1,378 research outputs found

    A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics

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    © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caiger, P. E., Dean, M. J., DeAngelis, A. I., Hatch, L. T., Rice, A. N., Stanley, J. A., Tholke, C., Zemeckis, D. R., & Van Parijs, S. M. A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics. Marine Ecology Progress Series, 635, (2020): 89-103, doi:10.3354/meps13219.Atlantic cod Gadus morhua populations in the northeast USA have failed to recover since major declines in the 1970s and 1990s. To rebuild these stocks, managers need reliable information on spawning dynamics in order to design and implement control measures; discovering cost-effective and non-invasive monitoring techniques is also favorable. Atlantic cod form dense, site-fidelic spawning aggregations during which they vocalize, permitting acoustic detection of their presence at such times. The objective of this study was to detect spawning activity of Atlantic cod using multiple fixed-station passive acoustic recorders to sample across Massachusetts Bay during the winter spawning period. A generalized linear modeling approach was used to investigate spatio-temporal trends of cod vocalizing over 10 consecutive winter spawning seasons (2007-2016), the longest such timeline of any passive acoustic monitoring of a fish species. The vocal activity of Atlantic cod was associated with diel, lunar, and seasonal cycles, with a higher probability of occurrence at night, during the full moon, and near the end of November. Following 2009 and 2010, there was a general decline in acoustic activity. Furthermore, the northwest corner of Stellwagen Bank was identified as an important spawning location. This project demonstrated the utility of passive acoustic monitoring in determining the presence of an acoustically active fish species, and provides valuable data for informing the management of this commercially, culturally, and ecologically important species.Thanks to Eli Bonnell, Genevieve Davis, Julianne Bonell, Samara Haver, and Eric Matzen for assistance in MARU deployments, Dana Gerlach and Heather Heenehan for help in passive acoustic data analysis, and the NEFSC passive acoustics group for useful discussions. Funding for 2007−2012 passive acoustic surveys was provided by Excelerate Energy and Neptune LNG to Cornell University. Fieldwork for 2013−2015 was funded through the 2013−2014 NOAA Saltonstall-Kennedy grant program (Award No. NA14NMF4270027), and jointly funded by The Nature Conservancy, Massachusetts Division of Marine Fisheries, and the Cabot Family Charitable Foundation. Funding for 2016 SoundTrap data was provided by NOAA’s Ocean Acoustics Program (4 Sanctuaries Project)

    Persistence, extinction and spatio-temporal synchronization of SIRS cellular automata models

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    Spatially explicit models have been widely used in today's mathematical ecology and epidemiology to study persistence and extinction of populations as well as their spatial patterns. Here we extend the earlier work--static dispersal between neighbouring individuals to mobility of individuals as well as multi-patches environment. As is commonly found, the basic reproductive ratio is maximized for the evolutionary stable strategy (ESS) on diseases' persistence in mean-field theory. This has important implications, as it implies that for a wide range of parameters that infection rate will tend maximum. This is opposite with present results obtained in spatial explicit models that infection rate is limited by upper bound. We observe the emergence of trade-offs of extinction and persistence on the parameters of the infection period and infection rate and show the extinction time having a linear relationship with respect to system size. We further find that the higher mobility can pronouncedly promote the persistence of spread of epidemics, i.e., the phase transition occurs from extinction domain to persistence domain, and the spirals' wavelength increases as the mobility increasing and ultimately, it will saturate at a certain value. Furthermore, for multi-patches case, we find that the lower coupling strength leads to anti-phase oscillation of infected fraction, while higher coupling strength corresponds to in-phase oscillation.Comment: 12page

    Bio-Assisted Tailored Synthesis of Plasmonic Silver Nanorings and Site-Selective Deposition on Graphene Arrays

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    The spontaneous interaction between noble metals and biological scaffolds enables simple and cost-effective synthesis of nanomaterials with unique features. Here, plasmonic silver nanorings are synthesized on a ring-like protein, i.e., a peroxiredoxin (PRX), and used to assemble large arrays of functional nanostructures. The PRX drives the seeding growth of metal silver under wet reducing conditions, yielding nanorings with outer and inner diameters down to 28 and 3 nm, respectively. The obtained hybrid nanostructures are selectively deposited onto a solid-state 2D membrane made of graphene in order to prepare plasmonic nanopores. In particular, the interaction between the graphene and the PRX allows for the simple preparation of ordered arrays of plasmonic nanorings on a 2D-material membrane. This fabrication process can be finalized by drilling a nanometer scale pore in the middle of the ring. Fluorescence spectroscopic measurements in combination with numerical simulations demonstrate the plasmonic effects induced in the metallic nanoring cavity. The prepared nanopores represent one of the first examples of hybrid plasmonic nanopore structures integrated on a 2D-material membrane. The diameter of the nanopore and the atomically thick substrate make this proof-of-concept approach particularly interesting for nanopore-based technologies and applications such as next-generation sequencing and single-molecule detection

    Disclosing conflicts of interest in German publications concerning health services research

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    <p>Abstract</p> <p>Background</p> <p>The influence of the pharmaceutical industry and other stakeholders on medical science has been increasingly criticised. When dealing with conflicts of interest in scientific publications it is important to ensure the best possible transparency. The objective of this work is to examine the disclosure practice of financial and non-financial conflicts of interest in German language publications concerning health services research for the first time.</p> <p>Methods</p> <p>We performed a systematic literature search in the PubMed data base using the MeSH term "health services research". The review was conducted on July 10, 2006, setting the limits "dates: published in the last 2 years" and "languages: German" (only articles with abstracts). 124 articles in 31 magazines were found. In the magazines the instructions for authors were examined as to whether a statement on conflicts of interest is expected – and if, in which form. Regarding the articles in the journals which require a statement, we examined whether the statement is explicitly published. The results are descriptively represented.</p> <p>Results</p> <p>13 magazines (42%) do not require any statement on conflicts of interest, whereas 18 journals (58%) expect a statement. Two of these 18 magazines refer explicitly to the uniform requirements of the <it>International Committee of the Medical Journal Editors </it>(ICMJE); the remaining 16 magazines give differently accentuated instructions on how to disclose conflicts of interest, whereby the focus is primarily on financial issues. A statement on conflicts of interest is explicitly published in 11 of the 71 articles (15%) which are found in the magazines that require a statement with the submission of a manuscript. Related to the total number of included articles, this means that the reader explicitly receives information on potential conflicts of interest in 9% of the cases (11 of 124 articles). Statements of others that are involved in the publication process (reviewers, editors) are not available in any of the articles examined.</p> <p>Conclusion</p> <p>A better sensitization for possible conflicts of interest in German publications concerning health services research is necessary. We suggest tightening the criteria for disclosure in the instructions for authors in the scientific journals. Among other things the equivalent consideration of financial and non-financial conflicts of interest as well as the obligatory publication of the statements should be part of good practice.</p

    Searching for the Slater Transition in the Pyrochlore Cd2_{2}Os2_{2}O7_{7} with Infrared Spectroscopy

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    Infrared reflectance measurements were made on the single crystal pyrochlore Cd2_{2}Os2_{2}O7_{7} in order to examine the transformations of the electronic structure and crystal lattice across the boundary of the metal insulator transition at TMIT=226KT_{MIT}=226K. All predicted IR active phonons are observed in the conductivity over all temperatures and the oscillator strength is found to be temperature independent. These results indicate that charge ordering plays only a minor role in the MIT and that the transition is strictly electronic in nature. The conductivity shows the clear opening of a gap with 2Δ=5.2kBTMIT2\Delta=5.2k_{B}T_{MIT}. The gap opens continuously, with a temperature dependence similar to that of BCS superconductors, and the gap edge having a distinct σ(ω)∼ω1/2\sigma(\omega)\thicksim\omega^{1/2} dependence. All of these observables support the suggestion of a Slater transition in Cd2_{2}% Os2_{2}O7_{7}.Comment: 4 pages, 4 figure

    Time Serial Analysis of the Induced LEO Environment within the ISS 6A

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    Anisotropies in the low Earth orbit (LEO) radiation environment were found to influence the thermoluminescence detectors (TLD) dose within the (International Space Station) ISS 7A Service Module. Subsequently, anisotropic environmental models with improved dynamic time extrapolation have been developed including westward and northern drifts using AP8 Min & Max as estimates of the historic spatial distribution of trapped protons in the 1965 and 1970 era, respectively. In addition, a directional dependent geomagnetic cutoff model was derived for geomagnetic field configurations from the 1945 to 2020 time frame. A dynamic neutron albedo model based on our atmospheric radiation studies has likewise been required to explain LEO neutron measurements. The simultaneous measurements of dose and dose rate using four Liulin instruments at various locations in the US LAB and Node 1 has experimentally demonstrated anisotropic effects in ISS 6A and are used herein to evaluate the adequacy of these revised environmental models

    In vitro synthesis of heparosan using recombinant Pasteurella multocida heparosan synthase PmHS2

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    In vertebrates and bacteria, heparosan the precursor of heparin is synthesized by glycosyltransferases via the stepwise addition of UDP-N-acetylglucosamine and UDP-glucuronic acid. As heparin-like molecules represent a great interest in the pharmaceutical area, the cryptic Pasteurella multocida heparosan synthase PmHS2 found to catalyze heparosan synthesis using substrate analogs has been studied. In this paper, we report an efficient way to purify PmHS2 and to maintain its activity stable during 6 months storage at −80 °C using His-tag purification and a desalting step. In the presence of 1 mM of each nucleotide sugar, purified PmHS2 synthesized polymers up to an average molecular weight of 130 kDa. With 5 mM of UDP-GlcUA and 5 mM of UDP-GlcNAc, an optimal specific activity, from 3 to 6 h of incubation, was found to be about 0.145 nmol/μg/min, and polymers up to an average of 102 kDa were synthesized in 24 h. In this study, we show that the chain length distribution of heparosan polymers can be controlled by change of the initial nucleotide sugar concentration. It was observed that low substrate concentration favors the formation of high molecular weight heparosan polymer with a low polydispersity while high substrate concentration did the opposite. Similarities in the polymerization mechanism between PmHS2, PmHS1, and PmHAS are discussed

    The NEI/NCBI dbGAP database: Genotypes and haplotypes that may specifically predispose to risk of neovascular age-related macular degeneration

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    <p>Abstract</p> <p>Background</p> <p>To examine if the significantly associated SNPs derived from the genome wide allelic association study on the AREDS cohort at the NEI (dbGAP) specifically confer risk for neovascular age-related macular degeneration (AMD). We ascertained 134 unrelated patients with AMD who had one sibling with an AREDS classification 1 or less and was past the age at which the affected sibling was diagnosed (268 subjects). Genotyping was performed by both direct sequencing and Sequenom iPLEX system technology. Single SNP analyses were conducted with McNemar's Test (both 2 × 2 and 3 × 3 tests) and likelihood ratio tests (LRT). Conditional logistic regression was used to determine significant gene-gene interactions. LRT was used to determine the best fit for each genotypic model tested (additive, dominant or recessive).</p> <p>Results</p> <p>Before release of individual data, <it>p</it>-value information was obtained directly from the AREDS dbGAP website. Of the 35 variants with <it>P </it>< 10<sup>-6 </sup>examined, 23 significantly modified risk of neovascular AMD. Many variants located in tandem on 1q32-q22 including those in <it>CFH</it>, <it>CFHR4</it>, <it>CFHR2</it>, <it>CFHR5</it>, <it>F13B</it>, <it>ASPM </it>and <it>ZBTB </it>were significantly associated with AMD risk. Of these variants, single SNP analysis revealed that <it>CFH </it>rs572515 was the most significantly associated with AMD risk (P < 10<sup>-6</sup>). Haplotype analysis supported our findings of single SNP association, demonstrating that the most significant haplotype, GATAGTTCTC, spanning <it>CFH</it>, <it>CFHR4</it>, and <it>CFHR2 </it>was associated with the greatest risk of developing neovascular AMD (<it>P </it>< 10<sup>-6</sup>). Other than variants on 1q32-q22, only two SNPs, rs9288410 (<it>MAP2</it>) on 2q34-q35 and rs2014307 (<it>PLEKHA1</it>/<it>HTRA1</it>) on 10q26 were significantly associated with AMD status (<it>P </it>= .03 and <it>P </it>< 10<sup>-6 </sup>respectively). After controlling for smoking history, gender and age, the most significant gene-gene interaction appears to be between rs10801575 (<it>CFH</it>) and rs2014307 (<it>PLEKHA1</it>/<it>HTRA1</it>) (<it>P </it>< 10<sup>-11</sup>). The best genotypic fit for rs10801575 and rs2014307 was an additive model based on LRT. After applying a Bonferonni correction, no other significant interactions were identified between any other SNPs.</p> <p>Conclusion</p> <p>This is the first replication study on the NEI dbGAP SNPs, demonstrating that alleles on 1q, 2q and 10q may predispose an individual to AMD.</p
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