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  • Public Library of Science  (34,884)
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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
    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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  • 3
    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.
    Repository Name: Woods Hole Open Access Server
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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): 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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  • 5
    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).
    Repository Name: Woods Hole Open Access Server
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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 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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  • 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): 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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  • 8
    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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  • 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): 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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  • 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): 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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  • 11
    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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  • 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 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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  • 13
    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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  • 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 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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  • 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): 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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  • 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): 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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  • 17
    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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  • 18
    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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  • 19
    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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  • 20
    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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  • 21
    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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  • 22
    Publication Date: 2013-09-07
    Description: Author(s): G. Berner, A. Müller, F. Pfaff, J. Walde, C. Richter, J. Mannhart, S. Thiess, A. Gloskovskii, W. Drube, M. Sing, and R. Claessen We present a detailed study of the electronic structure and band alignment in LaAlO 3 /SrTiO 3 oxide heterostructures by hard x-ray photoelectron spectroscopy. Our spectroscopic measurements find no evidence for the strong potential gradient within the polar LaAlO 3 film predicted by band theory. Due to... [Phys. Rev. B 88, 115111] Published Fri Sep 06, 2013
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
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  • 23
    Publication Date: 2013-09-07
    Description: Author(s): Jifa Tian, Yongjin Jiang, Isaac Childres, Helin Cao, Jiangping Hu, and Yong P. Chen The Hall resistance of a homogeneous electron system is well known to be antisymmetric with respect to the magnetic field and the sign of charge carriers. We have observed that such symmetries no longer hold in planar hybrid structures consisting of partly single layer graphene (SLG) and partly bila... [Phys. Rev. B 88, 125410] Published Fri Sep 06, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
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  • 24
    Publication Date: 2013-09-07
    Description: Author(s): A. Tan, J. Li, C. A. Jenkins, E. Arenholz, A. Scholl, C. Hwang, and Z. Q. Qiu Py/FeMn/Cu(001) and Py/FeMn/Ni/Cu(001) films were grown and studied as a function of both the FeMn and the Ni thicknesses using rotating magneto-optic Kerr effect and x-ray magnetic circular dichroism. For Py/FeMn/Cu(001), we find that the FeMn antiferromagnetic order switches the sign of the Py fou... [Phys. Rev. B 88, 104404] Published Fri Sep 06, 2013
    Keywords: Magnetism
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  • 25
    Publication Date: 2013-09-07
    Description: Author(s): Bettina Gertjerenken and Christoph Weiss For the dynamics of Bose-Einstein condensates (BECs), differences between mean-field (Gross-Pitaevskii) physics and N -particle quantum physics often disappear if the BEC becomes larger and larger. In particular, the time scale for which both dynamics agree should thus become larger if the particle n... [Phys. Rev. A 88, 033608] Published Fri Sep 06, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
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  • 26
    Publication Date: 2013-09-07
    Description: Author(s): J. Ignacio Cirac, Spyridon Michalakis, David Pérez-García, and Norbert Schuch We analyze a criterion which guarantees that the ground states of certain many-body systems are stable under perturbations. Specifically, we consider PEPS, which are believed to provide an efficient description, based on local tensors, for the low energy physics arising from local interactions. In o... [Phys. Rev. B 88, 115108] Published Fri Sep 06, 2013
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
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  • 27
    Publication Date: 2013-09-07
    Description: Author(s): N. Drichko, R. Hackl, and J. Schlueter We compare the photoluminescence spectra of the low-temperature Mott insulator κ -(BEDT–TTF) 2 Cu[N(CN) 2 ]Cl ( T MIT =40 K) with spectra of metallic κ -(BEDT–TTF) 2 Cu[N(CN) 2 ]Br, which is superconducting below T c =11.8 K, in the temperature range between 300 and 20 K. In the Mott insulating state of κ -(BEDT–TT... [Phys. Rev. B 88, 115109] Published Fri Sep 06, 2013
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
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  • 28
    Publication Date: 2013-09-07
    Description: Author(s): G. Scherrer, M. Hofman, W. Śmigaj, M. Kadic, T.-M. Chang, X. Mélique, D. Lippens, O. Vanbésien, B. Cluzel, F. de Fornel, S. Guenneau, and B. Gralak Ground-plane cloaks, which transform a curved mirror into a flat one, and recently reported at wavelengths ranging from the optical to the visible spectrum, bring the realm of optical illusion a step closer to reality. However, all carpet-cloaking experiments have thus far been carried out in the fa... [Phys. Rev. B 88, 115110] Published Fri Sep 06, 2013
    Keywords: Electronic structure and strongly correlated systems
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  • 29
    Publication Date: 2013-09-07
    Description: Author(s): V. Kokoouline, A. Wearne, R. Lefebvre, and O. Atabek Exceptional points (EPs) corresponding to resonance coalescence (i.e., complex energy degeneracy and identical wave functions) occur in many areas of non-Hermitian physics and, in particular, in laser-induced molecular dynamics for specific choices of two control parameters. We have previously shown... [Phys. Rev. A 88, 033408] Published Fri Sep 06, 2013
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
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  • 30
    Publication Date: 2013-09-07
    Description: Author(s): Yiyan Sun, Houchen Chang, Michael Kabatek, Young-Yeal Song, Zihui Wang, Michael Jantz, William Schneider, Mingzhong Wu, E. Montoya, B. Kardasz, B. Heinrich, Suzanne G. E. te Velthuis, Helmut Schultheiss, and Axel Hoffmann Strong damping enhancement in nm-thick yttrium iron garnet (YIG) films due to Pt capping layers was observed. This damping is substantially larger than the expected damping due to conventional spin pumping, is accompanied by a shift in the ferromagnetic resonance field, and can be suppressed by the ... [Phys. Rev. Lett. 111, 106601] Published Fri Sep 06, 2013
    Keywords: Condensed Matter: Electronic Properties, etc.
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  • 31
    Publication Date: 2013-09-07
    Description: Author(s): Rintaro Inoue, Makoto Nakamura, Kazuya Matsui, Toshiji Kanaya, Koji Nishida, and Masahiro Hino We studied the distribution of glass transition temperature ( T g ) through neutron reflectivity in a poly(methyl methacrylate) (PMMA) thin film supported on a silicon substrate with a five-layered PMMA thin film consisting of deuterated-PMMA and hydrogenated-PMMA. The depth distribution of T g was succ... [Phys. Rev. E 88, 032601] Published Fri Sep 06, 2013
    Keywords: Polymers
    Print ISSN: 1539-3755
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  • 32
    Publication Date: 2013-09-07
    Description: Author(s): Volodymyr Borshch, Sergij V. Shiyanovskii, and Oleg D. Lavrentovich Electrically induced reorientation of nematic liquid crystal (NLC) molecules caused by dielectric anisotropy of the material is a fundamental phenomenon widely used in modern technologies. Its Achilles heel is a slow (millisecond) relaxation from the field-on to the field-off state. We present an el... [Phys. Rev. Lett. 111, 107802] Published Fri Sep 06, 2013
    Keywords: Soft Matter, Biological, and Interdisciplinary Physics
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  • 33
    Publication Date: 2013-09-10
    Description: Author(s): Azadeh Moradinezhad Dizgah, Scott Dodelson, and Antonio Riotto We study the impact of primordial non-Gaussianity on the density profile of dark matter halos by using the semianalytical model introduced recently by Dalal et al. which relates the peaks of the initial linear density field to the final density profile of dark matter halos. Models with primordial no... [Phys. Rev. D 88, 063513] Published Mon Sep 09, 2013
    Keywords: Astrophysics & Cosmology
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
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  • 34
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    Publication Date: 2013-09-10
    Description: Author(s): Sandipan Sengupta Motivated by a recent proposal (by Koslowski-Sahlmann) of a kinematical representation in loop quantum gravity (LQG) with a nondegenerate vacuum metric, we construct a polymer quantization of the parametrized massless scalar field theory on a Minkowskian cylinder. The diffeomorphism covariant kinema... [Phys. Rev. D 88, 064016] Published Mon Sep 09, 2013
    Keywords: General relativity, gravitation
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  • 35
    facet.materialart.
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    Publication Date: 2013-09-10
    Description: Author(s): Koji Ishiwata and Mark B. Wise We study the impact that a heavy generation of vectorlike leptons can have on the value of the electric dipole moment of the electron, and the rates for the flavor violating processes μ → e γ and μ →3 e . The smallness of the charged lepton masses suggests that at least some of the Yukawa coupling constan... [Phys. Rev. D 88, 055009] Published Mon Sep 09, 2013
    Keywords: Beyond the standard model
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  • 36
    Publication Date: 2013-09-10
    Description: Author(s): Chiu Man Ho and Thomas J. Weiler [Phys. Rev. D 88, 069901] Published Mon Sep 09, 2013
    Keywords: Errata
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  • 37
    Publication Date: 2013-09-10
    Description: Author(s): Riccardo Borsato, Olof Ohlsson Sax, Alessandro Sfondrini, Bogdan Stefański, Jr., and Alessandro Torrielli We determine the all-loop dressing phases of the AdS 3 /CFT 2 integrable system related to type IIB string theory on AdS 3 ×S 3 ×T 4 by solving the recently found crossing relations and studying their singularity structure. The two resulting phases present a novel structure with respect to the ones appearin... [Phys. Rev. D 88, 066004] Published Mon Sep 09, 2013
    Keywords: String theory
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  • 38
    Publication Date: 2013-09-10
    Description: Author(s): Swetaprovo Chaudhuri, Fujia Wu, and Chung K. Law In this paper we clarify the role of Markstein diffusivity, which is the product of the planar laminar flame speed and the Markstein length, on the turbulent flame speed and its scaling, based on experimental measurements on constant-pressure expanding turbulent flames. Turbulent flame propagation d... [Phys. Rev. E 88, 033005] Published Mon Sep 09, 2013
    Keywords: Fluid Dynamics
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  • 39
    Publication Date: 2013-09-10
    Description: Author(s): Cyril Desjouy, Pauline Labelle, Bruno Gilles, Jean-Christophe Bera, and Claude Inserra Acoustic cavitation-induced microbubbles in a cylindrical resonator filled with water tend to concentrate into ring patterns due to the cylindrical geometry of the system. The shape of these ring patterns is directly linked to the Bjerknes force distribution in the resonator. Experimental observatio... [Phys. Rev. E 88, 033006] Published Mon Sep 09, 2013
    Keywords: Fluid Dynamics
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  • 40
    facet.materialart.
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    American Physical Society (APS)
    Publication Date: 2013-09-10
    Description: Author(s): M. D. Campanell Most works on plasma-wall interaction predict that with strong electron emission, a nonmonotonic “space-charge-limited” (SCL) sheath forms where the plasma potential is positive relative to the wall. We show that a fundamentally different sheath structure is possible where the potential monotonicall... [Phys. Rev. E 88, 033103] Published Mon Sep 09, 2013
    Keywords: Plasma Physics
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  • 41
    Publication Date: 2013-09-11
    Description: Author(s): R. Aaij et al. (LHCb Collaboration) A broad peaking structure is observed in the dimuon spectrum of B + → K + μ + μ - decays in the kinematic region where the kaon has a low recoil against the dimuon system. The structure is consistent with interference between the B + → K + μ + μ - decay and a resonance and has a statistical significance exceeding s... [Phys. Rev. Lett. 111, 112003] Published Tue Sep 10, 2013
    Keywords: Elementary Particles and Fields
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  • 42
    Publication Date: 2013-09-11
    Description: Author(s): Serge Mora, Corrado Maurini, Ty Phou, Jean-Marc Fromental, Basile Audoly, and Yves Pomeau Under the effect of surface tension, a blob of liquid adopts a spherical shape when immersed in another fluid. We demonstrate experimentally that soft, centimeter-size elastic solids can exhibit a similar behavior: when immersed into a liquid, a gel having a low elastic modulus undergoes large, reve... [Phys. Rev. Lett. 111, 114301] Published Tue Sep 10, 2013
    Keywords: Nonlinear Dynamics, Fluid Dynamics, Classical Optics, etc.
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  • 43
    Publication Date: 2013-09-11
    Description: Author(s): V. P. Bhallamudi, C. S. Wolfe, V. P. Amin, D. E. Labanowski, A. J. Berger, D. Stroud, J. Sinova, and P. C. Hammel We present a new tool for imaging spin properties. We show that a spatially averaged spin signal, measured as a function of a scanned magnetic probe’s position, contains information about the local spin properties. In this first demonstration we map the injected spin density in GaAs by measuring spi... [Phys. Rev. Lett. 111, 117201] Published Tue Sep 10, 2013
    Keywords: Condensed Matter: Electronic Properties, etc.
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  • 44
    Publication Date: 2013-09-11
    Description: Author(s): Nicolas Desreumaux, Jean-Baptiste Caussin, Raphael Jeanneret, Eric Lauga, and Denis Bartolo We address the collective dynamics of non-Brownian particles cruising in a confined microfluidic geometry and provide a comprehensive characterization of their spatiotemporal density fluctuations. We show that density excitations freely propagate at all scales, and in all directions even though the ... [Phys. Rev. Lett. 111, 118301] Published Tue Sep 10, 2013
    Keywords: Soft Matter, Biological, and Interdisciplinary Physics
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  • 45
    Publication Date: 2013-09-11
    Description: Author(s): Uwe Thiele, Desislava V. Todorova, and Hender Lopez A thermodynamically consistent gradient dynamics model for the evolution of thin layers of liquid mixtures, solutions, and suspensions on solid substrates is presented which is based on a film-height- and mean-concentration-dependent free energy functional. It is able to describe a large variety of ... [Phys. Rev. Lett. 111, 117801] Published Tue Sep 10, 2013
    Keywords: Soft Matter, Biological, and Interdisciplinary Physics
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  • 46
    Publication Date: 2013-09-12
    Description: Author(s): Mahdi Ebrahimi Kahou and David L. Feder One approach to the development of quantum search algorithms is the quantum walk. A spatial search can be effected by the continuous-time evolution of a single quantum particle on a graph containing a marked site. In many physical implementations, however, one might expect to have multiple particles... [Phys. Rev. A 88, 032310] Published Wed Sep 11, 2013
    Keywords: Quantum information
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  • 47
    Publication Date: 2013-09-12
    Description: Author(s): Jun Jiang and J. Mitroy The influence of hyperfine interactions on the tune-out wavelengths of the 39 K, 40 K, and 41 K isotopes of the potassium atom was investigated. The hyperfine interaction of the 4 s 1/2 ground state results in a shift and splitting of the primary tune-out wavelength near 769 nm. The 4 s 1/2 state hyperfine... [Phys. Rev. A 88, 032505] Published Wed Sep 11, 2013
    Keywords: Atomic and molecular structure and dynamics
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  • 48
    Publication Date: 2013-09-12
    Description: Author(s): Sougata Mukhopadhyay and C. Sinha We study quantum mechanically the influence of an external laser field on the antihydrogen (H̅ ) formation cross sections in ground and excited states (2 s ,2 p ) via the three-body recombination process inside a dense plasma of antiprotons and positrons, supposed to be the most efficient mechani... [Phys. Rev. A 88, 033414] Published Wed Sep 11, 2013
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
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  • 49
    Publication Date: 2013-09-12
    Description: Author(s): Wenchen Luo and R. Côté At half-filling of the fourfold degenerate Landau levels | n |≥1 in graphene, the ground states are spin-polarized quantum Hall states that support spin skyrmion excitations for | n |=1,2,3. Working in the Hartree-Fock approximation, we compute the excitation energy of an unbound spin skyrmion-antiskyrm... [Phys. Rev. B 88, 115417] Published Wed Sep 11, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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  • 50
    facet.materialart.
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    American Physical Society (APS)
    Publication Date: 2013-09-12
    Description: Author(s): Bruno Amorim and Francisco Guinea Out of plane vibrations are suppressed in graphene layers placed on a substrate. These vibrations, in suspended samples, are relevant for the understanding of properties such as the electrical resistivity, the thermal expansion coefficient, and others. We use a general framework to study the propert... [Phys. Rev. B 88, 115418] Published Wed Sep 11, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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  • 51
    Publication Date: 2013-09-12
    Description: Author(s): Andreas Vogler, Ralf Labouvie, Felix Stubenrauch, Giovanni Barontini, Vera Guarrera, and Herwig Ott We investigate the thermodynamics of one-dimensional (1D) Bose gases in the strongly correlated regime. To this end, we prepare ensembles of independent 1D Bose gases in a two-dimensional optical lattice and perform high-resolution in situ imaging of the column-integrated density distribution. Using... [Phys. Rev. A 88, 031603] Published Wed Sep 11, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
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  • 52
    Publication Date: 2013-09-12
    Description: Author(s): Sergii Strelchuk There exist memoryless zero-capacity quantum channels that when used jointly result in a channel with positive capacity. This phenomenon is called superactivation. Making use of Parrondo's paradox, we exhibit examples of the superactivation-like effect for the capacity of classical communication cha... [Phys. Rev. A 88, 032311] Published Wed Sep 11, 2013
    Keywords: Quantum information
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  • 53
    Publication Date: 2013-09-12
    Description: Author(s): Benkang Liu, Yanqiu Wang, and Li Wang The photoelectron velocity-map image technique was employed to examine the one-photon detachment of Cu monomer and dimer anions using a linearly polarized infrared femtosecond laser. While the photoelectron angular distribution (PAD) in a single-photon detachment experiment of Cu − shows no dependenc... [Phys. Rev. A 88, 033413] Published Wed Sep 11, 2013
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
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  • 54
    Publication Date: 2013-09-12
    Description: Author(s): Zhang-qi Yin, Tongcang Li, Xiang Zhang, and L. M. Duan We propose a method to generate and detect large quantum superposition states and arbitrary Fock states for the oscillational mode of an optically levitated nanocrystal diamond. The nonlinear interaction required for the generation of non-Gaussian quantum states is enabled through the spin-mechanica... [Phys. Rev. A 88, 033614] Published Wed Sep 11, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
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  • 55
    Publication Date: 2013-09-12
    Description: Author(s): Sung Sakong, Peter Kratzer, Simone Wall, Annika Kalus, and Michael Horn-von Hoegen The dynamics of vibrations localized in a monolayer of Pb on Si(111) is studied using density functional theory and molecular dynamics methods. Recently, a pump-probe experiment has given direct access to the relaxation dynamics of the vibrational excitations in Pb, revealing two distinct time scale... [Phys. Rev. B 88, 115419] Published Wed Sep 11, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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  • 56
    Publication Date: 2013-09-12
    Description: Author(s): R. L. Stillwell, D. E. Graf, W. A. Coniglio, T. P. Murphy, E. C. Palm, J. H. Park, D. VanGennep, P. Schlottmann, and S. W. Tozer We have observed a massive reconstruction of the Fermi surface of single crystal chromium as a function of high pressure and high magnetic fields caused by the spin-flip transition, with multiple new orbits appearing above 0.93 GPa. In addition, some orbits have field-induced effective masses of ∼0.... [Phys. Rev. B 88, 125119] Published Wed Sep 11, 2013
    Keywords: Electronic structure and strongly correlated systems
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  • 57
    facet.materialart.
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    American Physical Society (APS)
    Publication Date: 2013-09-12
    Description: Author(s): Florian Kühnel Stability about cosmological background solutions to the bimetric Hassan-Rosen theory is studied. The results of this analysis are presented, and it is shown that a large class of cosmological backgrounds is classically unstable. This sets serious doubts on the physical viability of the Hassan-Rosen... [Phys. Rev. D 88, 064024] Published Wed Sep 11, 2013
    Keywords: General relativity, gravitation
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  • 58
    Publication Date: 2013-09-12
    Description: Author(s): R. Raut, A. P. Tonchev, G. Rusev, W. Tornow, C. Iliadis, M. Lugaro, J. Buntain, S. Goriely, J. H. Kelley, R. Schwengner, A. Banu, and N. Tsoneva We have carried out photodisintegration cross-section measurements on 86 Kr using monoenergetic photon beams ranging from the neutron separation energy, S n =9.86  MeV, to 13 MeV. We combine our experimental 86 Kr( γ , n ) 85 Kr cross section with results from our recent 86 Kr( γ , γ ′ ) measurement below the neutr... [Phys. Rev. Lett. 111, 112501] Published Wed Sep 11, 2013
    Keywords: Nuclear Physics
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  • 59
    Publication Date: 2013-09-12
    Description: Author(s): Eric A. Bergshoeff, Sjoerd de Haan, Olaf Hohm, Wout Merbis, and Paul K. Townsend We present a generally covariant and parity-invariant two-frame field (“zwei-dreibein”) action for gravity in three space-time dimensions that propagates two massive spin-2 modes, unitarily, and we use Hamiltonian methods to confirm the absence of unphysical degrees of freedom. We show how zwei-drei... [Phys. Rev. Lett. 111, 111102] Published Wed Sep 11, 2013
    Keywords: Gravitation and Astrophysics
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  • 60
    Publication Date: 2013-09-13
    Description: Author(s): Easwar Magesan, Alexandre Cooper, Honam Yum, and Paola Cappellaro Quantum systems have shown great promise for precision metrology thanks to advances in their control. This has allowed not only the sensitive estimation of external parameters but also the reconstruction of their temporal profile. In particular, quantum control techniques and orthogonal function the... [Phys. Rev. A 88, 032107] Published Thu Sep 12, 2013
    Keywords: Fundamental concepts
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  • 61
    Publication Date: 2013-09-13
    Description: Author(s): Guang-Yin Chen, Neill Lambert, Che-Ming Li, Yueh-Nan Chen, and Franco Nori We investigate, using the hierarchy method, the entanglement and the excitation transfer efficiency of the Fenna-Matthews-Olson (FMO) complex under two different local modifications: the suppression of transitions between particular sites and localized changes to the protein environment. We find tha... [Phys. Rev. E 88, 032120] Published Thu Sep 12, 2013
    Keywords: Statistical Physics
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  • 62
    facet.materialart.
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    American Physical Society (APS)
    Publication Date: 2013-09-13
    Description: Author(s): M. J. B. Moura and M. Marder We examine the fracture mechanics of tearing graphene. We present a molecular dynamics simulation of the propagation of cracks in clamped, free-standing graphene as a function of the out-of-plane force. The geometry is motivated by experimental configurations that expose graphene sheets to out-of-pl... [Phys. Rev. E 88, 032405] Published Thu Sep 12, 2013
    Keywords: Films, Interfaces, and Crystal Growth
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  • 63
    Publication Date: 2013-09-13
    Description: Author(s): Fulvio Bisi, Giovanni De Matteis, and Silvano Romano We consider here a classical model, consisting of D 2 h -symmetric particles in a three-dimensional simple-cubic lattice; the pair potential is isotropic in orientation space, and restricted to nearest neighbors. The simplest potential model is written in terms of the squares of the scalar products bet... [Phys. Rev. E 88, 032502] Published Thu Sep 12, 2013
    Keywords: Liquid Crystals
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  • 64
    Publication Date: 2013-09-14
    Description: Author(s): Hanjie Guo, Hiroshi Tanida, Riki Kobayashi, Ikuto Kawasaki, Masafumi Sera, Takashi Nishioka, Masahiro Matsumura, Isao Watanabe, and Zhu-an Xu The magnetic ground state of the Rh-doped Kondo semiconductor CeRu 2 Al 10 [Ce(Ru 1− x Rh x ) 2 Al 10 ] is investigated with the muon spin relaxation method. Muon spin precession with two frequencies is observed in the x =0 sample, while only one frequency is present in the x =0.05 and 0.10 samples, which is attr... [Phys. Rev. B 88, 115206] Published Fri Sep 13, 2013
    Keywords: Semiconductors I: bulk
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  • 65
    Publication Date: 2013-09-14
    Description: Author(s): A. Hillion, A. Tamion, F. Tournus, O. Gaier, E. Bonet, C. Albin, and V. Dupuis We propose a theoretical framework enabling the simulation of isothermal remanence magnetization (IRM) curves, based on the Stoner-Wohlfarth model combined with the Néel macrospin relaxation time description. We show how low temperature IRM curves, which have many advantages compared to hysteresis l... [Phys. Rev. B 88, 094419] Published Fri Sep 13, 2013
    Keywords: Magnetism
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  • 66
    Publication Date: 2013-09-14
    Description: Author(s): C. W. Xiao, J. Nieves, and E. Oset We present a coupled channel unitary approach to obtain states dynamically generated from the meson-baryon interaction with hidden charm, using constraints of heavy quark spin symmetry. As a basis of states, we use D ̅ B , D ̅ * B states, with B baryon charmed states belonging to the 20 re... [Phys. Rev. D 88, 056012] Published Fri Sep 13, 2013
    Keywords: Field theory, general methods
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  • 67
    Publication Date: 2013-09-14
    Description: Author(s): A. A. Bush, N. Büttgen, A. A. Gippius, V. N. Glazkov, W. Kraetschmer, L. A. Prozorova, L. E. Svistov, A. M. Vasiliev, and A. Zheludev We present the results of magnetization, electron spin resonance (ESR), and nuclear magnetic resonance (NMR) measurements on single-crystal samples of the frustrated S =1/2 chain cuprate LiCu 2 O 2 doped with nonmagnetic Zn 2+ . As shown by the x-ray techniques, the crystals of Li(Cu 1− x Zn x ) 2 O 2 with x 〈0... [Phys. Rev. B 88, 104411] Published Fri Sep 13, 2013
    Keywords: Magnetism
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  • 68
    Publication Date: 2013-09-14
    Description: Author(s): Nicolai Friis, Antony R. Lee, and Jorma Louko We analyze quantized scalar, spinor, and photon fields in a mechanically rigid cavity that is accelerated in Minkowski spacetime, in a recently introduced perturbative small-acceleration formalism that allows the velocities to become relativistic, with a view to applications in relativistic quantum ... [Phys. Rev. D 88, 064028] Published Fri Sep 13, 2013
    Keywords: General relativity, gravitation
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  • 69
    Publication Date: 2013-09-14
    Description: Author(s): Parvendra Kumar and Amarendra K. Sarma We report a simple scheme to achieve ultrafast and selective population transfer in four-level atoms by utilizing a single nonlinearly chirped femtosecond pulse. It is demonstrated that the almost complete population may be transferred to the preselected state of atoms just by manipulating the so-ca... [Phys. Rev. A 88, 033823] Published Fri Sep 13, 2013
    Keywords: Quantum optics, physics of lasers, nonlinear optics, classical optics
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  • 70
    Publication Date: 2013-09-14
    Description: Author(s): G. H. Gossel, V. A. Dzuba, and V. V. Flambaum We calculate magnetic dipole transition amplitudes in s − s and s − d transitions of Rb, Cs, Ba + , Fr, Ra + , Yb + , Ac 2+ and Th 3+ . These transitions were used or considered to be used for parity-nonconservation (PNC) measurements. We also calculate the magnetic g -factor anomalies for a selection of states, ... [Phys. Rev. A 88, 034501] Published Fri Sep 13, 2013
    Keywords: Atomic and molecular structure and dynamics
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  • 71
    Publication Date: 2013-09-14
    Description: Author(s): X. P. Shen, S. D. Chen, Q. Q. Ge, Z. R. Ye, F. Chen, H. C. Xu, S. Y. Tan, X. H. Niu, Q. Fan, B. P. Xie, and D. L. Feng We studied the low-lying electronic structure of the newly discovered iron-platinum-arsenide superconductor, Ca 10 (Pt 4 As 8 )(Fe 2− x Pt x As 2 ) 5 ( T c =22 K) with angle-resolved photoemission spectroscopy. We found that the Pt 4 As 8 layer contributes to a small electronlike Fermi surface, indicative of metallic c... [Phys. Rev. B 88, 115124] Published Fri Sep 13, 2013
    Keywords: Electronic structure and strongly correlated systems
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  • 72
    Publication Date: 2013-09-14
    Description: Author(s): U. C. Mendes, M. Korkusinski, A. H. Trojnar, and P. Hawrylak We present a microscopic theory of the optical properties of self-assembled quantum dots doped with a single magnetic manganese (Mn) impurity and containing a controlled number of electrons. The single-particle electron and heavy-hole electronic shells are described by two-dimensional harmonic oscil... [Phys. Rev. B 88, 115306] Published Fri Sep 13, 2013
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
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  • 73
    Publication Date: 2013-09-14
    Description: Author(s): F. Nilsson, R. Sakuma, and F. Aryasetiawan In this work we have calculated U from first principles for the early lanthanides (Ce-Gd) using the constrained random phase approximation (cRPA). We compare the static limit of U with experimental estimations from x-ray photoemission spectroscopy (XPS) and bremsstrahlung isochromat spectroscopy (BI... [Phys. Rev. B 88, 125123] Published Fri Sep 13, 2013
    Keywords: Electronic structure and strongly correlated systems
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  • 74
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    American Physical Society (APS)
    Publication Date: 2013-09-14
    Description: Author(s): Lance J. Dixon and Ye Li We study the change in the diphoton-invariant-mass distribution for Higgs boson decays to two photons, due to interference between the Higgs resonance in gluon fusion and the continuum background amplitude for g g → γ γ . Previously, the apparent Higgs mass was found to shift by around 100 MeV in the sta... [Phys. Rev. Lett. 111, 111802] Published Fri Sep 13, 2013
    Keywords: Elementary Particles and Fields
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  • 75
    Publication Date: 2013-09-14
    Description: Author(s): M. R. Kamali, J. J. J. Gillissen, H. E. A. van den Akker, and Sankaran Sundaresan A lattice Boltzmann (LB) method is presented for solving the energy conservation equation in two phases when the phase change effects are included in the model. This approach employs multiple distribution functions, one for a pseudotemperature scalar variable and the rest for the various species. A ... [Phys. Rev. E 88, 033302] Published Fri Sep 13, 2013
    Keywords: Computational Physics
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  • 76
    Publication Date: 2013-09-14
    Description: Author(s): C. Stock, S. R. Dunsiger, R. A. Mole, X. Li, and H. Luo A neutron scattering investigation of the magnetoelectric coupling in PbFe 1/2 Nb 1/2 O 3 has been undertaken. Ferroelectric order occurs below 400 K, as evidenced by the softening with temperature and subsequent recovery of the zone center transverse optic phonon mode energy ( ℏ Ω 0 ). Over the same tempera... [Phys. Rev. B 88, 094105] Published Fri Sep 13, 2013
    Keywords: Structure, structural phase transitions, mechanical properties, defects
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  • 77
    Publication Date: 2013-09-14
    Description: Author(s): Alessandro Roggero, Francesco Pederiva, and Giuseppina Orlandini An ab initio method for determining the dynamical structure function of an interacting many-body quantum system has been devised by combining a generalized integral transform method with quantum Monte Carlo (QMC) methods. A kernel has been found that (i) lets the transform be calculable with QMC met... [Phys. Rev. B 88, 094302] Published Fri Sep 13, 2013
    Keywords: Dynamics, dynamical systems, lattice effects
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  • 78
    Publication Date: 2013-09-14
    Description: Author(s): D. T. Son and B. Z. Spivak We consider the classical magnetoresistance of a Weyl metal in which the electron Fermi surface possesses nonzero fluxes of the Berry curvature. Such a system may exhibit large negative magnetoresistance with unusual anisotropy as a function of the angle between the electric and magnetic fields. In ... [Phys. Rev. B 88, 104412] Published Fri Sep 13, 2013
    Keywords: Magnetism
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  • 79
    Publication Date: 2013-09-14
    Description: Author(s): P. Delugas, A. Filippetti, A. Gadaleta, I. Pallecchi, D. Marré, and V. Fiorentini Using advanced first-principles calculations we predict that the nonpolar SrTiO 3 /SrZrO 3 (001) interface, designed as either thin SrZrO 3 film deposited on SrTiO 3 or short-period (SrTiO 3 ) m /(SrZrO 3 ) n superlattice, hosts a two-dimensionally confined electron gas. Mobile electron charge due to native imp... [Phys. Rev. B 88, 115304] Published Fri Sep 13, 2013
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
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  • 80
    Publication Date: 2013-09-14
    Description: Author(s): Rafael Roldán and Luis Brey The screening properties and collective excitations (plasmons) in AA-stacked bilayer graphene are studied within the random phase approximation. Whereas long-lived plasmons in single-layer graphene and in AB-stacked bilayer graphene can exist only in doped samples, we find that coherent plasmons can... [Phys. Rev. B 88, 115420] Published Fri Sep 13, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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  • 81
    Publication Date: 2013-09-14
    Description: Author(s): Stephan Michael, Weng W. Chow, and Hans Christian Schneider The slowdown of optical pulses due to quantum-coherence effects is investigated theoretically for an “active material” consisting of InGaAs-based double quantum dot molecules. These are designed to exhibit a long-lived coherence between two electronic levels, which is an essential part of a quantum-... [Phys. Rev. B 88, 125305] Published Fri Sep 13, 2013
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
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  • 82
    Publication Date: 2013-09-14
    Description: Author(s): V. Vandone et al. The K hindrance to the γ decay is studied in the warm rotating 174 W nucleus, focusing on the weakening of the selection rules of the K quantum number with increasing excitation energy. 174 W was populated by the fusion reaction of 50 Ti (at 217 MeV) on a 128 Te target, and its γ decay was detected by t... [Phys. Rev. C 88, 034312] Published Fri Sep 13, 2013
    Keywords: Nuclear Structure
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  • 83
    Publication Date: 2013-09-14
    Description: Author(s): S. F. C. Shearer and M. R. Monteith The recent adiabatic saddle-point approach of Shearer et al. [ Phys. Rev. A 84 033409 (2011) ] is extended to multiphoton detachment of negative ions with outer p -state electrons. This theory is applied to investigate the strong-field photodetachment dynamics of F − ions exposed to few-cycle femtosec... [Phys. Rev. A 88, 033415] Published Fri Sep 13, 2013
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
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  • 84
    Publication Date: 2013-09-14
    Description: Author(s): H. Zhang, J. Tulpan, M. Shrestha, and D. M. Manley We present results of a new multichannel partial-wave analysis for K ̅ N scattering in the center-of-mass (c.m.) energy range from 1480 to 2100 MeV. Resonance parameters were extracted by fitting partial-wave amplitudes from all considered channels using a multichannel parametrization that is ... [Phys. Rev. C 88, 035205] Published Fri Sep 13, 2013
    Keywords: Hadronic Physics and QCD
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  • 85
    Publication Date: 2013-09-14
    Description: Author(s): Nikolaos G. Fytas and Víctor Martín-Mayor [Phys. Rev. Lett. 111, 119903] Published Fri Sep 13, 2013
    Keywords: Errata
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  • 86
    Publication Date: 2013-09-14
    Description: Author(s): Subir Biswas, Debjyoti Basu, Rabindranath Pal, and Nikhil Chakrabarti Excitation of low frequency drift waves in a radial region of a weak density gradient is demonstrated experimentally by strong temporal modulation of the plasma density. Though a parallel electron current can destabilize drift waves throughout the region, we observe mode selection at the resonant lo... [Phys. Rev. Lett. 111, 115004] Published Fri Sep 13, 2013
    Keywords: Plasma and Beam Physics
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  • 87
    Publication Date: 2013-09-14
    Description: Author(s): Oliver Bäumchen, Michael Benzaquen, Thomas Salez, Joshua D. McGraw, Matilda Backholm, Paul Fowler, Elie Raphaël, and Kari Dalnoki-Veress The surface of a thin liquid film with nonconstant curvature flattens as a result of capillary forces. While this leveling is driven by local curvature gradients, the global boundary conditions greatly influence the dynamics. Here, we study the evolution of rectangular trenches in a polystyrene nano... [Phys. Rev. E 88, 035001] Published Fri Sep 13, 2013
    Keywords: Fluid Dynamics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 88
    Publication Date: 2013-09-14
    Description: Author(s): J. Schachenmayer, B. P. Lanyon, C. F. Roos, and A. J. Daley Recent advances in quantum simulators allow the use of systems of trapped ions to create and simulate spin models with a controllable interaction range. Scientists report timely and counterintuitive theoretical findings about the temporal growth of quantum entanglement in a suddenly “quenched” quantum spin chain based on trapped ions. [Phys. Rev. X 3, 031015] Published Fri Sep 13, 2013
    Keywords: Research Articles
    Electronic ISSN: 2160-3308
    Topics: Physics
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  • 89
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    American Physical Society (APS)
    Publication Date: 2013-09-17
    Description: Author(s): V. Subrahmanyam Block entanglement entropy in the ground state of a quantum spin chain is investigated. The spins have Kitaev-type nearest-neighbor interaction, of strength J x or J y , through either x or y components of the spins on alternating bonds, along with a transverse magnetic field h . An exact solution is ob... [Phys. Rev. A 88, 032315] Published Mon Sep 16, 2013
    Keywords: Quantum information
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 90
    Publication Date: 2013-09-17
    Description: Author(s): Sergey N. Filippov and Mário Ziman We fully characterize bipartite entanglement-annihilating (EA) channels that destroy entanglement of any state shared by subsystems and, thus, should be avoided in any entanglement-enabled experiment. Our approach relies on extending the problem to EA positive maps, the cone of which remains invaria... [Phys. Rev. A 88, 032316] Published Mon Sep 16, 2013
    Keywords: Quantum information
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 91
    Publication Date: 2013-09-17
    Description: Author(s): Bernhard M. Breid and James R. Anglin We develop a Hamiltonian that describes the time-dependent formation of a molecular Bose-Einstein condensate from a Bardeen-Cooper-Schrieffer state of fermionic atoms as a result of slowly sweeping through a Feshbach resonance. In contrast to many other calculations in the field, our Hamiltonian inc... [Phys. Rev. A 88, 033617] Published Mon Sep 16, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 92
    Publication Date: 2013-09-17
    Description: Author(s): Swapan Rana and Preeti Parashar In a recent article [ Phys. Rev. A 87 022340 (2013) ], Yan et al. have studied geometric discord for a well-known class of bound entangled states. Based on their calculation, they claim “It is found that there exists a nondynamic sudden change in quantum discord” for these states. In this Comment, w... [Phys. Rev. A 88, 036301] Published Mon Sep 16, 2013
    Keywords: Quantum information
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 93
    Publication Date: 2013-09-17
    Description: Author(s): Thomas Lehmann, Dmitry A. Ryndyk, and Gianaurelio Cuniberti We investigate the combined influence of structural defects and uniaxial longitudinal strain on the electronic transport properties of armchair graphene nanoribbons using the numerical approach based on the semiempirical tight-binding model, the Landauer formalism, and the recursion method for Green... [Phys. Rev. B 88, 125420] Published Mon Sep 16, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 94
    Publication Date: 2013-09-17
    Description: Author(s): Thomas DeGrand, Yigal Shamir, and Benjamin Svetitsky We apply Schrödinger functional methods to two gauge theories with fermions in two-index representations: the SU(3) theory with N f =2 adjoint fermions, and the SU(4) theory with N f =6 fermions in the two-index antisymmetric representation. Each theory is believed to lie near the bottom of the conforma... [Phys. Rev. D 88, 054505] Published Mon Sep 16, 2013
    Keywords: Strong interactions & Lattice methods
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 95
    Publication Date: 2013-09-17
    Description: Author(s): Raphaël Chetrite and Hugo Touchette Generalizations of the microcanonical and canonical ensembles for paths of Markov processes have been proposed recently to describe the statistical properties of nonequilibrium systems driven in steady states. Here, we propose a theory of these ensembles that unifies and generalizes earlier results ... [Phys. Rev. Lett. 111, 120601] Published Mon Sep 16, 2013
    Keywords: General Physics: Statistical and Quantum Mechanics, Quantum Information, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 96
    Publication Date: 2013-09-17
    Description: Author(s): Rafael M. Fernandes and Andrew J. Millis In several families of iron-based superconducting materials, a d -wave pairing instability may compete with the leading s -wave instability. Here, we show that when both states have comparable free energies, superconducting and nematic degrees of freedom are strongly coupled. Whereas nematic order cau... [Phys. Rev. Lett. 111, 127001] Published Mon Sep 16, 2013
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 97
    Publication Date: 2013-09-17
    Description: Author(s): Marco Cristoforetti, Francesco Di Renzo, Abhishek Mukherjee, and Luigi Scorzato We present the first practical Monte Carlo calculations of the recently proposed Lefschetz thimble formulation of quantum field theories. Our results provide strong evidence that the numerical sign problem that afflicts Monte Carlo calculations of models with complex actions can be softened signific... [Phys. Rev. D 88, 051501] Published Mon Sep 16, 2013
    Keywords: Strong interactions & Lattice methods
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 98
    Publication Date: 2013-09-17
    Description: Author(s): I. McGregor and K. M. Hock We describe full wave simulation results for a compact, novel deflecting structure operating around 2 GHz. The structure consists of a pair of elliptical complementary split-ring resonators (CSRRs) etched into a copper rectangular waveguide along with outer rectangular cavities to maintain the vacuu... [Phys. Rev. ST Accel. Beams 16, 090101] Published Mon Sep 16, 2013
    Keywords: Low- and Intermediate-Energy Accelerators
    Electronic ISSN: 1098-4402
    Topics: Physics
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  • 99
    Publication Date: 2013-09-17
    Description: Author(s): Ivan V. Pechenezhskiy, Xiaoping Hong, Giang D. Nguyen, Jeremy E. P. Dahl, Robert M. K. Carlson, Feng Wang, and Michael F. Crommie We have developed a new scanning-tunneling-microscopy–based spectroscopy technique to characterize infrared (IR) absorption of submonolayers of molecules on conducting crystals. The technique employs a scanning tunneling microscope as a precise detector to measure the expansion of a molecule-decorat... [Phys. Rev. Lett. 111, 126101] Published Mon Sep 16, 2013
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 100
    Publication Date: 2013-09-18
    Description: Author(s): V. M. Abazov et al. (D0 Collaboration) We present a search for the Higgs boson in final states with two oppositely charged leptons and large missing transverse energy as expected in H → W W → ℓ ν ℓ ′ ν ′ decays. The events are selected from the full Run II data sample of 9.7  fb -1 of p p ̅ collisions collected with the D0 detector at the Fer... [Phys. Rev. D 88, 052006] Published Tue Sep 17, 2013
    Keywords: Experiment
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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