-01-01

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May–July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak. PMID:22315421

Lipid body accumulation alters calcium signaling dynamics in immune cells

PubMed Central

Greineisen, William E.; Speck, Mark; Shimoda, Lori M.N.; Sung, Carl; Phan, Nolwenn; Maaetoft-Udsen, Kristina; Stokes, Alexander J.; Turner, Helen

2014-01-01

Summary There is well-established variability in the numbers of lipid bodies (LB) in macrophages, eosinophils, and neutrophils. Similarly to the steatosis observed in adipocytes and hepatocytes during hyperinsulinemia and nutrient overload, immune cell LB hyper-accumulate in response to bacterial and parasitic infection and inflammatory presentations. Recently we described that hyperinsulinemia, both in vitro and in vivo, drives steatosis and phenotypic changes in primary and transformed mast cells and basophils. LB reach high numbers in these steatotic cytosols, and here we propose that they could dramatically impact the transcytoplasmic signaling pathways. We compared calcium release and influx responses at the population and single cell level in normal and steatotic model mast cells. At the population level, all aspects of FcεRI-dependent calcium mobilization, as well as activation of calcium-dependent downstream signalling targets such as NFATC1 phosphorylation are suppressed. At the single cell level, we demonstrate that LB are both sources and sinks of calcium following FcεRI cross-linking. Unbiased analysis of the impact of the presence of LB on the rate of trans-cytoplasmic calcium signals suggest that LB enrichment accelerates calcium propagation, which may reflect a Bernoulli effect. LB abundance thus impacts this fundamental signalling pathway and its downstream targets. PMID:25016314

Carry-over of thermophilic Campylobacter spp. between sequential and adjacent poultry flocks.

PubMed

Alter, Thomas; Weber, Rita Margarete; Hamedy, Ahmad; Glünder, Gerhard

2011-01-10

Nineteen flocks of four poultry species were monitored at a veterinary field station to investigate the distribution and spread of Campylobacter genotypes between sequential and adjacent flocks. Caecal and liver samples were obtained at frequent intervals from birds of all flocks and examined for Campylobacter. Amplified fragment length polymorphism (AFLP) analysis was performed to genotype Campylobacter isolates. Of the 1643 caecal and liver samples investigated, 452 (27.5%) caecal samples and 11 (0.7%) liver samples contained Campylobacter. Of the caecal isolates 76.3% were identified as Campylobacter jejuni and 23.7% were identified as Campylobacter coli. Poultry flocks were largely colonized by more than one AFLP type and an intense exchange of Campylobacter genotypes between different poultry flocks occurred. These findings indicate that multiple genotypes can constitute the Campylobacter population within single poultry flocks, hinting to different sources of exposure and/or genetic drifts within the Campylobacter population. Nevertheless, in most flocks single Campylobacter genotypes predominated. Some strains superseded others resulting in colonization by successive Campylobacter genotypes during the observation period. In conclusion, the data demonstrate that the large genetic diversity of Campylobacter must be considered in epidemiological evaluations and microbial risk assessments of Campylobacter in poultry. Copyright © 2010 Elsevier B.V. All rights reserved.

The Within-Year Concentration of Medical Care: Implications for Family Out-of-Pocket Expenditure Burdens

PubMed Central

Selden, Thomas M

2009-01-01

Objective To examine the within-year concentration of family health care and the resulting exposure of families to short periods of high expenditure burdens. Data Source Household data from the pooled 2003 and 2004 Medical Expenditure Panel Survey (MEPS) yielding nationally representative estimates for the nonelderly civilian noninstitutionalized population. Study Design The paper examines the within-year concentration of family medical care use and the frequency with which family out-of-pocket expenditures exceeded 20 percent of family income, computed at the annual, quarterly, and monthly levels. Principal Findings On average among families with medical care, 49 percent of all (charge-weighted) care occurred in a single month, and 63 percent occurred in a single quarter). Nationally, 27 percent of the study population experienced at least 1 month in which out-of-pocket expenditures exceeded 20 percent of income. Monthly 20 percent burden rates were highest among the poor, at 43 percent, and were close to or above 30 percent for all but the highest income group (families above four times the federal poverty line). Conclusions Within-year spikes in health care utilization can create financial pressures missed by conventional annual burden analyses. Within-year health-related financial pressures may be especially acute among lower-income families due to low asset holdings. PMID:19674431

[Prospects of the integration of dry blood spot technology with human health and environmental population studies].

PubMed

Pomelova, V G; Osin, N S

2007-01-01

This literature review is dedicated to prospects of the use of whole blood dried on special filter paper as a source of biological material for human health and environmental population studies. Evident advantages of this low-invasive approach include the following: it is easy to take a blood sample from a patient's finger ofa neonate's heel; the cost of sampling as well as transportation and storage of samples is low; paper blanks are safe to manipulate with and convenient to mail in sealed plastic packages. Many analytes, such as DNA, become more stable after drying, which allows for the detection of phenotypic and genotypic markers, as well as multiple gene mutations by multiplex DNA amplification. Modern diagnostic techniques make it possible to detect a wide spectrum of biomarkers characterizing the condition of the endocrine, cardiovascular, reproductive, and immune systems of the organism in a single drop of blood. This allows considering paper blanks with dry blood the key component of multilevel interdisciplinary population studies on neonatal screening, disease spread surveillance, seroepidemiological monitoring, and ecological and genetic research.

The effects of restricted glycolysis on stem-cell like characteristics of breast cancer cells

PubMed Central

Banerjee, Arindam; Arvinrad, Pardis; Darley, Matthew; Laversin, Stéphanie A.; Parker, Rachel; Rose-Zerilli, Matthew J.J.; Townsend, Paul A.; Cutress, Ramsey I.; Beers, Stephen A.; Houghton, Franchesca D.; Birts, Charles N.; Blaydes, Jeremy P.

2018-01-01

Altered glycolysis is a characteristic of many cancers, and can also be associated with changes in stem cell-like cancer (SCLC) cell populations. We therefore set out to directly examine the effect of glycolysis on SCLC cell phenotype, using a model where glycolysis is stably reduced by adapting the cells to a sugar source other than glucose. Restricting glycolysis using this approach consistently resulted in cells with increased oncogenic potential; including an increase in SCLC cells, proliferation in 3D matrigel, invasiveness, chemoresistance, and altered global gene expression. Tumorigenicity in vivo was also markedly increased. SCLC cells exhibited increased dependence upon alternate metabolic pathways. They also became c-KIT dependent, indicating that their apparent state of maturation is regulated by glycolysis. Single-cell mRNA sequencing identified altered networks of metabolic-, stem- and signaling- gene expression within SCLC-enriched populations in response to glycolytic restriction. Therefore, reduced glycolysis, which may occur in niches within tumors where glucose availability is limiting, can promote tumor aggressiveness by increasing SCLC cell populations, but can also introduce novel, potentially exploitable, vulnerabilities in SCLC cells. PMID:29796188

Isolation and Purification of Satellite Cells for Skeletal Muscle Tissue Engineering

PubMed Central

Syverud, Brian C; Lee, Jonah D; VanDusen, Keith W; Larkin, Lisa M

2015-01-01

Engineered skeletal muscle holds promise as a source of graft tissue for the repair of traumatic injuries such as volumetric muscle loss. The resident skeletal muscle stem cell, the satellite cell, has been identified as an ideal progenitor for tissue engineering due to its role as an essential player in the potent skeletal muscle regeneration mechanism. A significant challenge facing tissue engineers, however, is the isolation of sufficiently large satellite cell populations with high purity. The two common isolation techniques, single fiber explant culture and enzymatic dissociation, can yield either a highly pure satellite cell population or a suitably large number or cells but fail to do both simultaneously. As a result, it is often necessary to use a purification technique such as pre-plating or cell sorting to enrich the satellite cell population post-isolation. Furthermore, the absence of complex chemical and biophysical cues influencing the in vivo satellite cell “niche” complicates the culture of isolated satellite cells. Techniques under investigation to maximize myogenic proliferation and differentiation in vitro are described in this article, along with current methods for isolating and purifying satellite cells. PMID:26413555

Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis

PubMed Central

Landry, Zachary C.; Giovanonni, Stephen J.; Quake, Stephen R.; Blainey, Paul C.

2013-01-01

Genetic analysis of single cells is emerging as a powerful approach for studies of heterogeneous cell populations. Indeed, the notion of homogeneous cell populations is receding as approaches to resolve genetic and phenotypic variation between single cells are applied throughout the life sciences. A key step in single-cell genomic analysis today is the physical isolation of individual cells from heterogeneous populations, particularly microbial populations, which often exhibit high diversity. Here, we detail the construction and use of instrumentation for optical trapping inside microfluidic devices to select individual cells for analysis by methods including nucleic acid sequencing. This approach has unique advantages for analyses of rare community members, cells with irregular morphologies, small quantity samples, and studies that employ advanced optical microscopy. PMID:24060116

Transcriptional Networks in Single Perivascular Cells Sorted from Human Adipose Tissue Reveal a Hierarchy of Mesenchymal Stem Cells.

PubMed

Hardy, W Reef; Moldovan, Nicanor I; Moldovan, Leni; Livak, Kenneth J; Datta, Krishna; Goswami, Chirayu; Corselli, Mirko; Traktuev, Dmitry O; Murray, Iain R; Péault, Bruno; March, Keith

2017-05-01

Adipose tissue is a rich source of multipotent mesenchymal stem-like cells, located in the perivascular niche. Based on their surface markers, these have been assigned to two main categories: CD31 - /CD45 - /CD34 + /CD146 - cells (adventitial stromal/stem cells [ASCs]) and CD31 - /CD45 - /CD34 - /CD146 + cells (pericytes [PCs]). These populations display heterogeneity of unknown significance. We hypothesized that aldehyde dehydrogenase (ALDH) activity, a functional marker of primitivity, could help to better define ASC and PC subclasses. To this end, the stromal vascular fraction from a human lipoaspirate was simultaneously stained with fluorescent antibodies to CD31, CD45, CD34, and CD146 antigens and the ALDH substrate Aldefluor, then sorted by fluorescence-activated cell sorting. Individual ASCs (n = 67) and PCs (n = 73) selected from the extremities of the ALDH-staining spectrum were transcriptionally profiled by Fluidigm single-cell quantitative polymerase chain reaction for a predefined set (n = 429) of marker genes. To these single-cell data, we applied differential expression and principal component and clustering analysis, as well as an original gene coexpression network reconstruction algorithm. Despite the stochasticity at the single-cell level, covariation of gene expression analysis yielded multiple network connectivity parameters suggesting that these perivascular progenitor cell subclasses possess the following order of maturity: (a) ALDH br ASC (most primitive); (b) ALDH dim ASC; (c) ALDH br PC; (d) ALDH dim PC (least primitive). This order was independently supported by specific combinations of class-specific expressed genes and further confirmed by the analysis of associated signaling pathways. In conclusion, single-cell transcriptional analysis of four populations isolated from fat by surface markers and enzyme activity suggests a developmental hierarchy among perivascular mesenchymal stem cells supported by markers and coexpression networks. Stem Cells 2017;35:1273-1289. © 2017 AlphaMed Press.

[The contribution of the Italian association of cancer registries (AIRTUM)].

PubMed

Crocetti, Emanuele; Buzzoni, Carlotta

2016-01-01

The study of cluster requires the ability to identify, with accuracy and completeness, the health events of interest and their geographical location and time of occurrence. For rare and complex diseases, such as childhood cancers, it is possible to observe a significant health migration from the place of residence, which makes the detection even more complex. The best tool to identify these rare diseases is represented by cancer registries (CRs). In fact, CRs collect, through many sources, information related to tumours that arise in the population resident in their areas of activity. The number of the sources of information has increased thanks to the computerization of health services. The availability of multiple sources of information increases the completeness of data collection overcoming the limits of a single source, and makes it possible to describe the diagnostic-therapeutic course and the outcome of the cases. Among all data sources, for childhood cancers the model 1.01, which summarize the clinical information of the cases treated in one of the Italian Association of paediatric haematology and oncology (AIEOP) centres, is relevant. Moreover, CRs produce reliable and comparable data due to the use of international rules and classifications for the definition of the topography and morphology of cancer, for the date of diagnosis, and for quality checks. In Italy, the Italian association of cancer registries (AIRTUM) coordinates the activities of 45 population CRs, both general and specialized (by age or tumour type). AIRTUM involves a population of over 6.7 million citizens under the age of 20 years, approximately 60% of the total resident population. AIRTUM plays a role of coordination, support, and harmonization for Italian CRs through training, accreditation, and a shared database, it promotes and participates in national and international collaboration involving scientific societies (AIEOP, Italian Association of medical oncology - AIOM, Italian Federation of volunteer-based cancer organisations - FAVO) and institutions (Italian national Institute of health, Italian national cancer institute of Milan) and performs analysis on key epidemiological indicators (incidence, mortality, survival, and prevalence). The AIRTUM database contains 19,650 cancer cases in child/ adolescent patients diagnosed from 1967 to 2011. The epidemiology of childhood cancers has been the subject of two AIRTUM monographs published in 2008 and in 2013 in collaboration with AIEOP; the latter includes specific contributions on polluted sites, on the psychological side, and on the experience of the parents of young cancer patients. The collaboration between different professionals, needs, and knowledge is the policy followed by AIRTUM to build up a complete picture of cancer epidemiology, even of childhood cancer, in Italy.

Effects of binary stellar populations on direct collapse black hole formation

NASA Astrophysics Data System (ADS)

Agarwal, Bhaskar; Cullen, Fergus; Khochfar, Sadegh; Klessen, Ralf S.; Glover, Simon C. O.; Johnson, Jarrett

2017-06-01

The critical Lyman-Werner (LW) flux required for direct collapse blackholes (DCBH) formation, or Jcrit, depends on the shape of the irradiating spectral energy distribution (SED). The SEDs employed thus far have been representative of realistic single stellar populations. We study the effect of binary stellar populations on the formation of DCBH, as a result of their contribution to the LW radiation field. Although binary populations with ages > 10 Myr yield a larger LW photon output, we find that the corresponding values of Jcrit can be up to 100 times higher than single stellar populations. We attribute this to the shape of the binary SEDs as they produce a sub-critical rate of H- photodetaching 0.76 eV photons as compared to single stellar populations, reaffirming the role that H- plays in DCBH formation. This further corroborates the idea that DCBH formation is better understood in terms of a critical region in the H2-H- photodestruction rate parameter space, rather than a single value of LW flux.

The Chandra Source Catalog 2.0: Interfaces

NASA Astrophysics Data System (ADS)

D'Abrusco, Raffaele; Zografou, Panagoula; Tibbetts, Michael; Allen, Christopher E.; Anderson, Craig S.; Budynkiewicz, Jamie A.; Burke, Douglas; Chen, Judy C.; Civano, Francesca Maria; Doe, Stephen M.; Evans, Ian N.; Evans, Janet D.; Fabbiano, Giuseppina; Gibbs, Danny G., II; Glotfelty, Kenny J.; Graessle, Dale E.; Grier, John D.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; Houck, John C.; Lauer, Jennifer L.; Laurino, Omar; Lee, Nicholas P.; Martínez-Galarza, Rafael; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph; McLaughlin, Warren; Morgan, Douglas L.; Mossman, Amy E.; Nguyen, Dan T.; Nichols, Joy S.; Nowak, Michael A.; Paxson, Charles; Plummer, David A.; Primini, Francis Anthony; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Van Stone, David W.

2018-01-01

Easy-to-use, powerful public interfaces to access the wealth of information contained in any modern, complex astronomical catalog are fundamental to encourage its usage. In this poster,I present the public interfaces of the second Chandra Source Catalog (CSC2). CSC2 is the most comprehensive catalog of X-ray sources detected by Chandra, thanks to the inclusion of Chandra observations public through the end of 2014 and to methodological advancements. CSC2 provides measured properties for a large number of sources that sample the X-ray sky at fainter levels than the previous versions of the CSC, thanks to the stacking of single overlapping observations within 1’ before source detection. Sources from stacks are then crossmatched, if multiple stacks cover the same area of the sky, to create a list of unique, optimal CSC2 sources. The properties of sources detected in each single stack and each single observation are also measured. The layered structure of the CSC2 catalog is mirrored in the organization of the CSC2 database, consisting of three tables containing all properties for the unique stacked sources (“Master Source”), single stack sources (“Stack Source”) and sources in any single observation (“Observation Source”). These tables contain estimates of the position, flags, extent, significances, fluxes, spectral properties and variability (and associated errors) for all classes of sources. The CSC2 also includes source region and full-field data products for all master sources, stack sources and observation sources: images, photon event lists, light curves and spectra.CSCview, the main interface to the CSC2 source properties and data products, is a GUI tool that allows to build queries based on the values of all properties contained in CSC2 tables, query the catalog, inspect the returned table of source properties, browse and download the associated data products. I will also introduce the suite of command-line interfaces to CSC2 that can be used in alternative to CSCview, and will present the concept for an additional planned cone-search web-based interface.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

76 FR 46308 - Fiscal Year (FY) 2011 Funding Opportunity

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2011-08-02

... Administration, HHS. ACTION: Notice of intent to award a Single Source Grant to the National Association of State... Services Administration (SAMHSA) is seeking to award a single source grant to the National Association of State Alcohol and Drug Abuse Directors (NASADAD) to provide assistance to substance abuse Single State...

Spatial variation in anthropogenic mortality induces a source-sink system in a hunted mesopredator.

PubMed

Minnie, Liaan; Zalewski, Andrzej; Zalewska, Hanna; Kerley, Graham I H

2018-04-01

Lethal carnivore management is a prevailing strategy to reduce livestock predation. Intensity of lethal management varies according to land-use, where carnivores are more intensively hunted on farms relative to reserves. Variations in hunting intensity may result in the formation of a source-sink system where carnivores disperse from high-density to low-density areas. Few studies quantify dispersal between supposed sources and sinks-a fundamental requirement for source-sink systems. We used the black-backed jackal (Canis mesomelas) as a model to determine if heterogeneous anthropogenic mortality induces a source-sink system. We analysed 12 microsatellite loci from 554 individuals from lightly hunted and previously unhunted reserves, as well as heavily hunted livestock- and game farms. Bayesian genotype assignment showed that jackal populations displayed a hierarchical population structure. We identified two genetically distinct populations at the regional level and nine distinct subpopulations at the local level, with each cluster corresponding to distinct land-use types separated by various dispersal barriers. Migration, estimated using Bayesian multilocus genotyping, between reserves and farms was asymmetric and heterogeneous anthropogenic mortality induced source-sink dynamics via compensatory immigration. Additionally some heavily hunted populations also acted as source populations, exporting individuals to other heavily hunted populations. This indicates that heterogeneous anthropogenic mortality results in the formation of a complex series of interconnected sources and sinks. Thus, lethal management of mesopredators may not be an effective long-term strategy in reducing livestock predation, as dispersal and, more importantly, compensatory immigration may continue to affect population reduction efforts as long as dispersal from other areas persists.

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)

PubMed Central

2012-01-01

Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey. PMID:22891612

Addressing nutritional gaps with multivitamin and mineral supplements

PubMed Central

2014-01-01

A balanced and varied diet is the best source of essential vitamins and minerals; however, nutrient deficiencies occur, including in populations with bountiful food supplies and the means to procure nutrient-rich foods. For example, the typical American diet bears little resemblance to what experts recommend for fruit, vegetables, and whole grains, which serve as important sources of an array of vitamins and minerals. With time, deficiencies in one or more micronutrients may lead to serious health issues. A common reason people take multivitamin and mineral (MVM) supplements is to maintain or improve health, but research examining the effectiveness of MVMs in the prevention of certain chronic conditions is ongoing. In addition to the utility of MVMs for filling in relatively small but critical nutritional gaps, which may help prevent conditions such as anemia, neural tube defects, and osteoporosis, some evidence supports possible benefits of MVM supplementation with regard to cancer prevention (particularly in men) and prevention or delay of cataract, as well as some aspects of cognitive performance. Unlike some single-vitamin supplements, MVM supplements are generally well tolerated and do not appear to increase the risk of mortality, cerebrovascular disease, or heart failure. The potential benefits of MVM supplements likely outweigh any risk in the general population and may be particularly beneficial for older people. PMID:25027766

Addressing nutritional gaps with multivitamin and mineral supplements.

PubMed

Ward, Elizabeth

2014-07-15

A balanced and varied diet is the best source of essential vitamins and minerals; however, nutrient deficiencies occur, including in populations with bountiful food supplies and the means to procure nutrient-rich foods. For example, the typical American diet bears little resemblance to what experts recommend for fruit, vegetables, and whole grains, which serve as important sources of an array of vitamins and minerals. With time, deficiencies in one or more micronutrients may lead to serious health issues. A common reason people take multivitamin and mineral (MVM) supplements is to maintain or improve health, but research examining the effectiveness of MVMs in the prevention of certain chronic conditions is ongoing. In addition to the utility of MVMs for filling in relatively small but critical nutritional gaps, which may help prevent conditions such as anemia, neural tube defects, and osteoporosis, some evidence supports possible benefits of MVM supplementation with regard to cancer prevention (particularly in men) and prevention or delay of cataract, as well as some aspects of cognitive performance. Unlike some single-vitamin supplements, MVM supplements are generally well tolerated and do not appear to increase the risk of mortality, cerebrovascular disease, or heart failure. The potential benefits of MVM supplements likely outweigh any risk in the general population and may be particularly beneficial for older people.

Cytonuclear Theory for Haplodiploid Species and X-Linked Genes. I. Hardy-Weinberg Dynamics and Continent-Island, Hybrid Zone Models

PubMed Central

Goodisman, MAD.; Asmussen, M. A.

1997-01-01

We develop models that describe the cytonuclear structure for either a cytoplasmic and nuclear marker in a haplodiploid species or a cytoplasmic and X-linked marker in a diploid species. Sex-specific disequilibrium statistics that summarize nonrandom cytonuclear associations in such systems are defined, and their basic Hardy-Weinberg dynamics and admixture formulae are delimited. We focus on the context of hybrid zones and develop continent-island models whereby individuals from two genetically differentiated source populations migrate into and mate within a single zone of admixture. We examine the effects of differential migration of the sexes, assortative mating by pure type females, and census time (relative to mating and migration), as well as special cases of random mating and migration subsumed under the general models. We show that pure type individuals and nonzero cytonuclear disequilibria can be maintained within a hybrid zone if there is continued migration from both source populations, and that females generally have a greater influence over these cytonuclear variables than males. The resulting theoretical framework can be used to estimate the rates of assortative mating and sex-specific gene flow in hybrid zones and other zones of admixture involving haplodiploid or sex-linked cytonuclear data. PMID:9286692

Bridging the Timescales of Single-Cell and Population Dynamics

NASA Astrophysics Data System (ADS)

Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

2018-04-01

How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

Air toxics and early childhood acute lymphocytic leukemia in Texas, a population based case control study.

PubMed

Symanski, Elaine; Tee Lewis, P Grace; Chen, Ting-Yu; Chan, Wenyaw; Lai, Dejian; Ma, Xiaomei

2016-06-14

Traffic exhaust, refineries and industrial facilities are major sources of air toxics identified by the U.S. Environmental Protection Agency (U.S. EPA) for their potential risk to human health. In utero and early life exposures to air toxics such as benzene and 1,3-butadiene, which are known leukemogens in adults, may play an etiologic role in childhood leukemia that comprises the majority of pediatric cancers. We conducted a population based case-control study to examine individual effects of benzene, 1,3-butadiene and polycyclic organic matter (POM) in ambient residential air on acute lymphocytic leukemia (ALL) diagnosed in children under age 5 years in Texas from 1995-2011. Texas Cancer Registry cases were linked to birth records and then were frequency matched by birth month and year to 10 population-based controls. Maternal and infant characteristics from birth certificates were abstracted to obtain information about potential confounders. Modelled estimates of benzene, 1,3-butadiene and POM exposures at the census tract level were assigned by linking geocoded maternal addresses from birth certificates to U.S. EPA National-Scale Air Toxics Assessment data for single and co-pollutant statistical analyses. Mixed-effects logistic regression models were applied to evaluate associations between air toxics and childhood leukemia. In adjusted single pollutant models, odds of childhood leukemia among mothers with the highest ambient air exposures compared to those in the lowest quartile were 1.11 (95 % CI: 0.94-1.32) for POM, 1.17 (95 % CI: 0.98-1.39) for benzene and 1.29 (95 % CI: 1.08-1.52) for 1,3-butadiene. In co-pollutant models, odds ratios for childhood leukemia remained elevated for 1,3-butadiene but were close to the null value for benzene and POM. We observed positive associations between 1,3-butadiene and childhood leukemia in single and co-pollutant models whereas effect estimates from single pollutant models were diminished for benzene and POM in co-pollutant models. Early life exposure to 1,3-butadiene rather than benzene or POM appears to increase early childhood risk of acute lymphocytic leukemia.

Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

PubMed

Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

2017-07-07

The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

Turbulent aerosol fluxes over the Arctic Ocean: 2. Wind-driven sources from the sea

NASA Astrophysics Data System (ADS)

Nilsson, E. D.; Rannik, Ü.; Swietlicki, E.; Leck, C.; Aalto, P. P.; Zhou, J.; Norman, M.

2001-12-01

An eddy-covariance flux system was successfully applied over open sea, leads and ice floes during the Arctic Ocean Expedition in July-August 1996. Wind-driven upward aerosol number fluxes were observed over open sea and leads in the pack ice. These particles must originate from droplets ejected into the air at the bursting of small air bubbles at the water surface. The source flux F (in 106 m-2 s-1) had a strong dependency on wind speed, log>(F>)=0.20U¯-1.71 and 0.11U¯-1.93, over the open sea and leads, respectively (where U¯ is the local wind speed at about 10 m height). Over the open sea the wind-driven aerosol source flux consisted of a film drop mode centered at ˜100 nm diameter and a jet drop mode centered at ˜1 μm diameter. Over the leads in the pack ice, a jet drop mode at ˜2 μm diameter dominated. The jet drop mode consisted of sea-salt, but oxalate indicated an organic contribution, and bacterias and other biogenic particles were identified by single particle analysis. Particles with diameters less than -100 nm appear to have contributed to the flux, but their chemical composition is unknown. Whitecaps were probably the bubble source at open sea and on the leads at high wind speed, but a different bubble source is needed in the leads owing to their small fetch. Melting of ice in the leads is probably the best candidate. The flux over the open sea was of such a magnitude that it could give a significant contribution to the condensation nuclei (CCN) population. Although the flux from the leads were roughly an order of magnitude smaller and the leads cover only a small fraction of the pack ice, the local source may till be important for the CCN population in Arctic fogs. The primary marine aerosol source will increase both with increased wind speed and with decreased ice fraction and extent. The local CCN production may therefore increase and influence cloud or fog albedo and lifetime in response to greenhouse warming in the Arctic Ocean region.

Single-Molecule Sequencing Reveals Complex Genome Variation of Hepatitis B Virus during 15 Years of Chronic Infection following Liver Transplantation

PubMed Central

Betz-Stablein, B. D.; Töpfer, A.; Littlejohn, M.; Yuen, L.; Colledge, D.; Sozzi, V.; Angus, P.; Thompson, A.; Revill, P.; Beerenwinkel, N.; Warner, N.

2016-01-01

ABSTRACT Chronic hepatitis B (CHB) is prevalent worldwide. The infectious agent, hepatitis B virus (HBV), replicates via an RNA intermediate and is error prone, leading to the rapid generation of closely related but not identical viral variants, including those that can escape host immune responses and antiviral treatments. The complexity of CHB can be further enhanced by the presence of HBV variants with large deletions in the genome generated via splicing (spHBV variants). Although spHBV variants are incapable of autonomous replication, their replication is rescued by wild-type HBV. spHBV variants have been shown to enhance wild-type virus replication, and their prevalence increases with liver disease progression. Single-molecule deep sequencing was performed on whole HBV genomes extracted from samples, including the liver explant, longitudinally collected from a subject with CHB over a 15-year period after liver transplantation. By employing novel bioinformatics methods, this analysis showed that the dynamics of the viral population across a period of changing treatment regimens was complex. The spHBV variants detected in the liver explant remained present posttransplantation, and a highly diverse novel spHBV population as well as variants with multiple deletions in the pre-S genes emerged. The identification of novel mutations outside the HBV reverse transcriptase gene that co-occurred with known drug resistance-associated mutations highlights the relevance of using full-genome deep sequencing and supports the hypothesis that drug resistance involves interactions across the full length of the HBV genome. IMPORTANCE Single-molecule sequencing allowed the characterization, in unprecedented detail, of the evolution of HBV populations and offered unique insights into the dynamics of defective and spHBV variants following liver transplantation and complex treatment regimens. This analysis also showed the rapid adaptation of HBV populations to treatment regimens with evolving drug resistance phenotypes and evidence of purifying selection across the whole genome. Finally, the new open-source bioinformatics tools with the capacity to easily identify potential spliced variants from deep sequencing data are freely available. PMID:27252524

Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS

PubMed Central

Zimmermann, Matthias; Escrig, Stéphane; Hübschmann, Thomas; Kirf, Mathias K.; Brand, Andreas; Inglis, R. Fredrik; Musat, Niculina; Müller, Susann; Meibom, Anders; Ackermann, Martin; Schreiber, Frank

2015-01-01

Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N2 and CO2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with 15N2 and 13CO2 under in situ conditions with and without NH4+. Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation 15N and 13C stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N2 in the absence of NH4+, but not in the presence of NH4+ as has previously been suggested. N2 and CO2 fixation were heterogeneous among cells and positively correlated indicating that N2 and CO2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature. PMID:25932020

Ultrafast single photon emitting quantum photonic structures based on a nano-obelisk.

PubMed

Kim, Je-Hyung; Ko, Young-Ho; Gong, Su-Hyun; Ko, Suk-Min; Cho, Yong-Hoon

2013-01-01

A key issue in a single photon source is fast and efficient generation of a single photon flux with high light extraction efficiency. Significant progress toward high-efficiency single photon sources has been demonstrated by semiconductor quantum dots, especially using narrow bandgap materials. Meanwhile, there are many obstacles, which restrict the use of wide bandgap semiconductor quantum dots as practical single photon sources in ultraviolet-visible region, despite offering free space communication and miniaturized quantum information circuits. Here we demonstrate a single InGaN quantum dot embedded in an obelisk-shaped GaN nanostructure. The nano-obelisk plays an important role in eliminating dislocations, increasing light extraction, and minimizing a built-in electric field. Based on the nano-obelisks, we observed nonconventional narrow quantum dot emission and positive biexciton binding energy, which are signatures of negligible built-in field in single InGaN quantum dots. This results in efficient and ultrafast single photon generation in the violet color region.

Single-Cell Quantitative PCR: Advances and Potential in Cancer Diagnostics.

PubMed

Ok, Chi Young; Singh, Rajesh R; Salim, Alaa A

2016-01-01

Tissues are heterogeneous in their components. If cells of interest are a minor population of collected tissue, it would be difficult to obtain genetic or genomic information of the interested cell population with conventional genomic DNA extraction from the collected tissue. Single-cell DNA analysis is important in the analysis of genetics of cell clonality, genetic anticipation, and single-cell DNA polymorphisms. Single-cell PCR using Single Cell Ampligrid/GeXP platform is described in this chapter.

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

PubMed Central

Chen, Zixi; Chen, Lei; Zhang, Weiwen

2017-01-01

Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented. PMID:28979258

Prevalence of multiple sclerosis in Health District III, Murcia, Spain.

PubMed

Candeliere-Merlicco, Antonio; Valero-Delgado, Francisco; Martínez-Vidal, Salvadora; Lastres-Arias, María Del Carmen; Aparicio-Castro, Eladio; Toledo-Romero, Francisco; Villaverde-González, Ramón

2016-09-01

The prevalence of multiple sclerosis (MS) varies throughout the world, and available epidemiological data suggest a progressively increasing prevalence of MS in Spain. The objective of this study was to calculate MS prevalence in Health District III of the autonomous community of Murcia in Spain. This is an observational, cross-sectional, descriptive study. The prevalence of MS in Health District III in the Region of Murcia, which includes the municipalities of Lorca, Totana, Águilas, Puerto Lumbreras and Aledo, was calculated from the total population (171,040 inhabitants), and among native Spanish citizens only (137,659 persons). Healthcare and demographic data were obtained from three sources: 1) OMI-AP: the local primary care computer system containing the medical records of all subscribers; 2) the medical record database of the Hospital Rafael Mendez (the single hospital in the district); and 3) the records of the AEMA III Multiple Sclerosis Association to which patients from this healthcare district belong. Data from these three sources were combined to check the accuracy and completeness of the patient records. The prevalence of MS among the general population of this district, including non-Spanish individuals, was 71.9 per 100,000 inhabitants (95% CI=60-85). Prevalence among the native Spanish population was 82.0 per 100,000 (95% CI=68-98). Considering prevalence by sex, it was 118.1 per 100,000 (95% CI: 95-146) in the female native Spanish population, and 45.4 per 100,000 (95% CI: 31-64) in the male native Spanish population. The prevalence in the native Spanish population in this district was calculated by sex and age (grouped by decades). A peak was observed among women aged between 20 and 29 years: 234.2 per 100,000 inhabitants (95% CI: 151-361). Our results suggest that the population in this healthcare district presents a risk of MS similar to that recently reported in other regions of Spain, which is higher than in previous decades. Copyright © 2016 Elsevier B.V. All rights reserved.

Radiocarbon Records of Fossil Fuel Emissions From Urban Trees in the Greater Salt Lake Valley From Mid-Century to Present.

NASA Astrophysics Data System (ADS)

Chritz, K.; Buchert, M.; Walker, J. C.; Mendoza, D.; Pataki, D. E.; Xu, X.; Lin, J. C.

2017-12-01

Generating long term records of fossil fuel emissions of urban environments is complicated by the fact that direct observations of emissions and urban atmospheric CO2 concentrations were only collected in the recent past. Radiocarbon (14C) in tree rings from urban trees can provide archives of fossil fuel emissions that may track population growth over time, as higher population density is typically correlated with increased vehicular traffic and associated CO2 emissions, which are radiocarbon dead. We present radiocarbon measurements (n=125) from five roadside green ash trees (Fraxinus pennsylvanica) located in three cities of northern Utah - Salt Lake City (urban, 2016 population: 193,744), Logan City (agricultural, 2016 population: 49,110) and Heber (rural, 2016 population: 14,969). Urban trees were cored in four cardinal directions and ring widths were measured and counted to establish a chronology. One ring from every third year in a single core from each tree was removed and holocellulose was extracted from bulk wood of individual rings for 14C analysis. Fraction CO2 from fossil fuel burning (CO2-ff) was calculated using a simple mass-balance calculation from measured 14C values and remote background atmospheric 14CO2 values for NH Zone 2. The data from all three cities indicate a general trend of increasing CO2-ff uptake by the trees from 1980s to present, as expected with increased population growth and vehicular traffic. However, records in all three cities show unique elevated CO2-ff prior to the 1980s, assuming similar climate patterns through time, diverging from historic population size. We employed atmospheric simulations from the STILT (Stochastic Time-Inverted Lagrangian Transport) models for each of these trees to create footprints to determine source areas for CO2. These footprints reveal that atmospheric sampling areas can be large for certain trees, and other sources of 14C dead carbon, such as coal and natural gas from industrial emissions, should also be considered when building these records.

Protecting single-photon entanglement with practical entanglement source

NASA Astrophysics Data System (ADS)

Zhou, Lan; Ou-Yang, Yang; Wang, Lei; Sheng, Yu-Bo

2017-06-01

Single-photon entanglement (SPE) is important for quantum communication and quantum information processing. However, SPE is sensitive to photon loss. In this paper, we discuss a linear optical amplification protocol for protecting SPE. Different from the previous protocols, we exploit the practical spontaneous parametric down-conversion (SPDC) source to realize the amplification, for the ideal entanglement source is unavailable in current quantum technology. Moreover, we prove that the amplification using the entanglement generated from SPDC source as auxiliary is better than the amplification assisted with single photons. The reason is that the vacuum state from SPDC source will not affect the amplification, so that it can be eliminated automatically. This protocol may be useful in future long-distance quantum communications.

Particle swarm optimization and its application in MEG source localization using single time sliced data

NASA Astrophysics Data System (ADS)

Lin, Juan; Liu, Chenglian; Guo, Yongning

2014-10-01

The estimation of neural active sources from the magnetoencephalography (MEG) data is a very critical issue for both clinical neurology and brain functions research. A widely accepted source-modeling technique for MEG involves calculating a set of equivalent current dipoles (ECDs). Depth in the brain is one of difficulties in MEG source localization. Particle swarm optimization(PSO) is widely used to solve various optimization problems. In this paper we discuss its ability and robustness to find the global optimum in different depths of the brain when using single equivalent current dipole (sECD) model and single time sliced data. The results show that PSO is an effective global optimization to MEG source localization when given one dipole in different depths.

Population genetics features for persistent, but transient, Botryllus schlosseri (Urochordata) congregations in a central Californian marina.

PubMed

Karahan, Arzu; Douek, Jacob; Paz, Guy; Rinkevich, Baruch

2016-08-01

The colonial tunicate Botryllus schlosseri is a globally distributed, invasive ascidian that has colonized the Californian coasts of the USA during the mid-late 1940s and has, since the late 1980s, spread north to Washington. This study analyzes the population genetic characteristics of transient populations residing at the Elkhorn Yacht-Club (EYC), in central California (seven sessions, 1996-2008), which suffered periodic catastrophes caused by episodic fresh-water floods and a single sampling session (in the year 2001) of five West-Coast populations using the mtDNA COI gene and five microsatellite markers. EYC microsatellite results were further compared with the closely situated but persistent population of the Santa Cruz Harbor (SCH) to understand the impact on EYC population regeneration processes after the 2005-flood catastrophe. All microsatellites were highly polymorphic, revealing a large number of unique alleles at different sampling dates. Whereas pairwise θ did not reveal significant differences between the EYC time-series samplings, the overall θ was significant, as it was between all the 2001 West Coast populations. The most likely cluster number was 3 for the EYC samples whereas two K values were obtained (2 and 5) for the 2001 samples. Tajima's D and Fu's/Fs tests did not reject the null hypothesis for COI neutral evolution, except for in the EYC-2000, 2007 and two 2001 samplings. The wide geographical range of the analyses has indicated that following the EYC 2005-flood catastrophe, newcomers could have originated from neighboring populations, from deep-water colonies that may have escaped the 2005 low salinity event, or less expectedly, from far away West-Coast populations, while revealing that the SCH population is the most probable source for the EYC population. Copyright © 2016 Elsevier Inc. All rights reserved.

Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

PubMed Central

Kussell, Edo

2017-01-01

Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness landscapes of arbitrary phenotypic traits, using genealogical data in the form of population lineage trees which can include phenotypic data of various kinds. Our inference methodology for fitness landscapes determines how reproductivity is correlated to cellular phenotypes, and provides a natural generalization of bulk growth rate measures for single-cell histories. Using this technique, we quantify the strength of selection acting on different cellular phenotypic traits within populations, which allows us to determine whether a change in population growth is caused by individual cells’ response, selection within a population, or by a mixture of these two processes. By applying these methods to single-cell time-lapse data of growing bacterial populations that express a resistance-conferring protein under antibiotic stress, we show how the distributions, fitness landscapes, and selection strength of single-cell phenotypes are affected by the drug. Our work provides a unified and practical framework for quantitative measurements of fitness landscapes and selection strength for any statistical quantities definable on lineages, and thus elucidates the adaptive significance of phenotypic states in time series data. The method is applicable in diverse fields, from single cell biology to stem cell differentiation and viral evolution. PMID:28267748

Tri-channel single-mode terahertz quantum cascade laser.

PubMed

Wang, Tao; Liu, Jun-Qi; Liu, Feng-Qi; Wang, Li-Jun; Zhang, Jin-Chuan; Wang, Zhan-Guo

2014-12-01

We report on a compact THz quantum cascade laser source emitting at, individually controllable, three different wavelengths (92.6, 93.9, and 95.1 μm). This multiwavelength laser array can be used as a prototype of the emission source of THz wavelength division multiplex (WDM) wireless communication system. The source consists of three tapered single-mode distributed feedback (DFB) terahertz quantum cascade lasers fabricated monolithically on a single chip. All array elements feature longitudinal as well as lateral single-mode in the entire injection range. The peak output powers of individual lasers are 42, 73, and 37 mW at 10 K, respectively.

Thin Film CuInS2 Prepared by Spray Pyrolysis with Single-Source Precursors

NASA Technical Reports Server (NTRS)

Jin, Michael H.; Banger, Kulinder K.; Harris, Jerry D.; Cowen, Jonathan E.; Hepp, Aloysius F.; Lyons, Valerie (Technical Monitor)

2002-01-01

Both horizontal hot-wall and vertical cold-wall atmospheric chemical spray pyrolysis processes deposited near single-phase stoichiometric CuInS2 thin films. Single-source precursors developed for ternary chalcopyrite materials were used for this study, and a new liquid phase single-source precursor was tested with a vertical cold-wall reactor. The depositions were carried out under an argon atmosphere, and the substrate temperature was kept at 400 C. Columnar grain structure was obtained with vapor deposition, and the granular structure was obtained with (liquid) droplet deposition. Conductive films were deposited with planar electrical resistivities ranging from 1 to 30 Omega x cm.

Fused Silica Ion Trap Chip with Efficient Optical Collection System for Timekeeping, Sensing, and Emulation

DTIC Science & Technology

2015-01-22

applications in fast single photon sources, quantum repeater circuitry, and high fidelity remote entanglement of atoms for quantum information protocols. We...fluorescence for motion/force sensors through Doppler velocimetry; and for the efficient collection of single photons from trapped ions for...Doppler velocimetry; and for the efficient collection of single photons from trapped ions for applications in fast single photon sources, quantum

75 FR 62840 - Award of a Single-Source Expansion Supplement to the University of Southern Maine, Muskie School...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-13

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Administration for Children and Families Award of a Single...: Children's Bureau, ACYF, ACF, HHS. ACTION: Notice. CFDA Number: 93.658. Legislative Authority: Section 476..., the Administration for Children and Families (ACF), Children's Bureau (CB) is awarding a single-source...

Fast Purcell-enhanced single photon source in 1,550-nm telecom band from a resonant quantum dot-cavity coupling

PubMed Central

Birowosuto, Muhammad Danang; Sumikura, Hisashi; Matsuo, Shinji; Taniyama, Hideaki; van Veldhoven, Peter J.; Nötzel, Richard; Notomi, Masaya

2012-01-01

High-bit-rate nanocavity-based single photon sources in the 1,550-nm telecom band are challenges facing the development of fibre-based long-haul quantum communication networks. Here we report a very fast single photon source in the 1,550-nm telecom band, which is achieved by a large Purcell enhancement that results from the coupling of a single InAs quantum dot and an InP photonic crystal nanocavity. At a resonance, the spontaneous emission rate was enhanced by a factor of 5 resulting a record fast emission lifetime of 0.2 ns at 1,550 nm. We also demonstrate that this emission exhibits an enhanced anti-bunching dip. This is the first realization of nanocavity-enhanced single photon emitters in the 1,550-nm telecom band. This coupled quantum dot cavity system in the telecom band thus provides a bright high-bit-rate non-classical single photon source that offers appealing novel opportunities for the development of a long-haul quantum telecommunication system via optical fibres. PMID:22432053

Fast Purcell-enhanced single photon source in 1,550-nm telecom band from a resonant quantum dot-cavity coupling.

PubMed

Birowosuto, Muhammad Danang; Sumikura, Hisashi; Matsuo, Shinji; Taniyama, Hideaki; van Veldhoven, Peter J; Nötzel, Richard; Notomi, Masaya

2012-01-01

High-bit-rate nanocavity-based single photon sources in the 1,550-nm telecom band are challenges facing the development of fibre-based long-haul quantum communication networks. Here we report a very fast single photon source in the 1,550-nm telecom band, which is achieved by a large Purcell enhancement that results from the coupling of a single InAs quantum dot and an InP photonic crystal nanocavity. At a resonance, the spontaneous emission rate was enhanced by a factor of 5 resulting a record fast emission lifetime of 0.2 ns at 1,550 nm. We also demonstrate that this emission exhibits an enhanced anti-bunching dip. This is the first realization of nanocavity-enhanced single photon emitters in the 1,550-nm telecom band. This coupled quantum dot cavity system in the telecom band thus provides a bright high-bit-rate non-classical single photon source that offers appealing novel opportunities for the development of a long-haul quantum telecommunication system via optical fibres.

Separating Turbofan Engine Noise Sources Using Auto and Cross Spectra from Four Microphones

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2008-01-01

The study of core noise from turbofan engines has become more important as noise from other sources such as the fan and jet were reduced. A multiple-microphone and acoustic-source modeling method to separate correlated and uncorrelated sources is discussed. The auto- and cross spectra in the frequency range below 1000 Hz are fitted with a noise propagation model based on a source couplet consisting of a single incoherent monopole source with a single coherent monopole source or a source triplet consisting of a single incoherent monopole source with two coherent monopole point sources. Examples are presented using data from a Pratt& Whitney PW4098 turbofan engine. The method separates the low-frequency jet noise from the core noise at the nozzle exit. It is shown that at low power settings, the core noise is a major contributor to the noise. Even at higher power settings, it can be more important than jet noise. However, at low frequencies, uncorrelated broadband noise and jet noise become the important factors as the engine power setting is increased.

Energy Harvesting Research: The Road from Single Source to Multisource.

PubMed

Bai, Yang; Jantunen, Heli; Juuti, Jari

2018-06-07

Energy harvesting technology may be considered an ultimate solution to replace batteries and provide a long-term power supply for wireless sensor networks. Looking back into its research history, individual energy harvesters for the conversion of single energy sources into electricity are developed first, followed by hybrid counterparts designed for use with multiple energy sources. Very recently, the concept of a truly multisource energy harvester built from only a single piece of material as the energy conversion component is proposed. This review, from the aspect of materials and device configurations, explains in detail a wide scope to give an overview of energy harvesting research. It covers single-source devices including solar, thermal, kinetic and other types of energy harvesters, hybrid energy harvesting configurations for both single and multiple energy sources and single material, and multisource energy harvesters. It also includes the energy conversion principles of photovoltaic, electromagnetic, piezoelectric, triboelectric, electrostatic, electrostrictive, thermoelectric, pyroelectric, magnetostrictive, and dielectric devices. This is one of the most comprehensive reviews conducted to date, focusing on the entire energy harvesting research scene and providing a guide to seeking deeper and more specific research references and resources from every corner of the scientific community. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of dislocation pile-up on size-dependent yield strength in finite single-crystal micro-samples

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

Pan, Bo; Shibutani, Yoji, E-mail: sibutani@mech.eng.osaka-u.ac.jp; Zhang, Xu

2015-07-07

Recent research has explained that the steeply increasing yield strength in metals depends on decreasing sample size. In this work, we derive a statistical physical model of the yield strength of finite single-crystal micro-pillars that depends on single-ended dislocation pile-up inside the micro-pillars. We show that this size effect can be explained almost completely by considering the stochastic lengths of the dislocation source and the dislocation pile-up length in the single-crystal micro-pillars. The Hall–Petch-type relation holds even in a microscale single-crystal, which is characterized by its dislocation source lengths. Our quantitative conclusions suggest that the number of dislocation sources andmore » pile-ups are significant factors for the size effect. They also indicate that starvation of dislocation sources is another reason for the size effect. Moreover, we investigated the explicit relationship between the stacking fault energy and the dislocation “pile-up” effect inside the sample: materials with low stacking fault energy exhibit an obvious dislocation pile-up effect. Our proposed physical model predicts a sample strength that agrees well with experimental data, and our model can give a more precise prediction than the current single arm source model, especially for materials with low stacking fault energy.« less

Method of Promoting Single Crystal Growth During Melt Growth of Semiconductors

NASA Technical Reports Server (NTRS)

Su, Ching-Hua (Inventor)

2013-01-01

The method of the invention promotes single crystal growth during fabrication of melt growth semiconductors. A growth ampoule and its tip have a semiconductor source material placed therein. The growth ampoule is placed in a first thermal environment that raises the temperature of the semiconductor source material to its liquidus temperature. The growth ampoule is then transitioned to a second thermal environment that causes the semiconductor source material in the growth ampoule's tip to attain a temperature that is below the semiconductor source material's solidus temperature. The growth ampoule so-transitioned is then mechanically perturbed to induce single crystal growth at the growth ampoule's tip.

Single-source mechanical loading system produces biaxial stresses in cylinders

NASA Technical Reports Server (NTRS)

Flower, J. F.; Stafford, R. L.

1967-01-01

Single-source mechanical loading system proportions axial-to-hoop tension loads applied to cylindrical specimens. The system consists of hydraulic, pneumatic, and lever arrangements which produce biaxial loading ratios.

Reducing single-use plastic shopping bags in the USA.

PubMed

Wagner, Travis P

2017-12-01

In the USA, local governments have the primary responsibility to manage MSW. However, local governments lack the authority to explicitly shift costs or responsibility back onto the producer for specific problem wastes. A particularly problematic waste for local governments is the single-use plastic bag. In 2014, in the USA, 103.465 billion single-use plastic shopping bags were consumed. Because of their extremely low recyclability rate, plastic bags remain a significant source of land-based litter and marine debris and impair stormwater management systems. They also reduce the effectiveness of automated recycling systems. In response, local governments increasingly have adopted a variety of measures specifically intended to reduce the store-level consumption of single-use shopping bags in 5 major categories: bans, imposition of fees and taxes, establishing minimum product design of bags, requiring consumer education, and mandating retailer take-back programs. As of September 2017, there were 271 local governments in the USA with plastic bag ordinances covering 9.7% of the nation's population. The majority (95%) of the ordinances is a ban on single-use plastic bags; 56.9% of these bans also include a mandatory fee on paper and/or reusable bags. For the fee-based ordinances, the mode is $0.10 per bag; every tax/fee ordinance allows retailers to retain some or all the collected fee. As local governments continue to increase their actions on plastic bags, 11 states have enacted laws to prohibit local governments from regulating single-use plastic bags. Because of the success with single-use bags, local governments are also enacting similar ordinances on single-use expanded polystyrene consumer products and other single-use plastic products. Copyright © 2017 Elsevier Ltd. All rights reserved.

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

PubMed

Lan, Freeman; Demaree, Benjamin; Ahmed, Noorsher; Abate, Adam R

2017-07-01

The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

The design of a multisource americium-beryllium (Am-Be) neutron irradiation facility using MCNP for the neutronic performance calculation.

PubMed

Sogbadji, R B M; Abrefah, R G; Nyarko, B J B; Akaho, E H K; Odoi, H C; Attakorah-Birinkorang, S

2014-08-01

The americium-beryllium neutron irradiation facility at the National Nuclear Research Institute (NNRI), Ghana, was re-designed with four 20 Ci sources using Monte Carlo N-Particle (MCNP) code to investigate the maximum amount of flux that is produced by the combined sources. The results were compared with a single source Am-Be irradiation facility. The main objective was to enable us to harness the maximum amount of flux for the optimization of neutron activation analysis and to enable smaller sample sized samples to be irradiated. Using MCNP for the design construction and neutronic performance calculation, it was realized that the single-source Am-Be design produced a thermal neutron flux of (1.8±0.0007)×10(6) n/cm(2)s and the four-source Am-Be design produced a thermal neutron flux of (5.4±0.0007)×10(6) n/cm(2)s which is a factor of 3.5 fold increase compared to the single-source Am-Be design. The criticality effective, k(eff), of the single-source and the four-source Am-Be designs were found to be 0.00115±0.0008 and 0.00143±0.0008, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis.

PubMed

Jena, Kshirod K; Hechanova, Sherry Lou; Verdeprado, Holden; Prahalada, G D; Kim, Sung-Ryul

2017-11-01

A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BC 3 F 5 ) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.

Assessing the number of fire fatalities in a defined population.

PubMed

Jonsson, Anders; Bergqvist, Anders; Andersson, Ragnar

2015-12-01

Fire-related fatalities and injuries have become a growing governmental concern in Sweden, and a national vision zero strategy has been adopted stating that nobody should get killed or seriously injured from fires. There is considerable uncertainty, however, regarding the numbers of both deaths and injuries due to fires. Different national sources present different numbers, even on deaths, which obstructs reliable surveillance of the problem over time. We assume the situation is similar in other countries. This study seeks to assess the true number of fire-related deaths in Sweden by combining sources, and to verify the coverage of each individual source. By doing so, we also wish to demonstrate the possibilities of improved surveillance practices. Data from three national sources were collected and matched; a special database on fatal fires held by The Swedish Contingencies Agency (nationally responsible for fire prevention), a database on forensic medical examinations held by the National Board of Forensic Medicine, and the cause of death register held by the Swedish National Board of Health and Welfare. The results disclose considerable underreporting in the single sources. The national database on fatal fires, serving as the principal source for policy making on fire prevention matters, underestimates the true situation by 20%. Its coverage of residential fires appears to be better than other fires. Systematic safety work and informed policy-making presuppose access to correct and reliable numbers. By combining several different sources, as suggested in this study, the national database on fatal fires is now considerably improved and includes regular matching with complementary sources.

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

PubMed

Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

2017-10-27

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

PubMed Central

Ryall, Ben; Eydallin, Gustavo

2012-01-01

Summary: Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior. PMID:22933562

EHDViz: clinical dashboard development using open-source technologies.

PubMed

Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

2016-03-24

To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14,221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Falcon: a highly flexible open-source software for closed-loop neuroscience.

PubMed

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Falcon: a highly flexible open-source software for closed-loop neuroscience

NASA Astrophysics Data System (ADS)

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Single Quantum Dot with Microlens and 3D-Printed Micro-objective as Integrated Bright Single-Photon Source

PubMed Central

2017-01-01

Integrated single-photon sources with high photon-extraction efficiency are key building blocks for applications in the field of quantum communications. We report on a bright single-photon source realized by on-chip integration of a deterministic quantum dot microlens with a 3D-printed multilens micro-objective. The device concept benefits from a sophisticated combination of in situ 3D electron-beam lithography to realize the quantum dot microlens and 3D femtosecond direct laser writing for creation of the micro-objective. In this way, we obtain a high-quality quantum device with broadband photon-extraction efficiency of (40 ± 4)% and high suppression of multiphoton emission events with g(2)(τ = 0) < 0.02. Our results highlight the opportunities that arise from tailoring the optical properties of quantum emitters using integrated optics with high potential for the further development of plug-and-play fiber-coupled single-photon sources. PMID:28670600

Investigating the Keratinolytic Activities of the Bacteria Isolated from Different Sources

NASA Astrophysics Data System (ADS)

Chen, S. X.

2017-12-01

Background InformationThe development of microbial keratinase has gained increasing attention over the million tons of keratinous wastes generated by the worldwide livestock population. Keratinous wastes not only serve as the niche for pathogenic microorganisms, but also they collapse environmental balance for being the source of air, soil, and water pollutions. Conversely, microbial keratinases can convert the unexploited keratinous wastes into bioaccessible animal feed. However, because of the recalcitrant structure of keratin, the complete keratin degradation is difficult to achieve with one keratinase as opposed to recombinant keratinases. Therefore, this study is designed to isolate the bacteria from different sources and to evaluate their keratinolytic activities using azokeratin substrates. Materials and Methods Soil, horse hooves, penguin stool, and chicken stool are collected from different sites. These samples are serially diluted and then streaked on feather-meal agar plates. Single colonies are screened for the ability to hydrolyze keratin. The isolate of single colonies is cultivated in a whole-feather medium. The sample is then centrifuged, and the supernatant is used for crude enzyme preparation. Azokeratin is synthesized by coupling bristle keratin with diazotized laurent's acid, and it is used as a substrate for assaying keratinase activity by using a spectrophotometer. ConclusionThis study will compare the keratinase activities on bristle azokeratin substrates from three different samples and thus evaluate the bacterium with the best ability to hydrolyze keratin amongst the three. Further steps will be taken to produce a blend of enzymes generated and select the optimum combination that can most efficiently degrade keratin.

The voice of Holland: Dutch public and patient's opinion favours single-port laparoscopy.

PubMed

Fransen, Sofie Af; Broeders, Epm; Stassen, Lps; Bouvy, Nd

2014-07-01

Single-port laparoscopy is prospected as the future of minimal invasive surgery. It is hypothesised to cause less post operative pain, with a shorter hospitalisation period and improved cosmetic results. Population- and patient-based opinion is important for the adaptation of new techniques. This study aimed to assess the opinion and perception of a healthy population and a patient population on single-port laparoscopy compared with conventional laparoscopy. An anonymous 33-item questionnaire, describing conventional and single-port laparoscopy, was given to 101 patients and 104 healthy volunteers. The survey participants (median age 44 years; range 17-82 years) were asked questions about their personal situation and their expectations and perceptions of the two different surgical techniques; conventional multi-port laparoscopy and single-port laparoscopy. A total of 72% of the participants had never heard of single-port laparoscopy before. The most important concern in both groups was the risk of surgical complications. When complication risks remain similar, 80% prefers single-port laparoscopy to conventional laparoscopy. When the risk of complications increases from 1% to 10%, 43% of all participants prefer single-port laparoscopy. A total of 70% of the participants are prepared to receive treatment in another hospital if single-port surgery is not performed in their hometown hospital. The preference for single-port approach was higher in the female population. Although cure and safety remain the main concerns, the population and patients group have a favourable perception of single-port surgery. The impact of public opinion and patient perception towards innovative techniques is undeniable. If the safety of the two different procedures is similar, this study shows a positive attitude of both participant groups in favour of single-port laparoscopy. However, solid scientific proof for the safety and feasibility of this new surgical technique needs to be obtained before this procedure can be implemented into everyday practice.

Minimizing the Diameter of a Network Using Shortcut Edges

NASA Astrophysics Data System (ADS)

Demaine, Erik D.; Zadimoghaddam, Morteza

We study the problem of minimizing the diameter of a graph by adding k shortcut edges, for speeding up communication in an existing network design. We develop constant-factor approximation algorithms for different variations of this problem. We also show how to improve the approximation ratios using resource augmentation to allow more than k shortcut edges. We observe a close relation between the single-source version of the problem, where we want to minimize the largest distance from a given source vertex, and the well-known k-median problem. First we show that our constant-factor approximation algorithms for the general case solve the single-source problem within a constant factor. Then, using a linear-programming formulation for the single-source version, we find a (1 + ɛ)-approximation using O(klogn) shortcut edges. To show the tightness of our result, we prove that any ({3 over 2}-ɛ)-approximation for the single-source version must use Ω(klogn) shortcut edges assuming P ≠ NP.

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.

Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons

PubMed Central

Laloi, G.; Montarry, J.; Guibert, M.; Andrivon, D.; Michot, D.

2016-01-01

ABSTRACT Ascochyta blight, caused by the necrotrophic ascomycete Didymella pinodes, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520 D. pinodes strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses. IMPORTANCE Ascochyta blight, caused by Didymella pinodes, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. PMID:27208102

Scleroderma prevalence: demographic variations in a population-based sample.

PubMed

Bernatsky, S; Joseph, L; Pineau, C A; Belisle, P; Hudson, M; Clarke, A E

2009-03-15

To estimate the prevalence of systemic sclerosis (SSc) using population-based administrative data, and to assess the sensitivity of case ascertainment approaches. We ascertained SSc cases from Quebec physician billing and hospitalization databases (covering approximately 7.5 million individuals). Three case definition algorithms were compared, and statistical methods accounting for imperfect case ascertainment were used to estimate SSc prevalence and case ascertainment sensitivity. A hierarchical Bayesian latent class regression model that accounted for possible between-test dependence conditional on disease status estimated the effect of patient characteristics on SSc prevalence and the sensitivity of the 3 ascertainment algorithms. Accounting for error inherent in both the billing and the hospitalization data, we estimated SSc prevalence in 2003 at 74.4 cases per 100,000 women (95% credible interval [95% CrI] 69.3-79.7) and 13.3 cases per 100,000 men (95% CrI 11.1-16.1). Prevalence was higher for older individuals, particularly in urban women (161.2 cases per 100,000, 95% CrI 148.6-175.0). Prevalence was lowest in young men (in rural areas, as low as 2.8 cases per 100,000, 95% CrI 1.4-4.8). In general, no single algorithm was very sensitive, with point estimates for sensitivity ranging from 20-73%. We found marked differences in SSc prevalence according to age, sex, and region. In general, no single case ascertainment approach was very sensitive for SSc. Therefore, using data from multiple sources, with adjustment for the imperfect nature of each, is an important strategy in population-based studies of SSc and similar conditions.

Quantum dynamics of a BEC interacting with a single-mode quantized field under the influence of a dissipation process: thermal and squeezed vacuum reservoirs

NASA Astrophysics Data System (ADS)

Ghasemian, E.; Tavassoly, M. K.

2017-09-01

In this paper we consider a system consisting of a number of two-level atoms in a Bose-Einstein condensate (BEC) and a single-mode quantized field, which interact with each other in the presence of two different damping sources, i.e. cavity and atomic reservoirs. The reservoirs which we consider here are thermal and squeezed vacuum ones corresponding to field and atom modes. Strictly speaking, by considering both types of reservoirs for each of the atom and field modes, we investigate the quantum dynamics of the interacting bosons in the system. Then, via solving the quantum Langevin equations for such a dissipative BEC system, we obtain analytical expressions for the time dependence of atomic population inversion, mean atom as well as photon number and quadrature squeezing in the field and atom modes. Our investigations demonstrate that for modeling the real physical systems, considering the dissipation effects is essential. Also, numerical calculations which are presented show that the atomic population inversion, the mean number of atoms in the BEC and the photons in the cavity possess damped oscillatory behavior due to the presence of reservoirs. In addition, non-classical squeezing effects in the field quadrature can be observed especially when squeezed vacuum reservoirs are taken into account. As an outstanding property of this model, we may refer to the fact that one can extract the atom-field coupling constant from the frequency of oscillations in the mentioned quantities such as atomic population inversion.

Partial Failure of Milk Pasteurization as a Risk for the Transmission of Campylobacter From Cattle to Humans

PubMed Central

Fernandes, Anand M.; Balasegaram, Sooria; Willis, Caroline; Wimalarathna, Helen M. L.; Maiden, Martin C.; McCarthy, Noel D.

2015-01-01

Background. Cattle are the second most common source of human campylobacteriosis. However, routes to account for this scale of transmission have not been identified. In contrast to chicken, red meat is not heavily contaminated at point of sale. Although effective pasteurization prevents milk-borne infection, apparently sporadic infections may include undetected outbreaks from raw or perhaps incompletely pasteurized milk. Methods. A rise in Campylobacter gastroenteritis in an isolated population was investigated using whole-genome sequencing (WGS), an epidemiological study, and environmental investigations. Results. A single strain was identified in 20 cases, clearly distinguishable from other local strains and a reference population by WGS. A case-case analysis showed association of infection with the outbreak strain and milk from a single dairy (odds ratio, 8; Fisher exact test P value = .023). Despite temperature records indicating effective pasteurization, mechanical faults likely to lead to incomplete pasteurization of part of the milk were identified by further testing and examination of internal components of dairy equipment. Conclusions. Here, milk distribution concentrated on a small area, including school-aged children with low background incidence of campylobacteriosis, facilitated outbreak identification. Low-level contamination of widely distributed milk would not produce as detectable an outbreak signal. Such hidden outbreaks may contribute to the substantial burden of apparently sporadic Campylobacter from cattle where transmission routes are not certain. The effective discrimination of outbreak isolates from a reference population using WGS shows that integrating these data and approaches into surveillance could support the detection as well as investigation of such outbreaks. PMID:26063722

Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs.

PubMed

Hao, Wei-Qi; Liu, Jing; Jiang, Li; Han, Jun-Ping; Wang, Ling; Li, Jiu-Ling; Ma, Quan; Liu, Chao; Wang, Hui-Jun; Li, Cai-Xia

2018-06-07

Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

The role of local populations within a landscape context: Defining and classifying sources and sinks

USGS Publications Warehouse

Runge, J.P.; Runge, M.C.; Nichols, J.D.

2006-01-01

The interaction of local populations has been the focus of an increasing number of studies in the past 30 years. The study of source-sink dynamics has especially generated much interest. Many of the criteria used to distinguish sources and sinks incorporate the process of apparent survival (i.e., the combined probability of true survival and site fidelity) but not emigration. These criteria implicitly treat emigration as mortality, thus biasing the classification of sources and sinks in a manner that could lead to flawed habitat management. Some of the same criteria require rather restrictive assumptions about population equilibrium that, when violated, can also generate misleading inference. Here, we expand on a criterion (denoted ?contribution? or Cr) that incorporates successful emigration in differentiating sources and sinks and that makes no restrictive assumptions about dispersal or equilibrium processes in populations of interest. The metric Cr is rooted in the theory of matrix population models, yet it also contains clearly specified parameters that have been estimated in previous empirical research. We suggest that estimates of emigration are important for delineating sources and sinks and, more generally, for evaluating how local populations interact to generate overall system dynamics. This suggestion has direct implications for issues such as species conservation and habitat management.

Factors affecting GEBV accuracy with single-step Bayesian models.

PubMed

Zhou, Lei; Mrode, Raphael; Zhang, Shengli; Zhang, Qin; Li, Bugao; Liu, Jian-Feng

2018-01-01

A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated. Three models were implemented to analyze the simulated data: single-step genomic best linear unbiased prediction (GBLUP; SSGBLUP), single-step BayesA (SS-BayesA), and single-step BayesB (SS-BayesB). According to our results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for ungenotyped animals than for genotyped animals. SS-BayesA/BayesB showed an obvious advantage over SSGBLUP with the scenarios of 5 and 50 QTL. SS-BayesB model obtained the lowest accuracy with the 500 QTL in the simulation. SS-BayesA model was the most efficient and robust considering all QTL scenarios. Generally, both the relationships between training and validation populations and LD between markers and QTL contributed to GEBV accuracy in the single-step analysis, and the advantages of single-step Bayesian models were more apparent when the trait is controlled by fewer QTL.

Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations.

PubMed

Gómez-Villafuertes, Rosa; Paniagua-Herranz, Lucía; Gascon, Sergio; de Agustín-Durán, David; Ferreras, María de la O; Gil-Redondo, Juan Carlos; Queipo, María José; Menendez-Mendez, Aida; Pérez-Sen, Ráquel; Delicado, Esmerilda G; Gualix, Javier; Costa, Marcos R; Schroeder, Timm; Miras-Portugal, María Teresa; Ortega, Felipe

2017-12-16

Understanding the mechanisms that control critical biological events of neural cell populations, such as proliferation, differentiation, or cell fate decisions, will be crucial to design therapeutic strategies for many diseases affecting the nervous system. Current methods to track cell populations rely on their final outcomes in still images and they generally fail to provide sufficient temporal resolution to identify behavioral features in single cells. Moreover, variations in cell death, behavioral heterogeneity within a cell population, dilution, spreading, or the low efficiency of the markers used to analyze cells are all important handicaps that will lead to incomplete or incorrect read-outs of the results. Conversely, performing live imaging and single cell tracking under appropriate conditions represents a powerful tool to monitor each of these events. Here, a time-lapse video-microscopy protocol, followed by post-processing, is described to track neural populations with single cell resolution, employing specific software. The methods described enable researchers to address essential questions regarding the cell biology and lineage progression of distinct neural populations.

Analyzing Genetic Diversity for Virulence and Resistance Phenotypes in Populations of Stem Rust (Puccinia graminis f. sp. secalis) and Winter Rye (Secale cereale).

PubMed

Miedaner, Thomas; Schmitt, Ann-Kristin; Klocke, Bettina; Schmiedchen, Brigitta; Wilde, Peer; Spieß, Hartmut; Szabo, Lilla; Koch, Silvia; Flath, Kerstin

2016-11-01

Stem rust (Puccinia graminis f. sp. secalis) leads to considerable yield losses in rye-growing areas with continental climate, from Eastern Germany to Siberia. For implementing resistance breeding, it is of utmost importance to (i) analyze the diversity of stem rust populations in terms of pathotypes (= virulence combinations) and (ii) identify resistance sources in winter rye populations. We analyzed 323 single-uredinial isolates mainly collected from German rye-growing areas across 3 years for their avirulence/virulence on 15 rye inbred differentials. Out of these, 226 pathotypes were detected and only 56 pathotypes occurred more than once. This high diversity was confirmed by a Simpson index of 1.0, a high Shannon index (5.27), and an evenness index of 0.97. In parallel, we investigated stem rust resistance among and within 121 heterogeneous rye populations originating mainly from Russia, Poland, Austria, and the United States across 3 to 15 environments (location-year combinations). While German rye populations had an average stem rust severity of 49.7%, 23 nonadapted populations were significantly (P < 0.01) more resistant with a stem rust severity ranging from 3 to 40%. Out of these, two modern Russian breeding populations and two old Austrian landraces were the best harboring 32 to 70% fully resistant plants across 8 to 10 environments. These populations with the lowest disease severity in adult-plant stage in the field also displayed resistance in leaf segment tests. In conclusion, stem rust populations are highly diverse and the majority of resistances in rye populations seems to be race specific.

Accuracy of genomic prediction using deregressed breeding values estimated from purebred and crossbred offspring phenotypes in pigs.

PubMed

Hidalgo, A M; Bastiaansen, J W M; Lopes, M S; Veroneze, R; Groenen, M A M; de Koning, D-J

2015-07-01

Genomic selection is applied to dairy cattle breeding to improve the genetic progress of purebred (PB) animals, whereas in pigs and poultry the target is a crossbred (CB) animal for which a different strategy appears to be needed. The source of information used to estimate the breeding values, i.e., using phenotypes of CB or PB animals, may affect the accuracy of prediction. The objective of our study was to assess the direct genomic value (DGV) accuracy of CB and PB pigs using different sources of phenotypic information. Data used were from 3 populations: 2,078 Dutch Landrace-based, 2,301 Large White-based, and 497 crossbreds from an F1 cross between the 2 lines. Two female reproduction traits were analyzed: gestation length (GLE) and total number of piglets born (TNB). Phenotypes used in the analyses originated from offspring of genotyped individuals. Phenotypes collected on CB and PB animals were analyzed as separate traits using a single-trait model. Breeding values were estimated separately for each trait in a pedigree BLUP analysis and subsequently deregressed. Deregressed EBV for each trait originating from different sources (CB or PB offspring) were used to study the accuracy of genomic prediction. Accuracy of prediction was computed as the correlation between DGV and the DEBV of the validation population. Accuracy of prediction within PB populations ranged from 0.43 to 0.62 across GLE and TNB. Accuracies to predict genetic merit of CB animals with one PB population in the training set ranged from 0.12 to 0.28, with the exception of using the CB offspring phenotype of the Dutch Landrace that resulted in an accuracy estimate around 0 for both traits. Accuracies to predict genetic merit of CB animals with both parental PB populations in the training set ranged from 0.17 to 0.30. We conclude that prediction within population and trait had good predictive ability regardless of the trait being the PB or CB performance, whereas using PB population(s) to predict genetic merit of CB animals had zero to moderate predictive ability. We observed that the DGV accuracy of CB animals when training on PB data was greater than or equal to training on CB data. However, when results are corrected for the different levels of reliabilities in the PB and CB training data, we showed that training on CB data does outperform PB data for the prediction of CB genetic merit, indicating that more CB animals should be phenotyped to increase the reliability and, consequently, accuracy of DGV for CB genetic merit.

Efficient fiber-coupled single-photon source based on quantum dots in a photonic-crystal waveguide

PubMed Central

DAVEAU, RAPHAËL S.; BALRAM, KRISHNA C.; PREGNOLATO, TOMMASO; LIU, JIN; LEE, EUN H.; SONG, JIN D.; VERMA, VARUN; MIRIN, RICHARD; NAM, SAE WOO; MIDOLO, LEONARDO; STOBBE, SØREN; SRINIVASAN, KARTIK; LODAHL, PETER

2017-01-01

Many photonic quantum information processing applications would benefit from a high brightness, fiber-coupled source of triggered single photons. Here, we present a fiber-coupled photonic-crystal waveguide single-photon source relying on evanescent coupling of the light field from a tapered out-coupler to an optical fiber. A two-step approach is taken where the performance of the tapered out-coupler is recorded first on an independent device containing an on-chip reflector. Reflection measurements establish that the chip-to-fiber coupling efficiency exceeds 80 %. The detailed characterization of a high-efficiency photonic-crystal waveguide extended with a tapered out-coupling section is then performed. The corresponding overall single-photon source efficiency is 10.9 % ± 2.3 %, which quantifies the success probability to prepare an exciton in the quantum dot, couple it out as a photon in the waveguide, and subsequently transfer it to the fiber. The applied out-coupling method is robust, stable over time, and broadband over several tens of nanometers, which makes it a highly promising pathway to increase the efficiency and reliability of planar chip-based single-photon sources. PMID:28584859

Systematic study of target localization for bioluminescence tomography guided radiation therapy

PubMed Central

Yu, Jingjing; Zhang, Bin; Iordachita, Iulian I.; Reyes, Juvenal; Lu, Zhihao; Brock, Malcolm V.; Patterson, Michael S.; Wong, John W.

2016-01-01

Purpose: To overcome the limitation of CT/cone-beam CT (CBCT) in guiding radiation for soft tissue targets, the authors developed a spectrally resolved bioluminescence tomography (BLT) system for the small animal radiation research platform. The authors systematically assessed the performance of the BLT system in terms of target localization and the ability to resolve two neighboring sources in simulations, tissue-mimicking phantom, and in vivo environments. Methods: Multispectral measurements acquired in a single projection were used for the BLT reconstruction. The incomplete variables truncated conjugate gradient algorithm with an iterative permissible region shrinking strategy was employed as the optimization scheme to reconstruct source distributions. Simulation studies were conducted for single spherical sources with sizes from 0.5 to 3 mm radius at depth of 3–12 mm. The same configuration was also applied for the double source simulation with source separations varying from 3 to 9 mm. Experiments were performed in a standalone BLT/CBCT system. Two self-illuminated sources with 3 and 4.7 mm separations placed inside a tissue-mimicking phantom were chosen as the test cases. Live mice implanted with single-source at 6 and 9 mm depth, two sources at 3 and 5 mm separation at depth of 5 mm, or three sources in the abdomen were also used to illustrate the localization capability of the BLT system for multiple targets in vivo. Results: For simulation study, approximate 1 mm accuracy can be achieved at localizing center of mass (CoM) for single-source and grouped CoM for double source cases. For the case of 1.5 mm radius source, a common tumor size used in preclinical study, their simulation shows that for all the source separations considered, except for the 3 mm separation at 9 and 12 mm depth, the two neighboring sources can be resolved at depths from 3 to 12 mm. Phantom experiments illustrated that 2D bioluminescence imaging failed to distinguish two sources, but BLT can provide 3D source localization with approximately 1 mm accuracy. The in vivo results are encouraging that 1 and 1.7 mm accuracy can be attained for the single-source case at 6 and 9 mm depth, respectively. For the 2 sources in vivo study, both sources can be distinguished at 3 and 5 mm separations, and approximately 1 mm localization accuracy can also be achieved. Conclusions: This study demonstrated that their multispectral BLT/CBCT system could be potentially applied to localize and resolve multiple sources at wide range of source sizes, depths, and separations. The average accuracy of localizing CoM for single-source and grouped CoM for double sources is approximately 1 mm except deep-seated target. The information provided in this study can be instructive to devise treatment margins for BLT-guided irradiation. These results also suggest that the 3D BLT system could guide radiation for the situation with multiple targets, such as metastatic tumor models. PMID:27147371

A Chandra ACIS Study of 30 Doradus. II. X-Ray Point Sources in the Massive Star Cluster R136 and Beyond

NASA Astrophysics Data System (ADS)

Townsley, Leisa K.; Broos, Patrick S.; Feigelson, Eric D.; Garmire, Gordon P.; Getman, Konstantin V.

2006-04-01

We have studied the X-ray point-source population of the 30 Doradus (30 Dor) star-forming complex in the Large Magellanic Cloud using high spatial resolution X-ray images and spatially resolved spectra obtained with the Advanced CCD Imaging Spectrometer (ACIS) on board the Chandra X-Ray Observatory. Here we describe the X-ray sources in a 17'×17' field centered on R136, the massive star cluster at the center of the main 30 Dor nebula. We detect 20 of the 32 Wolf-Rayet stars in the ACIS field. The cluster R136 is resolved at the subarcsecond level into almost 100 X-ray sources, including many typical O3-O5 stars, as well as a few bright X-ray sources previously reported. Over 2 orders of magnitude of scatter in LX is seen among R136 O stars, suggesting that X-ray emission in the most massive stars depends critically on the details of wind properties and the binarity of each system, rather than reflecting the widely reported characteristic value LX/Lbol~=10-7. Such a canonical ratio may exist for single massive stars in R136, but our data are too shallow to confirm this relationship. Through this and future X-ray studies of 30 Dor, the complete life cycle of a massive stellar cluster can be revealed.

A MODEL FOR THE ORIGIN OF HIGH DENSITY IN LOOPTOP X-RAY SOURCES

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

Longcope, D. W.; Guidoni, S. E.

Super-hot (SH) looptop sources, detected in some large solar flares, are compact sources of HXR emission with spectra matching thermal electron populations exceeding 30 MK. High observed emission measure (EM) and inference of electron thermalization within the small source region both provide evidence of high densities at the looptop, typically more than an order of magnitude above ambient. Where some investigators have suggested such density enhancement results from a rapid enhancement in the magnetic field strength, we propose an alternative model, based on Petschek reconnection, whereby looptop plasma is heated and compressed by slow magnetosonic shocks generated self-consistently through fluxmore » retraction following reconnection. Under steady conditions such shocks can enhance density by no more than a factor of four. These steady shock relations (Rankine-Hugoniot relations) turn out to be inapplicable to Petschek's model owing to transient effects of thermal conduction. The actual density enhancement can in fact exceed a factor of 10 over the entire reconnection outflow. An ensemble of flux tubes retracting following reconnection at an ensemble of distinct sites will have a collective EM proportional to the rate of flux tube production. This rate, distinct from the local reconnection rate within a single tube, can be measured separately through flare ribbon motion. Typical flux transfer rates and loop parameters yield EMs comparable to those observed in SH sources.« less

Rupture characteristics of the 2016 Meinong earthquake revealed by the back projection and directivity analysis of teleseismic broadband waveforms

NASA Astrophysics Data System (ADS)

Jian, Pei-Ru; Hung, Shu-Huei; Meng, Lingsen; Sun, Daoyuan

2017-04-01

The 2016 Mw 6.4 Meinong earthquake struck a previously unrecognized fault zone in midcrust beneath south Taiwan and inflicted heavy causalities in the populated Tainan City about 30 km northwest of the epicenter. Because of its relatively short rupture duration and P wave trains contaminated by large-amplitude depth phases and reverberations generated in the source region, accurate characterization of the rupture process and source properties for such a shallow strong earthquake remains challenging. Here we present a first high-resolution MUltiple SIgnal Classification back projection source image by using both P and depth-phase sP waves recorded at two large and dense arrays to understand the source behavior and consequent hazards of this peculiar catastrophic event. The results further corroborated by the directivity analysis indicate a unilateral rupture propagating northwestward and slightly downward on the shallow NE-dipping fault plane. The source radiation process is primarily characterized by one single peak, 7 s duration, with a total rupture length of 17 km and average rupture speed of 2.4 km/s. The rupture terminated immediately east of the prominent off-fault aftershock cluster about 20 km northwest of the hypocenter. Synergistic amplification of ground shaking by the directivity and strong excitation of sP and reverberations mainly caused the destruction concentrated in the area further to the northwest away from the rupture zone.

Predominance of Movement Speed Over Direction in Neuronal Population Signals of Motor Cortex: Intracranial EEG Data and A Simple Explanatory Model

PubMed Central

Hammer, Jiří; Pistohl, Tobias; Fischer, Jörg; Kršek, Pavel; Tomášek, Martin; Marusič, Petr; Schulze-Bonhage, Andreas; Aertsen, Ad; Ball, Tonio

2016-01-01

How neuronal activity of motor cortex is related to movement is a central topic in motor neuroscience. Motor-cortical single neurons are more closely related to hand movement velocity than speed, that is, the magnitude of the (directional) velocity vector. Recently, there is also increasing interest in the representation of movement parameters in neuronal population activity, such as reflected in the intracranial EEG (iEEG). We show that in iEEG, contrasting to what has been previously found on the single neuron level, speed predominates over velocity. The predominant speed representation was present in nearly all iEEG signal features, up to the 600–1000 Hz range. Using a model of motor-cortical signals arising from neuronal populations with realistic single neuron tuning properties, we show how this reversal can be understood as a consequence of increasing population size. Our findings demonstrate that the information profile in large population signals may systematically differ from the single neuron level, a principle that may be helpful in the interpretation of neuronal population signals in general, including, for example, EEG and functional magnetic resonance imaging. Taking advantage of the robust speed population signal may help in developing brain–machine interfaces exploiting population signals. PMID:26984895

Health center financial performance: national trends and state variation, 1998-2004.

PubMed

Shi, Leiyu; Collins, Patricia B; Aaron, Kaytura Felix; Watters, Vanessa; Shah, Leslie Greenblat

2007-01-01

For four decades, health centers have provided quality, cost-effective primary healthcare to underserved populations. Using the Uniform Data System, this study analyzes national trends in health center patients, providers, and financial performance for 1998-2004, and state-specific data for 2004. Between 1998 and 2004, health centers served increasing numbers of underserved patients, which included patients who were uninsured or on Medicaid, minorities, and patients at or below poverty level. Even though the number of health center providers and patients increased, patient-to-provider ratios did not change significantly. Medicaid remained the single largest source of health center revenue, accounting for 36.4 percent of total revenue in 2004. Compared with Medicare, private insurance, and self-pay, Medicaid consistently reimbursed health centers at the highest rate per patient. Federal and nonfederal grants to support care for the uninsured as well as enabling services such as transportation, translation, and other support systems is one of many important sources of revenue. Financial challenges for health centers included increasing costs and varied or declining rates of reimbursement for services rendered. However, health centers became more self-sufficient over time, average net revenues increased, and operating margins were predominantly positive. Data on individual states, with different numbers and types of health centers, varied widely in all of these categories. In conclusion, health centers rely on federal and nonfederal grant support in concert with the Medicaid program as major funding sources and continued financial stability will be contingent upon health centers' ability to balance revenues with the cost of managing the vulnerable populations that they serve.

Food sources of free sugars in children's diet and identification of lifestyle patterns associated with free sugars intake: the GRECO (Greek Childhood Obesity) study.

PubMed

Farajian, Paul; Risvas, Grigoris; Panagiotakos, Demosthenes B; Zampelas, Antonis

2016-09-01

Excessive free sugars consumption has a possible role in health issues, diet quality and obesity development. The present cross-sectional study aimed to identify the major food sources of free sugars in Greek children's diet and investigate possible associations of dietary patterns with free sugars intake. Anthropometric measurements and information on dietary and physical activity habits were obtained. Energy and free sugars intake coming from foods were estimated and principal components analysis was applied to identify dietary patterns. The GRECO (Greek Childhood Obesity) study. Nationwide sample of 3089 children (aged 10-12 years). Adopting WHO criteria, 44·2 % of participants were categorized as having free sugars intake above 10 % of total energy intake. Mean contribution of free sugars to energy intake was 11·2 %, and the major food sources of free sugars differed from those of other childhood populations. Free sugars intake was not associated with overweight/obesity. Multiple linear regression analysis revealed that two lifestyle and dietary patterns, characterized by higher consumption of sweets, fast foods, fries, sugared drinks, frequently ordering/eating outside home and having meals in front of a screen (pattern 1) and higher consumption of whole fruits, 100 % fruit juices, vegetables, legumes and honey/jam (pattern 2), were positively associated with free sugars intake. A large proportion of children exceeded the recommended cut-off and free sugars intake was associated with lifestyle patterns rather than single foods. Public health programmes aiming to reduce free sugars consumption should be tailored on promoting the correct dietary habits of specific childhood populations.

Seasonal variation and principle of cyanobacterial biomass and forms in the water source area of Chaohu City, China

NASA Astrophysics Data System (ADS)

Xu, Xiangen; Ke, Fan; Li, Wenchao; Feng, Muhua; Shang, Lixia; Fan, Fan; He, Yanzhao

2016-01-01

We investigated seasonal variations in cyanobacterial biomass and the forms of its dominant population ( M. aeruginosa) and their correlation with environmental factors in the water source area of Chaohu City, China from December 2011 to October 2012. The results show that species belonging to the phylum Cyanophyta occupied the maximum proportion of phytoplankton biomass, and that the dominant population in the water source area of Chaohu City was M. aeruginosa. The variation in cyanobacterial biomass from March to August 2012 was well fitted to the logistic growth model. The growth rate of cyanobacteria was the highest in June, and the biomass of cyanobacteria reached a maximum in August. From February to March 2012, the main form of M. aeruginosa was the single-cell form; M. aeruginosa colonies began to appear from April, and blooms appeared on the water surface in May. The maximum diameter of the colonies was recorded in July, and then gradually decreased from August. The diameter range of M. aeruginosa colonies was 18.37-237.77 μm, and most of the colonies were distributed in the range 20-200 μm, comprising 95.5% of the total number of samples. Temperature and photosynthetically active radiation may be the most important factors that influenced the annual variation in M. aeruginosa biomass and forms. The suitable temperature for cyanobacterial growth was in the range of 15-30°C. In natural water bodies, photosynthetically active radiation had a significant positive influence on the colonial diameter of M. aeruginosa ( P <0.01).

Environmental and economic benefits of the recovery of materials in a municipal solid waste management system.

PubMed

De Feo, Giovanni; Ferrara, Carmen; Finelli, Alessio; Grosso, Alberto

2017-12-07

The main aim of this study was to perform a Life cycle assessment study as well as an economic evaluation of the recovery of recyclable materials in a municipal solid waste management system. If citizens separate erroneously waste fractions, they produce both environmental and economic damages. The environmental and economic evaluation was performed for the case study of Nola (34.349 inhabitants) in Southern Italy, with a kerbside system that assured a source separation of 62% in 2014. The economic analysis provided a quantification of the economic benefits obtainable for the population in function of the achievable percentage of source separation. The comparison among the environmental performance of four considered scenarios showed that the higher the level of source separation was, the lower the overall impacts were. This occurred because, even if the impacts of the waste collection and transport increased, they were overcome by the avoided impacts of the recycling processes. Increasing the source separation by 1% could avoid the emission of 5 kg CO 2 eq. and 5 g PM10 for each single citizen. The economic and environmental indicators defined in this study provide simple and effective information useful for a wide-ranging audience in a behavioural change programme perspective.

Spontaneous pregnancy loss in humans and exposure to arsenic in drinking water.

PubMed

Bloom, Michael S; Fitzgerald, Edward F; Kim, Keewan; Neamtiu, Iulia; Gurzau, Eugen S

2010-11-01

Maternal exposure to high concentrations of inorganic arsenic (iAs) in naturally contaminated drinking groundwater sources has been associated with an increased risk for the spontaneous loss of clinically recognized pregnancies in several epidemiologic studies. Whereas a large worldwide population depends on drinking groundwater sources with high levels of iAs contamination, in quantities exceeding 10 parts per billion (ppb), an even larger population is likely to be exposed to mild-moderate drinking groundwater iAs contamination, in quantities <10ppb. Only a single epidemiologic study to date has considered spontaneous pregnancy loss in association with consumption of drinking water with mild-moderate iAs contamination; the vast majority of published studies of spontaneous loss addressed populations with substantial exposure. The aim of this review is to evaluate the published literature to assess the plausibility for a causal association between exposure to iAs-contaminated drinking water and the spontaneous loss of clinically recognized pregnancy. In spite of numerous methodologic limitations resulting from circumstance or design, a consistent pattern of increased risk for loss is suggested by the epidemiologic literature. Moreover, these study results are corroborated by a large number of experimental studies, albeit usually conducted at concentrations exceeding that to which humans are exposed via contaminated drinking water. In this review, we discuss sources of human iAs exposure, highlight several experimental studies pertinent to a possible causal link between iAs and spontaneous pregnancy loss in humans, and provide a critical review of published epidemiologic studies of pregnancy loss and drinking water iAs exposures, and their limitations. Based on a review of the published literature, we recommend the future conduct of a two-stage comprehensive prospective study of low-moderate iAs drinking water exposure and spontaneous pregnancy loss. Copyright © 2010 Elsevier GmbH. All rights reserved.

Ablation of film stacks in solar cell fabrication processes

DOEpatents

Harley, Gabriel; Kim, Taeseok; Cousins, Peter John

2013-04-02

A dielectric film stack of a solar cell is ablated using a laser. The dielectric film stack includes a layer that is absorptive in a wavelength of operation of the laser source. The laser source, which fires laser pulses at a pulse repetition rate, is configured to ablate the film stack to expose an underlying layer of material. The laser source may be configured to fire a burst of two laser pulses or a single temporally asymmetric laser pulse within a single pulse repetition to achieve complete ablation in a single step.

Rethinking sources of representative controls for the conduct of case–control studies in minority populations

PubMed Central

2013-01-01

Background Recruitment of controls remains a challenge in case–control studies and particularly in studies involving minority populations. Methods We compared characteristics of controls recruited through random digit dialing (RDD) to those of community controls enrolled through churches, health events and other outreach sources among women of African ancestry (AA) participating in the Women’s Circle of Health Study, a case–control study of breast cancer. Odds ratios and 95% confidence intervals were also computed using unconditional logistic regression to evaluate the impact of including the community controls for selected variables relevant to breast cancer and for which there were significant differences in distribution between the two control groups. Results Compared to community controls (n=347), RDD controls (n=207) had more years of education and higher income, lower body mass index, were more likely to have private insurance, and less likely to be single. While the percentage of nulliparous women in the two groups was similar, community controls tended to have more children, have their first child at a younger age, and were less likely to breastfeed their children. Dietary intake was similar in the two groups. Compared to census data, the combination of RDD and community controls seems to be more representative of the general population than RDD controls alone. Furthermore, the inclusion of the community group had little impact on the magnitude of risk estimates for most variables, while enhancing statistical power. Conclusions Community-based recruitment was found to be an efficient and feasible method to recruit AA controls. PMID:23721229

Complex dynamics of selection and cellular memory in adaptation to a changing environment

NASA Astrophysics Data System (ADS)

Kussell, Edo; Lin, Wei-Hsiang

We study a synthetic evolutionary system in bacteria in which an antibiotic resistance gene is controlled by a stochastic on/off switching promoter. At the population level, this system displays all the basic ingredients for evolutionary selection, including diversity, fitness differences, and heritability. At the single cell level, physiological processes can modulate the ability of selection to act. We expose the stochastic switching strains to pulses of antibiotics of different durations in periodically changing environments using microfluidics. Small populations are tracked over a large number of periods at single cell resolution, allowing the visualization and quantification of selective sweeps and counter-sweeps at the population level, as well as detailed single cell analysis. A simple model is introduced to predict long-term population growth rates from single cell measurements, and reveals unexpected aspects of population dynamics, including cellular memory that acts on a fast timescale to modulate growth rates. This work is supported by NIH Grant No. R01-GM097356.

High-throughput SNP-genotyping analysis of the relationships among Ponto-Caspian sturgeon species

PubMed Central

Rastorguev, Sergey M; Nedoluzhko, Artem V; Mazur, Alexander M; Gruzdeva, Natalia M; Volkov, Alexander A; Barmintseva, Anna E; Mugue, Nikolai S; Prokhortchouk, Egor B

2013-01-01

Abstract Legally certified sturgeon fisheries require population protection and conservation methods, including DNA tests to identify the source of valuable sturgeon roe. However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species. We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon species from the Caspian Sea region (Volga and Ural Rivers), the Azov Sea, and two Siberian rivers. We found that Russian sturgeons from the Volga and Ural Rivers were essentially indistinguishable, but they differed from Russian sturgeons in the Azov Sea, and from Persian and Siberian sturgeons. We identified eight SNPs that were sufficient to distinguish these sturgeon populations with 80% confidence, and allowed the development of markers to distinguish sturgeon species. Finally, on the basis of our SNP data, we propose that the A. baerii-like mitochondrial DNA found in some Russian sturgeons from the Caspian Sea arose via an introgression event during the Pleistocene glaciation. In the present study, the high-throughput genotyping analysis of several sturgeon populations was performed. SNP markers for species identification were defined. The possible explanation of the baerii-like mitotype presence in some Russian sturgeons in the Caspian Sea was suggested. PMID:24567827

Aedes aegypti on Madeira Island (Portugal): genetic variation of a recently introduced dengue vector

PubMed Central

Seixas, Gonçalo; Salgueiro, Patrícia; Silva, Ana Clara; Campos, Melina; Spenassatto, Carine; Reyes-Lugo, Matías; Novo, Maria Teresa; Ribolla, Paulo Eduardo Martins; Pinto, João Pedro Soares da Silva; Sousa, Carla Alexandra

2013-01-01

The increasing population of Aedes aegypti mosquitoes on Madeira Island (Portugal) resulted in the first autochthonous dengue outbreak, which occurred in October 2012. Our study establishes the first genetic evaluation based on the mitochondrial DNA (mtDNA) genes [cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4)] and knockdown resistance ( kdr ) mutations exploring the colonisation history and the genetic diversity of this insular vector population. We included mosquito populations from Brazil and Venezuela in the analysis as putative geographic sources. The Ae. aegypti population from Madeira showed extremely low mtDNA genetic variability, with a single haplotype for COI and ND4. We also detected the presence of two important kdr mutations and the quasi-fixation of one of these mutations (F1534C). These results are consistent with a unique recent founder event that occurred on the island of Ae. aegypti mosquitoes that carry kdr mutations associated with insecticide resistance. Finally, we also report the presence of the F1534C kdr mutation in the Brazil and Venezuela populations. To our knowledge, this is the first time this mutation has been found in South American Ae. aegypti mosquitoes. Given the present risk of Ae. aegypti re-invading continental Europe from Madeira and the recent dengue outbreaks on the island, this information is important to plan surveillance and control measures. PMID:24473797

Aedes aegypti on Madeira Island (Portugal): genetic variation of a recently introduced dengue vector.

PubMed

Seixas, Gonçalo; Salgueiro, Patrícia; Silva, Ana Clara; Campos, Melina; Spenassatto, Carine; Reyes-Lugo, Matías; Novo, Maria Teresa; Ribolla, Paulo Eduardo Martins; Silva Pinto, João Pedro Soares da; Sousa, Carla Alexandra

2013-01-01

The increasing population of Aedes aegypti mosquitoes on Madeira Island (Portugal) resulted in the first autochthonous dengue outbreak, which occurred in October 2012. Our study establishes the first genetic evaluation based on the mitochondrial DNA (mtDNA) genes [cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4)] and knockdown resistance (kdr) mutations exploring the colonisation history and the genetic diversity of this insular vector population. We included mosquito populations from Brazil and Venezuela in the analysis as putative geographic sources. The Ae. aegypti population from Madeira showed extremely low mtDNA genetic variability, with a single haplotype for COI and ND4. We also detected the presence of two important kdr mutations and the quasi-fixation of one of these mutations (F1534C). These results are consistent with a unique recent founder event that occurred on the island of Ae. aegypti mosquitoes that carry kdr mutations associated with insecticide resistance. Finally, we also report the presence of the F1534C kdr mutation in the Brazil and Venezuela populations. To our knowledge, this is the first time this mutation has been found in South American Ae. aegypti mosquitoes. Given the present risk of Ae. aegypti re-invading continental Europe from Madeira and the recent dengue outbreaks on the island, this information is important to plan surveillance and control measures.

4P: fast computing of population genetics statistics from large DNA polymorphism panels

PubMed Central

Benazzo, Andrea; Panziera, Alex; Bertorelle, Giorgio

2015-01-01

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations. PMID:25628874

Symbiotic Stars in X-rays

NASA Technical Reports Server (NTRS)

Luna, G. J. M.; Sokoloski, J. L.; Mukai, K.; Nelson, T.

2014-01-01

Until recently, symbiotic binary systems in which a white dwarf accretes from a red giant were thought to be mainly a soft X-ray population. Here we describe the detection with the X-ray Telescope (XRT) on the Swift satellite of 9 white dwarf symbiotics that were not previously known to be X-ray sources and one that was previously detected as a supersoft X-ray source. The 9 new X-ray detections were the result of a survey of 41 symbiotic stars, and they increase the number of symbiotic stars known to be X-ray sources by approximately 30%. Swift/XRT detected all of the new X-ray sources at energies greater than 2 keV. Their X-ray spectra are consistent with thermal emission and fall naturally into three distinct groups. The first group contains those sources with a single, highly absorbed hard component, which we identify as probably coming from an accretion-disk boundary layer. The second group is composed of those sources with a single, soft X-ray spectral component, which likely arises in a region where low-velocity shocks produce X-ray emission, i.e. a colliding-wind region. The third group consists of those sources with both hard and soft X-ray spectral components. We also find that unlike in the optical, where rapid, stochastic brightness variations from the accretion disk typically are not seen, detectable UV flickering is a common property of symbiotic stars. Supporting our physical interpretation of the two X-ray spectral components, simultaneous Swift UV photometry shows that symbiotic stars with harder X-ray emission tend to have stronger UV flickering, which is usually associated with accretion through a disk. To place these new observations in the context of previous work on X-ray emission from symbiotic stars, we modified and extended the alpha/beta/gamma classification scheme for symbiotic-star X-ray spectra that was introduced by Muerset et al. based upon observations with the ROSAT satellite, to include a new sigma classification for sources with hard X-ray emission from the innermost accretion region. Since we have identified the elusive accretion component in the emission from a sample of symbiotic stars, our results have implications for the understanding of wind-fed mass transfer in wide binaries, and the accretion rate in one class of candidate progenitors of type Ia supernovae.

Unified method to integrate and blend several, potentially related, sources of information for genetic evaluation.

PubMed

Vandenplas, Jérémie; Colinet, Frederic G; Gengler, Nicolas

2014-09-30

A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated information and, therefore, more reliable estimated breeding values were obtained. The proposed unified method integrated and blended several sources of information well into a genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. The unified method can also be extended to other types of situations such as single-step genomic or multi-trait evaluations, combining information across different traits.

Design and simulation of ion optics for ion sources for production of singly charged ions

NASA Astrophysics Data System (ADS)

Zelenak, A.; Bogomolov, S. L.

2004-05-01

During the last 2 years different types of the singly charged ion sources were developed for FLNR (JINR) new projects such as Dubna radioactive ion beams, (Phase I and Phase II), the production of the tritium ion beam and the MASHA mass separator. The ion optics simulations for 2.45 GHz electron cyclotron resonance source, rf source, and the plasma ion source were performed. In this article the design and simulation results of the optics of new ion sources are presented. The results of simulation are compared with measurements obtained during the experiments.

The linac coherent light source single particle imaging road map

PubMed Central

Aquila, A.; Barty, A.; Bostedt, C.; Boutet, S.; Carini, G.; dePonte, D.; Drell, P.; Doniach, S.; Downing, K. H.; Earnest, T.; Elmlund, H.; Elser, V.; Gühr, M.; Hajdu, J.; Hastings, J.; Hau-Riege, S. P.; Huang, Z.; Lattman, E. E.; Maia, F. R. N. C.; Marchesini, S.; Ourmazd, A.; Pellegrini, C.; Santra, R.; Schlichting, I.; Schroer, C.; Spence, J. C. H.; Vartanyants, I. A.; Wakatsuki, S.; Weis, W. I.; Williams, G. J.

2015-01-01

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources. PMID:26798801

The linac coherent light source single particle imaging road map

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

Aquila, A.; Barty, A.; Bostedt, C.

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electronmore » laser sources.« less

Generation and transfer of single photons on a photonic crystal chip.

PubMed

Englund, Dirk; Faraon, Andrei; Zhang, Bingyang; Yamamoto, Yoshihisa; Vucković, Jelena

2007-04-30

We present a basic building block of a quantum network consisting of a quantum dot coupled to a source cavity, which in turn is coupled to a target cavity via a waveguide. The single photon emission from the high-Q/V source cavity is characterized by twelve-fold spontaneous emission (SE) rate enhancement, SE coupling efficiency beta ~ 0.98 into the source cavity mode, and mean wavepacket indistinguishability of ~67%. Single photons are efficiently transferred into the target cavity via the waveguide, with a target/source field intensity ratio of 0.12 +/- 0.01. This system shows great promise as a building block of future on-chip quantum information processing systems.

Mental health and support among young key populations: an ecological approach to understanding and intervention

PubMed Central

Mutumba, Massy; Harper, Gary W

2015-01-01

Introduction The patterning of the HIV epidemic within young key populations (YKPs) highlights disproportionate burden by mental disorders in these populations. The mental wellbeing of YKPs is closely associated with biological predispositions and psychosocial factors related to YKPs’ sexual and gender identities and socio-economic status. The purpose of this paper is to highlight sources of risk and resilience, as well as identify treatment and supports for mental health disorders (MHDs) among YKPs. Discussion This paper utilizes Bronfenbrenner's Bioecological Systems Theory and the Social Stress Model to explore the risk and protective factors for MHDs across YKPs’ ecological systems, and identify current gaps in treatment and support for MHDs among these youth. We emphasize the fluidity and intersections across these categorizations which reinforce the vulnerability of these populations, the lack of concrete data to inform mental health interventions among YKPs, and the need to ground YKP interventions and programmes with human rights principles stipulated in the convention on the rights of a child. Conclusions We put forth recommendations for future research and strategies to address the mental wellbeing of YKPs, including the need for integrated interventions that address the multiplicity of risk factors inherent in the multiple group membership, rather than single-focus interventions whilst addressing the unique needs or challenges of YKPs. PMID:25724505

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

PubMed Central

Ramachandran, Sohini; Deshpande, Omkar; Roseman, Charles C.; Rosenberg, Noah A.; Feldman, Marcus W.; Cavalli-Sforza, L. Luca

2005-01-01

Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by FST) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between FST and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation. PMID:16243969

A simple real-time polymerase chain reaction (PCR)-based assay for authentication of the Chinese Panax ginseng cultivar Damaya from a local ginseng population.

PubMed

Wang, H; Wang, J; Li, G

2016-06-27

Panax ginseng is one of the most important medicinal plants in the Orient. Owing to its increasing demand in the world market, cultivated ginseng has become the main source of medicinal material. Among the Chinese ginseng cultivars, Damaya commands higher prices and is grown in significant proportions among the local ginseng population. Due to the lack of rapid and accurate authentication methods, Damaya is distributed among different cultivars in the local ginseng population in China. Here, we identified a unique, Damaya-specific single nucleotide polymorphism (SNP) site present in the second intron of mitochondrial cytochrome c oxidase subunit 2 (cox2). Based on this SNP, a Damaya cultivar-specific primer was designed and an allele-specific polymerase chain reaction (PCR) was optimized for the effective molecular authentication of Damaya. We designed a method by combining a simple DNA isolation method with real-time allele-specific PCR using SYBR Green I fluorescent dye, and proved its efficacy in clearly discriminated Damaya cultivar from other Chinese ginseng cultivars according to the allelic discrimination analysis. Hence, this study provides a simple and rapid assay for the differentiation and conservation of Damaya from the local Chinese ginseng population.

Coexistence of the social types: genetic population structure in the ant Formica exsecta.

PubMed

Seppä, Perttu; Gyllenstrand, Niclas; Corander, Jukka; Pamilo, Pekka

2004-11-01

The ant Formica exsecta has two types of colonies that exist in sympatry but usually as separate subpopulations: colonies with simple social organization and single queens (M type) or colonial networks with multiple queens (P type). We used both nuclear (DNA microsatellites) and mitochondrial markers to study the transition between the social types, and the contribution of males and females in gene flow within and between the types. Our results showed that the social types had different spatial genetic structures. The M subpopulations formed a fairly uniform population, whereas the P subpopulations were, on average, more differentiated from each other than from the nearby M subpopulations and could have been locally established from the M-type colonies, followed by philopatric behavior and restricted emigration of females. Thus, the relationship between the two social types resembles that of source (M type) and sink (P type) populations. The comparison of mitochondrial (phiST) and nuclear (FST) differentiation indicates that the dispersal rate of males is four to five times larger than that of females both among the P-type subpopulations and between the social types. Our results suggest that evolution toward complex social organization can have an important effect on genetic population structure through changes in dispersal behavior associated with different sociogenetic organizations.

Two Populations of SiO Masers in the Galactic Bulge

NASA Astrophysics Data System (ADS)

Trapp, Adam; Rich, Robert Michael; Morris, Mark; Pihlstrom, Ylva; Sjouwerman, Lorant; Claussen, Mark J.; Stroh, Michael

2017-01-01

We present a summary of the kinematics of stellar SiO masers observed in the direction of the galactic bulge with ALMA (885 sources), and the JVLA (2,479 sources). These objects are selected by color from the MSX point source catalog, which has given an SiO detection rate of ~70%. The presented sample, along with the ~24,000 sources still being observed and reduced, enable radial velocity measurements even in regions with extreme optical extinction. These maser stars are compared to the known bulge surveys: APOGEE (~25,000 sources), BRAVA (~8000 sources), and GIBS (~6,400 sources). We have found that BAaDE stars in the direction of the bulge exist in two subpopulations: (1) A kinematically hot population exhibiting cylindrical rotation consistent with the other bulge surveys, and (2) a kinematically cold population more consistent with a disk population. In the ALMA data, we find evidence for a -200 km/s feature at (l,b) = (-9,0), possibly the symmetric complement to a previously proposed +200 km/s feature (Nidever 2012), that we do not confirm with our data.

A research on the positioning technology of vehicle navigation system from single source to "ASPN"

NASA Astrophysics Data System (ADS)

Zhang, Jing; Li, Haizhou; Chen, Yu; Chen, Hongyue; Sun, Qian

2017-10-01

Due to the suddenness and complexity of modern warfare, land-based weapon systems need to have precision strike capability on roads and railways. The vehicle navigation system is one of the most important equipments for the land-based weapon systems that have precision strick capability. There are inherent shortcomings for single source navigation systems to provide continuous and stable navigation information. To overcome the shortcomings, the multi-source positioning technology is developed. The All Source Positioning and Navigaiton (ASPN) program was proposed in 2010, which seeks to enable low cost, robust, and seamless navigation solutions for military to use on any operational platform and in any environment with or without GPS. The development trend of vehicle positioning technology was reviewed in this paper. The trend indicates that the positioning technology is developed from single source and multi-source to ASPN. The data fusion techniques based on multi-source and ASPN was analyzed in detail.

High-Efficiency Plug-and-Play Source of Heralded Single Photons

NASA Astrophysics Data System (ADS)

Montaut, Nicola; Sansoni, Linda; Meyer-Scott, Evan; Ricken, Raimund; Quiring, Viktor; Herrmann, Harald; Silberhorn, Christine

2017-08-01

Reliable generation of single photons is of key importance for fundamental physical experiments and to demonstrate quantum protocols. Waveguide-based photon-pair sources have shown great promise in this regard due to their large spectral tunability, high generation rates, and long temporal coherence of the photon wave packet. However, integrating such sources with fiber-optic networks often results in a strong degradation of performance. We answer this challenge by presenting an alignment-free source of photon pairs in the telecommunications band that maintains heralding efficiency >50 % even after fiber pigtailing, photon separation, and pump suppression. The source combines this outstanding performance in heralding efficiency with a compact, stable, and easy-to-use "plug-and-play" package: one simply connects a laser to the input and detectors to the output, and the source is ready to use. This high performance can be achieved even outside the lab without the need for alignment which makes the source extremely useful for any experiment or demonstration needing heralded single photons.

Single colloidal quantum dots as sources of single photons for quantum cryptography

NASA Astrophysics Data System (ADS)

Pisanello, Ferruccio; Qualtieri, Antonio; Leménager, Godefroy; Martiradonna, Luigi; Stomeo, Tiziana; Cingolani, Roberto; Bramati, Alberto; De Vittorio, Massimo

2011-02-01

Colloidal nanocrystals, i.e. quantum dots synthesized trough wet-chemistry approaches, are promising nanoparticles for photonic applications and, remarkably, their quantum nature makes them very promising for single photon emission at room temperature. In this work we describe two approaches to engineer the emission properties of these nanoemitters in terms of radiative lifetime and photon polarization, drawing a viable strategy for their exploitation as room-temperature single photon sources for quantum information and quantum telecommunications.

Background nuclei measurements and implications for cavitation inception in hydrodynamic test facilities

NASA Astrophysics Data System (ADS)

Venning, J. A.; Khoo, M. T.; Pearce, B. W.; Brandner, P. A.

2018-04-01

Water susceptibility and background nuclei content in a water tunnel are investigated using a cavitation susceptibility meter. The measured cumulative histogram of nuclei concentration against critical pressure shows a power law dependence over a large range of concentrations and pressures. These results show that the water strength is not characterised by a single tension but is susceptible to `all' tensions depending on the relevant timescale. This background nuclei population is invariant to tunnel conditions showing that it is stabilised against dissolution. Consideration of a practical cavitating flow about a sphere shows that although background nuclei may be activated, their numbers are so few compared with other sources that they are insignificant for this case.

Genetic effects of habitat restoration in the Laurentian Great Lakes: an assessment of lake sturgeon origin and genetic diversity

USGS Publications Warehouse

Jamie Marie Marranca,; Amy Welsh,; Roseman, Edward F.

2015-01-01

Lake sturgeon (Acipenser fulvescens) have experienced significant habitat loss, resulting in reduced population sizes. Three artificial reefs were built in the Huron-Erie corridor in the Great Lakes to replace lost spawning habitat. Genetic data were collected to determine the source and numbers of adult lake sturgeon spawning on the reefs and to determine if the founder effect resulted in reduced genetic diversity. DNA was extracted from larval tail clips and 12 microsatellite loci were amplified. Larval genotypes were then compared to 22 previously studied spawning lake sturgeon populations in the Great Lakes to determine the source of the parental population. The effective number of breeders (Nb) was calculated for each reef cohort. The larval genotypes were then compared to the source population to determine if there were any losses in genetic diversity that are indicative of the founder effect. The St. Clair and Detroit River adult populations were found to be the source parental population for the larvae collected on all three artificial reefs. There were large numbers of contributing adults relative to the number of sampled larvae. There was no significant difference between levels of genetic diversity in the source population and larval samples from the artificial reefs; however, there is some evidence for a genetic bottleneck in the reef populations likely due to the founder effect. Habitat restoration in the Huron-Erie corridor is likely resulting in increased habitat for the large lake sturgeon population in the system and in maintenance of the population's genetic diversity.

Resting-state fMRI correlations: From link-wise unreliability to whole brain stability.

PubMed

Pannunzi, Mario; Hindriks, Rikkert; Bettinardi, Ruggero G; Wenger, Elisabeth; Lisofsky, Nina; Martensson, Johan; Butler, Oisin; Filevich, Elisa; Becker, Maxi; Lochstet, Martyna; Kühn, Simone; Deco, Gustavo

2017-08-15

The functional architecture of spontaneous BOLD fluctuations has been characterized in detail by numerous studies, demonstrating its potential relevance as a biomarker. However, the systematic investigation of its consistency is still in its infancy. Here, we analyze within- and between-subject variability and test-retest reliability of resting-state functional connectivity (FC) in a unique data set comprising multiple fMRI scans (42) from 5 subjects, and 50 single scans from 50 subjects. We adopt a statistical framework that enables us to identify different sources of variability in FC. We show that the low reliability of single links can be significantly improved by using multiple scans per subject. Moreover, in contrast to earlier studies, we show that spatial heterogeneity in FC reliability is not significant. Finally, we demonstrate that despite the low reliability of individual links, the information carried by the whole-brain FC matrix is robust and can be used as a functional fingerprint to identify individual subjects from the population. Copyright © 2017 Elsevier Inc. All rights reserved.

Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics

DOE PAGES

Geng, Tao; Bredeweg, Erin L.; Szymanski, Craig J.; ...

2015-11-04

Here, interrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in conventional assays. Here we present a robust and high-performance microfluidic system that enables observations of polarized growth with enhanced temporal and spatial control over prolonged periods. The system has built-in tunability and versatility to accommodate a variety of science applications requiring precisely controlled environments. Using the model filamentous fungus, Neurospora crassa, this microfluidic system enabled direct visualization and analysis of cellular heterogeneity in a clonal fungal cell population, nuclear distribution and dynamics at the subhyphal level, and quantitative dynamics of gene expression withmore » single hyphal compartment resolution in response to carbon source starvation and exchange experiments. Although the microfluidic device is demonstrated on filamentous fungi, our technology is immediately extensible to a wide array of other biosystems that exhibit similar polarized cell growth with applications ranging from bioenergy production to human health.« less

Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

NASA Astrophysics Data System (ADS)

Bustamam, A.; Fitria, I.; Umam, K.

2017-07-01

Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

Ejection of rocky and icy material from binary star systems: implications for the origin and composition of 1I/`Oumuamua

NASA Astrophysics Data System (ADS)

Jackson, Alan P.; Tamayo, Daniel; Hammond, Noah; Ali-Dib, Mohamad; Rein, Hanno

2018-06-01

In single-star systems like our own Solar system, comets dominate the mass budget of bodies ejected into interstellar space, since they form further away and are less tightly bound. However, 1I/`Oumuamua, the first interstellar object detected, appears asteroidal in its spectra and lack of detectable activity. We argue that the galactic budget of interstellar objects like 1I/`Oumuamua should be dominated by planetesimal material ejected during planet formation in circumbinary systems, rather than in single-star systems or widely separated binaries. We further show that in circumbinary systems, rocky bodies should be ejected in comparable numbers to icy ones. This suggests that a substantial fraction of interstellar objects discovered in future should display an active coma. We find that the rocky population, of which 1I/`Oumuamua seems to be a member, should be predominantly sourced from A-type and late B-star binaries.

Single cell analysis of normal and leukemic hematopoiesis.

PubMed

Povinelli, Benjamin J; Rodriguez-Meira, Alba; Mead, Adam J

2018-02-01

The hematopoietic system is well established as a paradigm for the study of cellular hierarchies, their disruption in disease and therapeutic use in regenerative medicine. Traditional approaches to study hematopoiesis involve purification of cell populations based on a small number of surface markers. However, such population-based analysis obscures underlying heterogeneity contained within any phenotypically defined cell population. This heterogeneity can only be resolved through single cell analysis. Recent advances in single cell techniques allow analysis of the genome, transcriptome, epigenome and proteome in single cells at an unprecedented scale. The application of these new single cell methods to investigate the hematopoietic system has led to paradigm shifts in our understanding of cellular heterogeneity in hematopoiesis and how this is disrupted in disease. In this review, we summarize how single cell techniques have been applied to the analysis of hematopoietic stem/progenitor cells in normal and malignant hematopoiesis, with a particular focus on recent advances in single-cell genomics, including how these might be utilized for clinical application. Copyright © 2017. Published by Elsevier Ltd.

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.

PubMed

Pollen, Alex A; Nowakowski, Tomasz J; Shuga, Joe; Wang, Xiaohui; Leyrat, Anne A; Lui, Jan H; Li, Nianzhen; Szpankowski, Lukasz; Fowler, Brian; Chen, Peilin; Ramalingam, Naveen; Sun, Gang; Thu, Myo; Norris, Michael; Lebofsky, Ronald; Toppani, Dominique; Kemp, Darnell W; Wong, Michael; Clerkson, Barry; Jones, Brittnee N; Wu, Shiquan; Knutsson, Lawrence; Alvarado, Beatriz; Wang, Jing; Weaver, Lesley S; May, Andrew P; Jones, Robert C; Unger, Marc A; Kriegstein, Arnold R; West, Jay A A

2014-10-01

Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.

Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens

PubMed Central

Monteil, Caroline L.; Yahara, Koji; Studholme, David J.; Mageiros, Leonardos; Méric, Guillaume; Swingle, Bryan; Morris, Cindy E.

2016-01-01

Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae. PMID:28348830

Phylogeography of recently emerged DENV-2 in southern Viet Nam.

PubMed

Rabaa, Maia A; Ty Hang, Vu Thi; Wills, Bridget; Farrar, Jeremy; Simmons, Cameron P; Holmes, Edward C

2010-07-27

Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-length DENV-2 genome sequences obtained from hospitalized dengue cases from 10 provinces in southern Viet Nam, we reveal substantial genetic diversity in both urban and rural areas, with multiple lineages identified in individual provinces within a single season, and indicative of frequent viral migration among communities. Focusing on the recently introduced Asian I genotype, we observed particularly high rates of viral exchange between adjacent geographic areas, and between Ho Chi Minh City, the primary urban center of this region, and populations across southern Viet Nam. Within Ho Chi Minh City, patterns of DENV movement appear consistent with a gravity model of virus dispersal, with viruses traveling across a gradient of population density. Overall, our analysis suggests that Ho Chi Minh City may act as a source population for the dispersal of DENV across southern Viet Nam, and provides further evidence that urban areas of Southeast Asia play a primary role in DENV transmission. However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons.

Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens.

PubMed

Monteil, Caroline L; Yahara, Koji; Studholme, David J; Mageiros, Leonardos; Méric, Guillaume; Swingle, Bryan; Morris, Cindy E; Vinatzer, Boris A; Sheppard, Samuel K

2016-10-01

Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1 , to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae .

Determination of Jet Noise Radiation Source Locations using a Dual Sideline Cross-Correlation/Spectrum Technique

NASA Technical Reports Server (NTRS)

Allen, C. S.; Jaeger, S. M.

1999-01-01

The goal of our efforts is to extrapolate nearfield jet noise measurements to the geometric far field where the jet noise sources appear to radiate from a single point. To accomplish this, information about the location of noise sources in the jet plume, the radiation patterns of the noise sources and the sound pressure level distribution of the radiated field must be obtained. Since source locations and radiation patterns can not be found with simple single microphone measurements, a more complicated method must be used.

FR0CAT: a FIRST catalog of FR 0 radio galaxies

NASA Astrophysics Data System (ADS)

Baldi, R. D.; Capetti, A.; Massaro, F.

2018-01-01

With the aim of exploring the properties of the class of FR 0 radio galaxies, we selected a sample of 108 compact radio sources, called FR0CAT, by combining observations from the NVSS, FIRST, and SDSS surveys. We included in the catalog sources with redshift ≤0.05, with a radio size ≲5 kpc, and with an optical spectrum characteristic of low-excitation galaxies. Their radio luminosities at 1.4 GHz are in the range 1038 ≲ νL1.4 ≲ 1040 erg s-1. The FR0CAT hosts are mostly (86%) luminous (-21 ≳ Mr ≳ -23) red early-type galaxies with black hole masses 108 ≲ MBH ≲ 109M⊙. These properties are similar to those seen for the hosts of FR I radio galaxies, but they are on average a factor 1.6 less massive. The number density of FR0CAT sources is 5 times higher than that of FR Is, and thus they represent the dominant population of radio sources in the local Universe. Different scenarios are considered to account for the smaller sizes and larger abundance of FR 0s with respect to FR Is. An age-size scenario that considers FR 0s as young radio galaxies that will all eventually evolve into extended radio sources cannot be reconciled with the large space density of FR 0s. However, the radio activity recurrence, with the duration of the active phase covering a wide range of values and with short active periods strongly favored with respect to longer ones, might account for their large density number. Alternatively, the jet properties of FR 0s might be intrinsically different from those of the FR Is, the former class having lower bulk Lorentz factors, possibly due to lower black hole spins. Our study indicates that FR 0s and FR I/IIs can be interpreted as two extremes of a continuous population of radio sources that is characterized by a broad distribution of sizes and luminosities of their extended radio emission, but shares a single class of host galaxies.

Observations of galactic X-ray sources by OSO-7

NASA Technical Reports Server (NTRS)

Markert, T. H.; Canizares, C. R.; Clark, G. W.; Hearn, D. R.; Li, F. K.; Sprott, G. F.; Winkler, P. F.

1977-01-01

We present the MIT data from the OSO-7 satellite for observations of the galactic plane between 1971 and 1974. A number of sources discovered in the MIT all-sky survey are described in detail: MX 0049 + 59, MX 0836 - 42, MX 1353 - 64, MX 1406 - 61, MX 1418 - 61, MX 1709 - 40, and MX 1608 - 52 (the persistent source suggested to be associated with the X-ray burst source XB 1608 - 52). Upper limits to the X-ray emission from a number of interesting objects are also derived. General results describing all of our observations of galactic sources are presented. Specifically, we display the number-intensity diagrams, luminosity functions, and color-color diagrams for all of the sources we detected. The data are divided between disk and bulge populations, and the characteristics of the two groups are contrasted. Finally, the concept of X-ray source populations and the relationship of globular cluster sources and burst sources to the disk and bulge populations are discussed.

Beam current enhancement of microwave plasma ion source utilizing double-port rectangular cavity resonator

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

Lee, Yuna; Park, Yeong-Shin; Jo, Jong-Gab

2012-02-15

Microwave plasma ion source with rectangular cavity resonator has been examined to improve ion beam current by changing wave launcher type from single-port to double-port. The cavity resonators with double-port and single-port wave launchers are designed to get resonance effect at TE-103 mode and TE-102 mode, respectively. In order to confirm that the cavities are acting as resonator, the microwave power for breakdown is measured and compared with the E-field strength estimated from the HFSS (High Frequency Structure Simulator) simulation. Langmuir probe measurements show that double-port cavity enhances central density of plasma ion source by modifying non-uniform plasma density profilemore » of the single-port cavity. Correspondingly, beam current from the plasma ion source utilizing the double-port resonator is measured to be higher than that utilizing single-port resonator. Moreover, the enhancement in plasma density and ion beam current utilizing the double-port resonator is more pronounced as higher microwave power applied to the plasma ion source. Therefore, the rectangular cavity resonator utilizing the double-port is expected to enhance the performance of plasma ion source in terms of ion beam extraction.« less

Beam current enhancement of microwave plasma ion source utilizing double-port rectangular cavity resonator.

PubMed

Lee, Yuna; Park, Yeong-Shin; Jo, Jong-Gab; Yang, J J; Hwang, Y S

2012-02-01

Microwave plasma ion source with rectangular cavity resonator has been examined to improve ion beam current by changing wave launcher type from single-port to double-port. The cavity resonators with double-port and single-port wave launchers are designed to get resonance effect at TE-103 mode and TE-102 mode, respectively. In order to confirm that the cavities are acting as resonator, the microwave power for breakdown is measured and compared with the E-field strength estimated from the HFSS (High Frequency Structure Simulator) simulation. Langmuir probe measurements show that double-port cavity enhances central density of plasma ion source by modifying non-uniform plasma density profile of the single-port cavity. Correspondingly, beam current from the plasma ion source utilizing the double-port resonator is measured to be higher than that utilizing single-port resonator. Moreover, the enhancement in plasma density and ion beam current utilizing the double-port resonator is more pronounced as higher microwave power applied to the plasma ion source. Therefore, the rectangular cavity resonator utilizing the double-port is expected to enhance the performance of plasma ion source in terms of ion beam extraction.

Photon pair source via two coupling single quantum emitters

NASA Astrophysics Data System (ADS)

Peng, Yong-Gang; Zheng, Yu-Jun

2015-10-01

We study the two coupling two-level single molecules driven by an external field as a photon pair source. The probability of emitting two photons, P2, is employed to describe the photon pair source quality in a short time, and the correlation coefficient RAB is employed to describe the photon pair source quality in a long time limit. The results demonstrate that the coupling single quantum emitters can be considered as a stable photon pair source. Project supported by the National Natural Science Foundation of China (Grand Nos. 91021009, 21073110, and 11374191), the Natural Science Foundation of Shandong Province, China (Grant No. ZR2013AQ020), the Postdoctoral Science Foundation of China (Grant No. 2013M531584), the Doctoral Program of Higher Education of China (Grant Nos. 20130131110005 and 20130131120006), and the Taishan Scholarship Project of Shandong Province, China.

Reconciling PM10 analyses by different sampling methods for Iron King Mine tailings dust.

PubMed

Li, Xu; Félix, Omar I; Gonzales, Patricia; Sáez, Avelino Eduardo; Ela, Wendell P

2016-03-01

The overall project objective at the Iron King Mine Superfund site is to determine the level and potential risk associated with heavy metal exposure of the proximate population emanating from the site's tailings pile. To provide sufficient size-fractioned dust for multi-discipline research studies, a dust generator was built and is now being used to generate size-fractioned dust samples for toxicity investigations using in vitro cell culture and animal exposure experiments as well as studies on geochemical characterization and bioassay solubilization with simulated lung and gastric fluid extractants. The objective of this study is to provide a robust method for source identification by comparing the tailing sample produced by dust generator and that collected by MOUDI sampler. As and Pb concentrations of the PM10 fraction in the MOUDI sample were much lower than in tailing samples produced by the dust generator, indicating a dilution of Iron King tailing dust by dust from other sources. For source apportionment purposes, single element concentration method was used based on the assumption that the PM10 fraction comes from a background source plus the Iron King tailing source. The method's conclusion that nearly all arsenic and lead in the PM10 dust fraction originated from the tailings substantiates our previous Pb and Sr isotope study conclusion. As and Pb showed a similar mass fraction from Iron King for all sites suggesting that As and Pb have the same major emission source. Further validation of this simple source apportionment method is needed based on other elements and sites.

Photometric redshifts for the next generation of deep radio continuum surveys - I. Template fitting

NASA Astrophysics Data System (ADS)

Duncan, Kenneth J.; Brown, Michael J. I.; Williams, Wendy L.; Best, Philip N.; Buat, Veronique; Burgarella, Denis; Jarvis, Matt J.; Małek, Katarzyna; Oliver, S. J.; Röttgering, Huub J. A.; Smith, Daniel J. B.

2018-01-01

We present a study of photometric redshift performance for galaxies and active galactic nuclei detected in deep radio continuum surveys. Using two multiwavelength data sets, over the NOAO Deep Wide Field Survey Boötes and COSMOS fields, we assess photometric redshift (photo-z) performance for a sample of ∼4500 radio continuum sources with spectroscopic redshifts relative to those of ∼63 000 non-radio-detected sources in the same fields. We investigate the performance of three photometric redshift template sets as a function of redshift, radio luminosity and infrared/X-ray properties. We find that no single template library is able to provide the best performance across all subsets of the radio-detected population, with variation in the optimum template set both between subsets and between fields. Through a hierarchical Bayesian combination of the photo-z estimates from all three template sets, we are able to produce a consensus photo-z estimate that equals or improves upon the performance of any individual template set.

Recommendations for research design and reporting in computer-assisted diagnosis to facilitate meta-analysis.

PubMed

Eadie, Leila H; Taylor, Paul; Gibson, Adam P

2012-04-01

Computer-assisted diagnosis (CAD) describes a diverse, heterogeneous range of applications rather than a single entity. The aims and functions of CAD systems vary considerably and comparing studies and systems is challenging due to methodological and design differences. In addition, poor study quality and reporting can reduce the value of some publications. Meta-analyses of CAD are therefore difficult and may not provide reliable conclusions. Aiming to determine the major sources of heterogeneity and thereby what CAD researchers could change to allow this sort of assessment, this study reviews a sample of 147 papers concerning CAD used with imaging for cancer diagnosis. It discusses sources of variability, including the goal of the CAD system, learning methodology, study population, design, outcome measures, inclusion of radiologists, and study quality. Based upon this evidence, recommendations are made to help researchers optimize the quality and comparability of their trial design and reporting. Copyright © 2011 Elsevier Inc. All rights reserved.

Orbital evolution of 95/P Chiron, 39P/Oterma, 29P/Shwassmann-Wachmann 1, and of 33 Centaurs

NASA Astrophysics Data System (ADS)

Kovalenko, N. S.; Churyumov, K. I.; Babenko, Yu. G.

2011-12-01

The paper is devoted to numerical modeling of orbital evolution of 34 Centaurs, and 2 distant Jupiter-family comets - 39P/Oterma and 29P/Shwassmann-Wachmann 1. As a result the evolutionary tracks of orbital elements of 33 Centaurs and 3 comets (95/P Chiron (2060), 39P/Oterma and 29P/Shwassmann-Wachmann 1) are obtained. The integrations were produced for 1 Myr back and forth in time starting at epoch and using the implicit single sequence Everhart methods. The statistical analysis of numerical integrations results was done, trends in changes of Centaurs' orbital elements in the past and in the future are revealed. The part of Centaurs that are potential comets is defined by the values of perihelia distributions for modeled orbits. It is shown that Centaurs may transits into orbits typical for Jupiter-family comets, and vice versa. Centaurs represent one of possible sources for replenishment of JFCs population, but other sources are also necessary.

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics.

PubMed

Spyrou, Maria A; Tukhbatova, Rezeda I; Feldman, Michal; Drath, Joanna; Kacki, Sacha; Beltrán de Heredia, Julia; Arnold, Susanne; Sitdikov, Airat G; Castex, Dominique; Wahl, Joachim; Gazimzyanov, Ilgizar R; Nurgaliev, Danis K; Herbig, Alexander; Bos, Kirsten I; Krause, Johannes

2016-06-08

Ancient DNA analysis has revealed an involvement of the bacterial pathogen Yersinia pestis in several historical pandemics, including the second plague pandemic (Europe, mid-14(th) century Black Death until the mid-18(th) century AD). Here we present reconstructed Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks spanning Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1362-1400 AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for (1) a single entry of Y. pestis in Europe during the Black Death, (2) a wave of plague that traveled toward Asia to later become the source population for contemporary worldwide epidemics, and (3) the presence of an historical European plague focus involved in post-Black Death outbreaks that is now likely extinct. Copyright © 2016 Elsevier Inc. All rights reserved.

Polycyclic Aromatic Hydrocarbons Bound to PM 2.5 in Urban Coimbatore, India with Emphasis on Source Apportionment

PubMed Central

Mohanraj, R.; Dhanakumar, S.; Solaraj, G.

2012-01-01

Coimbatore is one of the fast growing industrial cities of Southern India with an urban population of 1.9 million. This study attempts to evaluate the trends of airborne fine particulates (PM 2.5) and polyaromatic hydrocarbons (PAH) on them. The PM 2.5 mass was collected in polytetra fluoroethylene filters using fine particulate sampler at monthly intervals during March 2009 to February 2010. PAHs were extracted from PM 2.5 and estimated by high-performance liquid chromatography. It is alarming to note that PM 2.5 values ranged between 27.85 and 165.75 μg/m3 and exceeded the air quality standards in many sampling events. The sum of 9 PAHs bound to PM 2.5 in a single sampling event ranged from 4.1 to 1632.3 ng/m3. PAH diagnostic ratios and principal component analysis results revealed vehicular emissions and diesel-powered generators as predominant sources of PAH in Coimbatore. PMID:22649329

[To educate and to inform the population about population].

PubMed

Levy, M L

1993-03-01

Each society has multiple institutions that inform members about themselves and their world. The quality of the information received depends on the balance between the political, religious, intellectual, educational, and media institutions that supply information. Population questions are almost always absent from public education programs, because they deal with themes traditionally reserved for family and religious education. But the contemporary world has changed so much that families and the clerical world are no longer necessarily the best sources of instruction. The ignorance and passivity of many families leave a void that is difficult to fill. The difficulty arises because the need is to assist families in filling their role, and not to substitute for them. Educators, development technicians, psychologists, physicians, and sociologists should not be allowed to monopolize the task of educating children in areas related to population, and morality any more than priests should. The central discipline for questions of population is demography. The use of figures and quantitative categories such as age cohorts gives a "scientific" air to demographic discourse which masks the arbitrariness of many terms. At what age, for example, does one became single, or when does one cease to be an orphan? Explaining the European term "household" to Africans, or the African term "concession" to Europeans, illustrates the semantic problems impeding, understanding and communication. The diffusion of demographic information, like that of all numeric information, assumes that the complexity of data gathering and the conventions of calculation are understood. The risk of error and misunderstanding is greater in population than, for example, for the economy, because of the simple and universal nature of demographic subjects: birth, death, illness. Good understanding of demographic information should lead to a deeper understanding of apparently evident notions such as age, duration of life, households, couples and parenthood. Demography is the statistical study of intimate life. Demography should play the same role in relation to social information that national accounts play in relation to economic information, that of a model requiring careful collection of statistics and mathematical rigor, without discouraging evaluation of sources and questioning of theories by the statistical administrators, the press, or the educational institutions.

Single-cell MALDI-MS as an analytical tool for studying intrapopulation metabolic heterogeneity of unicellular organisms.

PubMed

Amantonico, Andrea; Urban, Pawel L; Fagerer, Stephan R; Balabin, Roman M; Zenobi, Renato

2010-09-01

Heterogeneity is a characteristic feature of all populations of living organisms. Here we make an attempt to validate a single-cell mass spectrometric method for detection of changes in metabolite levels occurring in populations of unicellular organisms. Selected metabolites involved in central metabolism (ADP, ATP, GTP, and UDP-Glucose) could readily be detected in single cells of Closterium acerosum by means of negative-mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The analytical capabilities of this approach were characterized using standard compounds. The method was then used to study populations of individual cells with different levels of the chosen metabolites. With principal component analysis and support vector machine algorithms, it was possible to achieve a clear separation of individual C. acerosum cells in different metabolic states. This study demonstrates the suitability of mass spectrometric analysis of metabolites in single cells to measure cell-population heterogeneity.

Ice cloud formation potential by free tropospheric particles from long-range transport over the Northern Atlantic Ocean

NASA Astrophysics Data System (ADS)

China, Swarup; Alpert, Peter A.; Zhang, Bo; Schum, Simeon; Dzepina, Katja; Wright, Kendra; Owen, R. Chris; Fialho, Paulo; Mazzoleni, Lynn R.; Mazzoleni, Claudio; Knopf, Daniel A.

2017-03-01

Long-range transported free tropospheric particles can play a significant role on heterogeneous ice nucleation. Using optical and electron microscopy we examine the physicochemical characteristics of ice nucleating particles (INPs). Particles were collected on substrates from the free troposphere at the remote Pico Mountain Observatory in the Azores Islands, after long-range transport and aging over the Atlantic Ocean. We investigate four specific events to study the ice formation potential by the collected particles with different ages and transport patterns. We use single-particle analysis, as well as bulk analysis to characterize particle populations. Both analyses show substantial differences in particle composition between samples from the four events; in addition, single-particle microscopy analysis indicates that most particles are coated by organic material. The identified INPs contained mixtures of dust, aged sea salt and soot, and organic material acquired either at the source or during transport. The temperature and relative humidity (RH) at which ice formed, varied only by 5% between samples, despite differences in particle composition, sources, and transport patterns. We hypothesize that this small variation in the onset RH may be due to the coating material on the particles. This study underscores and motivates the need to further investigate how long-range transported and atmospherically aged free tropospheric particles impact ice cloud formation.

Ice cloud formation potential by free tropospheric particles from long-range transport over the Northern Atlantic Ocean

DOE PAGES

China, Swarup; Alpert, Peter A.; Zhang, Bo; ...

2017-02-27

Long-range transported free tropospheric particles can play a significant role on heterogeneous ice nucleation. Using optical and electron microscopy we examine the physicochemical characteristics of ice nucleating particles (INPs). Particles were collected on substrates from the free troposphere at the remote Pico Mountain Observatory in the Azores Islands, after long-range transport and aging over the Atlantic Ocean. We investigate four specific events to study the ice formation potential by the collected particles with different ages and transport patterns. We use single-particle analysis, as well as bulk analysis to characterize particle populations. Both analyses show substantial differences in particle composition betweenmore » samples from the four events; in addition, single-particle microscopy analysis indicates that most particles are coated by organic material. The identified INPs contained mixtures of dust, aged sea salt and soot, and organic material acquired either at the source or during transport. The temperature and relative humidity ( RH) at which ice formed, varied only by 5% between samples, despite differences in particle composition, sources, and transport patterns. We hypothesize that this small variation in the onset RH may be due to the coating material on the particles. Finally, this study underscores and motivates the need to further investigate how long-range transported and atmospherically aged free tropospheric particles impact ice cloud formation.« less

Ice cloud formation potential by free tropospheric particles from long-range transport over the Northern Atlantic Ocean

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

China, Swarup; Alpert, Peter A.; Zhang, Bo

Long-range transported free tropospheric particles can play a significant role on heterogeneous ice nucleation. Using optical and electron microscopy we examine the physicochemical characteristics of ice nucleating particles (INPs). Particles were collected on substrates from the free troposphere at the remote Pico Mountain Observatory in the Azores Islands, after long-range transport and aging over the Atlantic Ocean. We investigate four specific events to study the ice formation potential by the collected particles with different ages and transport patterns. We use single-particle analysis, as well as bulk analysis to characterize particle populations. Both analyses show substantial differences in particle composition betweenmore » samples from the four events; in addition, single-particle microscopy analysis indicates that most particles are coated by organic material. The identified INPs contained mixtures of dust, aged sea salt and soot, and organic material acquired either at the source or during transport. The temperature and relative humidity ( RH) at which ice formed, varied only by 5% between samples, despite differences in particle composition, sources, and transport patterns. We hypothesize that this small variation in the onset RH may be due to the coating material on the particles. Finally, this study underscores and motivates the need to further investigate how long-range transported and atmospherically aged free tropospheric particles impact ice cloud formation.« less

The derived population of luminous supersoft X-ray sources

NASA Technical Reports Server (NTRS)

Di Stefano, R.STEFANO; Rappaport, S.

1994-01-01

The existence of a new class of astrophysical object, luminous supersoft X-ray sources, has been established through ROSAT satellite observations and analysis during the past approximately 3 yr. Because most of the radiation emitted by supersoft sources spans a range of wavelengths readily absorbed by interstellar gas, a substantial fraction of these sources may not be detectable with present satellite instrumentation. It is therefore important to derive a reliable estimate of the underlying population, based on the approximately 30 sources that have been observed to date. The work reported here combines the observational results with a theoretical analysis, to obtain an estimate of the total number of sources likely to be present in M31, the Magellanic Clouds, and in our own Galaxy. We find that in M31, where approximately 15 supersoft sources have been identified and roughly an equal number of sources are being investigated as supersoft candidates, there are likely to be approximately 2500 active supersoft sources at the present time. In our own Galaxy, where about four supersoft sources have been detected in the Galactic plane, there are likely to be approximately 1000 active sources. Similarly, with about six and about four (nonforeground) sources observed in the Large (LMC) and Small Magellanic Clouds (SMC), respectively, there should be approximately 30 supersoft sources in the LMC, and approximately 20 in the SMC. The likely uncertainties in the numbers quoted above, and the properties of observable sources relative to those of the total underlying population, are also derived in detail. These results can be scaled to estimate the numbers of supersoft sources likely to be present in other galaxies. The results reported here on the underlying population of supersoft X-ray sources are in good agreement with the results of a prior population synthesis study of the white dwarf accretor model for luminous supersoft X-ray sources. It should be emphasized, however, that the questions asked in these two investigations are distinct, that the approaches taken to answer these questions are largely independent and that the findings of these two studies could in principle have been quite different.

Remotely measuring populations during a crisis by overlaying two data sources

PubMed Central

Bharti, Nita; Lu, Xin; Bengtsson, Linus; Wetter, Erik; Tatem, Andrew J.

2015-01-01

Background Societal instability and crises can cause rapid, large-scale movements. These movements are poorly understood and difficult to measure but strongly impact health. Data on these movements are important for planning response efforts. We retrospectively analyzed movement patterns surrounding a 2010 humanitarian crisis caused by internal political conflict in Côte d'Ivoire using two different methods. Methods We used two remote measures, nighttime lights satellite imagery and anonymized mobile phone call detail records, to assess average population sizes as well as dynamic population changes. These data sources detect movements across different spatial and temporal scales. Results The two data sources showed strong agreement in average measures of population sizes. Because the spatiotemporal resolution of the data sources differed, we were able to obtain measurements on long- and short-term dynamic elements of populations at different points throughout the crisis. Conclusions Using complementary, remote data sources to measure movement shows promise for future use in humanitarian crises. We conclude with challenges of remotely measuring movement and provide suggestions for future research and methodological developments. PMID:25733558

Fixation Times in Deme Structured, Finite Populations with Rare Migration

NASA Astrophysics Data System (ADS)

Hauert, Christoph; Chen, Yu-Ting; Imhof, Lorens A.

2014-08-01

Population structure affects both the outcome and the speed of evolutionary dynamics. Here we consider a finite population that is divided into subpopulations called demes. The dynamics within the demes are stochastic and frequency-dependent. Individuals can adopt one of two strategic types, or . The fitness of each individual is determined by interactions with other individuals in the same deme. With small probability, proportional to fitness, individuals migrate to other demes. The outcome of these dynamics has been studied earlier by analyzing the fixation probability of a single mutant in an otherwise homogeneous population. These results give only a partial picture of the dynamics, because the time when fixation occurs can be exceedingly large. In this paper, we study the impact of deme structures on the speed of evolution. We derive analytical approximations of fixation times in the limit of rare migration and rare mutation. In this limit, the conditional fixation time of a single mutant in a population is the same as that of a single in an population. For the prisoner's dilemma game, simulation results fit very well with our analytical predictions and demonstrate that fixation takes place in a moderate amount of time as compared to the expected waiting time until a mutant successfully invades and fixates. The simulations also confirm that the conditional fixation time of a single cooperator is indeed the same as that of a single defector.

SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.

PubMed

Li, Jiannong; Smalley, Inna; Schell, Michael J; Smalley, Keiran S M; Chen, Y Ann

2017-09-15

Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet ( gle ell erogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using S hannon P rofile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the P rofile of S hannon D ifference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and/or within cell populations. The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/ . ann.chen@moffitt.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Single Nucleotide Polymorphisms in B-Genome Specific UDP-Glucosyl Transferases Associated with Fusarium Head Blight Resistance and Reduced Deoxynivalenol Accumulation in Wheat Grain.

PubMed

Sharma, Pallavi; Gangola, Manu P; Huang, Chen; Kutcher, H Randy; Ganeshan, Seedhabadee; Chibbar, Ravindra N

2018-01-01

An in vitro spike culture method was optimized to evaluate Fusarium head blight (FHB) resistance in wheat (Triticum aestivum) and used to screen a population of ethyl methane sulfonate treated spike culture-derived variants (SCDV). Of the 134 SCDV evaluated, the disease severity score of 47 of the variants was ≤30%. Single nucleotide polymorphisms (SNP) in the UDP-glucosyltransferase (UGT) genes, TaUGT-2B, TaUGT-3B, and TaUGT-EST, differed between AC Nanda (an FHB-susceptible wheat variety) and Sumai-3 (an FHB-resistant wheat cultivar). SNP at 450 and 1,558 bp from the translation initiation site in TaUGT-2B and TaUGT-3B, respectively were negatively correlated with FHB severity in the SCDV population, whereas the SNP in TaUGT-EST was not associated with FHB severity. Fusarium graminearum strain M7-07-1 induced early expression of TaUGT-2B and TaUGT-3B in FHB-resistant SCDV lines, which were associated with deoxynivalenol accumulation and reduced FHB disease progression. At 8 days after inoculation, deoxynivalenol concentration varied from 767 ppm in FHB-resistant variants to 2,576 ppm in FHB-susceptible variants. The FHB-resistant SCDV identified can be used as new sources of FHB resistance in wheat improvement programs.

Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices.

PubMed

Zhou, L; Lund, M S; Wang, Y; Su, G

2014-08-01

This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G-matrices) across these two breeds. Single-trait genomic best linear unbiased prediction (GBLUP) model and two-trait GBLUP model were used for single-breed and two-breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two-breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two-breed predictions. Weighting the two-breed G-matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two-breed predictions. © 2014 Blackwell Verlag GmbH.

Origin of Japanese White-Eyes and Brown-Eared Bulbuls on the Volcano Islands.

PubMed

Sugita, Norimasa; Kawakami, Kazuto; Nishiumi, Isao

2016-04-01

The Ogasawara Archipelago comprises two groups of oceanic islands: the Bonin Islands, formed in the Paleogene, and the Volcano Islands, formed in the Quaternary. These groups are located within a moderate distance (ca. 160-270 km) of one another; thus, most land bird species are not distinguished as different subspecies. Two land birds, however, show unusual distribution. The Japanese white-eyes Zosterops japonicus originally inhabited only the Volcano Islands, but has been introduced to the Bonin Islands. The brown-eared bulbuls Hypsipetes amaurotis are distributed as a different subspecies. We investigated their genetic differences and divergences in the Ogasawara Archipelago using mitochondria DNA. The Volcano population of white-eyes had four endemic haplotypes that were divergent from one another, except for the Bonin population, which shared three haplotypes with the Volcano, Izu, and Ryukyu Islands and did not have any endemic haplotype. This is the first genetic suggestion that the Bonin population is a hybrid of introduced populations. With respect to bulbuls, the Volcano and Bonin Islands each had a single endemic haplotype. The Volcano haplotype is closest to a haplotype shared with Izu, the Japanese mainland, Daito and Ryukyu, whereas the Bonin haplotype is closest to one endemic to the south Ryukyu Islands. This indicates that the sources of the two bulbul populations can be geologically and temporally distinguished. The populations of the two species in the Ogasawara Archipelago are irreplaceable, owing to their genetic differences and should be regarded as evolutionarily significant units. In order to prevent introgression between the two populations, we must restrict interisland transfers.

Intraspecific variation in aphid resistance and constitutive phenolics exhibited by the wild blueberry Vaccinium darrowi.

PubMed

Ranger, C M; Singh, A P; Johnson-Cicalese, J; Polavarapu, S; Vorsa, N

2007-04-01

Illinoia pepperi (MacGillivray) infests cultivated highbush blueberries, Vaccinium corymbosum L., in the Northeastern United States. Allopatric resistance to I. pepperi was examined in Vaccinium darrowi Camp, which evolved in the absence of I. pepperi in the Southeastern U.S. V. corymbosum cv. "Elliott", was used as a susceptible control. Between population variability in I. pepperi resistance was assessed by measuring length of the prereproductive period, fecundity, and survivorship on 14 V. darrowi accessions representing 11 discrete wild populations. Length of I. pepperi's prereproductive period and survivorship were not significantly affected. However, differences were detected in fecundity and the intrinsic rate of increase (r ( m )). Within population variability in resistance was measured by confining first instars to 24 accessions from a single wild population of V. darrowi (NJ88-06). Significant differences in the mean total number of aphids occurring after 20 d were only detected between 2 of the 24 V. darrowi accessions. A greater degree of diversity in I. pepperi resistance exists between populations of V. darrowi compared to within a population. Constitutive leaf and stem polyphenolics were identified by HPLC-MS and quantified from 14 of the V. darrowi accessions. The accessions varied in concentrations of five phenolic acids and seven flavonol glycosides, but a correlation was not found between individual or total phenolics and aphid performance. Overall, screening within and between populations of V. darrowi identified promising sources of aphid resistance, but phenolic acid and flavonol glycoside profiles did not predict resistance levels. The mechanism of resistance remains to be identified.

Systematic study of target localization for bioluminescence tomography guided radiation therapy

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

Yu, Jingjing; Zhang, Bin; Reyes, Juvenal

Purpose: To overcome the limitation of CT/cone-beam CT (CBCT) in guiding radiation for soft tissue targets, the authors developed a spectrally resolved bioluminescence tomography (BLT) system for the small animal radiation research platform. The authors systematically assessed the performance of the BLT system in terms of target localization and the ability to resolve two neighboring sources in simulations, tissue-mimicking phantom, and in vivo environments. Methods: Multispectral measurements acquired in a single projection were used for the BLT reconstruction. The incomplete variables truncated conjugate gradient algorithm with an iterative permissible region shrinking strategy was employed as the optimization scheme to reconstructmore » source distributions. Simulation studies were conducted for single spherical sources with sizes from 0.5 to 3 mm radius at depth of 3–12 mm. The same configuration was also applied for the double source simulation with source separations varying from 3 to 9 mm. Experiments were performed in a standalone BLT/CBCT system. Two self-illuminated sources with 3 and 4.7 mm separations placed inside a tissue-mimicking phantom were chosen as the test cases. Live mice implanted with single-source at 6 and 9 mm depth, two sources at 3 and 5 mm separation at depth of 5 mm, or three sources in the abdomen were also used to illustrate the localization capability of the BLT system for multiple targets in vivo. Results: For simulation study, approximate 1 mm accuracy can be achieved at localizing center of mass (CoM) for single-source and grouped CoM for double source cases. For the case of 1.5 mm radius source, a common tumor size used in preclinical study, their simulation shows that for all the source separations considered, except for the 3 mm separation at 9 and 12 mm depth, the two neighboring sources can be resolved at depths from 3 to 12 mm. Phantom experiments illustrated that 2D bioluminescence imaging failed to distinguish two sources, but BLT can provide 3D source localization with approximately 1 mm accuracy. The in vivo results are encouraging that 1 and 1.7 mm accuracy can be attained for the single-source case at 6 and 9 mm depth, respectively. For the 2 sources in vivo study, both sources can be distinguished at 3 and 5 mm separations, and approximately 1 mm localization accuracy can also be achieved. Conclusions: This study demonstrated that their multispectral BLT/CBCT system could be potentially applied to localize and resolve multiple sources at wide range of source sizes, depths, and separations. The average accuracy of localizing CoM for single-source and grouped CoM for double sources is approximately 1 mm except deep-seated target. The information provided in this study can be instructive to devise treatment margins for BLT-guided irradiation. These results also suggest that the 3D BLT system could guide radiation for the situation with multiple targets, such as metastatic tumor models.« less

A high-power fiber-coupled semiconductor light source with low spatio-temporal coherence

NASA Astrophysics Data System (ADS)

Schittko, Robert; Mazurenko, Anton; Tai, M. Eric; Lukin, Alexander; Rispoli, Matthew; Menke, Tim; Kaufman, Adam M.; Greiner, Markus

2017-04-01

Interference-induced distortions pose a significant challenge to a variety of experimental techniques, ranging from full-field imaging applications in biological research to the creation of optical potentials in quantum gas microscopy. Here, we present a design of a high-power, fiber-coupled semiconductor light source with low spatio-temporal coherence that bears the potential to reduce the impact of such distortions. The device is based on an array of non-lasing semiconductor emitters mounted on a single chip whose optical output is coupled into a multi-mode fiber. By populating a large number of fiber modes, the low spatial coherence of the input light is further reduced due to the differing optical path lengths amongst the modes and the short coherence length of the light. In addition to theoretical calculations showcasing the feasibility of this approach, we present experimental measurements verifying the low degree of spatial coherence achievable with such a source, including a detailed analysis of the speckle contrast at the fiber end. We acknowledge support from the National Science Foundation, the Gordon and Betty Moore Foundation's EPiQS Initiative, an Air Force Office of Scientific Research MURI program and an Army Research Office MURI program.

Genetic Mapping of Resistance to Meloidogyne arenaria in Arachis stenosperma: A New Source of Nematode Resistance for Peanut

PubMed Central

Leal-Bertioli, Soraya C. M.; Moretzsohn, Márcio C.; Roberts, Philip A.; Ballén-Taborda, Carolina; Borba, Tereza C. O.; Valdisser, Paula A.; Vianello, Rosana P.; Araújo, Ana Cláudia G; Guimarães, Patricia M.; Bertioli, David J.

2015-01-01

Root-knot nematodes (RKN; Meloidogyne sp.) are a major threat to crops in tropical and subtropical regions worldwide. The use of resistant crop varieties is the preferred method of control because nematicides are expensive, and hazardous to humans and the environment. Peanut (Arachis hypogaea) is infected by four species of RKN, the most damaging being M. arenaria, and commercial cultivars rely on a single source of resistance. In this study, we genetically characterize RKN resistance of the wild Arachis species A. stenosperma using a population of 93 recombinant inbred lines developed from a cross between A. duranensis and A. stenosperma. Four quantitative trait loci (QTL) located on linkage groups 02, 04, and 09 strongly influenced nematode root galling and egg production. Drought-related, domestication and agronomically relevant traits were also evaluated, revealing several QTL. Using the newly available Arachis genome sequence, easy-to-use KASP (kompetitive allele specific PCR) markers linked to the newly identified RKN resistance loci were developed and validated in a tetraploid context. Therefore, we consider that A. stenosperma has high potential as a new source of RKN resistance in peanut breeding programs. PMID:26656152

The Massive Star-forming Regions Omnibus X-ray Catalog, Second Installment

NASA Astrophysics Data System (ADS)

Townsley, Leisa K.; Broos, Patrick S.; Garmire, Gordon P.; Anderson, Gemma E.; Feigelson, Eric D.; Naylor, Tim; Povich, Matthew S.

2018-04-01

We present the second installment of the Massive Star-forming Regions (MSFRs) Omnibus X-ray Catalog (MOXC2), a compilation of X-ray point sources detected in Chandra/ACIS observations of 16 Galactic MSFRs and surrounding fields. MOXC2 includes 13 ACIS mosaics, three containing a pair of unrelated MSFRs at different distances, with a total catalog of 18,396 point sources. The MSFRs sampled range over distances of 1.3 kpc to 6 kpc and populations varying from single massive protostars to the most massive Young Massive Cluster known in the Galaxy. By carefully detecting and removing X-ray point sources down to the faintest statistically significant limit, we facilitate the study of the remaining unresolved X-ray emission. Through comparison with mid-infrared images that trace photon-dominated regions and ionization fronts, we see that the unresolved X-ray emission is due primarily to hot plasmas threading these MSFRs, the result of feedback from the winds and supernovae of massive stars. The 16 MSFRs studied in MOXC2 more than double the MOXC1 sample, broadening the parameter space of ACIS MSFR explorations and expanding Chandra's substantial contribution to contemporary star formation science.

Detection of potential periodicities in the unique hard X-ray source Swift J0042.6+4112, dominating the hard X-ray emission in M31

NASA Astrophysics Data System (ADS)

Yukita, Mihoko; Tzanavaris, Panayiotis; Corbet, Robin; Ptak, Andrew; Hornschemeier, Ann; Pottschmidt, Katja; Ballhausen, Ralf; Enoto, Teruaki; Antoniou, Vallia; Lehmer, Bret; Maccarone, Thomas J.; Wik, Daniel; Williams, Ben; Zezas, Andreas

2018-01-01

Recent NuSTAR-Swift observations revealed that a single resolved X-ray source, Swift J0042.6+4112, with Lx of a few times 1038 erg/s dominates the hard X-ray emission from the Andromeda galaxy. HST-based stellar population synthesis modeling combined with the 0.5-50 keV spectral shape suggests that this might be an X-ray pulsar with an intermediate- (or low-) mass donor. Here we further explore the alternative scenario of a symbiotic or ultracompact X-ray binary, based on long-term variability from Swift observations between 2005 and 2016. We find that the soft (0.3-8.0 keV) X-ray flux varies within a factor of 4 but does not exhibit transient behavior. Its power spectrum suggests a 6.1-day period. Additionally, we find a strong 3s-period candidate from both NuSTAR and XMM observations taken in 2017. If interpreted as an orbital and spin period respectively, the source's temporal behavior would not support either the symbiotic or the ultracompact X-ray binary scenario. Rather, it is more consistent with an accreting pulsar with a higher mass donor.

Single-ring magnetic cusp low gas pressure ion source

DOEpatents

Bacon, Frank M.; Brainard, John P.; O'Hagan, James B.; Walko, Robert J.

1985-01-01

A single-ring magnetic cusp low gas pressure ion source designed for use in a sealed, nonpumped neutron generator utilizes a cathode and an anode, three electrically floating electrodes (a reflector behind the cathode, a heat shield around the anode, and an aperture plate), together with a single ring-cusp magnetic field, to establish and energy-filtering mechanism for producing atomic-hydrogen ions.

A high repetition deterministic single ion source

NASA Astrophysics Data System (ADS)

Sahin, C.; Geppert, P.; Müllers, A.; Ott, H.

2017-12-01

We report on a deterministic single ion source with high repetition rate and high fidelity. The source employs a magneto-optical trap, where ultracold rubidium atoms are photoionized. The electrons herald the creation of a corresponding ion, whose timing information is used to manipulate its trajectory in flight. We demonstrate an ion rate of up to 4× {10}4 {{{s}}}-1 and achieve a fidelity for single ion operation of 98%. The technique can be used for all atomic species, which can be laser-cooled, and opens up new applications in ion microscopy, ion implantation and surface spectroscopy.

Compact high-power red-green-blue laser light source generation from a single lithium tantalate with cascaded domain modulation.

PubMed

Xu, P; Zhao, L N; Lv, X J; Lu, J; Yuan, Y; Zhao, G; Zhu, S N

2009-06-08

1W quasi-white-light source has been generated from a single lithium tantalate with cascaded domain modulation. The quasi-white-light is combined by proper proportion of the red, green and blue laser light. The red and the blue result from a compact self-sum frequency optical parametric oscillation when pumped by a single green laser. The efficiency of quasi-white-light from the green pump reaches 27%. This compact design can be employed not only as a stable and powerful RGB light source but also an effective blue laser generator.

Single- and multi-channel underwater acoustic communication channel capacity: a computational study.

PubMed

Hayward, Thomas J; Yang, T C

2007-09-01

Acoustic communication channel capacity determines the maximum data rate that can be supported by an acoustic channel for a given source power and source/receiver configuration. In this paper, broadband acoustic propagation modeling is applied to estimate the channel capacity for a time-invariant shallow-water waveguide for a single source-receiver pair and for vertical source and receiver arrays. Without bandwidth constraints, estimated single-input, single-output (SISO) capacities approach 10 megabitss at 1 km range, but beyond 2 km range they decay at a rate consistent with previous estimates by Peloquin and Leinhos (unpublished, 1997), which were based on a sonar equation calculation. Channel capacities subject to source bandwidth constraints are approximately 30-90% lower than for the unconstrained case, and exhibit a significant wind speed dependence. Channel capacity is investigated for single-input, multi-output (SIMO) and multi-input, multi-output (MIMO) systems, both for finite arrays and in the limit of a dense array spanning the entire water column. The limiting values of the SIMO and MIMO channel capacities for the modeled environment are found to be about four times higher and up to 200-400 times higher, respectively, than for the SISO case. Implications for underwater acoustic communication systems are discussed.

MOBILE GAMMA IRRADIATORS FOR FRUIT PRODUCE (Engineering Materials)

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

None

1963-10-31

Mobile irradiators used for the radiopasteurization of strawberries, grapes, peaches, tomatoes, and lemons are described. The irradiators are mounted on trailers and each irradiator, including the trailer, weighs 70 to 80 tons. Radiatton doses range from 100,000 to 200,000 rads. Minimum production is 500 lb of fruit per hour. Drawings are included for four types of irradiators: the single-slab twopass, double-slab one-pass, single-slab four-pass, and line-source rotary. In the single-slab two-pass system, the packages make two passes in front of the source. The length of the packages is parallel to the direction of travel. The packages are irradiated on eachmore » side. This system is light in weight, has low capital cost, and is simple to fabricate. The double-slab one- pass system is the same as the above except the source strength is doubled and irradiation time is cut in half. The same arrangement is used in the single-slab four-pass system that is used in the singleslab two-pass system except the packages make two passes on each side of the source. The rotary system combines a linear and rotary motion to provide high dosage. It uses a small Co/sup 60/ source but costs more than a single-slab twopass system. (F.E.S.)« less

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

PubMed

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22-48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.

[Multicriteria evaluation of environmental risk exposure using a geographic information system in Argentina].

PubMed

Pietri, Diana De; Dietrich, Patricia; Mayo, Patricia; Carcagno, Alejandro

2011-10-01

Develop a spatial model that includes environmental factors posing a health hazard, for application in the Matanza-Riachuelo River Basin (MRB) in Argentina. Multicriteria evaluation procedures were used with geographic information systems to obtain territorial zoning based on the degree of suitability for residence. Variables that characterize the habitability of housing and potential sources of basin pollution were geographically referenced. Health information was taken from the Risk Factor Survey (RFS) to measure the relative risk of living in unsuitable areas (exposed population) compared with suitable areas (unexposed population). Sixty percent of the MRB area is in suitable condition, a situation that affects 40% of residents. The rest of the population lives in unsuitable territory, and 6% live in the basin's most unsuitable conditions. Environmental conditions that are detrimental to health in the unsuitable areas became evident during the interviews through three of the pathologies considered: diarrheal diseases, respiratory diseases, and cancer. A regional analysis that provides valid information to support decisionmaking was obtained. Considering the basin as a unit of analysis allowed the use of a single protocol to undertake comprehensive measurement of the magnitude of risk and, thus, set priorities.

Comparison of methods used to estimate numbers of walruses on sea ice

USGS Publications Warehouse

Udevitz, Mark S.; Gilbert, James R.; Fedoseev, Gennadii A.

2001-01-01

The US and former USSR conducted joint surveys of Pacific walruses on sea ice and at land haul-outs in 1975, 1980, 1985, and 1990. One of the difficulties in interpreting results of these surveys has been that, except for the 1990 survey, the Americans and Soviets used different methods for estimating population size from their respective portions of the sea ice data. We used data exchanged between Soviet and American scientists to compare and evaluate the two estimation procedures and to derive a set of alternative estimates from the 1975, 1980, and 1985 surveys based on a single consistent procedure. Estimation method had only a small effect on total population estimates because most walruses were found at land haul-outs. However, the Soviet method is subject to bias that depends on the distribution of the population on the sea ice and this has important implications for interpreting the ice portions of previously reported surveys for walruses and other pinniped species. We recommend that the American method be used in future surveys. Future research on survey methods for walruses should focus on other potential sources of bias and variation.

Portable atomic frequency standard based on coherent population trapping

NASA Astrophysics Data System (ADS)

Shi, Fan; Yang, Renfu; Nian, Feng; Zhang, Zhenwei; Cui, Yongshun; Zhao, Huan; Wang, Nuanrang; Feng, Keming

2015-05-01

In this work, a portable atomic frequency standard based on coherent population trapping is designed and demonstrated. To achieve a portable prototype, in the system, a single transverse mode 795nm VCSEL modulated by a 3.4GHz RF source is used as a pump laser which generates coherent light fields. The pump beams pass through a vapor cell containing atom gas and buffer gas. This vapor cell is surrounded by a magnetic shield and placed inside a solenoid which applies a longitudinal magnetic field to lift the Zeeman energy levels' degeneracy and to separate the resonance signal, which has no first-order magnetic field dependence, from the field-dependent resonances. The electrical control system comprises two control loops. The first one locks the laser wavelength to the minimum of the absorption spectrum; the second one locks the modulation frequency and output standard frequency. Furthermore, we designed the micro physical package and realized the locking of a coherent population trapping atomic frequency standard portable prototype successfully. The short-term frequency stability of the whole system is measured to be 6×10-11 for averaging times of 1s, and reaches 5×10-12 at an averaging time of 1000s.

Enhancing health care professionals' and trainees' knowledge of physical activity guidelines for adults with and without SCI.

PubMed

Shirazipour, Celina H; Tomasone, Jennifer R; Martin Ginis, Kathleen A

2018-01-11

Health care providers (HCPs) are preferred sources of physical activity (PA) information; however, minimal research has explored HCPs' knowledge of spinal cord injury (SCI) PA guidelines, and no research has examined HCP trainees' PA guideline knowledge. The current study explored HCPs' and trainees' initial knowledge of PA guidelines for both adults with SCI and the general population, and the utility of an event-based intervention for improving this knowledge. Participants (HCPs n = 129; trainees n = 573) reported guideline knowledge for both sets of guidelines (SCI and general population) immediately after, one-month, and six-months following the intervention. Frequencies determined guideline knowledge at each timepoint, while chi-squared tests examined differences in knowledge of both guidelines, as well as knowledge differences in the short- and long-term. Results demonstrated that HCPs and trainees lack knowledge of PA guidelines, particularly guidelines for adults with SCI. The results further suggest that a single event-based intervention is not effective for improving long-term guideline knowledge. Suggestions are made for future research with the aim of improving interventions that target HCP and HCP trainees' long-term guideline knowledge for adults with SCI and the general population.

Leveraging Hierarchical Population Structure in Discrete Association Studies

PubMed Central

Carlson, Jonathan; Kadie, Carl; Mallal, Simon; Heckerman, David

2007-01-01

Population structure can confound the identification of correlations in biological data. Such confounding has been recognized in multiple biological disciplines, resulting in a disparate collection of proposed solutions. We examine several methods that correct for confounding on discrete data with hierarchical population structure and identify two distinct confounding processes, which we call coevolution and conditional influence. We describe these processes in terms of generative models and show that these generative models can be used to correct for the confounding effects. Finally, we apply the models to three applications: identification of escape mutations in HIV-1 in response to specific HLA-mediated immune pressure, prediction of coevolving residues in an HIV-1 peptide, and a search for genotypes that are associated with bacterial resistance traits in Arabidopsis thaliana. We show that coevolution is a better description of confounding in some applications and conditional influence is better in others. That is, we show that no single method is best for addressing all forms of confounding. Analysis tools based on these models are available on the internet as both web based applications and downloadable source code at http://atom.research.microsoft.com/bio/phylod.aspx. PMID:17611623

Radiation exposure from consumer products and miscellaneous sources

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

Not Available

1977-01-01

This review of the literature indicates that there is a variety of consumer products and miscellaneous sources of radiation that result in exposure to the U.S. population. A summary of the number of people exposed to each such source, an estimate of the resulting dose equivalents to the exposed population, and an estimate of the average annual population dose equivalent are tabulated. A review of the data in this table shows that the total average annual contribution to the whole-body dose equivalent of the U.S. population from consumer products is less than 5 mrem; about 70 percent of this arisesmore » from the presence of naturally-occurring radionuclides in building materials. Some of the consumer product sources contribute exposure mainly to localized tissues or organs. Such localized estimates include: 0.5 to 1 mrem to the average annual population lung dose equivalent (generalized); 2 rem to the average annual population bronchial epithelial dose equivalent (localized); and 10 to 15 rem to the average annual population basal mucosal dose equivalent (basal mucosa of the gum). Based on these estimates, these sources may be grouped or classified as those that involve many people and the dose equivalent is relative large or those that involve many people but the dose equivalent is relatively small, or the dose equivalent is relatively large but the number of people involved is small.« less

Knowledge, attitude and practice of modern contraception among single women in a rural and urban community in southeast Nigeria.

PubMed

Ozumba, B C; Obi, S N; Ijioma, N N

2005-04-01

The contraceptive information and services offered to single women in most developing countries is compromised by stigma attached to premarital sex. This study was to ascertain the knowledge, attitude and practice of contraception among single women in a rural and urban community in southeast Nigeria, using a cross-sectional survey of 279 and 295 single women in Ngwo (rural) and Enugu (urban) community. The mean age of the population was 21.3 years. Contraceptive awareness was more among the urban than rural respondents (90.2% vs 34.1%). The major sources of contraceptive knowledge were mass media (68%) and peer groups (86.3%) for the urban and rural respondents, respectively. Most respondents in both groups had positive attitude towards contraception. More urban than rural respondents (68.3% vs 12.5%) began sexual activity during adolescence and the level of contraceptive use during first coitus were 48.4% and 13.7%, respectively. Of the currently sexually active respondents, 32.5% (rural) and 59.7% (urban) were using a form of modern contraception. Condoms, followed by oral pills were the most popular contraceptive method because they can easily procure them over the counter. Poor contraceptive information, highly critical behavior of family planning providers towards unmarried women seeking contraception and attitude of male partners militate against contraceptive practice. There is need to promote information and education on contraception among single women, their male partners and family planning providers.

A search for dispersed radio bursts in archival Parkes Multibeam Pulsar Survey data

NASA Astrophysics Data System (ADS)

Bagchi, Manjari; Nieves, Angela Cortes; McLaughlin, Maura

2012-10-01

A number of different classes of potentially extra-terrestrial bursts of radio emission have been observed in surveys with the Parkes 64-m radio telescope, including 'rotating radio transients', the 'Lorimer burst' and 'perytons'. Rotating radio transients are radio pulsars which are best detectable in single-pulse searches. The Lorimer burst is a highly dispersed isolated radio burst with properties suggestive of extragalactic origin. Perytons share the frequency-swept nature of the rotating radio transients and Lorimer burst, but unlike these events appear in all 13 beams of the Parkes multibeam receiver and are probably a form of peculiar radio frequency interference. In order to constrain these and other radio source populations further, we searched the archival Parkes Multibeam Pulsar Survey data for events similar to any of these. We did not find any new rotating radio transients or bursts like the Lorimer burst. We did, however, discover four peryton-like events. Similar to the perytons, these four bursts are highly dispersed, detected in all 13 beams of the Parkes multibeam receiver, and have pulse widths between 20 and 30 ms. Unlike perytons, these bursts are not associated with atmospheric events like rain or lightning. These facts may indicate that lightning was not responsible for the peryton phenomenon. Moreover, the lack of highly dispersed celestial signals is the evidence that the Lorimer burst is unlikely to belong to a cosmological source population.

Bilayer graphene phonovoltaic-FET: In situ phonon recycling

NASA Astrophysics Data System (ADS)

Melnick, Corey; Kaviany, Massoud

2017-11-01

A new heat harvester, the phonovoltaic (pV) cell, was recently proposed. The device converts optical phonons into power before they become heat. Due to the low entropy of a typical hot optical phonon population, the phonovoltaic can operate at high fractions of the Carnot limit and harvest heat more efficiently than conventional heat harvesting technologies such as the thermoelectric generator. Previously, the optical phonon source was presumed to produce optical phonons with a single polarization and momentum. Here, we examine a realistic optical phonon source in a potential pV application and the effects this has on pV operation. Supplementing this work is our investigation of bilayer graphene as a new pV material. Our ab initio calculations show that bilayer graphene has a figure of merit exceeding 0.9, well above previously investigated materials. This allows a room-temperature pV to recycle 65% of a highly nonequilibrium, minimum entropy population of phonons. However, full-band Monte Carlo simulations of the electron and phonon dynamics in a bilayer graphene field-effect transistor (FET) show that the optical phonons emitted by field-accelerated electrons can only be recycled in situ with an efficiency of 50%, and this efficiency falls as the field strength grows. Still, an appropriately designed FET-pV can recycle the phonons produced therein in situ with a much higher efficiency than a thermoelectric generator can harvest heat produced by a FET ex situ.

Diagnostic value of circulating microRNAs for gastric cancer in Asian populations: a meta-analysis.

PubMed

Liu, Lihua; Wang, Shan; Cao, Xiutang; Liu, Jianchao

2014-12-01

Gastric cancer (GC) accounts for one of the highest mortality worldwide and particularly in East Asia. Many studies have reported on the potential value of microRNAs (miRNAs) detection for diagnosing GC, but their results have proven inconclusive. The present meta-analysis was conducted to assess the diagnostic value of circulating miRNAs for GC diagnosis. A literature search was carried out in databases (PubMed, Embase, Web of Science, The Cochrane Library, and CNKI) and other sources using combinations of keywords relating to GC, miRNAs, and diagnosis. The values of sensitivity, specificity, positive likelihood ratios (PLR), negative likelihood ratios (NLR), and diagnostic odds ratio (DOR) reported in individual studies were pooled using random-effects models. Potential sources of heterogeneity were assessed with subgroup and meta-regression analyses. The summary receiver operating characteristic (SROC) curve and the area under the curve (AUC) were used to assess the diagnosis accuracy of miRNAs. This meta-analysis included 1,279 patients with GC and 954 healthy controls from 20 publications. The pooled sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.78 (95 % CI: 0.73-0.81), 0.80 (95 % CI: 0.76-0.84), 4.0 (95 % CI: 3.1-6.0), 0.28 (95 % CI: 0.23-0.34), 14 (95 % CI: 10-21), and 0.86 (95 % CI: 0.83-0.89), respectively. Subgroup analyses showed that early stages (I and II) GC were more easily detected than later stages and that multiple miRNAs assays were more accurate than single miRNA assays. Our meta-analysis suggests that miRNAs have a high diagnostic value for GC, especially in its early stages (I and II). In addition, multiple miRNAs assays have a better diagnosis value than single miRNA assays. In conclusion, circulating miRNAs might be used as noninvasive biomarkers for the confirmation of GC detection in Asian populations.

Using species abundance distribution models and diversity indices for biogeographical analyses

NASA Astrophysics Data System (ADS)

Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

2016-01-01

We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for biogeographical purposes.

Combining multiple sources of data to inform conservation of Lesser Prairie-Chicken populations

USGS Publications Warehouse

Ross, Beth; Haukos, David A.; Hagen, Christian A.; Pitman, James

2018-01-01

Conservation of small populations is often based on limited data from spatially and temporally restricted studies, resulting in management actions based on an incomplete assessment of the population drivers. If fluctuations in abundance are related to changes in weather, proper management is especially important, because extreme weather events could disproportionately affect population abundance. Conservation assessments, especially for vulnerable populations, are aided by a knowledge of how extreme events influence population status and trends. Although important for conservation efforts, data may be limited for small or vulnerable populations. Integrated population models maximize information from various sources of data to yield population estimates that fully incorporate uncertainty from multiple data sources while allowing for the explicit incorporation of environmental covariates of interest. Our goal was to assess the relative influence of population drivers for the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) in the core of its range, western and southern Kansas, USA. We used data from roadside lek count surveys, nest monitoring surveys, and survival data from telemetry monitoring combined with climate (Palmer drought severity index) data in an integrated population model. Our results indicate that variability in population growth rate was most influenced by variability in juvenile survival. The Palmer drought severity index had no measurable direct effects on adult survival or mean number of offspring per female; however, there were declines in population growth rate following severe drought. Because declines in population growth rate occurred at a broad spatial scale, declines in response to drought were likely due to decreases in chick and juvenile survival rather than emigration outside of the study area. Overall, our model highlights the importance of accounting for environmental and demographic sources of variability, and provides a thorough method for simultaneously evaluating population demography in response to long-term climate effects.

A framework for estimating the determinants of spatial and temporal variation in vital rates and inferring the occurrence of unobserved extreme events

PubMed Central

Jesenšek, Dušan; Crivelli, Alain J.

2018-01-01

We develop a general framework that combines long-term tag–recapture data and powerful statistical and modelling techniques to investigate how population, environmental and climate factors determine variation in vital rates and population dynamics in an animal species, using as a case study the population of brown trout living in Upper Volaja (Western Slovenia). This population has been monitored since 2004. Upper Volaja is a sink, receiving individuals from a source population living above a waterfall. We estimate the numerical contribution of the source population on the sink population and test the effects of temperature, population density and extreme events on variation in vital rates among 2647 individually tagged brown trout. We found that individuals dispersing downstream from the source population help maintain high population densities in the sink population despite poor recruitment. The best model of survival for individuals older than juveniles includes additive effects of birth cohort and sampling occasion. Fast growth of older cohorts and higher population densities in 2004–2005 suggest very low population densities in the late 1990s, which we hypothesize were caused by a flash flood that strongly reduced population size and created the habitat conditions for faster individual growth and transient higher population densities after the extreme event. PMID:29657746

A framework for estimating the determinants of spatial and temporal variation in vital rates and inferring the occurrence of unobserved extreme events.

PubMed

Vincenzi, Simone; Jesenšek, Dušan; Crivelli, Alain J

2018-03-01

We develop a general framework that combines long-term tag-recapture data and powerful statistical and modelling techniques to investigate how population, environmental and climate factors determine variation in vital rates and population dynamics in an animal species, using as a case study the population of brown trout living in Upper Volaja (Western Slovenia). This population has been monitored since 2004. Upper Volaja is a sink, receiving individuals from a source population living above a waterfall. We estimate the numerical contribution of the source population on the sink population and test the effects of temperature, population density and extreme events on variation in vital rates among 2647 individually tagged brown trout. We found that individuals dispersing downstream from the source population help maintain high population densities in the sink population despite poor recruitment. The best model of survival for individuals older than juveniles includes additive effects of birth cohort and sampling occasion. Fast growth of older cohorts and higher population densities in 2004-2005 suggest very low population densities in the late 1990s, which we hypothesize were caused by a flash flood that strongly reduced population size and created the habitat conditions for faster individual growth and transient higher population densities after the extreme event.

Single-photon emitting diode in silicon carbide.

PubMed

Lohrmann, A; Iwamoto, N; Bodrog, Z; Castelletto, S; Ohshima, T; Karle, T J; Gali, A; Prawer, S; McCallum, J C; Johnson, B C

2015-07-23

Electrically driven single-photon emitting devices have immediate applications in quantum cryptography, quantum computation and single-photon metrology. Mature device fabrication protocols and the recent observations of single defect systems with quantum functionalities make silicon carbide an ideal material to build such devices. Here, we demonstrate the fabrication of bright single-photon emitting diodes. The electrically driven emitters display fully polarized output, superior photon statistics (with a count rate of >300 kHz) and stability in both continuous and pulsed modes, all at room temperature. The atomic origin of the single-photon source is proposed. These results provide a foundation for the large scale integration of single-photon sources into a broad range of applications, such as quantum cryptography or linear optics quantum computing.

Low-Cost, Single-Frequency Sources for Spectroscopy using Conventional Fabry-Perot Diode Lasers

NASA Technical Reports Server (NTRS)

Duerksen, Gary L.; Krainak, Michael A.

1999-01-01

Commercial (uncoated) Fabry-Perot laser diodes are converted to single-frequency spectroscopy sources by passively locking the laser frequency to the band edge of a fiber Bragg grating, which phase-locks the laser oscillations through self-injection seeding.

Low-Cost, Single-Frequency Sources for Spectroscopy Using Conventional Fabry-Perot Diode Lasers

NASA Technical Reports Server (NTRS)

Krainak, Michael A.; Duerksen, Gary L.

1999-01-01

Commercial (uncoated) Fabry-Perot laser diodes are converted to single-frequency spectroscopy sources by passively locking the laser frequency to the band edge of a fiber Bragg grating, which phase-locks the laser oscillations through self-injection seeding.

Characterizing source-sink dynamics with genetic parentage assignments

Treesearch

M. Zachariah Peery; Steven R. Beissinger; Roger F. House; Martine Berube; Laurie A. Hall; Anna Sellas; Per J. Palsboll

2008-01-01

Source-sink dynamics have been suggested to characterize the population structure of many species, but the prevalence of source-sink systems in nature is uncertain because of inherent challenges in estimating migration rates among populations. Migration rates are often difficult to estimate directly with demographic methods, and indirect genetic methods are subject to...

Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.

PubMed

Ibstedt, Sebastian; Stenberg, Simon; Bagés, Sara; Gjuvsland, Arne B; Salinas, Francisco; Kourtchenko, Olga; Samy, Jeevan K A; Blomberg, Anders; Omholt, Stig W; Liti, Gianni; Beltran, Gemma; Warringer, Jonas

2015-01-01

Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Deep Chandra ACIS Survey of M51

NASA Astrophysics Data System (ADS)

Kuntz, K. D.; Long, Knox S.; Kilgard, Roy E.

2016-08-01

We have obtained a deep X-ray image of the nearby galaxy M51 using Chandra. Here we present the catalog of X-ray sources detected in these observations and provide an overview of the properties of the point-source population. We find 298 sources within the D 25 radii of NGC 5194/5, of which 20% are variable, a dozen are classical transients, and another half dozen are transient-like sources. The typical number of active ultraluminous X-ray sources in any given observation is ˜5, and only two of those sources persist in an ultraluminous state over the 12 yr of observations. Given reasonable assumptions about the supernova remnant population, the luminosity function is well described by a power law with an index between 1.55 and 1.7, only slightly shallower than that found for populations dominated by high-mass X-ray binaries (HMXBs), which suggests that the binary population in NGC 5194 is also dominated by HMXBs. The luminosity function of NGC 5195 is more consistent with a low-mass X-ray binary dominated population. Based on observations made with NASA's Chandra X-ray Observatory, which is operated by the Smithsonian Astrophysical Observatory under contract #NAS83060, and the data were obtained through program GO1-12115.

Gravitational wave hotspots: Ranking potential locations of single-source gravitational wave emission

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

Simon, Joseph; Polin, Abigail; Lommen, Andrea

2014-03-20

The steadily improving sensitivity of pulsar timing arrays (PTAs) suggests that gravitational waves (GWs) from supermassive black hole binary (SMBHB) systems in the nearby universe will be detectable sometime during the next decade. Currently, PTAs assume an equal probability of detection from every sky position, but as evidence grows for a non-isotropic distribution of sources, is there a most likely sky position for a detectable single source of GWs? In this paper, a collection of Galactic catalogs is used to calculate various metrics related to the detectability of a single GW source resolvable above a GW background, assuming that everymore » galaxy has the same probability of containing an SMBHB. Our analyses of these data reveal small probabilities that one of these sources is currently in the PTA band, but as sensitivity is improved regions of consistent probability density are found in predictable locations, specifically around local galaxy clusters.« less

Beyond the bulk: disclosing the life of single microbial cells

PubMed Central

Rosenthal, Katrin; Oehling, Verena

2017-01-01

Abstract Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples. PMID:29029257

Patterns of Genetic Variation among Populations of the Asian Longhorned Beetle in China and Korea

USDA-ARS?s Scientific Manuscript database

Central to the study of invasive species is identifying source populations in their native ranges. Source populations of invasive species can provide important information about species life cycles, host use and species-specific predators and parasites which could be deployed in a pest control prog...

Local source impacts on primary and secondary aerosols in the Midwestern United States

NASA Astrophysics Data System (ADS)

Jayarathne, Thilina; Rathnayake, Chathurika M.; Stone, Elizabeth A.

2016-04-01

Atmospheric particulate matter (PM) exhibits heterogeneity in composition across urban areas, leading to poor representation of outdoor air pollutants in human exposure assessments. To examine heterogeneity in PM composition and sources across an urban area, fine particulate matter samples (PM2.5) were chemically profiled in Iowa City, IA from 25 August to 10 November 2011 at two monitoring stations. The urban site is the federal reference monitoring (FRM) station in the city center and the peri-urban site is located 8.0 km to the west on the city edge. Measurements of PM2.5 carbonaceous aerosol, inorganic ions, molecular markers for primary sources, and secondary organic aerosol (SOA) tracers were used to assess statistical differences in composition and sources across the two sites. PM2.5 mass ranged from 3 to 26 μg m-3 during this period, averaging 11.2 ± 4.9 μg m-3 (n = 71). Major components of PM2.5 at the urban site included organic carbon (OC; 22%), ammonium (14%), sulfate (13%), nitrate (7%), calcium (2.9%), and elemental carbon (EC; 2.2%). Periods of elevated PM were driven by increases in ammonium, sulfate, and SOA tracers that coincided with hot and dry conditions and southerly winds. Chemical mass balance (CMB) modeling was used to apportion OC to primary sources; biomass burning, vegetative detritus, diesel engines, and gasoline engines accounted for 28% of OC at the urban site and 24% of OC at the peri-urban site. Secondary organic carbon from isoprene and monoterpene SOA accounted for an additional 13% and 6% of OC at the urban and peri-urban sites, respectively. Differences in biogenic SOA across the two sites were associated with enhanced combustion activities in the urban area and higher aerosol acidity at the urban site. Major PM constituents (e.g., OC, ammonium, sulfate) were generally well-represented by a single monitoring station, indicating a regional source influence. Meanwhile, nitrate, biomass burning, food cooking, suspended dust, and biogenic SOA were not well-represented by a single site and demonstrated local influences. For isoprene SOA, product distributions indicated a larger role for the high-NOx pathway at the urban site. These local sources are largely responsible for differences in population exposures to outdoor PM in the study domain located within the Midwestern US.