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The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

The demand for precise and efficient nuclear radiation detection has increased dramatically, particularly in numerous scientific disciplines, as well as homeland security and medical imaging applications. Modern methods by which ionizing radiation was sensed has now heavily considered using nano-scale materials for the sake of effective counting. Nanocrystalline (NC), or quantum dot (QD), semiconductors themselves exhibit exploitable properties—such as tunable energy band gap and charge carrier multiplication (multi-exciton generation) which arise due to strong quantum confinement. With this, fabricating a quantum-dot-based semiconductor to operate as a high-performance detector, via a low-cost solution-based manufacturing method, can truly alter the capabilities of radiation detectors. Using this NC approach which primarily focuses on high atomic number and density materials, was investigated as a means to maximize charge creation while minimizing the uncertainty in that conversion, as the approach is based on favorable features of NC materials for their application to the detection of ionizing radiation. The intrinsically high charge mobility combined with high atomic number and density of the lead chalcogenides makes them attractive for sensing applications with highly penetrating quanta, such as x-rays and gamma-rays, as the lead chalcogenide materials possesses an extensive literature of synthetic routes with which one can explore the strong confinement regime in quantum dots. By varying the reaction conditions, NCs of various sizes and shapes were synthesized, and their physical and opto-electric properties were investigated. Drop-, float-, or dip-coating NC dispersions on various metal contacts resulted in close-packed NC assemblies of lead chalcogenides. However, in sensing architectures, the exploitation of various properties for each individual nanocrystallite (NC) is hampered by the need to transport the charge carriers throughout the active volume, a motion that can be retarded by energetic surface barriers typically in the form of insulating oxides. Various synthetic routes are investigated to fabricate lead chalcogenide QDs while the feasibility of utilizing NC materials as a basis for detecting ionizing radiation is also explored. QDs and their assembled structures were carefully investigated through characterization to determine their overall quality. Methods to improve NC interconnectivity were studied and mentioned. The prevention of surface oxidation through the fabrication of NCs was also explored, resulting in chemically and optically stable NCs for at least 1.6 years. Overall, this study focuses on using solution-based methods to fabricate nano-semiconductor nuclear radiation detectors. Various recipes will be presented, as well as the electrical results of developed NC assembly samples, with the focus on improving the charge carrier transport properties of these NC assemblies.

In this work we propose Neuro-Nav, an open-source library for neurally plausible reinforcement learning (RL). RL is among the most common modeling frameworks for studying decision making, learning, and navigation in biological organisms. In utilizing RL, cognitive scientists often handcraft environments and agents to meet the needs of their particular studies. On the other hand, artificial intelligence researchers often struggle to find benchmarks for neurally and biologically plausible representation and behavior (e.g., in decision making or navigation). In order to streamline this process across both fields with transparency and reproducibility, Neuro-Nav offers a set of standardized environments and RL algorithms drawn from canonical behavioral and neural studies in rodents and humans. We demonstrate that the toolkit replicates relevant findings from a number of studies across both cognitive science and RL literatures. We furthermore describe ways in which the library can be extended with novel algorithms (including deep RL) and environments to address future research needs of the field.

The cross-cutting nature of microbiome research in environmental sciences, health, agriculture, energy, and natural and built environments, and the velocity at which microbiome data are generated has far outpaced current data infrastructure. Resources and solutions for collection, processing, and distribution of these data in an effective, uniform, accessible, and reproducible manner, are lacking even at the largest data centers. The National Microbiome Data Collaborative (NMDC) is a pilot initiative launched to support microbiome data exploration and discovery through a collaborative, integrative science gateway. The NMDC is tackling infrastructure challenges in microbiome data science by making use of distributed computational resources available across four Department of Energy National Laboratories, Lawrence Berkeley National Laboratory (LBNL), Los Alamos National Laboratory (LANL), Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory (ORNL). The NMDC team aims to deliver a set of unique microbiome data science capabilities, which include: leveraging existing ontology mapping software and curation resources to enable automated annotation of standardized metadata; developing workflows for metagenome, metatranscriptome, metaproteome, and metabolomics data processing leveraging HPC systems, and integrating the execution of these pipelines to produce NMDC-compliant data products; developing data registration, indexing, and access services to link data through a suite of publicly available APIs; and developing communication and sustainability strategies to assess current and future needs and capabilities to empower users, and promote the NMDC to the larger scientific community. To ensure that the NMDC data ecosystem supports and evolves with the needs of the microbiome research community, the NMDC team uses a community-centered design approach to seek feedback from the scientific research community throughout its phases of iterative development. Community feedback has informed the priorities of the NMDC data standards, bioinformatic workflows, and engagement activities, but perhaps the most visible contributions of the research community can be seen through the features and enhancements on the NMDC data portal. Here, we present an overview of the NMDC mission and vision, the distributed data infrastructure, and our community-centered design approach in developing the NMDC data portal.

In Syria, reports of Islamic State (ISIS) fighters utilizing small unmanned aerial systems (SUAS) to attack U.S. troops and their Syrian Democratic Forces (SDF) partners became a prevalent tactic. Failing to implement meaningful solutions to detect and counter this new application of SUASs by adversaries will cost American lives. The purpose of this project is to research and analyze the current capability gap in situational awareness technology, specifically focused on the integration of counter-UAS (C-UAS) sensors. Using the existing Tactical Assault Kit (TAK) situational awareness tool and developmental applications like the Defense Innovation Unit’s Dowding C-UAS System, the project explores solutions to these shortfalls by testing software solutions for integrating UAS sensors. Through field experiments with Norwegian SOF operators in collaboration with DoD partners, this project answers the question, “How can tactical situational awareness tools best enhance decision making and survivability of SOF teams in a threat UAS environment?” The researchers propose the development of a Dowding-based TAK plug-in capable of incorporating data from multiple sensors into a single common operating picture and recommends more rigorous, comprehensive testing of current C-UAS capabilities. http://archive.org/details/integrationofsit1094564130 Outstanding Thesis Major, United States Army Major, United States Army Approved for public release; distribution is unlimited.

This thesis analyzes the role of the Russian Orthodox Church (ROC) as an instrument of Russian soft power in the Putin era. Soft power is a means to attract allies and support for a nation’s objectives in foreign policy. Russia has a dwindling number of soft power weapons, with the ROC being one of its most remaining prominent soft power assets. The relationship between the ROC and Kremlin is nuanced, both gaining legitimacy and authority from one another. They share a similar conservative worldview and the narrative of a Russian world, which is seen to be Russia’s prominent ideology exported in its perceived near abroad. Investigated in-depth in Ukraine, the ROC’s influence has met failure there, demonstrated by the schism between the ROC and the Ukraine Church. This is contrasted by its use in Georgia, where, owing to the warm relationship between the ROC and the Georgian Orthodox Church, influence via the ROC appears to have found a measure of limited success. However, Russia’s ability to exert soft power through the ROC appears to be waning overall, particularly after the church schism in Ukraine. Ultimately, the future of the ROC as a mechanism of Russia’s soft power remains in doubt. http://archive.org/details/holywarhowputinw1094563444 Outstanding Thesis Lieutenant, United States Navy Approved for public release; distribution is unlimited.

Few areas across globe have escaped the pressures of militarization. Despite the many significant developments and repercussions tied to the military control of vast areas of national territories, the complex intersections between militarization and the environment have only recently attracted scholarly attention. This dissertation argues that the contemporary condition of global permanent war and ongoing state of emergency are rooted in the military control of land and other natural resources. During the mid-twentieth century buildup of North American defense forces, the practice of military land appropriation not only legitimized and expanded certain types of unilateral, emergency powers but also produced secret and legally permissive spaces in which the exercise of such extraordinary powers and related military land use practices could be more freely conducted. A major impetus driving these mid-century land use developments was the rise of unconventional weapons of mass destruction. Not only did such weapons technologies destabilize the global political order but they also brought about a multitude of disruptions at local sites. By investigating the establishment and operations of two of the world’s largest, most secretive, and longest-lasting chemical and biological weapons proving grounds—the U.S. Army’s Dugway Proving Ground in western Utah and the Canadian-and U.K.-controlled Suffield Experimental Station in southeastern Alberta—this study reveals how the imperatives of permanent war have had critical influence in shaping the workings of power between local citizens, government, and the environment in western North America. At its core, this dissertation pushes back against the various assumptions and prerogatives driving the establishment of a permanent military presence in the North American West. All four chapters examine how varying elements of exceptional, emergency executive and administrative powers have shaped military land claims and practices of military land use. The study uncovers and demystifies the procedures, policies, and practices governing the establishment, operational activities, and ongoing control of North American defense lands. It provides a critical examination of the legal, material, and figurative grounds of our continuing and permanent global state of war.

This thesis focuses on collection and preprocessing of streaming social media feeds for metadata as well as the visual and textual information. Today, news media has been the main source of immediate news events, large and small. However, the information conveyed on these news sources is delayed due to the lack of proximity and general knowledge of the event. Such news have started relying on social media sources for initial knowledge of these events. Previous works focused on captured textual data from social media as a data source to detect events. This preprocessing framework postures to facilitate the data fusion of images and text for event detection. Results from the preprocessing techniques explained in this work show the textual and visual data collected are able to be proceeded into a workable format for further processing. Moreover, the textual and visual data collected are transformed into bag-of-words vectors for future data fusion and event detection.

2013 annual AGU hydrology days was held at Colorado State University on March 25 - March 27, 2013., Includes bibliographical references., At the present time the vast majority of the stormwater generated on the Main Campus of Utah Valley University is exported to Utah Lake, which is only 1.4 miles from campus. Although there is a large boulder-lined detention pond on campus, it is used only as a holding pond before the stormwater is exported. The objective of this study was to determine what percentage of the average annual stormwater and the stormwater generated by a 100-year 24-hour precipitation event could be retained on campus and used for groundwater recharge by constructing a series of French drains. It was determined that the Main Campus could be divided into 33 watersheds that currently export stormwater (72.8% of the surface area) and 28 additional self-contained watersheds. Using the NRCS Runoff Curve Method, it was determined that the Main Campus exports 0.4998 ac·ft of stormwater annually and would export 23.2969 ac·ft of stormwater following a 100-year 24-hour precipitation event, while the self-contained watersheds capture 0.0330 ac·ft annually and would capture 2.7913 ac·ft following a 100-year 24-hour event. The construction of nine French drains (including subsurface expansion of the existing detention pond with discontinuation of pumping) with a combined surface area of 0.9260 ac would convert to groundwater recharge 0.1402 ac·ft annually (28.1% of current export) and 6.2083 ac·ft following a 100-year 24-hour precipitation event (26.6% of current export). Further reduction of stormwater export could not be accomplished without disruption to current paved areas or other built infrastructure.

Signal transduction mechanisms initiated by VEGF signaling leading to tight junction loss and redistribution of ZO-1 have not been fully elucidated. One potential transducer is vasodilator stimulated phosphoprotein (VASP). Site specific phosphorylation of VASP via PKG at s239 may be critical for tight junction loss in this pathway. Here we demonstrate the localization of VASP to tight junctions and changes in VASP phosphorylation following hypoxia and VEGF signaling. We also demonstrate that theses changes are dependent on VEGFR2 kinas activity. Further studies may give additional insight into molecular targets for modulating BBB integrity.

This study illustrates how the isolation and perceived worthlessness of the Great Basin’s West Desert led the military and livestock industry to create a sacrificial landscape. In focusing on the material activities of these two groups, this study also explores vital yet largely neglected issues regarding the tensions between the defense industry, economic prosperity, and ecological health, revealing the largely unacknowledged social and ecological costs of maintaining national security. The narrative traces the nineteenth-century rise of the sheep industry, growing friction between pastoral and national security landscapes in the mid twentieth century, and the social and environmental consequences of Army weapons testing programs during World War II and the Cold War. In focusing on Western settlement and early economic development, as well as the critical period during and after WWII, this study offers an extended view into North Americans’ largely dysfunctional relationship to arid lands.

In many areas of the United States, dairy and livestock farmers are facing lawsuits due to a variety of externalities, such as odor and other forms of non-point source pollution, caused by Confined animal feeding operations (CAFO's). Complaints include: general illness, unpleasant odor, headaches, and property devaluation. However, state and national law requires all CAFO's to have some form of waste storage facility. These facilities, mainly lagoons, increase the potential of pollution and run-off into streams and other water sources. As a result, large producers are beginning to install anaerobic digestive (A.D.) systems, which are a new form of waste management practices that reduces negative environmental effects. Therefore, the purpose of this study is to determine the future value of an ordinary annuity of an anaerobic digestive system by analyzing the joint probability of being sued and losing a litigation case. The analysis will also factor in potential policy incentives such as 100% grants with guaranteed electric buy-back premiums to determine a producer's joint probability of losing a litigation case.

In many areas of the United States, dairy and livestock farmers are facing lawsuits due to a variety of externalities, such as odor and other forms of non-point source pollution, caused by Confined animal feeding operations (CAFO's). Complaints include: general illness, unpleasant odor, headaches, and property devaluation. However, state and national law requires all CAFO's to have some form of waste storage facility. These facilities, mainly lagoons, increase the potential of pollution and run-off into streams and other water sources. As a result, large producers are beginning to install anaerobic digestive (A.D.) systems, which are a new form of waste management practices that reduces negative environmental effects. Therefore, the purpose of this study is to determine the future value of an ordinary annuity of an anaerobic digestive system by analyzing the joint probability of being sued and losing a litigation case. The analysis will also factor in potential policy incentives such as 100% grants with guaranteed electric buy-back premiums to determine a producer's joint probability of losing a litigation case.

This paper assesses the impact of the milk income loss contract program on U.S. dairy producers. The Milk Income Loss Contact (MILC) program was created through the 2002 farm bill, which financially compensates dairy producers when domestic milk prices fall below a predetermined Boston Class I trigger price. MILC payments were made to eligible dairy producers/farms on a per cwt basis at a rate equal to 45 percent of the difference between the trigger price of $16.94 and the Boston Class I milk price. In the analysis, the 20 major milk-producing states were analyzed to determine if MILC payments caused a milk supply response to be different across these states. By dividing the U.S. into states, this will give a better understanding of production decisions based on the availability of inputs. To test the hypothesis, milk production was regressed against each state's All Milk price, MILC payments, production trends, the milk-feed price ratio, and average productivity per dairy farm in each state. Data were collected over an 10-year period (1995-2004), and MILC variable was used as a dummy variable in the model. The a priori expectations suggest that, in certain states, MILC payments will dampen the state's milk supply response to low milk prices. However, results may also help explain why a state increased or decreased milk production after the implementation of the MILC program. Of the 20-states, those dairies located in the west and southwest regions of the U.S. experienced the largest increases of production during the selected eight years. OLS regression results obtained from the individual state models report mixed results and generally failed to support the hypothesis that MILC did alter the response of monthly milk production to All Milk prices.

This paper assesses the impact of the milk income loss contract program on U.S. dairy producers. The Milk Income Loss Contact (MILC) program was created through the 2002 farm bill, which financially compensates dairy producers when domestic milk prices fall below a predetermined Boston Class I trigger price. MILC payments were made to eligible dairy producers/farms on a per cwt basis at a rate equal to 45 percent of the difference between the trigger price of $16.94 and the Boston Class I milk price. In the analysis, the 20 major milk-producing states were analyzed to determine if MILC payments caused a milk supply response to be different across these states. By dividing the U.S. into states, this will give a better understanding of production decisions based on the availability of inputs. To test the hypothesis, milk production was regressed against each state's All Milk price, MILC payments, production trends, the milk-feed price ratio, and average productivity per dairy farm in each state. Data were collected over an 10-year period (1995-2004), and MILC variable was used as a dummy variable in the model. The a priori expectations suggest that, in certain states, MILC payments will dampen the state's milk supply response to low milk prices. However, results may also help explain why a state increased or decreased milk production after the implementation of the MILC program. Of the 20-states, those dairies located in the west and southwest regions of the U.S. experienced the largest increases of production during the selected eight years. OLS regression results obtained from the individual state models report mixed results and generally failed to support the hypothesis that MILC did alter the response of monthly milk production to All Milk prices.