62 research outputs found
COASTAL AND MARINE WAVE HAZARDS IN THE CHANGING ARCTIC
No full textThis work is embargoed by the author and will not be publicly available until May 2029.The rapid warming of the Arctic and consequential sea ice decline has resulted in growth in the regional wave climate. The increasing wave energy already has had marked impact on coastal regions, driving extreme rates of erosion and threatening coastal communities with unprecedented wave and flood hazards. Nonetheless, further growth in the regional wave climate is expected to continue well into the current century as sea ice decline proceeds and open-water area expands allowing for further generation and growth of ocean waves. In this context, this dissertation presents research investigating how future Arctic coastal and marine wave hazards will evolve in the coming decades in regions already affected by or expected to be impacted by wave hazards. To accomplish this objective, the latest generation of climate models’ projections of sea ice were assessed to gain insight towards bias inherent in the mean-state simulation of the Arctic sea ice and identify regions or seasons which models struggle to represent. Based on this analysis, a multi-model ensemble sea ice projection was utilized in conjunction with a dynamic wave model to simulate how Alaskan Arctic coastal wave exposure resulting from an extreme storm event would be modified under future sea ice conditions. Derived results predict that future coastal exposure into the fall could be extended by one month by 2050 and up to three months by 2070 for the high emissions scenario. Subsequently, an ensemble of pan-Arctic simulations was produced to investigate how future wave hazards would evolve along Arctic maritime sea routes. This investigation demonstrates that concurrent with increasing maritime accessibility resulting from sea ice retreat, there is a rapid and significant increase in extreme maritime wave hazards present in the late fall leading to unprecedented wave heights for the analyzed region. These projections and analyses advance the knowledge of future Arctic wave hazards by employing the latest modeling methodologies and utilizing the latest climate model data to derive assessments of wave hazards at scales applicable to user groups adapting to the rapidly changing Arctic.2029-05-1
Mineral Mountain Ranchos Market Wise Investors Inc. Cress Ferriera and June Ferriera v. The Division of Real Estate of the Department of Commerce of the State of Utah : Brief of Petitioners
No full textBRJEF OF PETITIONERS TO APPEAL FROM FINAL AND OTHER CEASE AND DESIST ORDERS ISSUED BY THE DIVISION OF REAL ESTATE AND THE DEPARTMENT OF COMMERCE, THE HONORABLE JUDGE J. STEVEN EKLUND, PRESIDIN
Ecotype diversity and conversion in Photobacterium profundum strains.
No full textPhotobacterium profundum is a cosmopolitan marine bacterium capable of growth at low temperature and high hydrostatic pressure. Multiple strains of P. profundum have been isolated from different depths of the ocean and display remarkable differences in their physiological responses to pressure. The genome sequence of the deep-sea piezopsychrophilic strain Photobacterium profundum SS9 has provided some clues regarding the genetic features required for growth in the deep sea. The sequenced genome of Photobacterium profundum strain 3TCK, a non-piezophilic strain isolated from a shallow-water environment, is now available and its analysis expands the identification of unique genomic features that correlate to environmental differences and define the Hutchinsonian niche of each strain. These differences range from variations in gene content to specific gene sequences under positive selection. Genome plasticity between Photobacterium bathytypes was investigated when strain 3TCK-specific genes involved in photorepair were introduced to SS9, demonstrating that horizontal gene transfer can provide a mechanism for rapid colonisation of new environments
Parameterized sequential decision making problems
No full textSubmission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2023-12-01The student, Amber Srivastava, accepted the attached license on 2021-07-27 at 12:27.The student, Amber Srivastava, submitted this Dissertation for approval on 2021-07-27 at 12:35.This Dissertation was approved for publication on 2021-07-29 at 11:37.DSpace SAF Submission Ingestion Package generated from Vireo submission #17020 on 2022-04-29 at 16:08:45Made available in DSpace on 2022-04-29T21:58:12Z (GMT). No. of bitstreams: 2
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Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemAuthor requested closed access (OA after 2yrs) in Vireo ETD systemLimitedThis thesis addresses a class of optimization problems that deals with the two-fold objective of making sequential decisions, and simultaneously determining the unknown problem parameters such that the associated cost function gets minimized. We refer to these problems as parameterized Sequential Decision Making (para-SDM) problems. The application areas are plenty; for instance, network design problems, job-shop scheduling, industrial process optimization, last mile delivery, vehicle routing, sensor networks, clustering and classification.
In this work, we develop a combinatorial optimization viewpoint for these problems - where the viewpoint is facilitated by the combinatorially large number of possible sequences of decisions - and use Maximum Entropy Principle (MEP) based framework to address them. The optimization problems considered in this thesis have been shown to be NP-hard, accompanied by a non-convex cost function whose surface that is riddled by multiple poor local minima. The combinatorially large number of possible sequences of decisions on top of the above mentioned challenges render para-SDM as a difficult class of optimization problems. Our proposed MEP-based framework is designed to overcome the aforesaid challenges in para-SDM. For instance, we employ annealing from a suitable convex function to the non-convex cost function to avoid getting stuck in a poor local minima. Additionally, we utilize the problem structures (such as the law of optimality of the paths) to represent the combinatorial number of possibilites using much smaller decision variable space. The proposed framework is flexible to incorporating application-specific capacity, inclusion-exclusion, and dynamic constraints. Our framework also extends to the class of problems where the information about the underlying model is lacking, and we develop suitable stochastic iterative updates that interacts with the underlying system to simultaneously learn the sequences and the parameter values.
A peculiar characteristic of the annealing process in our MEP-based frameworks is the phase transition phenomenon. In particular, these are the specific instances in the annealing procedure at which the solution undergoes significant changes. We demonstrate the utility of these phase transitions in determining certain design hyperparamters in para-SDMs, and in general, in combinatorial optimization problems; for instance, estimating the true number of clusters in a data set, or determining the appropriate choice of the sparsity level in sparse linear regression problems
Author Correction: Transcript expression-aware annotation improves rare variant interpretation
No full textIn this Article, author Marquis P. Vawter was missing from the Genome Aggregation Database Consortium list. They are associated with the affiliation: ‘Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, CA, USA’, and contributed to the generation of the primary data incorporated into the gnomAD resource. The original Article has been corrected online
Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche
No full textGene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA
Author Correction: The mutational constraint spectrum quantified from variation in 141,456 humanS
No full textIn this Article, author Marquis P. Vawter was missing from the Genome Aggregation Database Consortium list. They are associated with the affiliation: ‘Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, CA, USA’, and contributed to the generation of the primary data incorporated into the gnomAD resource. In addition, in the legend to Fig. 1, ‘ten’ should have been ‘seven’ in the sentence: “a, Uniform manifold approximation and projection (UMAP)46,47 plot depicting the ancestral diversity of all individuals in gnomAD, using seven principal components.” The original Article has been corrected online
Complete Genome Sequence of <i>Algoriphagus</i> sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate
No full textABSTRACT
Bacteria are the primary food source of choanoflagellates, the closest known relatives of animals. Studying signaling interactions between the Gram-negative
Bacteroidetes
bacterium
Algoriphagus
sp. PR1 and its predator, the choanoflagellate
Salpingoeca rosetta
, provides a promising avenue for testing hypotheses regarding the involvement of bacteria in animal evolution. Here we announce the complete genome sequence of
Algoriphagus
sp. PR1 and initial findings from its annotation.
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Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium
No full text© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e25386, doi:10.1371/journal.pone.0025386.Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.Funding has been provided by the NSF Microbial Observatories Program (KJE, DE), NSF’s Science and Technology Program, by the Gordon and Betty
Moore Foundation (KJE), the College of Letters, Arts, and Sciences at the University of Southern California (KJE), and by the NASA Astrobiology Institute (KJE, DE).
Advanced Light Source analyses at the Lawrence Berkeley National Lab are supported by the Office of Science, Basic Energy Sciences, Division of Materials Science
of the United States Department of Energy (DE-AC02-05CH11231)
Pulsed field gel electrophoresis of chromosomal plugs of <i>P. profundum</i> strains SS9, DSJ4 and 3TCK.
No full text<p>The plugs were digested overnight with <i>I-Ceu</i>I and run under the following conditions: (A) Voltage: 6 V/cm; Pulse-time: 3–18.5 s; Runtime: 18.5 h; Temperature: 14°C; Included angle: 120°; Gel: 0.95% PFGE agarose in 0.5x TBE (B) Voltage: 6 V/cm; Pulse-time: 6.7–54 s; Runtime: 28 h; Temperature: 14°C; Included angle: 120°; Gel: 0.95% PFGE agarose in 0.5x TBE.</p
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