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  • Public Library of Science  (34,884)
  • Oxford University Press  (21,988)
  • American Institute of Physics (AIP)  (14,366)
  • Cell Press  (10,827)
  • American Association for the Advancement of Science (AAAS)
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  • 1
    Publication Date: 2020-02-12
    Description: Background The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious “guilty-by-association” approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Cell Press
    In:  EPIC3Current Biology, Cell Press, 23(14), pp. 1330-1334, ISSN: 09609822
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56393, doi:10.1371/journal.pone.0056393.
    Description: Evolutionary constraints which limit the forces produced during bell contractions of medusae affect the overall medusan morphospace such that jet propulsion is limited to only small medusae. Cubomedusae, which often possess large prolate bells and are thought to swim via jet propulsion, appear to violate the theoretical constraints which determine the medusan morphospace. To examine propulsion by cubomedusae, we quantified size related changes in wake dynamics, bell shape, swimming and turning kinematics of two species of cubomedusae, Chironex fleckeri and Chiropsella bronzie. During growth, these cubomedusae transitioned from using jet propulsion at smaller sizes to a rowing-jetting hybrid mode of propulsion at larger sizes. Simple modifications in the flexibility and kinematics of their velarium appeared to be sufficient to alter their propulsive mode. Turning occurs during both bell contraction and expansion and is achieved by generating asymmetric vortex structures during both stages of the swimming cycle. Swimming characteristics were considered in conjunction with the unique foraging strategy used by cubomedusae.
    Description: This work was supported by an ONR MURI award (N000140810654) and National Science Foundation grant OCE 0623508 to JHC, SPC, JOD. And the work was supported by the Roger Williams University Foundation to Promote Scholarship.
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-25
    Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS ONE 8 (2013): e55273, doi:10.1371/journal.pone.0055273.
    Description: Georges Bank is a large, shallow feature separating the Gulf of Maine from the Atlantic Ocean. Previous studies demonstrated a strong tidal-mixing front during the warm season on the northern bank margin between thermally stratified water in the Gulf of Maine and mixed water on the bank. Tides transport warm water off the bank during flood tide and cool gulf water onto the bank during ebb tide. During 10 days in August 2009, we mapped frontal temperatures in five study areas along ~100 km of the bank margin. The seabed “frontal zone”, where temperature changed with frontal movment, experienced semidiurnal temperature maxima and minima. The tidal excursion of the frontal boundary between stratified and mixed water ranged 6 to 10 km. This “frontal boundary zone” was narrower than the frontal zone. Along transects perpendicular to the bank margin, seabed temperature change at individual sites ranged from 7.0°C in the frontal zone to 0.0°C in mixed bank water. At time series in frontal zone stations, changes during tidal cycles ranged from 1.2 to 6.1°C. The greatest rate of change (−2.48°C hr−1) occurred at mid-ebb. Geographic plots of seabed temperature change allowed the mapping of up to 8 subareas in each study area. The magnitude of temperature change in a subarea depended on its location in the frontal zone. Frontal movement had the greatest effect on seabed temperature in the 40 to 80 m depth interval. Subareas experiencing maximum temperature change in the frontal zone were not in the frontal boundary zone, but rather several km gulfward (off-bank) of the frontal boundary zone. These results provide a new ecological framework for examining the effect of tidally-driven temperature variability on the distribution, food resources, and reproductive success of benthic invertebrate and demersal fish species living in tidal front habitats.
    Description: This study was supported by salary funds from the regular annual salary budget from Northeast Fisheries Science Center (NEFSC) and United States Geological Survey Woods Hole Coastal and Marine Science Center (USGS WH C&MSC), respectively; ship time funds from the NEFSC annual budget for days-at-sea ship operations; equipment from the NEFSC and USGS WH C&MSC annual equipment budgets.
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e54443, doi:10.1371/journal.pone.0054443.
    Description: Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year−1, and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change.
    Description: This work was supported by grants from the German Science Foundation (DFG; www.dfg.de) to ML and SL (LA 884/10-1, LA 884/5-1).
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  • 8
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56993, doi:10.1371/journal.pone.0056993.
    Description: The mxaF gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene’s usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.
    Description: This work was supported in part by grants from the U.S. National Science Foundation Ecosystems Studies program (awards # DEB9708092 and DEB0089738).
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  • 9
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e61065, doi:10.1371/journal.pone.0061065.
    Description: Ocean acidification, characterized by elevated pCO2 and the associated decreases in seawater pH and calcium carbonate saturation state (Ω), has a variable impact on the growth and survival of marine invertebrates. Larval stages are thought to be particularly vulnerable to environmental stressors, and negative impacts of ocean acidification have been seen on fertilization as well as on embryonic, larval, and juvenile development and growth of bivalve molluscs. We investigated the effects of high CO2 exposure (resulting in pH = 7.39, Ωar = 0.74) on the larvae of the bay scallop Argopecten irradians from 12 h to 7 d old, including a switch from high CO2 to ambient CO2 conditions (pH = 7.93, Ωar = 2.26) after 3 d, to assess the possibility of persistent effects of early exposure. The survival of larvae in the high CO2 treatment was consistently lower than the survival of larvae in ambient conditions, and was already significantly lower at 1 d. Likewise, the shell length of larvae in the high CO2 treatment was significantly smaller than larvae in the ambient conditions throughout the experiment and by 7 d, was reduced by 11.5%. This study also demonstrates that the size effects of short-term exposure to high CO2 are still detectable after 7 d of larval development; the shells of larvae exposed to high CO2 for the first 3 d of development and subsequently exposed to ambient CO2 were not significantly different in size at 3 and 7 d than the shells of larvae exposed to high CO2 throughout the experiment.
    Description: This work was funded by a Woods Hole Oceanographic Institution Interdisciplinary Award to Mullineaux & McCorkle; and awards to Mullineaux & White, to McCorkle, and to Cohen & McCorkle through NOAA (National Oceanic and Admosphereic Administration) Sea Grant #NA10OAR4170083. White was funded through a National Defense Science and Engineering Graduate Fellowship through the American Society for Engineering Education.
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  • 10
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e76096, doi:10.1371/journal.pone.0076096.
    Description: DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8–11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.
    Description: LAZ and VS were funded by a Brown University Office of the Vice President of Research SEED grant (LAZ) entitled “Tracking disease spread through the wildlife trade: New techniques to identify infectious microbes in aquarium fishes.” SOO and MQ were funded by Wellcome Trust Sanger Institute grant numbers 098051 and 079355/Z/06/Z.
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  • 11
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50215, doi:10.1371/journal.pone.0050215.
    Description: The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.
    Description: This study was funded by CTM2009-00496 and CGL2011-23306 projects of the “Ministerio de Ciencia e Innovación” (Spain). Research at sea was partly supported by the European Commission F. P.VI Project HERMES Contract No. GOCE-CT-2005-511234-1) and the EU F.P. VII Project HERMIONE(contract number no. 226354).
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  • 12
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
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  • 13
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e53889, doi:10.1371/journal.pone.0053889.
    Description: Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the “DNA barcoding” region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of 〈3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (~19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (~24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species’ sensitivity to ocean acidification.
    Description: This material is based upon work supported by the National Science Foundation under Grant Number OCE-0928801. AEM was funded through the WHOI Postdoctoral Scholarship. Support to LBB was provided by the College of Liberal Arts & Sciences, University of Connecticut; and by the Census of Marine Life/Alfred P. Sloan Foundation.
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  • 14
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
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  • 15
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e63714, doi:10.1371/journal.pone.0063714.
    Description: Anthropogenic carbon dioxide (CO2) is being absorbed into the ocean, altering seawater chemistry, with potentially negative impacts on a wide range of marine organisms. The early life stages of invertebrates with internal and external aragonite structures may be particularly vulnerable to this ocean acidification. Impacts to cephalopods, which form aragonite cuttlebones and statoliths, are of concern because of the central role they play in many ocean ecosystems and because of their importance to global fisheries. Atlantic longfin squid (Doryteuthis pealeii), an ecologically and economically valuable taxon, were reared from eggs to hatchlings (paralarvae) under ambient and elevated CO2 concentrations in replicated experimental trials. Animals raised under elevated pCO2 demonstrated significant developmental changes including increased time to hatching and shorter mantle lengths, although differences were small. Aragonite statoliths, critical for balance and detecting movement, had significantly reduced surface area and were abnormally shaped with increased porosity and altered crystal structure in elevated pCO2-reared paralarvae. These developmental and physiological effects could alter squid paralarvae behavior and survival in the wild, directly and indirectly impacting marine food webs and commercial fisheries.
    Description: This study was supported by a WHOI Student Summer Fellowship and WHOI-MIT Joint Program, the Penzance Endowed Fund, the John E. and Anne W. Sawyer Endowed Fund and NSF Research Grant No. EF-1220034. Additional support came from NSF OCE 1041106 to ALC and DCM, and NOAA Sea Grant award #NA10OAR4170083 to ALC and DCM.
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  • 16
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e79574, doi:10.1371/journal.pone.0079574.
    Description: Transcription factors in the CNC-bZIP family (NFE2, NRF1, NRF2 and NRF3) regulate genes with a wide range of functions in response to both physiological and exogenous signals, including those indicating changes in cellular redox status. Given their role in helping to maintain cellular homeostasis, it is imperative to understand the expression, regulation, and function of CNC-bZIP genes during embryonic development. We explored the expression and function of six nrf genes (nfe2, nrf1a, nrf1b, nrf2a, nrf2b, and nrf3) using zebrafish embryos as a model system. Analysis by microarray and quantitative RT-PCR showed that genes in the nrf family were expressed throughout development from oocytes to larvae. The spatial expression of nrf3 suggested a role in regulating the development of the brain, brachia and pectoral fins. Knock-down by morpholino anti-sense oligonucleotides suggested that none of the genes were necessary for embryonic viability, but nfe2 was required for proper cellular organization in the pneumatic duct and subsequent swim bladder function, as well as for proper formation of the otic vesicles. nrf genes were induced by the oxidant tert-butylhydroperoxide, and some of this response was regulated through family members Nrf2a and Nrf2b. Our results provide a foundation for understanding the role of nrf genes in normal development and in regulating the response to oxidative stress in vertebrate embryos.
    Description: This work was supported, in whole or in part, by National Institutes of Health grants F32ES019832 (to L.M.W.), F32ES017585 (to A.R.T.-L.), R01ES015912 (to J.J.S.), and R01ES016366 (to M.E.H.). This work was also supported by Walter A. and Hope Noyes Smith and the J. Seward Johnson Fund.
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  • 17
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e49474, doi:10.1371/journal.pone.0049474.
    Description: Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (〈2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region.
    Description: This work was funded in part by a Fulbright Fellowship administered by Fulbright New Zealand and the U.S. Department of State, awarded in 2011 to EKB. Funding and support for research expedition was provided by Land Information New Zealand, New Zealand Ministry of Fisheries, NIWA, Census of Marine Life on Seamounts (CenSeam), and the Foundation for Research, Science and Technology. Other research funding was provided by the New Zealand Ministry of Science and Innovation project “Impacts of resource use on vulnerable deep-sea communities” (FRST contract CO1X0906), the National Science Foundation (OCE-0647612), and the Deep Ocean Exploration Institute (Fellowship support to TMS).
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  • 18
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Public Library of Science, doi:10.1371/journal.pone.0052072.
    Description: The low-frequency, powerful vocalizations of blue and fin whales may potentially be detected by conspecifics across entire ocean basins. In contrast, humpback and bowhead whales produce equally powerful, but more complex broadband vocalizations composed of higher frequencies that suffer from higher attenuation. Here we evaluate the active space of high frequency song notes of bowhead whales (Balaena mysticetus) in Western Greenland using measurements of song source levels and ambient noise. Four independent, GPS-synchronized hydrophones were deployed through holes in the ice to localize vocalizing bowhead whales, estimate source levels and measure ambient noise. The song had a mean apparent source level of 185±2 dB rms re 1 µPa @ 1 m and a high mean centroid frequency of 444±48 Hz. Using measured ambient noise levels in the area and Arctic sound spreading models, the estimated active space of these song notes is between 40 and 130 km, an order of magnitude smaller than the estimated active space of low frequency blue and fin whale songs produced at similar source levels and for similar noise conditions. We propose that bowhead whales spatially compensate for their smaller communication range through mating aggregations that co-evolved with broadband song to form a complex and dynamic acoustically mediated sexual display.
    Description: This work was funded by the Oticon Foundation (grant # 08-3469 to Arctic Station, OT). OT and MC were additionally funded by AP Møller og Hustru Chastine Mc-Kinney Møllers Fond til almene Formaal, MS by a PhD scholarship from the Oticon Foundation, FHJ by a Danish Council for Independent Research, Natural Sciences post-doctoral grant, SEP by a grant from the U.S. Office of Naval Research, and PTM by frame grants from the Danish Natural Science Research Council.
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  • 19
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e54069, doi:10.1371/journal.pone.0054069.
    Description: Structural change in both the habitat and reef-associated fish assemblages within spatially managed coral reefs can provide key insights into the benefits and limitations of Marine Protected Areas (MPAs). While MPA zoning effects on particular target species are well reported, we are yet to fully resolve the various affects of spatial management on the structure of coral reef communities over decadal time scales. Here, we document mixed affects of MPA zoning on fish density, biomass and species richness over the 21 years since establishment of the Saba Marine Park (SMP). Although we found significantly greater biomass and species richness of reef-associated fishes within shallow habitats (5 meters depth) closed to fishing, this did not hold for deeper (15 m) habitats, and there was a widespread decline (38% decrease) in live hard coral cover and a 68% loss of carnivorous reef fishes across all zones of the SMP from the 1990s to 2008. Given the importance of live coral for the maintenance and replenishment of reef fishes, and the likely role of chronic disturbance in driving coral decline across the region, we explore how local spatial management can help protect coral reef ecosystems within the context of large-scale environmental pressures and disturbances outside the purview of local MPA management.
    Description: Funding was provided by the Saba Conservation Foundation ((SCF), King Abdullah University of Science and Technology, The Australian National University and Australian Research Council.
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  • 20
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e70966, doi:10.1371/journal.pone.0070966.
    Description: Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms. This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19–100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance. Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of host anemones to cope with rising sea temperatures associated with climate change.
    Description: This work was supported by funding from the Red Sea Research Center at the King Abdullah University of Science and Technology (KAUST), The ARC Centre of Excellence for Coral Reef Studies, the National Science Foundation (OCE 0424688), the Coral Reef Initiatives for the Pacific (CRISP), the TOTAL Foundation, Populations Fractionees et Insulares (PPF EPHE), the Connectivity Working Group of the Global University of Queensland – World Bank – Global Environmental Facility Project, Coral Reef Target Research and Capacity Building for Management, Great Barrier Reef Marine Park Authority, and the Australian Government Department of Sustainability, Environment, Water, Population and Communities. J-P Hobbs is supported by a UWA-AIMS-CSIRO fellowship.
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  • 21
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e78275, doi:10.1371/journal.pone.0078275.
    Description: Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.
    Description: National Science Foundation (OCE #0961098) Hong Kong Research Grants Council (661911 and 661912) Chinese Academy of Science (SIDSSE-BR-201301).
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  • 22
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e77671, doi:10.1371/journal.pone.0077671.
    Description: Bottlenose dolphins (Tursiops truncatus) produce many vocalisations, including whistles that are unique to the individual producing them. Such “signature whistles” play a role in individual recognition and maintaining group integrity. Previous work has shown that humans can successfully group the spectrographic representations of signature whistles according to the individual dolphins that produced them. However, attempts at using mathematical algorithms to perform a similar task have been less successful. A greater understanding of the encoding of identity information in signature whistles is important for assessing similarity of whistles and thus social influences on the development of these learned calls. We re-examined 400 signature whistles from 20 individual dolphins used in a previous study, and tested the performance of new mathematical algorithms. We compared the measure used in the original study (correlation matrix of evenly sampled frequency measurements) to one used in several previous studies (similarity matrix of time-warped whistles), and to a new algorithm based on the Parsons code, used in music retrieval databases. The Parsons code records the direction of frequency change at each time step, and is effective at capturing human perception of music. We analysed similarity matrices from each of these three techniques, as well as a random control, by unsupervised clustering using three separate techniques: k-means clustering, hierarchical clustering, and an adaptive resonance theory neural network. For each of the three clustering techniques, a seven-level Parsons algorithm provided better clustering than the correlation and dynamic time warping algorithms, and was closer to the near-perfect visual categorisations of human judges. Thus, the Parsons code captures much of the individual identity information present in signature whistles, and may prove useful in studies requiring quantification of whistle similarity.
    Description: Arik Kershenbaum is a Postdoctoral Fellow at the National Institute for Mathematical and Biological Synthesis, an Institute sponsored by the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture through NSF Award #EF-0832858, with additional support from The University of Tennessee, Knoxville. Part of this work was conducted while Arik Kershenbaum was provided with a doctoral scholarship by the University of Haifa. Funding for access to the dolphins for recordings was provided by Dolphin Quest and the Chicago Zoological Society.
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  • 23
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
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  • 24
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50221, doi:10.1371/journal.pone.0050221.
    Description: Lymphocytes are a key component of the immune system and their differentiation and function are directly influenced by cancer. We examined peripheral blood lymphocyte (PBL) gene expression as a biomarker of illness and treatment effect using the Affymetrix Human Gene ST1 platform in patients with metastatic renal cell carcinoma (mRCC) who received combined treatment with IL-2, interferon-?-2a and dendritic cell vaccine. We examined gene expression, cytokine levels in patient serum and lymphocyte subsets as determined by flow cytometry (FCM). Pre-treatment PBLs from patients with mRCC exhibit a gene expression profile and serum cytokine profile consistent with inflammation and proliferation not found in healthy donors (HD). PBL gene expression from patients with mRCC showed increased mRNA of genes involved with T-cell and TREG-cell activation pathways, which was also reflected in lymphocyte subset distribution. Overall, PBL gene expression post-treatment (POST) was not significantly different than pre-treatment (PRE). Nevertheless, treatment related changes in gene expression (post-treatment minus pre-treatment) revealed an increased expression of T-cell and B-cell receptor signaling pathways in responding (R) patients compared to non-responding (NR) patients. In addition, we observed down-regulation of TREG-cell pathways post-treatment in R vs. NR patients. While exploratory in nature, this study supports the hypothesis that enhanced inflammatory cytotoxic pathways coupled with blunting of the regulatory pathways is necessary for effective anti-cancer activity associated with immune therapy. This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC.
    Description: This work was supported by grants from the National Institutes of Health (RO1 CA5648, R21CA112761, P20RR016437, and P30CA023108).
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  • 25
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e59284, doi:10.1371/journal.pone.0059284.
    Description: Toothed whales (Cetacea, odontoceti) use biosonar to navigate their environment and to find and catch prey. All studied toothed whale species have evolved highly directional, high-amplitude ultrasonic clicks suited for long-range echolocation of prey in open water. Little is known about the biosonar signals of toothed whale species inhabiting freshwater habitats such as endangered river dolphins. To address the evolutionary pressures shaping the echolocation signal parameters of non-marine toothed whales, we investigated the biosonar source parameters of Ganges river dolphins (Platanista gangetica gangetica) and Irrawaddy dolphins (Orcaella brevirostris) within the river systems of the Sundarban mangrove forest. Both Ganges and Irrawaddy dolphins produced echolocation clicks with a high repetition rate and low source level compared to marine species. Irrawaddy dolphins, inhabiting coastal and riverine habitats, produced a mean source level of 195 dB (max 203 dB) re 1 µPapp whereas Ganges river dolphins, living exclusively upriver, produced a mean source level of 184 dB (max 191) re 1 µPapp. These source levels are 1–2 orders of magnitude lower than those of similar sized marine delphinids and may reflect an adaptation to a shallow, acoustically complex freshwater habitat with high reverberation and acoustic clutter. The centroid frequency of Ganges river dolphin clicks are an octave lower than predicted from scaling, but with an estimated beamwidth comparable to that of porpoises. The unique bony maxillary crests found in the Platanista forehead may help achieve a higher directionality than expected using clicks nearly an octave lower than similar sized odontocetes.
    Description: This study was made possible through the logistical and field support of the Bangladesh Cetacean Diversity Project of the Wildlife Conservation Society, and funded by frame grants from the Danish Natural Science Foundation to PTM. FHJ was supported by the PhD School of Aquatic Sciences, Denmark, and is currently funded by a postdoctoral fellowship from the Danish Council for Independent Research | Natural Sciences. VMJ was supported by a fellowship of the Wissenschaftskolleg Berlin. PTM was supported by frame grants from the Danish Natural Science Foundation.
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  • 26
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56335, doi:10.1371/journal.pone.0056335.
    Description: The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.
    Description: This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359).
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  • 27
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50015, doi:10.1371/journal.pone.0050015.
    Description: Deep-sea hydrothermal vents are subject to major disturbances that alter the physical and chemical environment and eradicate the resident faunal communities. Vent fields are isolated by uninhabitable deep seafloor, so recolonization via dispersal of planktonic larvae is critical for persistence of populations. We monitored colonization near 9°50′N on the East Pacific Rise following a catastrophic eruption in order to address questions of the relative contributions of pioneer colonists and environmental change to variation in species composition, and the role of pioneers at the disturbed site in altering community structure elsewhere in the region. Pioneer colonists included two gastropod species: Ctenopelta porifera, which was new to the vent field, and Lepetodrilus tevnianus, which had been rare before the eruption but persisted in high abundance afterward, delaying and possibly out-competing the ubiquitous pre-eruption congener L. elevatus. A decrease in abundance of C. porifera over time, and the arrival of later species, corresponded to a decrease in vent fluid flow and in the sulfide to temperature ratio. For some species these successional changes were likely due to habitat requirements, but other species persisted (L. tevnianus) or arrived (L. elevatus) in patterns unrelated to their habitat preferences. After two years, disturbed communities had started to resemble pre-eruption ones, but were lower in diversity. When compared to a prior (1991) eruption, the succession of foundation species (tubeworms and mussels) appeared to be delayed, even though habitat chemistry became similar to the pre-eruption state more quickly. Surprisingly, a nearby community that had not been disturbed by the eruption was invaded by the pioneers, possibly after they became established in the disturbed vents. These results indicate that the post-eruption arrival of species from remote locales had a strong and persistent effect on communities at both disturbed and undisturbed vents.
    Description: The authors received funding from National Science Foundation grant OCE-0424953, WHOI Deep Ocean Exploration Institute, WHOI Summer Student Fellow program, Woods Hole Partnership in Education Program, IFREMER and CNRS, Fondation TOTAL Chair Extreme Marine Environment, Biodiversity and Global change.
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  • 28
    Publication Date: 1980-08-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 29
    Publication Date: 1980-08-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 30
    Publication Date: 1980-02-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 31
    Publication Date: 1980-08-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 32
    Publication Date: 1980-08-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 33
    Publication Date: 1980-02-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 34
    Publication Date: 1980-02-01
    Print ISSN: 0968-0004
    Electronic ISSN: 1362-4326
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Cell Press
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  • 35
    Publication Date: 2013-09-07
    Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 36
    Publication Date: 2013-09-07
    Description: J. Tuma, O. Lyutakov, I. Huttel, P. Slepicka, and V. Svorcik Thin poly(methylmethacrylate) films doped by or covalently attached to disperse Red 1 acrylate (DR1) were patterned by laser scanning and simultaneous sample movement in confocal microscope. In both cases, periodical structure due to Marangoni effect is created. Modified polymers surfaces were analy ... [J. Appl. Phys. 114, 093104 (2013)] published Fri Sep 6, 2013.
    Print ISSN: 0021-8979
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  • 37
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: L. Kilanski, K. Szalowski, R. Szymczak, M. Gorska, E. Dynowska et al. We present the studies of electrical transport and magnetic interactions in ZnMnGeAs crystals with low Mn content 0
    Print ISSN: 0021-8979
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  • 38
    Publication Date: 2013-09-07
    Description: G. Y. Gao, Z. B. Yang, W. Huang, H. Z. Zeng, Y. Wang et al. Epitaxial Mn-doped BiFeO (MBFO) thin films were grown on GaAs (001) substrate with SrTiO (STO) buffer layer by pulsed laser deposition. X-ray diffraction results demonstrate that the films show pure (00l) orientation, and MBFO (100)//STO(100), whereas STO (100)//GaAs (110). Piezoresponse force micro ... [J. Appl. Phys. 114, 094106 (2013)] published Fri Sep 6, 2013.
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  • 39
    Publication Date: 2013-09-07
    Description: Yanan Huang, Bangchuan Zhao, Shuai Lin, Wenhai Song, and Yuping Sun The effects of Ir doping on the low-temperature thermal and electrical transport properties of CaCoIrO (0
    Print ISSN: 0021-8979
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  • 40
    facet.materialart.
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: P. Orlandi In this paper, it is demonstrated by DNS of turbulent rough channels that a proportionality between u-tilde| (the wall-normal Reynolds stress u-tilde= at the top of the roughness elements) and the roughness function does exist. This observation confirmed by experiments allows the derivation of a sim ... [Phys. Fluids 25, 110813 (2013)] published Fri Sep 6, 2013.
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
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  • 41
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Alessandra Adrover We investigate the effects of secondary (transverse) flows on convection-dominated dispersion of pressure driven, open column laminar flow in a conduit with rectangular cross-section. We show that secondary flows significantly reduce dispersion (enhancing transverse diffusion) in Taylor-Aris regime ... [Phys. Fluids 25, 093601 (2013)] published Fri Sep 6, 2013.
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  • 42
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Michael E. Mueller and Heinz Pitsch An integrated kinetics-based Large Eddy Simulation (LES) approach for soot evolution in turbulent reacting flows is applied to the simulation of a Pratt & Whitney aircraft gas turbine combustor, and the results are analyzed to provide insights into the complex interactions of the hydrodynamics, mixi ... [Phys. Fluids 25, 110812 (2013)] published Fri Sep 6, 2013.
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  • 43
    facet.materialart.
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: D. M. Valiev, V. Bychkov, V. Akkerman, L.-E. Eriksson, and C. K. Law The present paper addresses the phenomenon of spontaneous acceleration of a premixed flame front propagating in micro-channels, with subsequent deflagration-to-detonation transition. It has recently been shown experimentally [M. Wu, M. Burke, S. Son, and R. Yetter, Proc. Combust. Inst. 31, 2429 (200 ... [Phys. Fluids 25, 096101 (2013)] published Fri Sep 6, 2013.
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  • 44
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Young-Min Shin and Michael Church A deflecting mode cavity is the integral element for six-dimensional phase-space beam control in bunch compressors and emittance transformers at high energy beam test facilities. RF performance of a high-Q device is, however, highly sensitive to operational conditions, in particular in a cryo-coolin ... [Phys. Plasmas 20, 093101 (2013)] published Fri Sep 6, 2013.
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  • 45
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Marcus Weinwurm, Simon N. Bland, and Jeremy P. Chittenden Properties of degenerate hydrogen and deuterium (D) at pressures of the order of terapascals are of key interest to Planetary Science and Inertial Confinement Fusion. In order to recreate these conditions in the laboratory, we present a scheme, where a metal liner drives a cylindrically convergent q ... [Phys. Plasmas 20, 092701 (2013)] published Fri Sep 6, 2013.
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  • 46
    Publication Date: 2013-09-07
    Description: Jaetae Seo, Sangram Raut, Mahmoud Abdel-Fattah, Quinton Rice, Bagher Tabibi et al. Time-resolved and temperature-dependent photoluminescence (PL) spectroscopy of ternary compound copper indium disulfide (CuInS, or CIS) core materials, CIS/ZnS coreshells, and quaternary compound ZnCuInS (ZnCIS) revealed their optical properties with spectral, temporal, and thermal characteristics, ... [J. Appl. Phys. 114, 094310 (2013)] published Fri Sep 6, 2013.
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  • 47
    Publication Date: 2013-09-07
    Description: D. H. Feng, X. Q. Pan, X. Li, T. Q. Jia, and Z. R. Sun We report experiments of coherent acoustic phonon generations and detections using a two-color femtosecond pump-probe technique in [001] and [110] oriented ZnTe single crystals. The above-bandgap pump excitation initiates strain waves to yield coherent acoustic phonons. The generation and propagatio ... [J. Appl. Phys. 114, 093513 (2013)] published Fri Sep 6, 2013.
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  • 48
    Publication Date: 2013-09-07
    Description: Kun Gao, S. Prucnal, W. Skorupa, M. Helm, and Shengqiang Zhou GaAs and GaAs based materials have outstanding optoelectronic properties and are widely used as light emitting media in devices. Many approaches have been applied to GaAs to generate luminescence at 0.88, 1.30, and 1.55 [mu]m which are transmission windows of optical fibers. In this paper, we presen ... [J. Appl. Phys. 114, 093511 (2013)] published Fri Sep 6, 2013.
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  • 49
    Publication Date: 2013-09-07
    Description: Xinliang Gao, Quanming Lu, Xin Tao, Yufei Hao, and Shui Wang Alfven waves with a finite amplitude are found to be unstable to a parametric decay in low beta plasmas. In this paper, the parametric decay of a circularly polarized Alfven wave in a proton-electron-alpha plasma system is investigated with one-dimensional (1-D) hybrid simulations. In cases without ... [Phys. Plasmas 20, 092106 (2013)] published Fri Sep 6, 2013.
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  • 50
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Brian M. Haines, Fernando F. Grinstein, Leslie WelserSherrill, James R. Fincke, and Forrest W. Doss We perform an ensemble of simulations of a laser-driven shear experiment [L. Welser-Sherrill et al., Two laser-driven mix experiments to study reshock and shear, High Energy Density Phys. J. 9(3), 496499 (2013)] in the strong-shock high energy-density regime to better understand material mixing driv ... [Phys. Plasmas 20, 092301 (2013)] published Fri Sep 6, 2013.
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  • 51
    Publication Date: 2013-09-07
    Description: Anthony Ballandras, Guy Weber, Christian Paulin, Jean-Pierre Bellat, and Maud Rotger The adsorption of trichloroethylene, perchloroethylene, and p-xylene on a MFI (Mobile-FIve) zeolite is studied using in situ FTIR spectroscopy at 298 K. Spectra of self-supported zeolites in contact with increasing pressures of pure gas were recorded at equilibrium in the mid-infrared domain. Analys ... [J. Chem. Phys. 139, 091103 (2013)] published Fri Sep 6, 2013.
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    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 52
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Y. Zheng (郑轶) , L. N. Su (苏鲁宁) , M. Liu (刘梦) , B. C. Liu (刘必成) , Z. W. Shen (沈忠伟) et al. In typical laser-driven proton acceleration experiments Thomson parabola proton spectrometers are used to measure the proton spectra with very small acceptance angle in specific directions. Stacks composed of CR-39 nuclear track detectors, imaging plates, or radiochromic films are used to measure th ... [Rev. Sci. Instrum. 84, 096103 (2013)] published Fri Sep 6, 2013.
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    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 53
    Publication Date: 2013-09-07
    Description: E. K. Michailidou, M. J. Assael, M. L. Huber, and R. A. Perkins This paper contains new, representative reference equations for the viscosity of n-hexane. The equations are based in part upon a body of experimental data that has been critically assessed for internal consistency and for agreement with theory whenever possible. The correlations are valid from the ... [J. Phys. Chem. Ref. Data 42, 033104 (2013)] published Fri Sep 6, 2013.
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    Electronic ISSN: 1529-7845
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  • 54
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-07
    Description: Hong-Biao Zhang, Lin Yang, and San-Xing Guo We construct so(3) algebra associated with the Morse potential and show that these operators obey so(3) commutation relations. A so(3) algebraic method is proposed in order to obtain the eigenvalues and eigenfunctions of the Morse potential. This method exhibits that Cartan operator J, the lowering ... [J. Math. Phys. 54, 092104 (2013)] published Fri Sep 6, 2013.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
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  • 55
    Publication Date: 2013-09-08
    Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.
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  • 56
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    Oxford University Press
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
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  • 57
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
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  • 58
    Publication Date: 2013-09-08
    Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.
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  • 59
    Publication Date: 2013-09-08
    Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.
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  • 60
    Publication Date: 2013-09-08
    Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.
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  • 61
    Publication Date: 2013-09-08
    Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.
    Print ISSN: 0964-6906
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  • 62
    Publication Date: 2013-09-08
    Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.
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  • 63
    Publication Date: 2013-09-09
    Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 64
    Publication Date: 2013-09-10
    Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 65
    Publication Date: 2013-09-10
    Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.
    Print ISSN: 0956-540X
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    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 66
    Publication Date: 2013-09-10
    Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.
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    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 67
    Publication Date: 2013-09-10
    Description: We have developed a network optimization method for regional-scale microseismic monitoring networks and applied it to optimize the densification of the existing seismic network in northeastern Switzerland. The new network will build the backbone of a 10-yr study on the neotectonic activity of this area that will help to better constrain the seismic hazard imposed on nuclear power plants and waste repository sites. This task defined the requirements regarding location precision (0.5 km in epicentre and 2 km in source depth) and detection capability [magnitude of completeness M c  = 1.0 ( M L )]. The goal of the optimization was to find the geometry and size of the network that met these requirements. Existing stations in Switzerland, Germany and Austria were considered in the optimization procedure. We based the optimization on the simulated annealing approach proposed by Hardt & Scherbaum, which aims to minimize the volume of the error ellipsoid of the linearized earthquake location problem ( D -criterion). We have extended their algorithm to: calculate traveltimes of seismic body waves using a finite difference ray tracer and the 3-D velocity model of Switzerland, calculate seismic body-wave amplitudes at arbitrary stations assuming the Brune source model and using scaling and attenuation relations recently derived for Switzerland, and estimate the noise level at arbitrary locations within Switzerland using a first-order ambient seismic noise model based on 14 land-use classes defined by the EU-project CORINE and open GIS data. We calculated optimized geometries for networks with 10–35 added stations and tested the stability of the optimization result by repeated runs with changing initial conditions. Further, we estimated the attainable magnitude of completeness ( M c ) for the different sized optimal networks using the Bayesian Magnitude of Completeness (BMC) method introduced by Mignan et al. The algorithm developed in this study is also applicable to smaller optimization problems, for example, small local monitoring networks. Possible applications are volcano monitoring, the surveillance of induced seismicity associated with geotechnical operations and many more. Our algorithm is especially useful to optimize networks in populated areas with heterogeneous noise conditions and if complex velocity structures or existing stations have to be considered.
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    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 68
    Publication Date: 2013-09-10
    Description: Fluid injection in and withdrawal from wells are basic procedures in mining activities and deep resources exploitation, such as oil and gas extraction, permeability enhancement for geothermal exploitation and waste fluid disposal. All of these activities have the potential to induce seismicity, as exemplified by the 2006 Basel earthquake ( M L 3.4). Despite several decades of experience, the mechanisms of induced seismicity are not known in detail, which prevents effective risk assessment and/or mitigation. In this study, we provide an interpretation of induced seismicity based on computation of Coulomb stress changes that result from fluid injection/withdrawal at depth, mainly focused on the interpretation of induced seismicity due to stimulation of a geothermal reservoir. Seismicity is, theoretically, more likely where Coulomb stress changes are larger. For modeling purposes, we simulate the thermodynamic evolution of a system after fluid injection/withdrawal. The associated changes in pressure and temperature are subsequently considered as sources of incremental stress changes, which are then converted to Coulomb stress changes on favourably oriented faults, taking into account the background regional stress. Numerical results are applied to the water injection that was performed to create the fractured reservoir at the enhanced-geothermal-system site, Soultz-sous-Forets (France). Our approach describes well the observed seismicity, and provides an explanation for the different behaviors of a system when fluids are injected or withdrawn.
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    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 69
    Publication Date: 2013-09-10
    Description: We report on a broad-band high-resolution attenuation model for the North China Craton and surrounding regions based on regional Lg -wave data. Vertical broad-band waveforms recorded at 39 stations from 176 crustal earthquakes are collected to extract the Lg -wave amplitude spectra between 0.05 and 10.0 Hz. We use the dual-station method to generate a preliminary Q Lg model and use it as the initial model. Then, we combine the dual- and single-station data together to jointly invert the Q Lg distribution and Lg source excitation functions. These inversions are conducted independently at individual frequencies without using any a priori assumption about the frequency dependences in Q Lg and source terms. The maximum spatial resolution is approximately 1° x 1° in well-covered areas for frequencies between 0.05 and 2.0 Hz. The Q Lg image is then used to determine the relationship between the attenuation and different geological structures. Results show an average Q 0 (1 Hz Q Lg ) of 374 for the entire North China Craton with an increasing trend from east to west. Average Q 0 values are 337, 361 and 421 for the east, central and west blocks, respectively. For the surrounding regions, the Eastern Tibetan plateau has a very low Q 0 of 188, while the Northeast China Plate and the Tianshan–Xingmeng fold belts are characterized by high Q 0 values of 506 and 424, respectively. We also investigate regional variations of the Lg attenuation in low-frequency band between 0.2 and 1.0 Hz.
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 70
    Publication Date: 2013-09-10
    Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750–1200 °C), carbon dioxide fugacity (log f CO 2  = –4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 °C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.
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  • 71
    Publication Date: 2013-09-10
    Description: The scattering of plane SH waves incident on a circular sectorial canyon is considered. An accurate region-matching technique is applied to derive a rigorous series solution. Appropriate wavefunctions are employed to describe antiplane motions. Judicious basis functions, involving Gegenbauer polynomials, are well utilized to correctly capture the singular behaviour in stress fields near the canyon bottom. The enforcement of matching conditions on the auxiliary boundary leads to the determination of unknown coefficients. Plotted results demonstrate the influence of pertinent parameters on surface and subsurface motions. Both steady-state and transient results are included. The solution technique proposed achieves a considerable reduction in the computational effort, facilitating benchmark computations. The derived series solution enriches the limited list of series solutions presently known for canyon problems related to SH -wave scattering.
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  • 72
    Publication Date: 2013-09-10
    Description: We present 3-D models of the P- and S -wave velocity distributions in the crust and uppermost mantle beneath Sicily, Calabria (Southern Italy), and surrounding submerged areas, obtained by tomographic inversion of traveltimes of regional body waves phases. Our method combines double-difference tomographic inversion with a post-processing procedure [Weighted Average Model method (WAM)]. This procedure was applied to a set of models consistent with the experimental data. We tested the ability of the WAM procedure to mitigate the uncertainty associated with the arbitrary nature of the many input parameters required for each inversion. The local reliability and resolution of the obtained models have been assessed through: synthetic tests, experimental tests carried out with independent data sets and unconventional tests based on the analysis of the internal consistency of the P - and S -velocity models. The tomographic images provide a detailed sketch of P- and S- wave velocity anomalies. These clearly show the shape of the Sicilian-Maghrebian belt beneath Sicily and Calabrian Arc at different depths. Low V P and Vs bodies are imaged beneath Stromboli and Marsili volcanoes in the southern Tyrrhenian, whereas high and low seismic velocities alternate beneath the Etna giving inferences on the possible depth of the mantle melting feeding the volcano. In the upper crust, the main sedimentary basins and tectonic features are also well imaged. Finally, tomographic cross sections show the trend of the Moho in the study area, where its depth ranges between 35 and 40 km beneath the Sicilian belt and between 15 and 22 km in the southern Tyrrhenian basin and Ionian Sea.
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  • 73
    Publication Date: 2013-09-10
    Description: We used two tracks of ALOS PALSAR images to investigate the focal mechanism and slip distribution of the 2011 March 24, M W 6.8 Burma strike-slip earthquake. Three different SAR techniques, namely conventional interferometry, SAR pixel offsets (SPO) and multiple-aperture InSAR (MAI), were employed to obtain the coseismic surface deformation fields along the ~30 km length of the fault rupture. Along-track measurements from SPO and MAI techniques show a high correlation, and were subsequently used to precisely determine the location and extent of the surface fault trace. The best-fitting fault model geometry derived from an iterative inversion technique suggests that the rupture occurred on a near-vertical sinistral strike-slip fault west of the Nam Ma fault with a strike of 70°. A maximum slip of 4.2 m occurs at a depth of 2.5 km, with significant slip constrained only to the upper 10 km of the crust.
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  • 74
    Publication Date: 2013-09-10
    Description: Knowledge of the mantle reflectivity structure is highly dependent on our ability to efficiently extract, and properly interpret, small seismic arrivals. Among the various data types and techniques, long-period SS/PP precursors and high-frequency receiver functions are routinely utilized to increase the confidence of the recovered mantle stratifications at distinct spatial scales. However, low resolution and a complex Fresnel zone are glaring weaknesses of SS precursors, while over-reliance on receiver distribution is a formidable challenge for the analysis of converted waves from oceanic regions. A promising high frequency alternative to receiver functions is P ' P ' precursors, which are capable of resolving mantle structures at vertical and lateral resolution of ~5 and ~200 km, respectively, owing to their spectral content, shallow angle of incidence and near-symmetric Fresnel zones. This study presents a novel processing method for both SS (or PP) and P ' P ' precursors based on deconvolution, stacking, Radon transform and depth migration. A suite of synthetic tests is performed to quantify the fidelity and stability of this method under different data conditions. Our multiresolution survey of the mantle at targeted areas near Nazca-South America subduction zone reveal both olivine and garnet related transitions at depths below 400 km. We attribute a depressed 660 to thermal variations, whereas compositional variations atop the upper-mantle transition zone are needed to explain the diminished or highly complex reflected/scattered signals from the 410 km discontinuity. We also observe prominent P ' P ' reflections within the transition zone, and the anomalous amplitudes near the plate boundary zone indicate a sharp (~10 km thick) transition that likely resonates with the frequency content of P ' P ' precursors. The migration of SS precursors in this study shows no evidence of split 660 reflections, but potential majorite–ilmenite (590–640 km) and ilmenite–perovskite transitions (740–750 km) are identified based on similarly processed high-frequency P ' P ' precursors. Additional findings of severely scattered energy in the lithosphere and distinct lower mantle reflections at ~800 km could be potentially important but require further verifications. Overall, our improved imaging methods and the strong sensitivity of P ' P ' precursors to the existence, depth, sharpness and strength of reflective structures offer significant future promise for the understanding of mantle mineralogy and dynamics.
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  • 75
    Publication Date: 2013-09-10
    Description: Time-dependent probabilistic seismic hazard assessment requires a stochastic description of earthquake occurrences. While short-term seismicity models are well-constrained by observations, the recurrences of characteristic on-fault earthquakes are only derived from theoretical considerations, uncertain palaeo-events or proxy data. Despite the involved uncertainties and complexity, simple statistical models for a quasi-period recurrence of on-fault events are implemented in seismic hazard assessments. To test the applicability of statistical models, such as the Brownian relaxation oscillator or the stress release model, we perform a systematic comparison with deterministic simulations based on rate- and state-dependent friction, high-resolution representations of fault systems and quasi-dynamic rupture propagation. For the specific fault network of the Lower Rhine Embayment, Germany, we run both stochastic and deterministic model simulations based on the same fault geometries and stress interactions. Our results indicate that the stochastic simulators are able to reproduce the first-order characteristics of the major earthquakes on isolated faults as well as for coupled faults with moderate stress interactions. However, we find that all tested statistical models fail to reproduce the characteristics of strongly coupled faults, because multisegment rupturing resulting from a spatiotemporally correlated stress field is underestimated in the stochastic simulators. Our results suggest that stochastic models have to be extended by multirupture probability distributions to provide more reliable results.
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  • 76
    Publication Date: 2013-09-10
    Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.
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  • 77
    Publication Date: 2013-09-10
    Description: We used strong-motion records from the 2012 May 20 and 29 Emilia-Romagna earthquakes ( M w 6.1 and 5.9, respectively) and four aftershocks with magnitudes ranging between 4.9 and 5.5 to analyse the S -wave spectral amplitude decay with distance and estimate acceleration source functions and site effects. The data set consists of six earthquakes, 44 stations and 248 records with hypocentral distances in the range 10 〈 r  〈 100 km. We rotated the accelerograms to calculate transverse and radial components of the acceleration spectrum. We found non-parametric attenuation functions that describe the spectral amplitude decay of SH and SV waves with distance at 60 different frequencies between 0.1 and 40 Hz. These attenuation functions provide an estimate of the quality factor Q at each frequency analysed. Assuming that geometrical spreading is 1/ r for r  ≤ r x and 1/( r x r ) 0.5 for r  〉 r x with r x  = 60 km and normalizing at 15 km (the recording distance where the attenuation functions start to decay), we find that the average Q for SH waves can be approximated by Q SH  = 82 ± 1 f  1.2±0.02 and by Q SV  = 79 ± 1 f  1.24±0.03 for SV waves in the frequency range 0.10 ≤ f  ≤ 10.7 Hz. At higher frequencies, 11.8 ≤ f  ≤ 40 Hz, the frequency dependence of Q weakens and is approximated by Q SH  = 301 ± 1 f   0.36±0.04 and Q SV  = 384 ± 1 f  0.28±0.04 . These results indicate that the S -wave attenuation is radially isotropic at local distances in the epicentral area. Nevertheless, we used these attenuation parameters separately to correct the radial (with Q SV ) and transverse (with Q SH ) components of the acceleration spectra and to separate source and site effects using a non-parametric spectral inversion scheme. We found that the source function of the main event and the bigger aftershocks show enhanced low frequency radiation between 0.4 and 3.0 Hz. We converted the source functions into far-field source acceleration spectra and interpreted the resulting source spectra in terms of Brune's model. The stress drops obtained range between approximately 0.9 and 2.9 MPa. Although all the recording stations used are located in the Po Plain, the site functions obtained from the spectral inversion show important amplification variability between the sites. We compared these site functions with the average horizontal to vertical spectral ratios calculated for each station, and we found consistent results for most stations.
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  • 78
    Publication Date: 2013-09-10
    Description: H. Perez, T. Cordova-Fraga, S. Lopez-Briones, J. C. Martinez-Espinosa, E. F. Rosas et al. A device's instrumentation for magnetic stimulation on human lymphocytes is presented. This is a new procedure to stimulate growing cells with ferrofluid in vortices of magnetic field. The stimulation of magnetic vortices was provided at five different frequencies, from 100 to 2500 Hz and intensitie ... [Rev. Sci. Instrum. 84, 094701 (2013)] published Mon Sep 9, 2013.
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  • 79
    Publication Date: 2013-09-10
    Description: Kui Wang, Jianchun Jiang, Zhan Si, and Xinyu Liang A solid acid catalyst SO/TiO/La was prepared via sol-gel method using tetrabutyl titanate as TiO precursor. The catalyst simultaneously catalyzed esterification and transesterification resulting in the synthesis of biodiesel from waste cooking oil with high content of free fatty acids as feedstock. ... [J. Renewable Sustainable Energy 5, 052001 (2013)] published Mon Sep 9, 2013.
    Electronic ISSN: 1941-7012
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 80
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-11
    Description: Hanping Hu, Jun Xu, Xiang Xia, Shaobin Wu, Yanlong Liu et al. A singular resonance is discovered in investigating the features of high-frequency photoacoustic (PA) effect with multilayers. Theoretical analysis of its formation is carried out and reveals that it is a result of interaction between the resonance of gas-heat and that of solid-heat, while they happ ... [J. Appl. Phys. 114, 104902 (2013)] published Tue Sep 10, 2013.
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  • 81
    Publication Date: 2013-09-11
    Description: Punam Silwal, Ludi Miao, Jin Hu, Leonard Spinu, Dae Ho Kim et al. We present the thickness dependent structural, magnetic, and transport properties of transparent conducting spinel NiCoO thin films on MgAlO (001) substrates. The structural examination of the films reveals that the epitaxial stain is independent of the films' thickness. Electric and magnetic measur ... [J. Appl. Phys. 114, 103704 (2013)] published Tue Sep 10, 2013.
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  • 82
    Publication Date: 2013-09-11
    Description: Junbo Guo, Zhanghua Gan, Zhihong Lu, Jing Liu, Jingjing Xi et al. Low visible light absorption and high charge carrier recombination rate are two main disadvantages of TiO as a photocatalyst which severely limit its practical applications. To overcome the problems, Fe mono-doped and (Fe+Mo) co-doped TiO were synthesized and studied. It was found that (Fe+Mo) co-do ... [J. Appl. Phys. 114, 104903 (2013)] published Tue Sep 10, 2013.
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  • 83
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-11
    Description: L. Li, A. Nikiforov, Q. Xiong, N. Britun, R. Snyders et al. Recently, plasma jet systems found numerous applications in the field of biomedicine and treatment of temperature-sensitive materials. OH radicals are one of the main active species produced by these plasmas. Present study deals with the investigation of RF atmospheric pressure plasma jet in terms o ... [Phys. Plasmas 20, 093502 (2013)] published Tue Sep 10, 2013.
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  • 84
    Publication Date: 2013-09-11
    Description: H. Comişel, D. Verscharen, Y. Narita, and U. Motschmann We present a method for studying the evolution of plasma turbulence by tracking dispersion relations in the energy spectrum in the wavenumber-frequency domain. We apply hybrid plasma simulations in a simplified two-dimensional geometry to demonstrate our method and its applicability to plasma turbul ... [Phys. Plasmas 20, 090701 (2013)] published Tue Sep 10, 2013.
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  • 85
    Publication Date: 2013-09-11
    Description: Yi Zhang, Hayaki Murata, Yoshimi Hatsukade, and Saburo Tanaka We introduce a method to improve the detection sensitivity for the magnetization M of superparamagnetic nanoparticles (MNP). The M response of MNP to an applied magnetic field H (MH characteristics) could be divided into a linear region and a saturation region, which are separated at a transition po ... [Rev. Sci. Instrum. 84, 094702 (2013)] published Tue Sep 10, 2013.
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  • 86
    Publication Date: 2013-09-11
    Description: J. M. Gao, Y. Liu, W. Li, J. Lu, Y. B. Dong et al. An infrared imaging bolometer diagnostic has been developed recently for the HL-2A tokamak to measure the temporal and spatial distribution of plasma radiation. The three-dimensional tomography, reduced to a two-dimensional problem by the assumption of plasma radiation toroidal symmetry, has been pe ... [Rev. Sci. Instrum. 84, 093503 (2013)] published Tue Sep 10, 2013.
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  • 87
    Publication Date: 2013-09-12
    Description: G. C. Schmidt, D. Hoft, M. Bhuie, K. Haase, M. Bellmann et al. The influence of post-press treatment on the modification of printed source/drain electrodes made of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) with ethylene glycol is presented. Beside changes of the geometry and the conductivity of these mass printed structures, the work f ... [Appl. Phys. Lett. 103, 113302 (2013)] published Wed Sep 11, 2013.
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  • 88
    Publication Date: 2013-09-12
    Description: Hideki Gotoh, Haruki Sanada, Hiroshi Yamaguchi, and Tetsuomi Sogawa The distinctive effects of coherent phonons (groups of phase-matched phonons) on exciton states are reported by using single dot photoluminescence (PL) spectroscopy in semiconductor quantum dots (QDs). Coherent phonons that were induced with titanium thin metal films close to QDs by irradiating ultr ... [Appl. Phys. Lett. 103, 112104 (2013)] published Wed Sep 11, 2013.
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  • 89
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: O. V. Bilousov, H. Geaney, J. J. Carvajal, V. Z. Zubialevich, P. J. Parbrook et al. Porous GaN layers are grown on silicon from gold or platinum catalyst seed layers, and self-catalyzed on epitaxial GaN films on sapphire. Using a Mg-based precursor, we demonstrate p-type doping of the porous GaN. Electrical measurements for p-type GaN on Si show Ohmic and Schottky behavior from gol ... [Appl. Phys. Lett. 103, 112103 (2013)] published Wed Sep 11, 2013.
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  • 90
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: Roberto Rosati and Fausto Rossi In spite of their intrinsic validity limits, a number of Boltzmann-like simulation schemes are extensively employed in the investigation of semiconductor nanomaterials and nanodevices. Such modeling strategies, based on the neglect of carrier phase coherence, are definitely unable to describe space- ... [Appl. Phys. Lett. 103, 113105 (2013)] published Wed Sep 11, 2013.
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  • 91
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: Mohammad Arif Ishtiaque Shuvo, Tzu-Liang (Bill) Tseng, Md. Ashiqur Rahaman Khan, Hasanul Karim, Philip Morton et al. The study of electrochemical super-capacitors has become one of the most attractive topics in both academia and industry as energy storage devices because of their high power density, long life cycles, and high charge/discharge efficiency. Recently, there has been increasing interest in the developm ... [J. Appl. Phys. 114, 104306 (2013)] published Wed Sep 11, 2013.
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  • 92
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: Atreyee Banerjee, Suman Chakrabarty, and Sarika Maitra Bhattacharyya In this work we explore the interplay between crystallization and glass transition in different binary mixtures by changing their inter-species interaction length and also the composition. We find that only those systems which form bcc crystal in the equimolar mixture and whose global structure for ... [J. Chem. Phys. 139, 104501 (2013)] published Wed Sep 11, 2013.
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  • 93
    Publication Date: 2013-09-12
    Description: S. Vigne, S. Delprat, M. Chaker, and J. Margot It is found that in specific Cl plasma conditions, using a nickel hard mask over calcium barium niobate, CBN (a material particularly difficult to etch) significantly improves both sidewall angles and etching selectivity. This mask hardening is due to the competition between NiCl growth and etching ... [J. Appl. Phys. 114, 103303 (2013)] published Wed Sep 11, 2013.
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  • 94
    Publication Date: 2013-09-12
    Description: S. Agnello, D. Di Francesca, A. Alessi, G. Iovino, M. Cannas et al. The O content and emission properties in silica nanoparticles after thermal treatments in oxygen rich atmosphere have been investigated by Raman and photoluminescence measurements. The nanoparticles have different sizes with average diameter ranging from 7 up to 40 nm. It is found that O concentrati ... [J. Appl. Phys. 114, 104305 (2013)] published Wed Sep 11, 2013.
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  • 95
    Publication Date: 2013-09-12
    Description: S. Maidul Haque, A. Biswas, Debarati Bhattacharya, R. B. Tokas, D. Bhattacharyya et al. Using an indigenously built r.f. magnetron sputtering system, several single layer Ti and Ni films have been deposited at varying deposition conditions. All the samples have been characterized by Grazing Incidence X-ray Reflectivity (GIXR) and Atomic Force Microscopy to estimate their thickness, den ... [J. Appl. Phys. 114, 103508 (2013)] published Wed Sep 11, 2013.
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  • 96
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: Larisa V. Arapkina and Vladimir A. Yuryev Structural models of growing Ge hut clusterspyramids and wedgesare proposed on the basis of data of recent STM investigations of nucleation and growth of Ge huts on the Si(001) surface in the process of molecular beam epitaxy. It is shown that extension of a hut base along directions goes non-unifo ... [J. Appl. Phys. 114, 104304 (2013)] published Wed Sep 11, 2013.
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  • 97
    Publication Date: 2013-09-12
    Description: Jorg Schormann, Pascal Hille, Markus Schafer, Jan Mussener, Pascal Becker et al. Germanium doping of GaN nanowires grown by plasma-assisted molecular beam epitaxy on Si(111) substrates is studied. Time of flight secondary ion mass spectrometry measurements reveal a constant Ge-concentration along the growth axis. A linear relationship between the applied Ge-flux and the resultin ... [J. Appl. Phys. 114, 103505 (2013)] published Wed Sep 11, 2013.
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  • 98
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    American Institute of Physics (AIP)
    Publication Date: 2013-09-12
    Description: Younes Achaoui, Vincent Laude, Sarah Benchabane, and Abdelkrim Khelif The propagation of surface acoustic waves in two-dimensional phononic crystals of pillars on a surface is investigated experimentally for hexagonal and honeycomb lattice symmetries. A random array of pillars is also compared to the periodic phononic crystals. Taking into account that the geometrical ... [J. Appl. Phys. 114, 104503 (2013)] published Wed Sep 11, 2013.
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  • 99
    Publication Date: 2013-09-12
    Description: Yating Chai, Howard C. Wikle, Zhenyu Wang, Shin Horikawa, Steve Best et al. The real-time, in-situ bacteria detection on food surfaces was achieved by using a magnetoelastic biosensor combined with a surface-scanning coil detector. This paper focuses on the coil design for signal optimization. The coil was used to excite the sensor's vibration and detect its resonant freque ... [J. Appl. Phys. 114, 104504 (2013)] published Wed Sep 11, 2013.
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  • 100
    Publication Date: 2013-09-12
    Description: Frederik Westergaard Osterberg, Anders Dahl Henriksen, Giovanni Rizzi, and Mikkel Fougt Hansen Abstract not available. [J. Appl. Phys. 114, 106101 (2013)] published Wed Sep 11, 2013.
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