Characterization of impact pile driving signals during installation of offshore wind turbine foundations

Author Posting. © Acoustical Society of America, 2020. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 147(4), (2020): 2323, doi:10.1121/10.0001035.Impact pile driving creates intense, impulsive sound that radiates into the surrounding environment. Piles driven vertically into the seabed generate an azimuthally symmetric underwater sound field whereas piles driven on an angle will generate an azimuthally dependent sound field. Measurements were made during pile driving of raked piles to secure jacket foundation structures to the seabed in waters off the northeastern coast of the U.S. at ranges between 500 m and 15 km. These measurements were analyzed to investigate variations in rise time, decay time, pulse duration, kurtosis, and sound received levels as a function of range and azimuth. Variations in the radiated sound field along opposing azimuths resulted in differences in measured sound exposure levels of up to 10 dB and greater due to the pile rake as the sound propagated in range. The raked pile configuration was modeled using an equivalent axisymmetric FEM model to describe the azimuthally dependent measured sound fields. Comparable sound level differences in the model results confirmed that the azimuthal discrepancy observed in the measured data was due to the inclination of the pile being driven relative to the receiver.This paper was presented at the fifth International Meeting on The Effects of Noise on Aquatic Life held in Den Haag, July 2019. Study concept, oversight, and funding for the experiment were provided by the U.S. Department of the Interior, Bureau of Ocean Energy Management (BOEM), Environmental Studies Program, Washington, DC, under Contract No. M15PC00002, Task Order M16PD00025. Collaborators in this project include Randy Gallien and Anwar Khan (HDR, Inc.).2020-10-1

Managing human activity and marine mammals: A biologically based, relativistic risk assessment framework

Presented here is a broadly applicable, transparent, repeatable analytical framework for assessing relative risk of anthropogenic disturbances on marine vertebrates, with the emphasis on the sound generating aspects of the activity. The objectives are to provide managers and action-proponents tools with which to objectively evaluate drivers of potential biological risk, to identify data gaps that limit assessment, and to identify actionable measures to reduce risk. Current regulatory assessments of how human activities (particularly those that produce sound) influence the likelihood of marine mammal behavioral responses and potential injury, rely principally on generalized characterizations of exposure and effect using simple, threshold-based criteria. While this is relatively straightforward in regulatory applications, this approach fails to adequately address realistic site and seasonal scenarios, other potential stressors, and scalable outcome probabilities. The risk assessment presented here is primarily based on a common and broad understanding of the spatial-temporal-spectral intersections of animals and anthropogenic activities, and specific examples of its application to hypothetical offshore wind farms are given. The resulting species- and activity-specific framework parses risk into two discrete factors: a population’s innate ‘vulnerability’ (potential degree of susceptibility to disturbance) and an ‘exposure index’ (magnitude-duration severity resulting from exposure to an activity). The classic intersection of these factors and their multi-dimensional components provides a relativistic risk assessment process for realistic evaluation of specified activity contexts, sites, and schedules, convolved with species-specific seasonal presence, behavioral-ecological context, and natural history. This process is inherently scalable, allowing a relativistic means of assessing potential disturbance scenarios, tunable to animal distribution, region, context, and degrees of spatial-temporal-spectral resolution

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): G03013, doi:10.1029/2005JG000121.The 18S ribosomal DNA (rDNA) sequences of haptophyte algae were successfully amplified using the polymerase chain reaction (PCR) from water filtrate, surface sediments, and a late-Holocene sediment sample (∼1000 years old) from a group of lakes in the Søndre Strømfjord region of west Greenland. The DNA of the algal primary producer is extremely well preserved in the laminated lake sediments which have been deposited in cold (1°–2°C), anoxic, and sulphidic bottom water. Phylogenetic analyses of the Greenland haptophyte rDNA sequences suggest that alkenones in the Greenland lake sediments are produced by haptophyte algae of the class Prymnesiophyceae. The 18S rDNA sequences from the Greenland samples cluster within a distinct phylotype, differing from both marine haptophytes and from those reported previously from Ace Lake, Antarctica. The similarity of haptophyte rDNA sequences among all samples in this study suggests a single alkenone-based temperature calibration may be applied to these lakes for at least the past 1000 years. These sedimentary archives hold great promise for high-resolution, alkenone-based paleotemperature reconstruction of southern west Greenland, a region sensitive to atmospheric-oceanic climate phenomena such as the North Atlantic Oscillation (NAO).This work was supported by grants from the National Science Foundation (NSF0081478, 0318050, 0318123, 0402383, 0520718), NASA (NAG5-10665, NNG04GJ34G) and the American Chemical Society, Petroleum Research Fund (ACS-PRF38878-AC2) to Y. Huang

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

Evaluating the pathogenicity of a variant is challenging given the plethora of types of genetic evidence that laboratories consider. Deciding how to weigh each type of evidence is difficult, and standards have been needed. In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for the assessment of variants in genes associated with Mendelian diseases. Nine molecular diagnostic laboratories involved in the Clinical Sequencing Exploratory Research (CSER) consortium piloted these guidelines on 99 variants spanning all categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign). Nine variants were distributed to all laboratories, and the remaining 90 were evaluated by three laboratories. The laboratories classified each variant by using both the laboratory's own method and the ACMG-AMP criteria. The agreement between the two methods used within laboratories was high (K-alpha = 0.91) with 79% concordance. However, there was only 34% concordance for either classification system across laboratories. After consensus discussions and detailed review of the ACMG-AMP criteria, concordance increased to 71%. Causes of initial discordance in ACMG-AMP classifications were identified, and recommendations on clarification and increased specification of the ACMG-AMP criteria were made. In summary, although an initial pilot of the ACMG-AMP guidelines did not lead to increased concordance in variant interpretation, comparing variant interpretations to identify differences and having a common framework to facilitate resolution of those differences were beneficial for improving agreement, allowing iterative movement toward increased reporting consistency for variants in genes associated with monogenic disease

ESIIL Strategic Plan

The 5 year plan (2022-2027) for the Environmental Data Science Innovation &amp; Inclusion Lab (ESIIL). ESIIL is a next-generation NSF synthesis center led by the University of Colorado Boulder in collaboration with NSF&rsquo;s CyVerse at the University of Arizona, and the University of Oslo. ESIIL enables a global community of environmental data scientists to leverage the wealth of environmental data and emerging analytics to develop science-based solutions to solve pressing challenges in the environmental sciences. This plan highlights ESIIL's mission, vision, and objectives, outlining a roadmap that will guide our efforts towards fulfilling the mission of accelerating innovation and driving just and equitable solutions through the power of data and technology. </p

Intracranial injection of dengue virus induces interferon stimulated genes and CD8(+) T cell infiltration by sphingosine kinase 1 independent pathways

We have previously reported that the absence of sphingosine kinase 1 (SK1) affects both dengue virus (DENV) infection and innate immune responses in vitro. Here we aimed to define SK1-dependancy of DENV-induced disease and the associated innate responses in vivo. The lack of a reliable mouse model with a fully competent interferon response for DENV infection is a challenge, and here we use an experimental model of DENV infection in the brain of immunocompetent mice. Intracranial injection of DENV-2 into C57BL/6 mice induced body weight loss and neurological symptoms which was associated with a high level of DENV RNA in the brain. Body weight loss and DENV RNA level tended to be greater in SK1-/- compared with wildtype (WT) mice. Brain infection with DENV-2 is associated with the induction of interferon-β (IFN-β) and IFN-stimulated gene (ISG) expression including viperin, Ifi27l2a, IRF7, and CXCL10 without any significant differences between WT and SK1-/- mice. The SK2 and sphingosine-1-phosphate (S1P) levels in the brain were unchanged by DENV infection or the lack of SK1. Histological analysis demonstrated the presence of a cellular infiltrate in DENV-infected brain with a significant increase in mRNA for CD8 but not CD4 suggesting this infiltrate is likely CD8+ but not CD4+ T-lymphocytes. This increase in T-cell infiltration was not affected by the lack of SK1. Overall, DENV-infection in the brain induces IFN and T-cell responses but does not influence the SK/S1P axis. In contrast to our observations in vitro, SK1 has no major influence on these responses following DENV-infection in the mouse brain.Wisam H. Al-Shujairi, Jennifer N. Clarke, Lorena T. Davies, Mohammed Alsharifi, Stuart M. Pitson, Jillian M. Car

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed

Modulation of dendritic spine development and plasticity by BDNF and vesicular trafficking: fundamental roles in neurodevelopmental disorders associated with mental retardation and autism

The process of axonal and dendritic development establishes the synaptic circuitry of the central nervous system (CNS) and is the result of interactions between intrinsic molecular factors and the external environment. One growth factor that has a compelling function in neuronal development is the neurotrophin brain-derived neurotrophic factor (BDNF). BDNF participates in axonal and dendritic differentiation during embryonic stages of neuronal development, as well as in the formation and maturation of dendritic spines during postnatal development. Recent studies have also implicated vesicular trafficking of BDNF via secretory vesicles, and both secretory and endosomal trafficking of vesicles containing synaptic proteins, such as neurotransmitter and neurotrophin receptors, in the regulation of axonal and dendritic differentiation, and in dendritic spine morphogenesis. Several genes that are either mutated or deregulated in neurodevelopmental disorders associated with mental retardation have now been identified, and several mouse models of these disorders have been generated and characterized. Interestingly, abnormalities in dendritic and synaptic structure are consistently observed in human neurodevelopmental disorders associated with mental retardation, and in mouse models of these disorders as well. Abnormalities in dendritic and synaptic differentiation are thought to underlie altered synaptic function and network connectivity, thus contributing to the clinical outcome. Here, we review the roles of BDNF and vesicular trafficking in axonal and dendritic differentiation in the context of dendritic and axonal morphological impairments commonly observed in neurodevelopmental disorders associated with mental retardation