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At least 199 records · Page 11

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes

The gut microbiome plays a fundamental role in the human host’s overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn’s disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn’s disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn’s disease patients’ post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition. As a result, the measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products. In conclusion, the human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome’s metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Spatial Heterogeneity in Human Activities Favors the Persistence of Wolves in Agroecosystems

As human populations expand, there is increasing demand and pressure for land. Under this scenario, behavioural flexibility and adaptation become important processes leading to the persistence of large carnivores in human-dominated landscapes such as agroecosystems. A growing interest has recently emerged on the outcome of the coexistence between wolves and humans in these systems. It has been suggested that spatial heterogeneity in human activities would be a major environmental factor modulating vulnerability and persistence of this contentious species in agroecosystems. Here, we combined information from 35 den sites detected between 2011 and 2012 in agroecosystems of western Iran (Hamedan province), a set of environmental variables measured at landscape and fine spatial scales, and generalized linear models to identify patterns of den site selection by wolves in a highly-modified agroecosystem. On a landscape level, wolves selected a mixture of rangelands with scattered dry-farms on hillsides (showing a low human use) to locate their dens, avoiding areas with high densities of settlements and primary roads. On a fine spatial scale, wolves primarily excavated dens into the sides of elevated steep-slope hills with availability of water bodies in the vicinity of den sites, and wolves were relegated to dig in places with coarse-soil particles. Our results suggest that vulnerability of wolves in human-dominated landscapes could be compensated by the existence of spatial heterogeneity in human activities. Such heterogeneity would favor wolf persistence in agroecosystems favoring a land sharing model of coexistence between wolves and people.

59 BASIC BIOLOGICAL SCIENCES↗

Uranium-Bearing Evaporite Mineralization Influencing Plume Persistence. Literature Review and DOE-LM Site Surveys

This report on evaporite mineralization was completed as an Ancillary Work Plan for the Applied Studies and Technology program under the U.S. Department of Energy (DOE) Office of Legacy Management (LM). This study reviews all LM sites under Title I and Title II of the Uranium Mill Tailings Radiation Control Act (UMTRCA) and one Decontamination and Decommissioning site to provide (1) a summary of which sites have evaporite deposits, (2) any available quantitative geochemical and mineralogical analyses, and (3) references to relevant reports. In this study, “evaporite” refers to any secondary mineral precipitate that occurs due to a loss of water through evaporative processes. This includes efflorescent salt crusts, where this term refers to a migration of dissolved constituents to the surface with a resulting salt crust, where “salt” can refer to any secondary precipitate, regardless of constituents. The potential for the formation of evaporites at LM sites has been identified, and may have relevance to plume persistence issues. Evaporite deposits have the potential to concentrate and store contaminants at LM sites that could later be re-released. These deposits can also provide a temporary storage mechanism for carbonate, chloride, and sulfate salts along with uranium and other contaminants of concern (COCs). Identification of sites with evaporites will be used in a new technical task plan (TTP), Persistent Secondary Contaminant Sources (PeSCS), for any proposed additional sampling and analyses. This additional study is currently under development and will focus on determining if the dissolution of evaporites has the potential to hinder natural flushing strategies and impact plume persistence. This report provides an initial literature review on evaporites followed by details for each site with identified evaporites. The final summary includes a table listing of all relevant LM sites regardless of evaporite identification.

54 ENVIRONMENTAL SCIENCES↗

Literature Review of Documented Persistent Secondary Uranium Sources at DOE LM Sites

The U.S. Department of Energy Office of Legacy Management (LM) has the responsibility to protect human health and the environment at 101 legacy uranium sites across the nation by implementing long-term surveillance and maintenance requirements. Included in these responsibilities is to provide for the safe and environmentally sound disposal, long-term stabilization, and control of uranium mill tailings in a manner that minimizes or eliminates radiation health hazards to the public at 21 Uranium Mill Tailings Radiation Control Act (UMTRCA) Title I sites; 6 UMTRCA Title II sites; and 9 Comprehensive Environmental Response, Compensation, and Liability Act/Resource Conservation and Recovery Act sites. These sites are former uranium mills (processing sites), or sites with wastes from processing sites encapsulated in engineered disposal cells (disposal sites), or sites where components of atomic weapons were manufactured. During site characterization, groundwater contamination was often discovered and evaluated or modeled for future movement with the inclusion of uranium sorption in the groundwater plume. Much of this original work did identify uranium processing wastes as the original contaminant source. However, more recent work has identified the existence and influence of persistent secondary uranium sources that may prevent uranium in groundwater from attenuating as quickly as initial evaluations or modeling indicated. By understanding these processes, better decisions can be made to choose the appropriate remediation and closure strategies, identify long-term surveillance and maintenance activities, and more accurately estimate life-cycle costs. The purpose of this report is to summarize the literature available on documented persistence secondary uranium sources at LM sites as part of the Applied Studies and Technology Persistent Secondary Contaminant Sources Project.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A Short-Term Solar Forecasting Platform Using a Physics-Based Smart Persistence Model and Data Imputation Method

Electrical energy plays vital role in our socio-economic activity and therefore ensuring the reliability of the electric grid, from the generation, transmission and distribution level is critical. In order to maintain the power system parameter viz., frequency, voltage, etc., optimally, balancing of generation and consumption is very much essential. However, solar energy is infirm power by nature this is due to cloud cover / other local phenomena. Hence, Photovoltaic (PV) power generation brings a significant challenge to the grid operator due to the variability of the solar energy. The complexity of this challenge in terms of planning and dispatch ability of PV resources, aggravates with the high penetration of solar energy into the electric grid. In this setting, reliable solar radiation forecasting models based on accurate and quality input data become essential. In order to develop a suitable model for predicting solar radiation, quality historical / real time measurement is also needed. Under this study NIWE and NREL jointly developed / tested short-term solar forecasting frameworks using a smart persistence and physics-based smart persistence models for intra-hour forecasting of solar radiation (PSPI) and benchmarked 9 different data imputation techniques in 15 Solar Radiation Resource Assessment (SRRA) stations, located at different parts of India. During any measurement campaign, due to various technical reasons, we may miss few observations. However, the missing observation often reduce the performance of any forecasting model. Therefore, suitable data imputation method would assist us to obtain continuous observation of solar radiation. A station-by-station and method-by-method analysis was carried out to understand the performance of each model. Based on our analysis, among all the data imputation methods, the Kalman data imputation method is better for Indian Weather condition. In addition, Kalman StructTS, Linear, Stine and Arima methods yield slightly inferior accuracy compared to Kalman, but outperform the other methods. The extended solar radiation data are used by solar forecasting models to provide the prediction of solar radiation at 15 SRRA stations. As far as short term forecasting model is concerned, the PSPI model outperforms the Smart Persistence model. However, the forecast error is increases with the forecasting horizon.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Hot Spots and Persistence of Nitrate in Aquifers Across Scales

Here, nitrate-N (NO 3 - - N) is one of the most pervasive contaminants in groundwater. Nitrate in groundwater exhibits long-term behavior due to complex interactions at multiple scales among various geophysical factors, such as sources of nitrate-N, characteristics of the vadose zone and aquifer attributes. To minimize contamination of nitrate-N in groundwater, it is important to estimate hot spots (>10 mg/L of NO 3 - - N), trends and persistence of nitrate-N in groundwater. To analyze the trends and persistence of nitrate-N in groundwater at multiple spatio-temporal scales, we developed and used an entropy-based method along with the Hurst exponent in two different hydrogeologic settings: The Trinity and Ogallala Aquifers in Texas at fine (2 km × 2 km), intermediate (10 km × 10 km) and coarse (100 km × 100 km) scales. Results show that nitrate-N exhibits long-term persistence at the intermediate and coarse scales. In the Trinity Aquifer, overall mean nitrate-N has declined with a slight increase in normalized marginal entropy (NME) over each decade from 1940 to 2008; however, the number of hot spots has increased over time. In the Ogallala Aquifer, overall mean nitrate-N has increased with slight moderation in NME since 1940; however, the number of hot spots has significantly decreased for the same period at all scales.

58 GEOSCIENCES↗

Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents

The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a persistent chemical agent simulation system

A Persistent Chemical Agent Simulation System was developed (PCASS) to simulate, for force-on-force training exercises, the field environment produced by the presence of persistent chemical agents. Such a simulant system must satisfy several requirements to be of value as a training aid. Specifically, it must provide for realistic training which will generate competency in at least the following areas: (1) detection of the persistent agent presence; (2) proper use of protective equipment and procedures; (3) determination of the extent of contamination; and (4) decontamination of equipment and personnel.

Source record↗

Persistent anomalies of the extratropical Northern Hemisphere wintertime circulation - Structure

A study identifying horizontal and vertical structures of low patterns occurring with persistent 500 mb height anomalies in the central North Pacific, eastern North Atlantic, and northern Soviet Union regions is presented. The flow patterns of positive and negative anomalies are compared. The relationship between persistent anomalies and small recurrent anomaly patterns is examined. The temporal fluctuations of the persistent patterns are analyzed.

Dole, R. M.↗

On the relation between X-ray burst properties and the persistent X-ray luminosity

Published data on X-ray bursts is analyzed, assuming that the peak luminosity of X-ray bursts with radius expansion is a standard candle and that the ratio of the anisotropy factors, xi(b) and xi(p) (Sztajno et al., 1987) is the same for all burst sources. It is shown that the effective burst duration, defined as the ratio of burst fluence to maximum burst flux, is strongly anticorrelated with the persistent luminosity. A positive correlation with the persistent luminosity of the ratio of the average persistent flux to the time-averaged burst flux is found. It is concluded that, independent of the accretion rate, after a given waiting time burst sources produce bursts with approximately the same (average) energy. This suggests that continuous stable burning of a sizeable fraction of the nuclear fuel is a general phenomenon on the surface of accreting neutron stars. It is suggested that this fraction is a gradually increasing function of the accretion rate.

Van Paradijs, J.↗

Persistence and predictability in a perfect model

A realistic two-level GCM is used to examine the relationship between predictability and persistence. Predictability is measured by the average divergence of ensembles of solutions starting from perturbed initial conditions, and persistence is defined in terms of the autocorrelation function based on a single long-term model integration. The average skill of the dynamical forecasts is compared with the skill of simple persistence-based statistical forecasts. For initial errors comparable in magnitude to present-day analysis errors, the statistical forecast loses all skill after about one week, reflecting the lifetime of the lowest frequency fluctuations in the model. Large ensemble mean dynamical forecasts would be expected to remain skillful for about 3 wk. The disparity between the skill of the statistical and dynamical forecasts is greater for the higher frequency modes, which have little memory beyond 1 d, yet remain predictable for about 2 wk. The results are analyzed in terms of two characteristic time scales.

Schubert, Siegfried D.↗

Path planning by querying persistent stores of trajectory segments

We introduce an algorithm for path planning (long duration) paths of dynamical systems, given a persistent object store containing suitable collections of short duration trajectory segments. We also describe experimental results from a proof-of-concept implementation of the algorithm. The basic idea is to interpret a path planning algorithm as a suitable query on a persistent object store consisting of short duration trajectory segments. The query returns a concatenation of short duration trajectory segments which is close to the desired path. The needed short duration segments are computed by using a divide and conquer algorithm to break up the original path into shorter paths; each shorter path is then matched to a nearby trajectory segment which is part of the persistent object store by using a suitable index function.

Grossman, Robert L.↗

Simulated life cycles of persistent anticyclonic anomalies over the North Pacific: Role of synoptic-scale eddies

This study examines the role of synoptic-scale eddies during the development of persistent anticyclonic height anomalies over the central North Pacific in a general circulation model under perpetual January conditions. The General Circulation Model (GCM) replicates the basic characteristics of the evolution of the anomaly patterns found in observations. The life cycle is characterized by the rapid establishment of the major anomaly center and considerably longer maintenance and decay phases, which include the development of downstream anomaly centers. The simulation also shows a realistic evolution of synoptic-scale activity beginning with enhanced activity off the east coast of Asia prior to onset, followed by a northward shift of the Pacific storm track, which lasts throughout the maintenance phase. The initial enhancement of synoptic-scale eddy activity is associated with a large-scale cyclonic anomaly that developes over Siberia several days prior to the onset of the main anticyclonic anomaly over the central North Pacific. The observations, however, show considerable interdecadel variability in the details of the composite onset behavior; it is unclear whether this variability is real or whether it reflects differences in the data assimilation systems. The role of the time mean flow and synoptic-scale eddies in the development of the persistent Pacific anomalies is studied within the context of a kinetic energy budget in which the flow is decomposed into the time-mean, low-frequency (timescales longer than 10 days), and synoptic (timescales less than 6 days) components. The budget, which is carried out for the simulation at 500 mb, shows that the initial growth of the persistent anticyclonic anomalies is associated with barotropic conversions of energy, with approximately equal contributions coming from the mean flow and the synoptic-scale eddies. After onset the barotropic conversion from the mean flow dominates, whereas the decay phase is associated with baroclinic processes within the low-frequency flow.

Higgins, R. W.↗

Characteristics of the persistent emission of SGR 1806-20

Earlier, using the X-ray satellite ASCA, we had identified the soft gamma-ray burst repeater (SGR) 1806-20 with a persistent X-ray source, AX 1805.7-2025 which is located close to the center of the radio supernova remnant G10.0-0.3. A burst seen by Burst and Transient Source Experiment (BATSE) was shown to be centered on G10.0-0.3. Here we report detailed temporal and spectral analysis of the persistent source. We find that AX 1805.7-2025 is a very compact source, size less than 30 sec in diameter, with a power-law spectrum. The count rate from AX 1805.7-2025 is steady on timescales of minutes, days, and 1 week. Most supernova remnants have extended X-ray emission ascribed to shocked gas. We set an upper limit to an extended X-ray emission both in continuum and line emission. We conclude that an isolated neutron star, most likely a pulsar, powers the radio remnant G10.0-0.3. Finally, we note that the persistent spectrum appears to be less absorbed than the burst spectrum.

Sonobe, T.↗

A Cryogenic Magnetostrictive Actuator Using a Persistent High Temperature Superconducting Magnet: Concept and Design - Part 1

Cryogenic magnetostrictive materials, such as rare earth zinc crystals, offer high strains and high forces with minimally applied magnetic fields, making the material ideally suited for deformable optics applications. For cryogenic temperature applications the use of superconducting magnets offer the possibility of a persistent mode of operation, i.e., the magnetostrictive material will maintain a strain field without power. High temperature superconductors (HTS) are attractive options if the temperature of operation is higher than 10 degrees Kelvin (K) and below 77 K. However, HTS wires have constraints that limit the minimum radius of winding, and even if good wires can be produced, the technology for joining superconducting wires does not exist. In this paper, the design and capabilities of a rare earth zinc magnetostrictive actuator using bulk HTS is described. Bulk superconductors can be fabricated in the sizes required with excellent superconducting properties. Equivalent permanent magnets, made with this inexpensive material, are persistent, do not require a persistent switch as in HTS wires, and can be made very small. These devices are charged using a technique which is similar to the one used for charging permanent magnets, e.g., by driving them into saturation. A small normal conducting coil can be used for charging or discharging. Because of the magnetic field capability of the superconductor material, a very small amount of superconducting magnet material is needed to actuate the rare earth zinc. In this paper, several designs of actuators using YBCO and BSCCO 2212 superconducting materials are presented. Designs that include magnetic shielding to prevent interaction between adjacent actuators will also be described. Preliminary experimental results and comparison with theory for BSCCO 2212 with a magnetostrictive element will be discussed.

Horner, Garnett↗

A Cryogenic Magnetostrictive Actuator using a Persistent High Temperature Superconducting Magnet, Part 1: Concept and Design: Concept and Design - Part 1

Cryogenic magnetostrictive materials, such as rare earth zinc crystals, offer high strains and high forces with minimally applied magnetic fields, making the material ideally suited for deformable optics applications. For cryogenic temperature applications, such as Next Generation Space Telescope (NGST), the use of superconducting magnets offer the possibility of a persistent mode of operation, i.e., the magnetostrictive material will maintain a strain field without power. High temperature superconductors (HTS) are attractive options if the temperature of operation is higher than 10 degrees Kelvin (K) and below 77 K. However, HTS wires have constraints that limit the minimum radius of winding, and even if good wires can be produced, the technology for joining superconducting wires does not exist. In this paper, the design and capabilities of a rare earth zinc magnetostrictive actuator using bulk HTS is described. Bulk superconductors can be fabricated in the sizes required with excellent superconducting properties. Equivalent permanent magnets, made with this inexpensive material, are persistent, do not require a persistent switch as in HTS wires, and can be made very small. These devices are charged using a technique which is similar to the one used for charging permanent magnets, e.g., by driving them into saturation. A small normal conducting coil can be used for charging or discharging. Very fast charging and discharging of HTS tubes, as short as 100 microseconds, has been demonstrated. Because of the magnetic field capability of the superconductor material, a very small amount of superconducting magnet material is needed to actuate the rare earth zinc. In this paper, several designs of actuators using YBCO and BSCCO 2212 superconducting materials are presented. Designs that include magnetic shielding to prevent interaction between adjacent actuators will also be described. Preliminary experimental results and comparison with theory for BSSCO 2212 with a magnetostrictive element will be discussed.

Horner, Garnett C.↗

Muscle organizers in Drosophila: the role of persistent larval fibers in adult flight muscle development

In many organisms muscle formation depends on specialized cells that prefigure the pattern of the musculature and serve as templates for myoblast organization and fusion. These include muscle pioneers in insects and muscle organizing cells in leech. In Drosophila, muscle founder cells have been proposed to play a similar role in organizing larval muscle development during embryogenesis. During metamorphosis in Drosophila, following histolysis of most of the larval musculature, there is a second round of myogenesis that gives rise to the adult muscles. It is not known whether muscle founder cells organize the development of these muscles. However, in the thorax specific larval muscle fibers do not histolyze at the onset of metamorphosis, but instead serve as templates for the formation of a subset of adult muscles, the dorsal longitudinal flight muscles (DLMs). Because these persistent larval muscle fibers appear to be functioning in many respects like muscle founder cells, we investigated whether they were necessary for DLM development by using a microbeam laser to ablate them singly and in combination. We found that, in the absence of the larval muscle fibers, DLMs nonetheless develop. Our results show that the persistent larval muscle fibers are not required to initiate myoblast fusion, to determine DLM identity, to locate the DLMs in the thorax, or to specify the total DLM fiber volume. However, they are required to regulate the number of DLM fibers generated. Thus, while the persistent larval muscle fibers are not obligatory for DLM fiber formation and differentiation, they are necessary to ensure the development of the correct number of fibers.

Non-NASA Center↗

Persistent Structures in the Turbulent Boundary Layer

Persistent structures in the turbulent boundary layer are located and analyzed. The data are taken from flight experiments on large commercial aircraft. An interval correlation technique is introduced which is able to locate the structures. The Morlet continuous wavelet is shown to not only locates persistent structures but has the added benefit that the pressure data are decomposed in time and frequency. To better understand how power is apportioned among these structures, a discrete Coiflet wavelet is used to decompose the pressure data into orthogonal frequency bands. Results indicate that some structures persist a great deal longer in the TBL than would be expected. These structure contain significant power and may be a primary source of vibration energy in the airframe.

Palumbo, Dan↗